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Fernández JD, Miño I, Canales J, Vidal EA. Gene regulatory networks underlying sulfate deficiency responses in plants. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:2781-2798. [PMID: 38366662 DOI: 10.1093/jxb/erae051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 02/14/2024] [Indexed: 02/18/2024]
Abstract
Sulfur (S) is an essential macronutrient for plants and its availability in soils is an important determinant for growth and development. Current regulatory policies aimed at reducing industrial S emissions together with changes in agronomical practices have led to a decline in S contents in soils worldwide. Deficiency of sulfate-the primary form of S accessible to plants in soil-has adverse effects on both crop yield and nutritional quality. Hence, recent research has increasingly focused on unraveling the molecular mechanisms through which plants detect and adapt to a limiting supply of sulfate. A significant part of these studies involves the use of omics technologies and has generated comprehensive catalogs of sulfate deficiency-responsive genes and processes, principally in Arabidopsis together with a few studies centering on crop species such as wheat, rice, or members of the Brassica genus. Although we know that sulfate deficiency elicits an important reprogramming of the transcriptome, the transcriptional regulators orchestrating this response are not yet well understood. In this review, we summarize our current knowledge of gene expression responses to sulfate deficiency and recent efforts towards the identification of the transcription factors that are involved in controlling these responses. We further compare the transcriptional response and putative regulators between Arabidopsis and two important crop species, rice and tomato, to gain insights into common mechanisms of the response to sulfate deficiency.
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Affiliation(s)
- José David Fernández
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Ingeniería y Tecnología, Universidad Mayor, 8580745, Santiago, Chile
- Agencia Nacional de Investigación y Desarrollo - Millennium Science Initiative Program, Millennium Institute for Integrative Biology, 7500565, Santiago, Chile
- Programa de Doctorado en Genómica Integrativa, Vicerrectoría de Investigación, Universidad Mayor, 8580745, Santiago, Chile
| | - Ignacio Miño
- Agencia Nacional de Investigación y Desarrollo - Millennium Science Initiative Program, Millennium Institute for Integrative Biology, 7500565, Santiago, Chile
- Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, 5110566, Valdivia, Chile
| | - Javier Canales
- Agencia Nacional de Investigación y Desarrollo - Millennium Science Initiative Program, Millennium Institute for Integrative Biology, 7500565, Santiago, Chile
- Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, 5110566, Valdivia, Chile
| | - Elena A Vidal
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Ingeniería y Tecnología, Universidad Mayor, 8580745, Santiago, Chile
- Agencia Nacional de Investigación y Desarrollo - Millennium Science Initiative Program, Millennium Institute for Integrative Biology, 7500565, Santiago, Chile
- Escuela de Biotecnología, Facultad de Ciencias, Ingeniería y Tecnología, Universidad Mayor, 8580745, Santiago, Chile
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2
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Yu E, Liu Q, Gao Y, Li Y, Zang P, Zhao Y, He Z. An exploration of mechanism of high quality and yield of Gastrodia elata Bl. f. glauca by the isolation, identification, and evaluation of Mycena. Front Microbiol 2023; 14:1220670. [PMID: 37928654 PMCID: PMC10620705 DOI: 10.3389/fmicb.2023.1220670] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 10/06/2023] [Indexed: 11/07/2023] Open
Abstract
Gastrodia elata Bl. f. glauca is an important traditional Chinese medicinal plant. The yield and quality of Gastrodia elata Bl. have significantly decreased due to multigenerational asexual reproduction. Therefore, it is necessary to have sexual reproduction of Gastrodia elata Bl. to supplement the market supply. Seeds of G. elata Bl. have no endosperm, and their sexual reproduction depends on the nutrients provided by the embryo cells infected by Mycena fungi to complete seed germination. However, Mycena fungi are small and have many species, and not all Mycena fungi can promote the germination of G. elata Bl. seeds. Therefore, it is of great significance to isolate and identify suitable germination fungi and explore the mechanism for improving the production performance and yield, and quality of G. elata Bl. Six closely related Mycena isolates, JFGL-01, JFGL-02, JFGL-03, JFGL-04, JFGL-05, and JFGL-06, were isolated from the leaves and protocorms of G. elata Bl. f. glauca and were identified as Mycena purpureofusca. The mycelial state and number of germinating protocorms were used as indicators to preferentially select Mycena fungi, and it was concluded that JFGL-06 had the best mycelial state and ability to germinate G. elata Bl. seeds. Finally, a mechanism to increase the yield of G. elata Bl. was explored by comparing the changes in nutrient elements and microbial diversity in the soil around G. elata Bl. with different strains. JFGL-06 proved to be an excellent Mycena fungal strain suitable for G. elata Bl. f. glauca. Compared with the commercial strain, JFGL-06 significantly increased the C, N, Na, Mg, S, Cl, K, Ca, and Fe contents of the soil surrounding the protocorms of G. elata Bl. f. glauca. JFGL-06 improved the composition, diversity, and metabolic function of the surrounding soil microbial community of G. elata Bl. f. glauca protocorms at the phylum, class, and genus levels, significantly increased the relative abundance of bacteria such as Acidobacteria and fungi such as Trichoderma among the dominant groups, and increased the abundance of functional genes in metabolic pathways such as nucleotide metabolism and energy metabolism. There was a significant reduction in the relative abundance of bacteria, such as Actinomycetes, and fungi, such as Fusarium, in the dominant flora, and a reduced abundance of functional genes, such as amino acid metabolism and xenobiotic biodegradation and metabolism. This is the main reason why the JFGL-06 strain promoted high-quality and high-yield G. elata Bl. f. glauca in Changbai Mountain.
