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Zhang L, Sun W, Gao W, Zhang Y, Zhang P, Liu Y, Chen T, Yang D. Genome-wide identification and analysis of the GGCT gene family in wheat. BMC Genomics 2024; 25:32. [PMID: 38177998 PMCID: PMC10768367 DOI: 10.1186/s12864-023-09934-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 12/21/2023] [Indexed: 01/06/2024] Open
Abstract
BACKGROUND γ-glutamylcyclotransferase (GGCT), an enzyme to maintain glutathione homeostasis, plays a vital role in the response to plant growth and development as well as the adaptation to various stresses. Although the GGCT gene family analysis has been conducted in Arabidopsis and rice, the family genes have not yet been well identified and analyzed at the genome-wide level in wheat (Triticum aestivum L.). RESULTS In the present study, 20 TaGGCT genes were identified in the wheat genome and widely distributed on chromosomes 2A, 2B, 2D, 3A, 4A, 5A, 5B, 5D, 6A, 6B, 6D, 7A, 7B, and 7D. Phylogenetic and structural analyses showed that these TaGGCT genes could be classified into three subfamilies: ChaC, GGGACT, and GGCT-PS. They exhibited similar motif compositions and distribution patterns in the same subgroup. Gene duplication analysis suggested that the expansion of TaGGCT family genes was facilitated by segmental duplications and tandem repeats in the wheat evolutionary events. Identification of diverse cis-acting response elements in TaGGCT promoters indicated their potential fundamental roles in response to plant development and abiotic stresses. The analysis of transcriptome data combined with RT-qPCR results revealed that the TaGGCTs genes exhibited ubiquitous expression across plant organs, with highly expressed in roots, stems, and developing grains. Most TaGGCT genes were up-regulated after 6 h under 20% PEG6000 and ABA treatments. Association analysis revealed that two haplotypes of TaGGCT20 gene displayed significantly different Thousand-kernel weight (TKW), Kernel length (KL), and Kernel width (KW) in wheat. The geographical and annual distribution of the two haplotypes of TaGGCT20 gene further revealed that the frequency of the favorable haplotype TaGGCT20-Hap-I was positively selected in the historical breeding process of wheat. CONCLUSION This study investigated the genome-wide identification, structure, evolution, and expression analysis of TaGGCT genes in wheat. The motifs of TaGGCTs were highly conserved throughout the evolutionary history of wheat. Most TaGGCT genes were highly expressed in roots, stems, and developing grains, and involved in the response to drought stresses. Two haplotypes were developed in the TaGGCT20 gene, where TaGGCT20-Hap-I, as a favorable haplotype, was significantly associated with higher TKW, KL, and KW in wheat, suggesting that the haplotype is used as a function marker for the selection in grain yield in wheat breeding.
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Affiliation(s)
- Long Zhang
- State Key Laboratory of Aridland Crop Science, Lanzhou, Gansu, 730070, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, 730070, China
| | - Wanting Sun
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, 730070, China
| | - Weidong Gao
- State Key Laboratory of Aridland Crop Science, Lanzhou, Gansu, 730070, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, 730070, China
| | - Yanyan Zhang
- State Key Laboratory of Aridland Crop Science, Lanzhou, Gansu, 730070, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, 730070, China
| | - Peipei Zhang
- State Key Laboratory of Aridland Crop Science, Lanzhou, Gansu, 730070, China
| | - Yuan Liu
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, 730070, China
| | - Tao Chen
- State Key Laboratory of Aridland Crop Science, Lanzhou, Gansu, 730070, China.
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, 730070, China.
| | - Delong Yang
- State Key Laboratory of Aridland Crop Science, Lanzhou, Gansu, 730070, China.
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, 730070, China.
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Apodiakou A, Hoefgen R. New insights into the regulation of plant metabolism by O-acetylserine: sulfate and beyond. J Exp Bot 2023; 74:3361-3378. [PMID: 37025061 DOI: 10.1093/jxb/erad124] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 04/04/2023] [Indexed: 06/08/2023]
Abstract
Under conditions of sulfur deprivation, O-acetylserine (OAS) accumulates, which leads to the induction of a common set of six genes, called OAS cluster genes. These genes are induced not only under sulfur deprivation, but also under other conditions where OAS accumulates, such as shift to darkness and stress conditions leading to reactive oxygen species (ROS) or methyl-jasmonate accumulation. Using the OAS cluster genes as a query in ATTED-II, a co-expression network is derived stably spanning several hundred conditions. This allowed us not only to describe the downstream function of the OAS cluster genes but also to score for functions of the members of the co-regulated co-expression network and hence the effects of the OAS signal on the sulfate assimilation pathway and co-regulated pathways. Further, we summarized existing knowledge on the regulation of the OAS cluster and the co-expressed genes. We revealed that the known sulfate deprivation-related transcription factor EIL3/SLIM1 exhibits a prominent role, as most genes are subject to regulation by this transcription factor. The role of other transcription factors in response to OAS awaits further investigation.
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Affiliation(s)
- Anastasia Apodiakou
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Rainer Hoefgen
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
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Pavlů J, Kerchev P, Černý M, Novák J, Berka M, Jobe TO, López Ramos JM, Saiz-Fernández I, Rashotte AM, Kopriva S, Brzobohatý B. Cytokinin modulates the metabolic network of sulfur and glutathione. J Exp Bot 2022; 73:7417-7433. [PMID: 36226742 DOI: 10.1093/jxb/erac391] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 10/12/2022] [Indexed: 06/16/2023]
Abstract
The phytohormone cytokinin is implicated in a range of growth, developmental, and defense processes. A growing body of evidence supports a crosstalk between cytokinin and nutrient signaling pathways, such as nitrate availability. Cytokinin signaling regulates sulfur-responsive gene expression, but the underlying molecular mechanisms and their impact on sulfur-containing metabolites have not been systematically explored. Using a combination of genetic and pharmacological tools, we investigated the interplay between cytokinin signaling and sulfur homeostasis. Exogenous cytokinin triggered sulfur starvation-like gene expression accompanied by a decrease in sulfate and glutathione content. This process was uncoupled from the activity of the major transcriptional regulator of sulfate starvation signaling SULFUR LIMITATION 1 and an important glutathione-degrading enzyme, γ-glutamyl cyclotransferase 2;1, expression of which was robustly up-regulated by cytokinin. Conversely, glutathione accumulation was observed in mutants lacking the cytokinin receptor ARABIDOPSIS HISTIDINE KINASE 3 and in cytokinin-deficient plants. Cytokinin-deficient plants displayed improved root growth upon exposure to glutathione-depleting chemicals which was attributed to a higher capacity to maintain glutathione levels. These results shed new light on the interplay between cytokinin signaling and sulfur homeostasis. They position cytokinin as an important modulator of sulfur uptake, assimilation, and remobilization in plant defense against xenobiotics and root growth.