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Affiliation(s)
- En Yu
- College of Chinese Medicinal Materials, Jilin Agricultural University, Changchun, China
| | - Qun Liu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Memorial Sun Yat-Sen), Nanjing, China
| | - Yugang Gao
- College of Chinese Medicinal Materials, Jilin Agricultural University, Changchun, China
| | - Yaqi Li
- College of Chinese Medicinal Materials, Jilin Agricultural University, Changchun, China
| | - Pu Zang
- College of Chinese Medicinal Materials, Jilin Agricultural University, Changchun, China
| | - Yan Zhao
- College of Chinese Medicinal Materials, Jilin Agricultural University, Changchun, China
| | - Zhongmei He
- College of Chinese Medicinal Materials, Jilin Agricultural University, Changchun, China
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Yurkov AP, Afonin AM, Kryukov AA, Gorbunova AO, Kudryashova TR, Kovalchuk AI, Gorenkova AI, Bogdanova EM, Kosulnikov YV, Laktionov YV, Kozhemyakov AP, Romanyuk DA, Zhukov VA, Puzanskiy RK, Mikhailova YV, Yemelyanov VV, Shishova MF. The Effects of Rhizophagus irregularis Inoculation on Transcriptome of Medicago lupulina Leaves at Early Vegetative and Flowering Stages of Plant Development. PLANTS (BASEL, SWITZERLAND) 2023; 12:3580. [PMID: 37896043 PMCID: PMC10610208 DOI: 10.3390/plants12203580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Revised: 10/02/2023] [Accepted: 10/13/2023] [Indexed: 10/29/2023]
Abstract
The study is aimed at revealing the effects of Rhizophagus irregularis inoculation on the transcriptome of Medicago lupulina leaves at the early (second leaf formation) and later (flowering) stages of plant development. A pot experiment was conducted under conditions of low phosphorus (P) level in the substrate. M. lupulina plants were characterized by high mycorrhizal growth response and mycorrhization parameters. Library sequencing was performed on the Illumina HiseqXTen platform. Significant changes in the expression of 4863 (padj < 0.01) genes from 34049 functionally annotated genes were shown by Massive Analysis of cDNA Ends (MACE-Seq). GO enrichment analysis using the Kolmogorov-Smirnov test was performed, and 244 functional GO groups were identified, including genes contributing to the development of effective AM symbiosis. The Mercator online tool was used to assign functional classes of differentially expressed genes (DEGs). The early stage was characterized by the presence of six functional classes that included only upregulated GO groups, such as genes of carbohydrate metabolism, cellular respiration, nutrient uptake, photosynthesis, protein biosynthesis, and solute transport. At the later stage (flowering), the number of stimulated GO groups was reduced to photosynthesis and protein biosynthesis. All DEGs of the GO:0016036 group were downregulated because AM plants had higher resistance to phosphate starvation. For the first time, the upregulation of genes encoding thioredoxin in AM plant leaves was shown. It was supposed to reduce ROS level and thus, consequently, enhance the mechanisms of antioxidant protection in M. lupulina plants under conditions of low phosphorus level. Taken together, the obtained results indicate genes that are the most important for the effective symbiosis with M. lupulina and might be engaged in other plant species.
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Affiliation(s)
- Andrey P. Yurkov
- Laboratory of Ecology of Symbiotic and Associative Rhizobacteria, All-Russia Research Institute for Agricultural Microbiology, Pushkin, St. Petersburg 196608, Russia; (A.M.A.); (A.A.K.); (A.O.G.); (T.R.K.); (A.I.K.); (A.I.G.); (E.M.B.); (Y.V.K.); (Y.V.L.); (A.P.K.)
| | - Alexey M. Afonin
- Laboratory of Ecology of Symbiotic and Associative Rhizobacteria, All-Russia Research Institute for Agricultural Microbiology, Pushkin, St. Petersburg 196608, Russia; (A.M.A.); (A.A.K.); (A.O.G.); (T.R.K.); (A.I.K.); (A.I.G.); (E.M.B.); (Y.V.K.); (Y.V.L.); (A.P.K.)
| | - Alexey A. Kryukov
- Laboratory of Ecology of Symbiotic and Associative Rhizobacteria, All-Russia Research Institute for Agricultural Microbiology, Pushkin, St. Petersburg 196608, Russia; (A.M.A.); (A.A.K.); (A.O.G.); (T.R.K.); (A.I.K.); (A.I.G.); (E.M.B.); (Y.V.K.); (Y.V.L.); (A.P.K.)
| | - Anastasia O. Gorbunova
- Laboratory of Ecology of Symbiotic and Associative Rhizobacteria, All-Russia Research Institute for Agricultural Microbiology, Pushkin, St. Petersburg 196608, Russia; (A.M.A.); (A.A.K.); (A.O.G.); (T.R.K.); (A.I.K.); (A.I.G.); (E.M.B.); (Y.V.K.); (Y.V.L.); (A.P.K.)
| | - Tatyana R. Kudryashova
- Laboratory of Ecology of Symbiotic and Associative Rhizobacteria, All-Russia Research Institute for Agricultural Microbiology, Pushkin, St. Petersburg 196608, Russia; (A.M.A.); (A.A.K.); (A.O.G.); (T.R.K.); (A.I.K.); (A.I.G.); (E.M.B.); (Y.V.K.); (Y.V.L.); (A.P.K.)
- Graduate School of Biotechnology and Food Science, Peter the Great St. Petersburg Polytechnic University, St. Petersburg 194064, Russia
| | - Anastasia I. Kovalchuk
- Laboratory of Ecology of Symbiotic and Associative Rhizobacteria, All-Russia Research Institute for Agricultural Microbiology, Pushkin, St. Petersburg 196608, Russia; (A.M.A.); (A.A.K.); (A.O.G.); (T.R.K.); (A.I.K.); (A.I.G.); (E.M.B.); (Y.V.K.); (Y.V.L.); (A.P.K.)
- Graduate School of Biotechnology and Food Science, Peter the Great St. Petersburg Polytechnic University, St. Petersburg 194064, Russia
| | - Anastasia I. Gorenkova
- Laboratory of Ecology of Symbiotic and Associative Rhizobacteria, All-Russia Research Institute for Agricultural Microbiology, Pushkin, St. Petersburg 196608, Russia; (A.M.A.); (A.A.K.); (A.O.G.); (T.R.K.); (A.I.K.); (A.I.G.); (E.M.B.); (Y.V.K.); (Y.V.L.); (A.P.K.)
- Faculty of Biology, St. Petersburg State University, St. Petersburg 199034, Russia; (R.K.P.); (V.V.Y.); (M.F.S.)
| | - Ekaterina M. Bogdanova
- Laboratory of Ecology of Symbiotic and Associative Rhizobacteria, All-Russia Research Institute for Agricultural Microbiology, Pushkin, St. Petersburg 196608, Russia; (A.M.A.); (A.A.K.); (A.O.G.); (T.R.K.); (A.I.K.); (A.I.G.); (E.M.B.); (Y.V.K.); (Y.V.L.); (A.P.K.)
- Faculty of Biology, St. Petersburg State University, St. Petersburg 199034, Russia; (R.K.P.); (V.V.Y.); (M.F.S.)
| | - Yuri V. Kosulnikov
- Laboratory of Ecology of Symbiotic and Associative Rhizobacteria, All-Russia Research Institute for Agricultural Microbiology, Pushkin, St. Petersburg 196608, Russia; (A.M.A.); (A.A.K.); (A.O.G.); (T.R.K.); (A.I.K.); (A.I.G.); (E.M.B.); (Y.V.K.); (Y.V.L.); (A.P.K.)
| | - Yuri V. Laktionov
- Laboratory of Ecology of Symbiotic and Associative Rhizobacteria, All-Russia Research Institute for Agricultural Microbiology, Pushkin, St. Petersburg 196608, Russia; (A.M.A.); (A.A.K.); (A.O.G.); (T.R.K.); (A.I.K.); (A.I.G.); (E.M.B.); (Y.V.K.); (Y.V.L.); (A.P.K.)
| | - Andrey P. Kozhemyakov
- Laboratory of Ecology of Symbiotic and Associative Rhizobacteria, All-Russia Research Institute for Agricultural Microbiology, Pushkin, St. Petersburg 196608, Russia; (A.M.A.); (A.A.K.); (A.O.G.); (T.R.K.); (A.I.K.); (A.I.G.); (E.M.B.); (Y.V.K.); (Y.V.L.); (A.P.K.)
| | - Daria A. Romanyuk
- Laboratory of Genetics of Plant-Microbe Interactions, All-Russia Research Institute for Agricultural Microbiology, Pushkin, St. Petersburg 196608, Russia; (D.A.R.); (V.A.Z.)
| | - Vladimir A. Zhukov
- Laboratory of Genetics of Plant-Microbe Interactions, All-Russia Research Institute for Agricultural Microbiology, Pushkin, St. Petersburg 196608, Russia; (D.A.R.); (V.A.Z.)
| | - Roman K. Puzanskiy
- Faculty of Biology, St. Petersburg State University, St. Petersburg 199034, Russia; (R.K.P.); (V.V.Y.); (M.F.S.)
- Laboratory of Analytical Phytochemistry, Komarov Botanical Institute of the Russian Academy of Sciences, St. Petersburg 197022, Russia
| | - Yulia V. Mikhailova
- Laboratory of Biosystematics and Cytology, Komarov Botanical Institute of the Russian Academy of Sciences, St. Petersburg 197022, Russia;
| | - Vladislav V. Yemelyanov
- Faculty of Biology, St. Petersburg State University, St. Petersburg 199034, Russia; (R.K.P.); (V.V.Y.); (M.F.S.)
| | - Maria F. Shishova
- Faculty of Biology, St. Petersburg State University, St. Petersburg 199034, Russia; (R.K.P.); (V.V.Y.); (M.F.S.)
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4
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Cope KR, Kafle A, Yakha JK, Pfeffer PE, Strahan GD, Garcia K, Subramanian S, Bücking H. Physiological and transcriptomic response of Medicago truncatula to colonization by high- or low-benefit arbuscular mycorrhizal fungi. MYCORRHIZA 2022; 32:281-303. [PMID: 35511363 DOI: 10.1007/s00572-022-01077-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 04/20/2022] [Indexed: 06/14/2023]
Abstract
Arbuscular mycorrhizal (AM) fungi form a root endosymbiosis with many agronomically important crop species. They enhance the ability of their host to obtain nutrients from the soil and increase the tolerance to biotic and abiotic stressors. However, AM fungal species can differ in the benefits they provide to their host plants. Here, we examined the putative molecular mechanisms involved in the regulation of the physiological response of Medicago truncatula to colonization by Rhizophagus irregularis or Glomus aggregatum, which have previously been characterized as high- and low-benefit AM fungal species, respectively. Colonization with R. irregularis led to greater growth and nutrient uptake than colonization with G. aggregatum. These benefits were linked to an elevated expression in the roots of strigolactone biosynthesis genes (NSP1, NSP2, CCD7, and MAX1a), mycorrhiza-induced phosphate (PT8), ammonium (AMT2;3), and nitrate (NPF4.12) transporters and the putative ammonium transporter NIP1;5. R. irregularis also stimulated the expression of photosynthesis-related genes in the shoot and the upregulation of the sugar transporters SWEET1.2, SWEET3.3, and SWEET 12 and the lipid biosynthesis gene RAM2 in the roots. In contrast, G. aggregatum induced the expression of biotic stress defense response genes in the shoots, and several genes associated with abiotic stress in the roots. This suggests that either the host perceives colonization by G. aggregatum as pathogen attack or that G. aggregatum can prime host defense responses. Our findings highlight molecular mechanisms that host plants may use to regulate their association with high- and low-benefit arbuscular mycorrhizal symbionts.
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Affiliation(s)
- Kevin R Cope
- Biology and Microbiology Department, South Dakota State University, Brookings, SD, 57007, USA
- Biosciences Division, Oak Ridge National Lab, Oak Ridge, TN, 37830, USA
| | - Arjun Kafle
- Biology and Microbiology Department, South Dakota State University, Brookings, SD, 57007, USA
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC, 27695, USA
| | - Jaya K Yakha
- Biology and Microbiology Department, South Dakota State University, Brookings, SD, 57007, USA
| | - Philip E Pfeffer
- Agricultural Research Service, Eastern Regional Research Center, USDA, 600 East Mermaid Lane, Wyndmoor, PA, 19038, USA
| | - Gary D Strahan
- Agricultural Research Service, Eastern Regional Research Center, USDA, 600 East Mermaid Lane, Wyndmoor, PA, 19038, USA
| | - Kevin Garcia
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC, 27695, USA
| | - Senthil Subramanian
- Biology and Microbiology Department, South Dakota State University, Brookings, SD, 57007, USA
- Department of Agronomy, Horticulture, and Plant Science, South Dakota State University, Brookings, SD, 57007, USA
| | - Heike Bücking
- Biology and Microbiology Department, South Dakota State University, Brookings, SD, 57007, USA.
- Division of Plant Science and Technology, University of Missouri, Columbia, MO, 65211, USA.
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Kafle A, Frank HER, Rose BD, Garcia K. Split down the middle: studying arbuscular mycorrhizal and ectomycorrhizal symbioses using split-root assays. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:1288-1300. [PMID: 34791191 DOI: 10.1093/jxb/erab489] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 11/05/2021] [Indexed: 06/13/2023]
Abstract
Most land plants symbiotically interact with soil-borne fungi to ensure nutrient acquisition and tolerance to various environmental stressors. Among these symbioses, arbuscular mycorrhizal and ectomycorrhizal associations can be found in a large proportion of plants, including many crops. Split-root assays are widely used in plant research to study local and systemic signaling responses triggered by local treatments, including nutrient availability, interaction with soil microbes, or abiotic stresses. However, split-root approaches have only been occasionally used to tackle these questions with regard to mycorrhizal symbioses. This review compiles and discusses split-root assays developed to study arbuscular mycorrhizal and ectomycorrhizal symbioses, with a particular emphasis on colonization by multiple beneficial symbionts, systemic resistance induced by mycorrhizal fungi, water and nutrient transport from fungi to colonized plants, and host photosynthate allocation from the host to fungal symbionts. In addition, we highlight how the use of split-root assays could result in a better understanding of mycorrhizal symbioses, particularly for a broader range of essential nutrients, and for multipartite interactions.
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Affiliation(s)
- Arjun Kafle
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC 27695, USA
| | - Hannah E R Frank
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC 27695, USA
| | - Benjamin D Rose
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC 27695, USA
| | - Kevin Garcia
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC 27695, USA
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Zhang H, Hao X, Zhang J, Wang L, Wang Y, Li N, Guo L, Ren H, Zeng J. Genome-wide identification of SULTR genes in tea plant and analysis of their expression in response to sulfur and selenium. PROTOPLASMA 2022; 259:127-140. [PMID: 33884505 DOI: 10.1007/s00709-021-01643-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 04/01/2021] [Indexed: 06/12/2023]
Abstract
Sulfur (S) is an essential macronutrient required by plants. Plants absorb and transport S through sulfate transporters (SULTRs). In this study, we cloned 8 SULTR genes (CsSULTR1;1/1;2/2;1/3;1/3;2/3;3/3;5/4;1) from tea plant (Camellia sinensis), all of which contain a typical sulfate transporter and antisigma factor antagonist (STAS) conserved domain. Phylogenetic tree analysis further divided the CsSULTRs into four main groups. Many cis-acting elements related to hormones and environmental stresses were found within the promoter sequence of CsSULTRs. Subcellular localization results showed that CsSULTR4;1 localized in the vacuolar membrane and that other CsSULTRs localized to the cellular membrane. The tissue-specific expression of the 8 CsSULTR genes showed different expression patterns during the active growing period and dormancy period. In particular, the expression of CsSULTR1;1 was highest in the roots, but that of CsSULTR1;2 was lowest in the dormancy period. The expression of CsSULTR1;1/1;2/2;1/3;2 was stimulated under different concentrations of selenium (Se) and S; moreover, CsSULTR1;2/2;1/3;3/3;5 was upregulated in response to different valences of Se.