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Affiliation(s)
- Jaroslav Pavlů
- Department of Molecular Biology and Radiobiology, Faculty of AgriSciences, Mendel University in Brno, Brno, Czech Republic
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Pavel Kerchev
- Department of Molecular Biology and Radiobiology, Faculty of AgriSciences, Mendel University in Brno, Brno, Czech Republic
| | - Martin Černý
- Department of Molecular Biology and Radiobiology, Faculty of AgriSciences, Mendel University in Brno, Brno, Czech Republic
| | - Jan Novák
- Department of Molecular Biology and Radiobiology, Faculty of AgriSciences, Mendel University in Brno, Brno, Czech Republic
| | - Miroslav Berka
- Department of Molecular Biology and Radiobiology, Faculty of AgriSciences, Mendel University in Brno, Brno, Czech Republic
| | - Timothy O Jobe
- Institute for Plant Sciences, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne, Germany
| | - José Maria López Ramos
- Institute for Plant Sciences, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne, Germany
| | - Iñigo Saiz-Fernández
- Department of Molecular Biology and Radiobiology, Faculty of AgriSciences, Mendel University in Brno, Brno, Czech Republic
| | - Aaron Michael Rashotte
- Department of Molecular Biology and Radiobiology, Faculty of AgriSciences, Mendel University in Brno, Brno, Czech Republic
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
| | - Stanislav Kopriva
- Institute for Plant Sciences, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne, Germany
| | - Břetislav Brzobohatý
- Department of Molecular Biology and Radiobiology, Faculty of AgriSciences, Mendel University in Brno, Brno, Czech Republic
- Central European Institute of Technology (CEITEC), Mendel University in Brno, Brno, Czech Republic
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Wawrzyńska A, Piotrowska J, Apodiakou A, Brückner F, Hoefgen R, Sirko A. The SLIM1 transcription factor affects sugar signaling during sulfur deficiency in Arabidopsis. J Exp Bot 2022; 73:7362-7379. [PMID: 36099003 PMCID: PMC9730805 DOI: 10.1093/jxb/erac371] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 09/12/2022] [Indexed: 06/08/2023]
Abstract
The homeostasis of major macronutrient metabolism needs to be tightly regulated, especially when the availability of one or more nutrients fluctuates in the environment. Both sulfur metabolism and glucose signaling are important processes throughout plant growth and development, as well as during stress responses. Still, very little is known about how these processes affect each other, although they are positively connected. Here, we showed in Arabidopsis that the crucial transcription factor of sulfur metabolism, SLIM1, is involved in glucose signaling during shortage of sulfur. The germination rate of the slim1_KO mutant was severely affected by high glucose and osmotic stress. The expression of SLIM1-dependent genes in sulfur deficiency appeared to be additionally induced by a high concentration of either mannitol or glucose, but also by sucrose, which is not only the source of glucose but another signaling molecule. Additionally, SLIM1 affects PAP1 expression during sulfur deficiency by directly binding to its promoter. The lack of PAP1 induction in such conditions leads to much lower anthocyanin production. Taken together, our results indicate that SLIM1 is involved in the glucose response by modulating sulfur metabolism and directly controlling PAP1 expression in Arabidopsis during sulfur deficiency stress.
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Affiliation(s)
| | - Justyna Piotrowska
- Laboratory of Plant Protein Homeostasis, Institute of Biochemistry and Biophysics Polish Academy of Sciences, Warsaw, Poland
| | - Anastasia Apodiakou
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Franziska Brückner
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Rainer Hoefgen
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Agnieszka Sirko
- Laboratory of Plant Protein Homeostasis, Institute of Biochemistry and Biophysics Polish Academy of Sciences, Warsaw, Poland
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Han B, Wang F, Liu Z, Chen L, Yue D, Sun W, Lin Z, Zhang X, Zhou X, Yang X. Transcriptome and metabolome profiling of interspecific CSSLs reveals general and specific mechanisms of drought resistance in cotton. Theor Appl Genet 2022; 135:3375-3391. [PMID: 35999283 DOI: 10.1007/s00122-022-04174-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 07/05/2022] [Indexed: 06/15/2023]
Abstract
In order to understand the molecular mechanism of cotton's response to drought during the flowering and boll stage, transcriptomics and metabolomics were carried out for two introgression lines (drought-tolerant line: T307; drought-sensitive line: S48) which were screened from Gossypium hirsutum cv. 'Emian22' with some gene fragments imported from Gossypium barbadense acc. 3-79, under drought stress by withdrawing water at flowering and boll stage. Results showed that the basic drought response in cotton included a series of broad-spectrum responses, such as amino acid synthesis, hormone (abscisic acid, ABA) signal transduction, and mitogen-activated protein kinases signal transduction pathway, which activated in both drought-tolerant and drought-sensitive lines. However, the difference of their imported fragments and diminished sequences triggers endoplasmic reticulum (ER) protein processing, photosynthetic-related pathways (in leaves), and membrane solute transport (in roots) in drought-tolerant line T307, while these are missed or not activated in drought-sensitive line S48, reflecting the different drought tolerance of the two genotypes. Virus-induced gene silencing assay of drought-tolerant differentially expressed heat shock protein (HSP) genes (mainly in leaf) and ATP-binding cassette (ABC) transporter genes (mainly in roots) indicated that those genes play important role in cotton drought tolerant. Combined analysis of transcriptomics and metabolomics highlighted the important roles of ER-stress-related HSP genes and root-specific ABC transporter genes in plants drought tolerance. These results provide new insights into the molecular mechanisms underlying the drought stress adaptation in cotton.