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Affiliation(s)
- Haojie Zhang
- National Center for Tea Improvement, Tea Research Institute of Chinese Academy of Agricultural Sciences/Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture and Rural Affairs, Hangzhou, 310008, China
- Huaiyin Institute of Agricultural Sciences of Xuhuai District in Jiangsu, Huai'an, 223001, China
| | - Xinyuan Hao
- National Center for Tea Improvement, Tea Research Institute of Chinese Academy of Agricultural Sciences/Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture and Rural Affairs, Hangzhou, 310008, China
| | - Jingjing Zhang
- National Center for Tea Improvement, Tea Research Institute of Chinese Academy of Agricultural Sciences/Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture and Rural Affairs, Hangzhou, 310008, China
| | - Lu Wang
- National Center for Tea Improvement, Tea Research Institute of Chinese Academy of Agricultural Sciences/Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture and Rural Affairs, Hangzhou, 310008, China
| | - Yuchun Wang
- National Center for Tea Improvement, Tea Research Institute of Chinese Academy of Agricultural Sciences/Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture and Rural Affairs, Hangzhou, 310008, China
| | - Nana Li
- National Center for Tea Improvement, Tea Research Institute of Chinese Academy of Agricultural Sciences/Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture and Rural Affairs, Hangzhou, 310008, China
| | - Lina Guo
- National Center for Tea Improvement, Tea Research Institute of Chinese Academy of Agricultural Sciences/Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture and Rural Affairs, Hangzhou, 310008, China
| | - Hengze Ren
- National Center for Tea Improvement, Tea Research Institute of Chinese Academy of Agricultural Sciences/Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture and Rural Affairs, Hangzhou, 310008, China
| | - Jianming Zeng
- National Center for Tea Improvement, Tea Research Institute of Chinese Academy of Agricultural Sciences/Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture and Rural Affairs, Hangzhou, 310008, China.
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7
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Shuai M, He D, Chen X. Optimizing weighted gene co-expression network analysis with a multi-threaded calculation of the topological overlap matrix. Stat Appl Genet Mol Biol 2021; 20:145-153. [PMID: 34757703 DOI: 10.1515/sagmb-2021-0025] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 10/08/2021] [Indexed: 02/06/2023]
Abstract
Biomolecular networks are often assumed to be scale-free hierarchical networks. The weighted gene co-expression network analysis (WGCNA) treats gene co-expression networks as undirected scale-free hierarchical weighted networks. The WGCNA R software package uses an Adjacency Matrix to store a network, next calculates the topological overlap matrix (TOM), and then identifies the modules (sub-networks), where each module is assumed to be associated with a certain biological function. The most time-consuming step of WGCNA is to calculate TOM from the Adjacency Matrix in a single thread. In this paper, the single-threaded algorithm of the TOM has been changed into a multi-threaded algorithm (the parameters are the default values of WGCNA). In the multi-threaded algorithm, Rcpp was used to make R call a C++ function, and then C++ used OpenMP to start multiple threads to calculate TOM from the Adjacency Matrix. On shared-memory MultiProcessor systems, the calculation time decreases as the number of CPU cores increases. The algorithm of this paper can promote the application of WGCNA on large data sets, and help other research fields to identify sub-networks in undirected scale-free hierarchical weighted networks. The source codes and usage are available at https://github.com/do-somethings-haha/multi-threaded_calculate_unsigned_TOM_from_unsigned_or_signed_Adjacency_Matrix_of_WGCNA.
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Affiliation(s)
- Min Shuai
- State Key Laboratory of Characteristic Chinese Medicine Resources in Southwest China, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, People's Republic of China.,Pharmacy College, Chengdu University of Traditional Chinese Medicine, Ministry of Education Key Laboratory of Standardization of Chinese Herbal Medicine, Key Laboratory of Systematic Research, Development and Utilization of Chinese Medicine Resources in Sichuan Province - Key Laboratory Breeding Base of Co-founded by Sichuan Province and MOST, Chengdu 611137, China
| | - Dongmei He
- State Key Laboratory of Characteristic Chinese Medicine Resources in Southwest China, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, People's Republic of China.,Pharmacy College, Chengdu University of Traditional Chinese Medicine, Ministry of Education Key Laboratory of Standardization of Chinese Herbal Medicine, Key Laboratory of Systematic Research, Development and Utilization of Chinese Medicine Resources in Sichuan Province - Key Laboratory Breeding Base of Co-founded by Sichuan Province and MOST, Chengdu 611137, China.,Center for Post-doctoral research, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, State Key Laboratory Breeding Base of Dao-di Herbs, Beijing 100700, China
| | - Xin Chen
- State Key Laboratory of Characteristic Chinese Medicine Resources in Southwest China, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, People's Republic of China.,Pharmacy College, Chengdu University of Traditional Chinese Medicine, Ministry of Education Key Laboratory of Standardization of Chinese Herbal Medicine, Key Laboratory of Systematic Research, Development and Utilization of Chinese Medicine Resources in Sichuan Province - Key Laboratory Breeding Base of Co-founded by Sichuan Province and MOST, Chengdu 611137, China
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8
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Fan X, Zhou X, Chen H, Tang M, Xie X. Cross-Talks Between Macro- and Micronutrient Uptake and Signaling in Plants. FRONTIERS IN PLANT SCIENCE 2021; 12:663477. [PMID: 34721446 PMCID: PMC8555580 DOI: 10.3389/fpls.2021.663477] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 08/30/2021] [Indexed: 05/05/2023]
Abstract
In nature, land plants as sessile organisms are faced with multiple nutrient stresses that often occur simultaneously in soil. Nitrogen (N), phosphorus (P), sulfur (S), zinc (Zn), and iron (Fe) are five of the essential nutrients that affect plant growth and health. Although these minerals are relatively inaccessible to plants due to their low solubility and relative immobilization, plants have adopted coping mechanisms for survival under multiple nutrient stress conditions. The double interactions between N, Pi, S, Zn, and Fe have long been recognized in plants at the physiological level. However, the molecular mechanisms and signaling pathways underlying these cross-talks in plants remain poorly understood. This review preliminarily examined recent progress and current knowledge of the biochemical and physiological interactions between macro- and micro-mineral nutrients in plants and aimed to focus on the cross-talks between N, Pi, S, Zn, and Fe uptake and homeostasis in plants. More importantly, we further reviewed current studies on the molecular mechanisms underlying the cross-talks between N, Pi, S, Zn, and Fe homeostasis to better understand how these nutrient interactions affect the mineral uptake and signaling in plants. This review serves as a basis for further studies on multiple nutrient stress signaling in plants. Overall, the development of an integrative study of multiple nutrient signaling cross-talks in plants will be of important biological significance and crucial to sustainable agriculture.
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Affiliation(s)
| | | | | | - Ming Tang
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Xianan Xie
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
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9
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Combined Effects of Water Deficit, Exogenous Ethylene Application and Root Symbioses on Trigonelline and ABA Accumulation in Fenugreek. APPLIED SCIENCES-BASEL 2020. [DOI: 10.3390/app10072338] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Secondary metabolites (SMs) have high economic impact thanks to their exploitability in chemical, pharmaceutical and cosmetic industries. Trigonella foenum-graecum has an importance due to the production of bioactive compounds with pharmaceutical values. Among them, the alkaloid trigonelline is known for its role in the treatment of different human diseases. SM accumulation is influenced by environmental factors but is modulated by the application of exogenous compounds. Ethephon, a precursor of the phytohormone ethylene, was already used to influence SM accumulation. Our work is aimed at evaluating the accumulation of trigonelline and the phytohormone abscisic acid (ABA) when three factors were combined: i) two levels of water regimes (well-watered and water deficit), ii) ethephon treatments and iii) inoculation with an arbuscular mycorrhizal (AM)-based inoculum also leading to nodulation. The content of trigonelline and ABA was significantly affected by symbioses, showing high accumulation in AM-colonized plants irrespective of the water regimes applied. In terms of trigonelline accumulation with respect to ethephon treatments, while symbiotic plants showed a dose-dependent trend, non-symbiotic plants showed a significantly difference only when 550 ppm of ethephon was applied. In conclusion, our work provides new information on the effects of both ethephon and symbioses on plant growth and accumulation of valuable compounds, such as trigonelline, in fenugreek.
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10
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Courbet G, Gallardo K, Vigani G, Brunel-Muguet S, Trouverie J, Salon C, Ourry A. Disentangling the complexity and diversity of crosstalk between sulfur and other mineral nutrients in cultivated plants. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:4183-4196. [PMID: 31055598 DOI: 10.1093/jxb/erz214] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 04/29/2019] [Indexed: 05/02/2023]
Abstract
A complete understanding of ionome homeostasis requires a thorough investigation of the dynamics of the nutrient networks in plants. This review focuses on the complexity of interactions occurring between S and other nutrients, and these are addressed at the level of the whole plant, the individual tissues, and the cellular compartments. With regards to macronutrients, S deficiency mainly acts by reducing plant growth, which in turn restricts the root uptake of, for example, N, K, and Mg. Conversely, deficiencies in N, K, or Mg reduce uptake of S. TOR (target of rapamycin) protein kinase, whose involvement in the co-regulation of C/N and S metabolism has recently been unravelled, provides a clue to understanding the links between S and plant growth. In legumes, the original crosstalk between N and S can be found at the level of nodules, which show high requirements for S, and hence specifically express a number of sulfate transporters. With regards to micronutrients, except for Fe, their uptake can be increased under S deficiency through various mechanisms. One of these results from the broad specificity of root sulfate transporters that are up-regulated during S deficiency, which can also take up some molybdate and selenate. A second mechanism is linked to the large accumulation of sulfate in the leaf vacuoles, with its reduced osmotic contribution under S deficiency being compensated for by an increase in Cl uptake and accumulation. A third group of broader mechanisms that can explain at least some of the interactions between S and micronutrients concerns metabolic networks where several nutrients are essential, such as the synthesis of the Mo co-factor needed by some essential enzymes, which requires S, Fe, Zn and Cu for its synthesis, and the synthesis and regulation of Fe-S clusters. Finally, we briefly review recent developments in the modelling of S responses in crops (allocation amongst plant parts and distribution of mineral versus organic forms) in order to provide perspectives on prediction-based approaches that take into account the interactions with other minerals such as N.
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Affiliation(s)
- Galatéa Courbet
- Normandie Université, UNICAEN, INRA, UMR 950 Ecophysiologie Végétale, Agronomie et Nutritions N, C, S, Esplanade de la Paix, Caen Cedex, France
- Agroécologie, AgroSup Dijon, INRA, Université Bourgogne, Franche-Comté, Dijon, France
| | - Karine Gallardo
- Agroécologie, AgroSup Dijon, INRA, Université Bourgogne, Franche-Comté, Dijon, France
| | - Gianpiero Vigani
- Plant Physiology Unit, Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
| | - Sophie Brunel-Muguet
- Normandie Université, UNICAEN, INRA, UMR 950 Ecophysiologie Végétale, Agronomie et Nutritions N, C, S, Esplanade de la Paix, Caen Cedex, France
| | - Jacques Trouverie
- Normandie Université, UNICAEN, INRA, UMR 950 Ecophysiologie Végétale, Agronomie et Nutritions N, C, S, Esplanade de la Paix, Caen Cedex, France
| | - Christophe Salon
- Agroécologie, AgroSup Dijon, INRA, Université Bourgogne, Franche-Comté, Dijon, France
| | - Alain Ourry
- Normandie Université, UNICAEN, INRA, UMR 950 Ecophysiologie Végétale, Agronomie et Nutritions N, C, S, Esplanade de la Paix, Caen Cedex, France
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11
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Avio L, Turrini A, Giovannetti M, Sbrana C. Designing the Ideotype Mycorrhizal Symbionts for the Production of Healthy Food. FRONTIERS IN PLANT SCIENCE 2018; 9:1089. [PMID: 30154803 PMCID: PMC6102486 DOI: 10.3389/fpls.2018.01089] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 07/05/2018] [Indexed: 05/03/2023]
Abstract
The new paradigm in agriculture, sustainable intensification, is focusing back onto beneficial soil microorganisms, for the role played in reducing the input of chemical fertilizers and pesticides and improving plant nutrition and health. Worldwide, more and more attention is deserved to arbuscular mycorrhizal fungi (AMF), which establish symbioses with the roots of most land plants and facilitate plant nutrient uptake, by means of a large network of extraradical hyphae spreading from colonized roots to the surrounding soil and functioning as a supplementary absorbing system. AMF protect plants from biotic and abiotic stresses and are able to modulate the activity of antioxidant enzymes and the biosynthesis of secondary metabolites (phytochemicals), such as polyphenols, anthocyanins, phytoestrogens and carotenoids, that play a fundamental role in promoting human health. An increasing number of studies focused on the use of AMF symbionts for the production of functional food, with enhanced nutritional and nutraceutical value. Yet, while several plant species were investigated, only few AMF were utilized, thus limiting the full exploitation of their wide physiological and genetic diversity. Here, we will focus on AMF effects on the biosynthesis of plant secondary metabolites with health-promoting activity, and on the criteria for a finely tuned, targeted selection of the best performing symbionts, to be utilized as sustainable biotechnological tools for the production of safe and healthy plant foods.