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Affiliation(s)
- Bei Han
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, People's Republic of China
| | - Fengjiao Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, People's Republic of China
| | - Zhilin Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, People's Republic of China
| | - Lin Chen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, People's Republic of China
| | - Dandan Yue
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, People's Republic of China
| | - Weinan Sun
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, People's Republic of China
| | - Zhongxu Lin
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, People's Republic of China
| | - Xianlong Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, People's Republic of China
| | - Xiaofeng Zhou
- Xinjiang Academy of Agriculture and Reclamation Science, Cotton Institute, Shihezi, 832000, Xinjiang, People's Republic of China.
| | - Xiyan Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, People's Republic of China.
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Liu Z, Liu D, Fu X, Du X, Zhang Y, Zhen W, Li S, Yang H, He S, Li R. Integrated transcriptomic and metabolomic analyses revealed the regulatory mechanism of sulfur application in grain yield and protein content in wheat ( Triticum aestivum L.). Front Plant Sci 2022; 13:935516. [PMID: 36186031 PMCID: PMC9523790 DOI: 10.3389/fpls.2022.935516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 08/24/2022] [Indexed: 06/16/2023]
Abstract
Sulfur fertilizers play an important role in increasing the yield and improving the dough quality of bread wheat, but their regulatory mechanism remains unclear. In this study, 0 kg·ha-1 (S0) and 60 kg·ha-1 (S60) of sulfur were applied on the anthesis date; subsequently, immature wheat grains at 8, 13, and 18 days post-anthesis (DPA) were subjected to integrated transcriptomic and metabolomic analyses to investigate the changes in the gene/metabolite activity in a typical strong-gluten wheat, Gaoyou2018 (GY2018). Our data show that the S60 treatment could significantly increase the grain yield and grain protein content by 13.2 and 3.6%, respectively. The transcriptomic analysis revealed that 10,694 differentially expressed genes (DEGs) were induced by S60 from 8 to 18 DPA when compared with their corresponding no-sulfur controls, and most DEGs were mainly involved in lipid metabolism and amino acid metabolism pathways. Ninety-seven MYB transcription factors (TFs) were identified as responsive to the S60 treatment; of these, 66 showed significantly differential expression at 13 DPA, and MYB118 might participate in the process of sulfur metabolism by regulating glucosinolate synthesis. In total, 542 significantly enriched differentially expressed (DE) metabolites (DEMs) were identified following the S60 treatment, which mainly included secondary metabolites, carbohydrates, and amino acids. Several metabolites (e.g., glutathione, sucrose, GDP-alpha-D-glucose, and amino acids) exhibited altered abundances following the S60 treatment. The combination of transcriptomic and metabolomic analyses highlighted the important role of amino acid metabolism (especially cysteine, methionine, and glutathione metabolism) and starch and sucrose metabolism pathways after S60 application. Our results provide valuable information enhancing our understanding of the molecular mechanism of the response to sulfur and provide useful clues for grain protein quality formation and yield improvement in bread wheat.
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Affiliation(s)
- Zhilian Liu
- State Key Laboratory of North China Crop Improvement and Regulation, College of Agronomy, Hebei Agricultural University, Baoding, China
- Wheat Breeding Center, Gaocheng Institute of Agricultural Sciences, Shijiazhuang, China
| | - Dongcheng Liu
- State Key Laboratory of North China Crop Improvement and Regulation, College of Agronomy, Hebei Agricultural University, Baoding, China
| | - Xiaoyi Fu
- Wheat Research Center, Shijiazhuang Academy of Agriculture and Forestry Sciences, Shijiazhuang, China
| | - Xiong Du
- State Key Laboratory of North China Crop Improvement and Regulation, College of Agronomy, Hebei Agricultural University, Baoding, China
| | - Yuechen Zhang
- State Key Laboratory of North China Crop Improvement and Regulation, College of Agronomy, Hebei Agricultural University, Baoding, China
| | - Wenchao Zhen
- State Key Laboratory of North China Crop Improvement and Regulation, College of Agronomy, Hebei Agricultural University, Baoding, China
| | - Shan Li
- State Key Laboratory of North China Crop Improvement and Regulation, College of Agronomy, Hebei Agricultural University, Baoding, China
| | - Haichuan Yang
- Wheat Breeding Center, Gaocheng Institute of Agricultural Sciences, Shijiazhuang, China
| | - Suqin He
- Agricultural Technology Promotion Center, Gaocheng Agricultural and Rural Bureau of Shijiazhuang City, Shijiazhuang, China
| | - Ruiqi Li
- State Key Laboratory of North China Crop Improvement and Regulation, College of Agronomy, Hebei Agricultural University, Baoding, China
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Ito T, Kitaiwa T, Nishizono K, Umahashi M, Miyaji S, Agake S, Kuwahara K, Yokoyama T, Fushinobu S, Maruyama‐Nakashita A, Sugiyama R, Sato M, Inaba J, Hirai MY, Ohkama‐Ohtsu N. Glutathione degradation activity of γ-glutamyl peptidase 1 manifests its dual roles in primary and secondary sulfur metabolism in Arabidopsis. Plant J 2022; 111:1626-1642. [PMID: 35932489 PMCID: PMC9804317 DOI: 10.1111/tpj.15912] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 07/09/2022] [Accepted: 07/20/2022] [Indexed: 06/08/2023]
Abstract
Glutathione (GSH) functions as a major sulfur repository and hence occupies an important position in primary sulfur metabolism. GSH degradation results in sulfur reallocation and is believed to be carried out mainly by γ-glutamyl cyclotransferases (GGCT2;1, GGCT2;2, and GGCT2;3), which, however, do not fully explain the rapid GSH turnover. Here, we discovered that γ-glutamyl peptidase 1 (GGP1) contributes to GSH degradation through a yeast complementation assay. Recombinant proteins of GGP1, as well as GGP3, showed high degradation activity of GSH, but not of oxidized glutathione (GSSG), in vitro. Notably, the GGP1 transcripts were highly abundant in rosette leaves, in agreement with the ggp1 mutants constantly accumulating more GSH regardless of nutritional conditions. Given the lower energy requirements of the GGP- than the GGCT-mediated pathway, the GGP-mediated pathway could be a more efficient route for GSH degradation than the GGCT-mediated pathway. Therefore, we propose a model wherein cytosolic GSH is degraded chiefly by GGP1 and likely also by GGP3. Another noteworthy fact is that GGPs are known to process GSH conjugates in glucosinolate and camalexin synthesis; indeed, we confirmed that the ggp1 mutant contained higher levels of O-acetyl-l-Ser, a signaling molecule for sulfur starvation, and lower levels of glucosinolates and their degradation products. The predicted structure of GGP1 further provided a rationale for this hypothesis. In conclusion, we suggest that GGP1 and possibly GGP3 play vital roles in both primary and secondary sulfur metabolism.
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Affiliation(s)
- Takehiro Ito
- United Graduate School of Agricultural ScienceTokyo University of Agriculture and Technology3‐5‐8, Saiwai‐choFuchuTokyo183‐8509Japan
- RIKEN Center for Sustainable Resource Science1‐7‐22, Suehiro‐cho, Tsurumi‐kuYokohamaKanagawa230‐0045Japan
| | - Taisuke Kitaiwa
- Graduate School of AgricultureTokyo University of Agriculture and Technology3‐5‐8, Saiwai‐choFuchuTokyo183‐8509Japan
| | - Kosuke Nishizono
- Graduate School of AgricultureTokyo University of Agriculture and Technology3‐5‐8, Saiwai‐choFuchuTokyo183‐8509Japan
| | - Minori Umahashi
- Graduate School of AgricultureTokyo University of Agriculture and Technology3‐5‐8, Saiwai‐choFuchuTokyo183‐8509Japan
| | - Shunsuke Miyaji
- Graduate School of AgricultureTokyo University of Agriculture and Technology3‐5‐8, Saiwai‐choFuchuTokyo183‐8509Japan
| | - Shin‐ichiro Agake
- Institute of Global Innovation ResearchTokyo University of Agriculture and Technology3‐5‐8, Saiwai‐choFuchuTokyo183‐8509Japan
| | - Kana Kuwahara
- Faculty of AgricultureTokyo University of Agriculture and Technology3‐5‐8, Saiwai‐choFuchuTokyo183‐8509Japan
| | - Tadashi Yokoyama
- Institute of AgricultureTokyo University of Agriculture and Technology3‐5‐8, Saiwai‐choFuchuTokyo183‐8509Japan
- Faculty of Food and Agricultural SciencesFukushima UniversityKanayagawa 1Fukushima‐shiFukushima960‐1296Japan
| | - Shinya Fushinobu
- Department of BiotechnologyThe University of Tokyo1‐1‐1 YayoiBunkyo‐kuTokyo113‐8657Japan
- Collaborative Research Institute for Innovative MicrobiologyThe University of Tokyo1‐1‐1 YayoiBunkyo‐kuTokyo113‐8657Japan
| | - Akiko Maruyama‐Nakashita
- Graduate School of Bioresource and Bioenvironmental ScienceKyushu University744 MotookaNishi‐kuFukuoka819‐0395Japan
| | - Ryosuke Sugiyama
- RIKEN Center for Sustainable Resource Science1‐7‐22, Suehiro‐cho, Tsurumi‐kuYokohamaKanagawa230‐0045Japan
- Department of PharmacyNational University of Singapore4 Science Drive 2117544SingaporeSingapore
- Present address:
Graduate School of Pharmaceutical SciencesChiba University1‐8‐1, Inohana, Chuo‐kuChiba260‐8675Japan
| | - Muneo Sato
- RIKEN Center for Sustainable Resource Science1‐7‐22, Suehiro‐cho, Tsurumi‐kuYokohamaKanagawa230‐0045Japan
| | - Jun Inaba
- RIKEN Center for Sustainable Resource Science1‐7‐22, Suehiro‐cho, Tsurumi‐kuYokohamaKanagawa230‐0045Japan
| | - Masami Yokota Hirai
- RIKEN Center for Sustainable Resource Science1‐7‐22, Suehiro‐cho, Tsurumi‐kuYokohamaKanagawa230‐0045Japan
- Graduate School of Bioagricultural ScienceNagoya UniversityFuro‐cho, Chikusa‐kuNagoyaAichi464‐8601Japan
| | - Naoko Ohkama‐Ohtsu
- Institute of Global Innovation ResearchTokyo University of Agriculture and Technology3‐5‐8, Saiwai‐choFuchuTokyo183‐8509Japan
- Institute of AgricultureTokyo University of Agriculture and Technology3‐5‐8, Saiwai‐choFuchuTokyo183‐8509Japan
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Dormatey R, Qin T, Wang Y, Karikari B, Dekomah SD, Fan Y, Bi Z, Yao P, Ali K, Sun C, Bai J. Comparative Transcriptome Profiling Reveals Potential Candidate Genes, Transcription Factors, and Biosynthetic Pathways for Phosphite Response in Potato (Solanum tuberosum L.). Genes (Basel) 2022; 13:1379. [PMID: 36011289 PMCID: PMC9407107 DOI: 10.3390/genes13081379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Revised: 07/28/2022] [Accepted: 07/29/2022] [Indexed: 12/10/2022] Open
Abstract
The study was conducted with C31 and C80 genotypes of the potato (Solanum tuberosum L.), which are tolerant and susceptible to phosphite (Phi, H2PO3), respectively. To decipher the molecular mechanisms underlying tolerance and susceptibility to Phi in the potato, RNA sequencing was used to study the global transcriptional patterns of the two genotypes. Media were prepared with 0.25 and 0.50 mM Phi, No-phosphorus (P), and 1.25 mM (phosphate, Pi as control). The values of fragments per kilobase of exon per million mapped fragments of the samples were also subjected to a principal component analysis, grouping the biological replicates of each sample. Using stringent criteria, a minimum of 819 differential (DEGs) were detected in both C80-Phi-0.25_vs_C80-Phi-0.50 (comprising 517 upregulated and 302 downregulated) and C80-Phi-0.50_vs_C80-Phi-0.25 (comprising 302 upregulated and 517 downregulated) and a maximum of 5214 DEGs in both C31-Con_vs_C31-Phi-0.25 (comprising 1947 upregulated and 3267 downregulated) and C31-Phi-0.25_vs_C31-Con (comprising 3267 upregulated and 1947 downregulated). DEGs related to the ribosome, plant hormone signal transduction, photosynthesis, and plant–pathogen interaction performed important functions under Phi stress, as shown by the Kyoto Encyclopedia of Genes and Genomes annotation. The expressions of transcription factors increased significantly in C31 compared with C80. For example, the expressions of Soltu.DM.01G047240, Soltu.DM.08G015900, Soltu.DM.06G012130, and Soltu.DM.08G012710 increased under P deficiency conditions (Phi-0.25, Phi-0.50, and No-P) relative to the control (P sufficiency) in C31. This study adds to the growing body of transcriptome data on Phi stress and provides important clues to the Phi tolerance response of the C31 genotype.