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Affiliation(s)
- Luciano Avio
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
| | - Alessandra Turrini
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
- Interdepartmental Research Center “Nutraceuticals and Food for Health”, University of Pisa, Pisa, Italy
| | - Manuela Giovannetti
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
- Interdepartmental Research Center “Nutraceuticals and Food for Health”, University of Pisa, Pisa, Italy
| | - Cristiana Sbrana
- Institute of Agricultural Biology and Biotechnology, C.N.R., UOS Pisa, Pisa, Italy
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12
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de Bang TC, Lundquist PK, Dai X, Boschiero C, Zhuang Z, Pant P, Torres-Jerez I, Roy S, Nogales J, Veerappan V, Dickstein R, Udvardi MK, Zhao PX, Scheible WR. Genome-Wide Identification of Medicago Peptides Involved in Macronutrient Responses and Nodulation. PLANT PHYSIOLOGY 2017; 175:1669-1689. [PMID: 29030416 PMCID: PMC5717731 DOI: 10.1104/pp.17.01096] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 10/10/2017] [Indexed: 05/18/2023]
Abstract
Growing evidence indicates that small, secreted peptides (SSPs) play critical roles in legume growth and development, yet the annotation of SSP-coding genes is far from complete. Systematic reannotation of the Medicago truncatula genome identified 1,970 homologs of established SSP gene families and an additional 2,455 genes that are potentially novel SSPs, previously unreported in the literature. The expression patterns of known and putative SSP genes based on 144 RNA sequencing data sets covering various stages of macronutrient deficiencies and symbiotic interactions with rhizobia and mycorrhiza were investigated. Focusing on those known or suspected to act via receptor-mediated signaling, 240 nutrient-responsive and 365 nodulation-responsive Signaling-SSPs were identified, greatly expanding the number of SSP gene families potentially involved in acclimation to nutrient deficiencies and nodulation. Synthetic peptide applications were shown to alter root growth and nodulation phenotypes, revealing additional regulators of legume nutrient acquisition. Our results constitute a powerful resource enabling further investigations of specific SSP functions via peptide treatment and reverse genetics.
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Affiliation(s)
- Thomas C de Bang
- Noble Research Institute, Ardmore, Oklahoma 73401
- Department of Plant and Environmental Sciences and Copenhagen Plant Science Center, Faculty of Science, University of Copenhagen, DK-1871 Frederiksberg C, Denmark
| | | | - Xinbin Dai
- Noble Research Institute, Ardmore, Oklahoma 73401
| | | | | | - Pooja Pant
- Noble Research Institute, Ardmore, Oklahoma 73401
| | | | - Sonali Roy
- Noble Research Institute, Ardmore, Oklahoma 73401
| | | | - Vijaykumar Veerappan
- Department of Biological Sciences, BioDiscovery Institute, University of North Texas, Denton, Texas 76203
| | - Rebecca Dickstein
- Department of Biological Sciences, BioDiscovery Institute, University of North Texas, Denton, Texas 76203
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13
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Wang W, Shi J, Xie Q, Jiang Y, Yu N, Wang E. Nutrient Exchange and Regulation in Arbuscular Mycorrhizal Symbiosis. MOLECULAR PLANT 2017; 10:1147-1158. [PMID: 28782719 DOI: 10.1016/j.molp.2017.07.012] [Citation(s) in RCA: 190] [Impact Index Per Article: 27.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 07/29/2017] [Accepted: 07/31/2017] [Indexed: 05/19/2023]
Abstract
Most land plants form symbiotic associations with arbuscular mycorrhizal (AM) fungi. These are the most common and widespread terrestrial plant symbioses, which have a global impact on plant mineral nutrition. The establishment of AM symbiosis involves recognition of the two partners and bidirectional transport of different mineral and carbon nutrients through the symbiotic interfaces within the host root cells. Intriguingly, recent discoveries have highlighted that lipids are transferred from the plant host to AM fungus as a major carbon source. In this review, we discuss the transporter-mediated transfer of carbon, nitrogen, phosphate, potassium and sulfate, and present hypotheses pertaining to the potential regulatory mechanisms of nutrient exchange in AM symbiosis. Current challenges and future perspectives on AM symbiosis research are also discussed.
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Affiliation(s)
- Wanxiao Wang
- College of Life and Environment Sciences, Shanghai Normal University, Shanghai 200234, China; National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Jincai Shi
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Qiujin Xie
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Yina Jiang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Nan Yu
- College of Life and Environment Sciences, Shanghai Normal University, Shanghai 200234, China.
| | - Ertao Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China.
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14
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Burghardt LT, Guhlin J, Chun CL, Liu J, Sadowsky MJ, Stupar RM, Young ND, Tiffin P. Transcriptomic basis of genome by genome variation in a legume‐rhizobia mutualism. Mol Ecol 2017; 26:6122-6135. [DOI: 10.1111/mec.14285] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 07/10/2017] [Indexed: 02/01/2023]
Affiliation(s)
- Liana T. Burghardt
- Department of Plant and Microbial Biology University of Minnesota St. Paul MN USA
| | - Joseph Guhlin
- Department of Plant and Microbial Biology University of Minnesota St. Paul MN USA
| | - Chan Lan Chun
- BioTechnology Institute University of Minnesota St. Paul MN USA
| | - Junqi Liu
- Department of Agronomy and Plant Genetics University of Minnesota St. Paul MN USA
| | | | - Robert M. Stupar
- Department of Agronomy and Plant Genetics University of Minnesota St. Paul MN USA
| | - Nevin D. Young
- Department of Plant and Microbial Biology University of Minnesota St. Paul MN USA
- Department of Plant Pathology University of Minnesota St. Paul MN USA
| | - Peter Tiffin
- Department of Plant and Microbial Biology University of Minnesota St. Paul MN USA
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15
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Kurmanbayeva A, Bekturova A, Srivastava S, Soltabayeva A, Asatryan A, Ventura Y, Khan MS, Salazar O, Fedoroff N, Sagi M. Higher Novel L-Cys Degradation Activity Results in Lower Organic-S and Biomass in Sarcocornia than the Related Saltwort, Salicornia. PLANT PHYSIOLOGY 2017; 175:272-289. [PMID: 28743765 PMCID: PMC5580768 DOI: 10.1104/pp.17.00780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 07/22/2017] [Indexed: 05/08/2023]
Abstract
Salicornia and Sarcocornia are almost identical halophytes whose edible succulent shoots hold promise for commercial production in saline water. Enhanced sulfur nutrition may be beneficial to crops naturally grown on high sulfate. However, little is known about sulfate nutrition in halophytes. Here we show that Salicornia europaea (ecotype RN) exhibits a significant increase in biomass and organic-S accumulation in response to supplemental sulfate, whereas Sarcocornia fruticosa (ecotype VM) does not, instead exhibiting increased sulfate accumulation. We investigated the role of two pathways on organic-S and biomass accumulation in Salicornia and Sarcoconia: the sulfate reductive pathway that generates Cys and l-Cys desulfhydrase that degrades Cys to H2S, NH3, and pyruvate. The major function of O-acetyl-Ser-(thiol) lyase (OAS-TL; EC 2.5.1.47) is the formation of l-Cys, but our study shows that the OAS-TL A and OAS-TL B of both halophytes are enzymes that also degrade l-Cys to H2S. This activity was significantly higher in Sarcocornia than in Salicornia, especially upon sulfate supplementation. The activity of the sulfate reductive pathway key enzyme, adenosine 5'-phosphosulfate reductase (APR, EC 1.8.99.2), was significantly higher in Salicornia than in Sarcocornia These results suggest that the low organic-S level in Sarcocornia is the result of high l-Cys degradation rate by OAS-TLs, whereas the greater organic-S and biomass accumulation in Salicornia is the result of higher APR activity and low l-Cys degradation rate, resulting in higher net Cys biosynthesis. These results present an initial road map for halophyte growers to attain better growth rates and nutritional value of Salicornia and Sarcocornia.