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Laîné P, Coquerel R, Arkoun M, Trouverie J, Etienne P. Assessing the Effect of Silicon Supply on Root Sulfur Uptake in S-Fed and S-Deprived Brassica napus L. Plants (Basel) 2022; 11:1606. [PMID: 35736757 PMCID: PMC9227570 DOI: 10.3390/plants11121606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 06/15/2022] [Accepted: 06/16/2022] [Indexed: 06/15/2023]
Abstract
Silicon (Si) is known to alleviate many nutritional stresses. However, in Brassica napus, which is a highly S-demanding species, the Si effect on S deficiency remains undocumented. The aim of this study was to assess whether Si alleviates the negative effects of S deficiency on Brassica napus and modulates root sulfate uptake capacity and S accumulation. For this, Brassica napus plants were cultivated with or without S and supplied or not supplied with Si. The effects of Si on S content, growth, expression of sulfate transporter genes (BnaSultr1.1; BnaSultr1.2) and sulfate transporters activity in roots were monitored. Si supply did not mitigate growth or S status alterations due to S deprivation but moderated the expression of BnaSultr1.1 in S-deprived plants without affecting the activity of root sulfate transporters. The effects of Si on the amount of S taken-up and on S transporter gene expression were also evaluated after 72 h of S resupply. In S-deprived plants, S re-feeding led to a strong decrease in the expression of both S transporter genes as expected, except in Si-treated plants where BnaSultr1.1 expression was maintained over time. This result is discussed in relation to the similar amount of S accumulated regardless of the Si treatment.
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Affiliation(s)
- Philippe Laîné
- Unicaen, INRAE, UMR 950 EVA, SF Normandie Végétal (FED4277), Normandie Université, 14000 Caen, France; (P.L.); (R.C.); (J.T.)
| | - Raphaël Coquerel
- Unicaen, INRAE, UMR 950 EVA, SF Normandie Végétal (FED4277), Normandie Université, 14000 Caen, France; (P.L.); (R.C.); (J.T.)
| | - Mustapha Arkoun
- Laboratoire de Nutrition Végétale, Agro Innovation International-TIMAC AGRO, 35400 Saint-Malo, France;
| | - Jacques Trouverie
- Unicaen, INRAE, UMR 950 EVA, SF Normandie Végétal (FED4277), Normandie Université, 14000 Caen, France; (P.L.); (R.C.); (J.T.)
| | - Philippe Etienne
- Unicaen, INRAE, UMR 950 EVA, SF Normandie Végétal (FED4277), Normandie Université, 14000 Caen, France; (P.L.); (R.C.); (J.T.)
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Uribe F, Henríquez-Valencia C, Arenas-M A, Medina J, Vidal EA, Canales J. Evolutionary and Gene Expression Analyses Reveal New Insights into the Role of LSU Gene-Family in Plant Responses to Sulfate-Deficiency. Plants 2022; 11:plants11121526. [PMID: 35736678 PMCID: PMC9229004 DOI: 10.3390/plants11121526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 05/30/2022] [Accepted: 06/04/2022] [Indexed: 11/16/2022]
Abstract
LSU proteins belong to a plant-specific gene family initially characterized by their strong induction in response to sulfate (S) deficiency. In the last few years, LSUs have arisen as relevant hubs in protein–protein interaction networks, in which they play relevant roles in the response to abiotic and biotic stresses. Most of our knowledge on LSU genomic organization, expression and function comes from studies in Arabidopsis and tobacco, while little is known about the LSU gene repertoire and evolution of this family in land plants. In this work, a total of 270 LSU family members were identified using 134 land plant species with whole-genome sequences available. Phylogenetic analysis revealed that LSU genes belong to a Spermatophyta-specific gene family, and their homologs are distributed in three major groups, two for dicotyledons and one group for monocotyledons. Protein sequence analyses showed four new motifs that further support the subgroup classification by phylogenetic analyses. Moreover, we analyzed the expression of LSU genes in one representative species of each phylogenetic group (wheat, tomato and Arabidopsis) and found a conserved response to S deficiency, suggesting that these genes might play a key role in S stress responses. In summary, our results indicate that LSU genes belong to the Spermatophyta-specific gene family and their response to S deficiency is conserved in angiosperms.
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Affiliation(s)
- Felipe Uribe
- Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Valdivia 5110566, Chile; (F.U.); (C.H.-V.); (A.A.-M.)
| | - Carlos Henríquez-Valencia
- Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Valdivia 5110566, Chile; (F.U.); (C.H.-V.); (A.A.-M.)
| | - Anita Arenas-M
- Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Valdivia 5110566, Chile; (F.U.); (C.H.-V.); (A.A.-M.)
- ANID-Millennium Science Initiative Program-Millennium Institute for Integrative Biology (iBio), Santiago 8331150, Chile;
| | - Joaquín Medina
- Centro de Biotecnología y Genómica de Plantas, INIA-CSIC-Universidad Politécnica de Madrid, 28223 Madrid, Spain;
| | - Elena A. Vidal
- ANID-Millennium Science Initiative Program-Millennium Institute for Integrative Biology (iBio), Santiago 8331150, Chile;
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Santiago 8580745, Chile
- Escuela de Biotecnología, Facultad de Ciencias, Universidad Mayor, Santiago 8580745, Chile
| | - Javier Canales
- Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Valdivia 5110566, Chile; (F.U.); (C.H.-V.); (A.A.-M.)