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Affiliation(s)
- Assylay Kurmanbayeva
- Plant Stress Laboratory, French Associates Institute for Agriculture and Biotechnology of Drylands, Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, 84990, Israel
| | - Aizat Bekturova
- Plant Stress Laboratory, French Associates Institute for Agriculture and Biotechnology of Drylands, Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, 84990, Israel
| | - Sudhakar Srivastava
- Plant Stress Laboratory, French Associates Institute for Agriculture and Biotechnology of Drylands, Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, 84990, Israel
| | - Aigerim Soltabayeva
- Plant Stress Laboratory, French Associates Institute for Agriculture and Biotechnology of Drylands, Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, 84990, Israel
| | - Armine Asatryan
- Plant Stress Laboratory, French Associates Institute for Agriculture and Biotechnology of Drylands, Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, 84990, Israel
| | - Yvonne Ventura
- Plant Stress Laboratory, French Associates Institute for Agriculture and Biotechnology of Drylands, Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, 84990, Israel
| | - Mohammad Suhail Khan
- King Abdullah University of Science and Technology, Biological and Environmental Science and Engineering Division (BESE), Thuwal, 23955-6900, Saudi Arabia
| | - Octavio Salazar
- King Abdullah University of Science and Technology, Biological and Environmental Science and Engineering Division (BESE), Thuwal, 23955-6900, Saudi Arabia
| | - Nina Fedoroff
- King Abdullah University of Science and Technology, Biological and Environmental Science and Engineering Division (BESE), Thuwal, 23955-6900, Saudi Arabia
- Evan Pugh Professor Emerita, Penn State University, State College, Pennsylvania
| | - Moshe Sagi
- Plant Stress Laboratory, French Associates Institute for Agriculture and Biotechnology of Drylands, Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, 84990, Israel
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16
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Peinado-Guevara LI, López-Meyer M, López-Valenzuela JA, Maldonado-Mendoza IE, Galindo-Flores H, Campista-León S, Medina-Godoy S. Comparative proteomic analysis of leaf tissue from tomato plants colonized with Rhizophagus irregularis. Symbiosis 2017. [DOI: 10.1007/s13199-016-0470-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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17
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Desalegn G, Turetschek R, Kaul HP, Wienkoop S. Microbial symbionts affect Pisum sativum proteome and metabolome under Didymella pinodes infection. J Proteomics 2016; 143:173-187. [PMID: 27016040 DOI: 10.1016/j.jprot.2016.03.018] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Revised: 02/18/2016] [Accepted: 03/15/2016] [Indexed: 11/15/2022]
Abstract
UNLABELLED The long cultivation of field pea led to an enormous diversity which, however, seems to hold just little resistance against the ascochyta blight disease complex. The potential of below ground microbial symbiosis to prime the immune system of Pisum for an upcoming pathogen attack has hitherto received little attention. This study investigates the effect of beneficial microbes on the leaf proteome and metabolome as well as phenotype characteristics of plants in various symbiont interactions (mycorrhiza, rhizobia, co-inoculation, non-symbiotic) after infestation by Didymella pinodes. In healthy plants, mycorrhiza and rhizobia induced changes in RNA metabolism and protein synthesis. Furthermore, metal handling and ROS dampening was affected in all mycorrhiza treatments. The co-inoculation caused the synthesis of stress related proteins with concomitant adjustment of proteins involved in lipid biosynthesis. The plant's disease infection response included hormonal adjustment, ROS scavenging as well as synthesis of proteins related to secondary metabolism. The regulation of the TCA, amino acid and secondary metabolism including the pisatin pathway, was most pronounced in rhizobia associated plants which had the lowest infection rate and the slowest disease progression. BIOLOGICAL SIGNIFICANCE A most comprehensive study of the Pisum sativum proteome and metabolome infection response to Didymella pinodes is provided. Several distinct patterns of microbial symbioses on the plant metabolism are presented for the first time. Upon D. pinodes infection, rhizobial symbiosis revealed induced systemic resistance e.g. by an enhanced level of proteins involved in pisatin biosynthesis.
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Affiliation(s)
- G Desalegn
- University of Natural Resources and Life Sciences, Department of Crop Sciences, Austria
| | - R Turetschek
- University of Vienna, Department of Ecogenomics and Systems Biology, Austria
| | - H-P Kaul
- University of Natural Resources and Life Sciences, Department of Crop Sciences, Austria
| | - S Wienkoop
- University of Vienna, Department of Ecogenomics and Systems Biology, Austria.
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18
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Damiani I, Drain A, Guichard M, Balzergue S, Boscari A, Boyer JC, Brunaud V, Cottaz S, Rancurel C, Da Rocha M, Fizames C, Fort S, Gaillard I, Maillol V, Danchin EGJ, Rouached H, Samain E, Su YH, Thouin J, Touraine B, Puppo A, Frachisse JM, Pauly N, Sentenac H. Nod Factor Effects on Root Hair-Specific Transcriptome of Medicago truncatula: Focus on Plasma Membrane Transport Systems and Reactive Oxygen Species Networks. FRONTIERS IN PLANT SCIENCE 2016; 7:794. [PMID: 27375649 PMCID: PMC4894911 DOI: 10.3389/fpls.2016.00794] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 05/22/2016] [Indexed: 05/18/2023]
Abstract
Root hairs are involved in water and nutrient uptake, and thereby in plant autotrophy. In legumes, they also play a crucial role in establishment of rhizobial symbiosis. To obtain a holistic view of Medicago truncatula genes expressed in root hairs and of their regulation during the first hours of the engagement in rhizobial symbiotic interaction, a high throughput RNA sequencing on isolated root hairs from roots challenged or not with lipochitooligosaccharides Nod factors (NF) for 4 or 20 h was carried out. This provided a repertoire of genes displaying expression in root hairs, responding or not to NF, and specific or not to legumes. In analyzing the transcriptome dataset, special attention was paid to pumps, transporters, or channels active at the plasma membrane, to other proteins likely to play a role in nutrient ion uptake, NF electrical and calcium signaling, control of the redox status or the dynamic reprogramming of root hair transcriptome induced by NF treatment, and to the identification of papilionoid legume-specific genes expressed in root hairs. About 10% of the root hair expressed genes were significantly up- or down-regulated by NF treatment, suggesting their involvement in remodeling plant functions to allow establishment of the symbiotic relationship. For instance, NF-induced changes in expression of genes encoding plasma membrane transport systems or disease response proteins indicate that root hairs reduce their involvement in nutrient ion absorption and adapt their immune system in order to engage in the symbiotic interaction. It also appears that the redox status of root hair cells is tuned in response to NF perception. In addition, 1176 genes that could be considered as "papilionoid legume-specific" were identified in the M. truncatula root hair transcriptome, from which 141 were found to possess an ortholog in every of the six legume genomes that we considered, suggesting their involvement in essential functions specific to legumes. This transcriptome provides a valuable resource to investigate root hair biology in legumes and the roles that these cells play in rhizobial symbiosis establishment. These results could also contribute to the long-term objective of transferring this symbiotic capacity to non-legume plants.