- ANID-Millennium Science Initiative Program-Millennium Institute for Integrative Biology (iBio), Santiago 8331150, Chile;
- Correspondence:
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11
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Rakpenthai A, Apodiakou A, Whitcomb SJ, Hoefgen R. In silico analysis of cis-elements and identification of transcription factors putatively involved in the regulation of the OAS cluster genes SDI1 and SDI2. Plant J 2022; 110:1286-1304. [PMID: 35315155 DOI: 10.1111/tpj.15735] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 02/09/2022] [Accepted: 03/01/2022] [Indexed: 06/14/2023]
Abstract
Arabidopsis thaliana sulfur deficiency-induced 1 and sulfur deficiency-induced 2 (SDI1 and SDI2) are involved in partitioning sulfur among metabolite pools during sulfur deficiency, and their transcript levels strongly increase in this condition. However, little is currently known about the cis- and trans-factors that regulate SDI expression. We aimed at identifying DNA sequence elements (cis-elements) and transcription factors (TFs) involved in regulating expression of the SDI genes. We performed in silico analysis of their promoter sequences cataloging known cis-elements and identifying conserved sequence motifs. We screened by yeast-one-hybrid an arrayed library of Arabidopsis TFs for binding to the SDI1 and SDI2 promoters. In total, 14 candidate TFs were identified. Direct association between particular cis-elements in the proximal SDI promoter regions and specific TFs was established via electrophoretic mobility shift assays: sulfur limitation 1 (SLIM1) was shown to bind SURE cis-element(s), the basic domain/leucine zipper (bZIP) core cis-element was shown to be important for HY5-homolog (HYH) binding, and G-box binding factor 1 (GBF1) was shown to bind the E box. Functional analysis of GBF1 and HYH using mutant and over-expressing lines indicated that these TFs promote a higher transcript level of SDI1 in vivo. Additionally, we performed a meta-analysis of expression changes of the 14 TF candidates in a variety of conditions that alter SDI expression. The presented results expand our understanding of sulfur pool regulation by SDI genes.
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Affiliation(s)
- Apidet Rakpenthai
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Anastasia Apodiakou
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Sarah J Whitcomb
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Rainer Hoefgen
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
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Wang R, Liu L, Zhao F, Huang X. Local and Systemic Response to Heterogeneous Sulfate Resupply after Sulfur Deficiency in Rice. Int J Mol Sci 2022; 23:6203. [PMID: 35682882 PMCID: PMC9181796 DOI: 10.3390/ijms23116203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 05/24/2022] [Accepted: 05/31/2022] [Indexed: 11/29/2022] Open
Abstract
Sulfur (S) is an essential mineral nutrient required for plant growth and development. Plants usually face temporal and spatial variation in sulfur availability, including the heterogeneous sulfate content in soils. As sessile organisms, plants have evolved sophisticated mechanisms to modify their gene expression and physiological processes in order to optimize S acquisition and usage. Such plasticity relies on a complicated network to locally sense S availability and systemically respond to S status, which remains poorly understood. Here, we took advantage of a split-root system and performed transcriptome-wide gene expression analysis on rice plants in S deficiency followed by sulfate resupply. S deficiency altered the expressions of 6749 and 1589 genes in roots and shoots, respectively, accounting for 18.07% and 4.28% of total transcripts detected. Homogeneous sulfate resupply in both split-root halves recovered the expression of 27.06% of S-deficiency-responsive genes in shoots, while 20.76% of S-deficiency-responsive genes were recovered by heterogeneous sulfate resupply with only one split-root half being resupplied with sulfate. The local sulfate resupply response genes with expressions only recovered in the split-root half resupplied with sulfate but not in the other half remained in S deficiency were identified in roots, which were mainly enriched in cellular amino acid metabolic process and root growth and development. Several systemic response genes were also identified in roots, whose expressions remained unchanged in the split-root half resupplied with sulfate but were recovered in the other split-root half without sulfate resupply. The systemic response genes were mainly related to calcium signaling and auxin and ABA signaling. In addition, a large number of S-deficiency-responsive genes exhibited simultaneous local and systemic responses to sulfate resupply, such as the sulfate transporter gene OsSULTR1;1 and the O-acetylserine (thiol) lyase gene, highlighting the existence of a systemic regulation of sulfate uptake and assimilation in S deficiency plants followed by sulfate resupply. Our studies provided a comprehensive transcriptome-wide picture of a local and systemic response to heterogeneous sulfate resupply, which will facilitate an understanding of the systemic regulation of S homeostasis in rice.
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Kurmanbayeva A, Bekturova A, Soltabayeva A, Oshanova D, Nurbekova Z, Srivastava S, Tiwari P, Dubey AK, Sagi M. Active O-acetylserine-(thiol) lyase A and B confer improved selenium resistance and degrade l-Cys and l-SeCys in Arabidopsis. J Exp Bot 2022; 73:2525-2539. [PMID: 35084469 DOI: 10.1093/jxb/erac021] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 01/26/2022] [Indexed: 06/14/2023]
Abstract
The roles of cytosolic O-acetylserine-(thiol)-lyase A (OASTLA), chloroplastic OASTLB, and mitochondrial OASTLC in plant selenate resistance were studied in Arabidopsis. Impairment in OASTLA and OASTLB resulted in reduced biomass, chlorophyll and soluble protein content compared with selenate-treated OASTLC-impaired and wild-type plants. The generally lower total selenium (Se), protein-Se, organic-sulfur and protein-sulfur (S) content in oastlA and oastlB compared with wild-type and oastlC leaves indicated that Se accumulation was not the main cause for the stress symptoms in these mutants. Notably, the application of selenate positively induced S-starvation markers and the OASTLs, followed by increased sulfite reductase, sulfite oxidase activities, and increased sulfite and sulfide concentrations. Taken together, our results indicate a futile anabolic S-starvation response that resulted in lower glutathione and increased oxidative stress symptoms in oastlA and oastlB mutants. In-gel assays of l-cysteine and l-seleno-cysteine, desulfhydrase activities revealed that two of the three OASTL activity bands in each of the oastl single mutants were enhanced in response to selenate, whereas the impaired proteins exhibited a missing activity band. The absence of differently migrated activity bands in each of the three oastl mutants indicates that these OASTLs are major components of desulfhydrase activity, degrading l-cysteine and l-seleno-cysteine in Arabidopsis.