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Affiliation(s)
- Isabelle Damiani
- Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, UMR 1355-7254 Institut Sophia Agrobiotech, Université Nice Sophia AntipolisSophia Antipolis, France
| | - Alice Drain
- Biochimie and Physiologie Moléculaire des Plantes, UMR 5004 Centre National de la Recherche Scientifique/386 Institut National de la Recherche Agronomique/SupAgro Montpellier/Université de Montpellier, Campus SupAgro-Institut National de la Recherche AgronomiqueMontpellier, France
| | - Marjorie Guichard
- Institute for Integrative Biology of the Cell, CEA, Centre National de la Recherche Scientifique, Université Paris-Sud, Université Paris-SaclayGif sur Yvette, France
| | - Sandrine Balzergue
- POPS Transcriptomic Platform, Centre National de la Recherche Scientifique, Institute of Plant Sciences Paris-Saclay, Institut National de la Recherche Agronomique, Université Paris-Sud, Université Evry, Université Paris-SaclayOrsay, France
- POPS Transcriptomic Platform, Institute of Plant Sciences Paris-Saclay, Paris DiderotOrsay, France
| | - Alexandre Boscari
- Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, UMR 1355-7254 Institut Sophia Agrobiotech, Université Nice Sophia AntipolisSophia Antipolis, France
| | - Jean-Christophe Boyer
- Biochimie and Physiologie Moléculaire des Plantes, UMR 5004 Centre National de la Recherche Scientifique/386 Institut National de la Recherche Agronomique/SupAgro Montpellier/Université de Montpellier, Campus SupAgro-Institut National de la Recherche AgronomiqueMontpellier, France
| | - Véronique Brunaud
- POPS Transcriptomic Platform, Centre National de la Recherche Scientifique, Institute of Plant Sciences Paris-Saclay, Institut National de la Recherche Agronomique, Université Paris-Sud, Université Evry, Université Paris-SaclayOrsay, France
- POPS Transcriptomic Platform, Institute of Plant Sciences Paris-Saclay, Paris DiderotOrsay, France
| | - Sylvain Cottaz
- Université Grenoble Alpes, CERMAVGrenoble, France
- Centre National de la Recherche Scientifique, CERMAVGrenoble, France
| | - Corinne Rancurel
- Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, UMR 1355-7254 Institut Sophia Agrobiotech, Université Nice Sophia AntipolisSophia Antipolis, France
| | - Martine Da Rocha
- Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, UMR 1355-7254 Institut Sophia Agrobiotech, Université Nice Sophia AntipolisSophia Antipolis, France
| | - Cécile Fizames
- Biochimie and Physiologie Moléculaire des Plantes, UMR 5004 Centre National de la Recherche Scientifique/386 Institut National de la Recherche Agronomique/SupAgro Montpellier/Université de Montpellier, Campus SupAgro-Institut National de la Recherche AgronomiqueMontpellier, France
| | - Sébastien Fort
- Université Grenoble Alpes, CERMAVGrenoble, France
- Centre National de la Recherche Scientifique, CERMAVGrenoble, France
| | - Isabelle Gaillard
- Biochimie and Physiologie Moléculaire des Plantes, UMR 5004 Centre National de la Recherche Scientifique/386 Institut National de la Recherche Agronomique/SupAgro Montpellier/Université de Montpellier, Campus SupAgro-Institut National de la Recherche AgronomiqueMontpellier, France
| | - Vincent Maillol
- Université Grenoble Alpes, CERMAVGrenoble, France
- Laboratoire d'Informatique, de Robotique et de Microélectronique de Montpellier and Institut de Biologie Computationnelle, Centre National de la Recherche Scientifique and Université MontpellierMontpellier, France
| | - Etienne G. J. Danchin
- Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, UMR 1355-7254 Institut Sophia Agrobiotech, Université Nice Sophia AntipolisSophia Antipolis, France
| | - Hatem Rouached
- Biochimie and Physiologie Moléculaire des Plantes, UMR 5004 Centre National de la Recherche Scientifique/386 Institut National de la Recherche Agronomique/SupAgro Montpellier/Université de Montpellier, Campus SupAgro-Institut National de la Recherche AgronomiqueMontpellier, France
| | - Eric Samain
- Université Grenoble Alpes, CERMAVGrenoble, France
- Centre National de la Recherche Scientifique, CERMAVGrenoble, France
| | - Yan-Hua Su
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of SciencesNanjing, China
| | - Julien Thouin
- Biochimie and Physiologie Moléculaire des Plantes, UMR 5004 Centre National de la Recherche Scientifique/386 Institut National de la Recherche Agronomique/SupAgro Montpellier/Université de Montpellier, Campus SupAgro-Institut National de la Recherche AgronomiqueMontpellier, France
| | - Bruno Touraine
- Biochimie and Physiologie Moléculaire des Plantes, UMR 5004 Centre National de la Recherche Scientifique/386 Institut National de la Recherche Agronomique/SupAgro Montpellier/Université de Montpellier, Campus SupAgro-Institut National de la Recherche AgronomiqueMontpellier, France
| | - Alain Puppo
- Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, UMR 1355-7254 Institut Sophia Agrobiotech, Université Nice Sophia AntipolisSophia Antipolis, France
| | - Jean-Marie Frachisse
- Institute for Integrative Biology of the Cell, CEA, Centre National de la Recherche Scientifique, Université Paris-Sud, Université Paris-SaclayGif sur Yvette, France
| | - Nicolas Pauly
- Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, UMR 1355-7254 Institut Sophia Agrobiotech, Université Nice Sophia AntipolisSophia Antipolis, France
- *Correspondence: Nicolas Pauly
| | - Hervé Sentenac
- Biochimie and Physiologie Moléculaire des Plantes, UMR 5004 Centre National de la Recherche Scientifique/386 Institut National de la Recherche Agronomique/SupAgro Montpellier/Université de Montpellier, Campus SupAgro-Institut National de la Recherche AgronomiqueMontpellier, France
- Hervé Sentenac
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