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Affiliation(s)
- Assylay Kurmanbayeva
- Department of Biotechnology and Microbiology, L. N. Gumilyov Eurasian National University, Nur-Sultan, Kazakhstan
| | - Aizat Bekturova
- The Albert Katz International School for Desert Studies, The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, Israel
| | - Aigerim Soltabayeva
- The Albert Katz International School for Desert Studies, The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, Israel
| | - Dinara Oshanova
- The Albert Katz International School for Desert Studies, The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, Israel
| | - Zhadyrassyn Nurbekova
- The Albert Katz International School for Desert Studies, The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, Israel
| | - Sudhakar Srivastava
- Jacob Blaustein Center for Scientific Cooperation, The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, Israel
| | - Poonam Tiwari
- Jacob Blaustein Center for Scientific Cooperation, The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, Israel
| | - Arvind Kumar Dubey
- Jacob Blaustein Center for Scientific Cooperation, The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, Israel
| | - Moshe Sagi
- The Albert Katz Department of Dryland Biotechnologies, French Associates Institute for Agriculture and Biotechnology of Dryland, The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, Israel
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14
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Yu T, Zhang J, Cao J, Li X, Li S, Liu C, Wang L. Metabolic Insight into Cold Stress Response in Two Contrasting Maize Lines. Life (Basel) 2022; 12:282. [PMID: 35207570 PMCID: PMC8875087 DOI: 10.3390/life12020282] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 02/08/2022] [Accepted: 02/11/2022] [Indexed: 02/04/2023] Open
Abstract
Maize (Zea mays L.) is sensitive to a minor decrease in temperature at early growth stages, resulting in deteriorated growth at later stages. Although there are significant variations in maize germplasm in response to cold stress, the metabolic responses as stress tolerance mechanisms are largely unknown. Therefore, this study aimed at providing insight into the metabolic responses under cold stress at the early growth stages of maize. Two inbred lines, tolerant (B144) and susceptible (Q319), were subjected to cold stress at the seedling stage, and their corresponding metabolic profiles were explored. The study identified differentially accumulated metabolites in both cultivars in response to induced cold stress with nine core conserved cold-responsive metabolites. Guanosine 3′,5′-cyclic monophosphate was detected as a potential biomarker metabolite to differentiate cold tolerant and sensitive maize genotypes. Furthermore, Quercetin-3-O-(2″′-p-coumaroyl)sophoroside-7-O-glucoside, Phloretin, Phloretin-2′-O-glucoside, Naringenin-7-O-Rutinoside, L-Lysine, L-phenylalanine, L-Glutamine, Sinapyl alcohol, and Feruloyltartaric acid were regulated explicitly in B144 and could be important cold-tolerance metabolites. These results increase our understanding of cold-mediated metabolic responses in maize that can be further utilized to enhance cold tolerance in this significant crop.
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Ying S, Blancaflor EB, Liao F, Scheible W. A phosphorus-limitation induced, functionally conserved DUF506 protein is a repressor of root hair elongation in plants. New Phytol 2022; 233:1153-1171. [PMID: 34775627 PMCID: PMC9300206 DOI: 10.1111/nph.17862] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 11/07/2021] [Indexed: 06/13/2023]
Abstract
Root hairs (RHs) function in nutrient and water acquisition, root metabolite exudation, soil anchorage and plant-microbe interactions. Longer or more abundant RHs are potential breeding traits for developing crops that are more resource-use efficient and can improve soil health. While many genes are known to promote RH elongation, relatively little is known about genes and mechanisms that constrain RH growth. Here we demonstrate that a DOMAIN OF UNKNOWN FUNCTION 506 (DUF506) protein, AT3G25240, negatively regulates Arabidopsis thaliana RH growth. The AT3G25240 gene is strongly and specifically induced during phosphorus (P)-limitation. Mutants of this gene, which we call REPRESSOR OF EXCESSIVE ROOT HAIR ELONGATION 1 (RXR1), have much longer RHs, higher phosphate content and seedling biomass, while overexpression of the gene exhibits opposite phenotypes. Co-immunoprecipitation, pull-down and bimolecular fluorescence complementation (BiFC) analyses reveal that RXR1 physically interacts with a RabD2c GTPase in nucleus, and a rabd2c mutant phenocopies the rxr1 mutant. Furthermore, N-terminal variable region of RXR1 is crucial for inhibiting RH growth. Overexpression of a Brachypodium distachyon RXR1 homolog results in repression of RH elongation in Brachypodium. Taken together, our results reveal a novel DUF506-GTPase module with a prominent role in repression of plant RH elongation especially under P stress.
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Affiliation(s)
- Sheng Ying
- Noble Research Institute LLCArdmoreOK73401USA
- Present address:
Department of Biochemistry and Molecular BiologyMichigan State UniversityEast LansingMI48823USA
| | | | - Fuqi Liao
- Noble Research Institute LLCArdmoreOK73401USA
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16
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Courbet G, D'Oria A, Maillard A, Jing L, Pluchon S, Arkoun M, Pateyron S, Paysant Le Roux C, Diquélou S, Ourry A, Trouverie J, Etienne P. Comparative Omics Analysis of Brassica napus Roots Subjected to Six Individual Macronutrient Deprivations Reveals Deficiency-Specific Genes and Metabolomic Profiles. Int J Mol Sci 2021; 22:11679. [PMID: 34769110 DOI: 10.3390/ijms222111679] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 10/19/2021] [Accepted: 10/21/2021] [Indexed: 12/12/2022] Open
Abstract
The early and specific diagnosis of a macronutrient deficiency is challenging when seeking to better manage fertilizer inputs in the context of sustainable agriculture. Consequently, this study explored the potential for transcriptomic and metabolomic analysis of Brassica napus roots to characterize the effects of six individual macronutrient deprivations (N, Mg, P, S, K, and Ca). Our results showed that before any visual phenotypic response, all macronutrient deprivations led to a large modulation of the transcriptome and metabolome involved in various metabolic pathways, and some were common to all macronutrient deprivations. Significantly, comparative transcriptomic analysis allowed the definition of a subset of 3282, 2011, 6325, 1384, 439, and 5157 differentially expressed genes (DEGs) specific to N, Mg, P, S, K, and Ca deprivations, respectively. Surprisingly, gene ontology term enrichment analysis performed on this subset of specific DEGs highlighted biological processes that are common to a number of these macronutrient deprivations, illustrating the complexity of nutrient interactions. In addition, a set of 38 biochemical compounds that discriminated the macronutrient deprivations was identified using a metabolic approach. The opportunity to use these specific DEGs and/or biochemical compounds as potential molecular indicators to diagnose macronutrient deficiency is discussed.
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Marcos-Barbero EL, Pérez P, Martínez-Carrasco R, Arellano JB, Morcuende R. Genotypic Variability on Grain Yield and Grain Nutritional Quality Characteristics of Wheat Grown under Elevated CO 2 and High Temperature. Plants (Basel) 2021; 10:1043. [PMID: 34064280 PMCID: PMC8224326 DOI: 10.3390/plants10061043] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 05/11/2021] [Accepted: 05/19/2021] [Indexed: 11/24/2022]
Abstract
The progressive rise in atmospheric CO2 concentrations and temperature associated with climate change is predicted to have a major impact on the productivity and quality of food crops. Therefore, food security is highly dependent on climate change. Following a survey with 60 bread wheat genotypes, here we investigated the genetic variation in grain yield and nutritional quality among 10 of these genotypes grown under elevated CO2 and temperature. With this purpose, the biomass production, grain yield-related traits, the grain concentration of starch, total protein, phenolic compounds, and mineral nutrients, together with the total antioxidant capacity, were determined. Variation among genotypes was found for almost all the studied traits. Higher grain and ear numbers were associated with increased grain yield but decreased grain total protein concentration and minerals such as Cu, Fe, Mg, Na, P, and Zn. Mineral nutrients were mainly associated with wheat biomass, whereas protein concentration was affected by plant biomass and yield-related traits. Associations among different nutrients and promising nutrient concentrations in some wheat genotypes were also found. This study demonstrates that the exploration of genetic diversity is a powerful approach, not only for selecting genotypes with improved quality, but also for dissecting the effect of the environment on grain yield and nutritional composition.
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Affiliation(s)
| | | | | | | | - Rosa Morcuende
- Institute of Natural Resources and Agrobiology of Salamanca (IRNASA), Consejo Superior de Investigaciones Científicas (CSIC), 37008 Salamanca, Spain; (E.L.M.-B.); (P.P.); (R.M.-C.); (J.B.A.)
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18
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Beleggia R, Omranian N, Holtz Y, Gioia T, Fiorani F, Nigro FM, Pecchioni N, De Vita P, Schurr U, David JL, Nikoloski Z, Papa R. Comparative Analysis Based on Transcriptomics and Metabolomics Data Reveal Differences between Emmer and Durum Wheat in Response to Nitrogen Starvation. Int J Mol Sci 2021; 22:4790. [PMID: 33946478 DOI: 10.3390/ijms22094790] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 04/27/2021] [Accepted: 04/28/2021] [Indexed: 12/04/2022] Open
Abstract
Mounting evidence indicates the key role of nitrogen (N) on diverse processes in plant, including development and defense. Using a combined transcriptomics and metabolomics approach, we studied the response of seedlings to N starvation of two different tetraploid wheat genotypes from the two main domesticated subspecies: emmer and durum wheat. We found that durum wheat exhibits broader and stronger response in comparison to emmer as seen from the expression pattern of both genes and metabolites and gene enrichment analysis. They showed major differences in the responses to N starvation for transcription factor families, emmer showed differential reduction in the levels of primary metabolites while durum wheat exhibited increased levels of most of them to N starvation. The correlation-based networks, including the differentially expressed genes and metabolites, revealed tighter regulation of metabolism in durum wheat in comparison to emmer. We also found that glutamate and γ-aminobutyric acid (GABA) had highest values of centrality in the metabolic correlation network, suggesting their critical role in the genotype-specific response to N starvation of emmer and durum wheat, respectively. Moreover, this finding indicates that there might be contrasting strategies associated to GABA and glutamate signaling modulating shoot vs. root growth in the two different wheat subspecies.
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Abstract
This article comments on:Henriet C, Balliau T, Aime D, Le Signor C, Kreplak J, Zivy M, Gallardo K, Vernoud V. 2021. Proteomics of developing pea seeds reveals a complex antioxidant network underlying the response to sulfur deficiency and water stress. Journal of Experimental Botany 72, 2611–2626.
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Affiliation(s)
- Elmien Heyneke
- Max Planck Institute of Molecular Plant Physiology, D-14476 Potsdam-Golm, Germany
| | - Rainer Hoefgen
- Max Planck Institute of Molecular Plant Physiology, D-14476 Potsdam-Golm, Germany
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20
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Aarabi F, Naake T, Fernie AR, Hoefgen R. Coordinating Sulfur Pools under Sulfate Deprivation. Trends Plant Sci 2020; 25:1227-1239. [PMID: 32800669 DOI: 10.1016/j.tplants.2020.07.007] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 07/09/2020] [Accepted: 07/14/2020] [Indexed: 05/22/2023]
Abstract
Plants display manifold metabolic changes on sulfate deficiency (S deficiency) with all sulfur-containing pools of primary and secondary metabolism affected. O-Acetylserine (OAS), whose levels are rapidly altered on S deficiency, is correlated tightly with novel regulators of plant sulfur metabolism that have key roles in balancing plant sulfur pools, including the Sulfur Deficiency Induced genes (SDI1 and SDI2), More Sulfur Accumulation1 (MSA1), and GGCT2;1. Despite the importance of OAS in the coordination of S pools under stress, mechanisms of OAS perception and signaling have remained elusive. Here, we put particular focus on the general OAS-responsive genes but also elaborate on the specific roles of SDI1 and SDI2 genes, which downregulate the glucosinolate (GSL) pool size. We also highlight the key open questions in sulfur partitioning.
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Affiliation(s)
- Fayezeh Aarabi
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Thomas Naake
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany.
| | - Rainer Hoefgen
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany.
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21
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Dietzen C, Koprivova A, Whitcomb SJ, Langen G, Jobe TO, Hoefgen R, Kopriva S. The Transcription Factor EIL1 Participates in the Regulation of Sulfur-Deficiency Response. Plant Physiol 2020; 184:2120-2136. [PMID: 33060195 PMCID: PMC7723090 DOI: 10.1104/pp.20.01192] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 10/07/2020] [Indexed: 06/08/2023]
Abstract
Sulfur, an indispensable constituent of many cellular components, is a growth-limiting macronutrient for plants. Thus, to successfully adapt to changing sulfur availability and environmental stress, a sulfur-deficiency response helps plants to cope with the limited supply. On the transcriptional level, this response is controlled by SULFUR LIMITATION1 (SLIM1), a member of the ETHYLENE-INSENSITIVE3-LIKE (EIL) transcription factor family. In this study, we identified EIL1 as a second transcriptional activator regulating the sulfur-deficiency response, subordinate to SLIM1/EIL3. Our comprehensive RNA sequencing analysis in Arabidopsis (Arabidopsis thaliana) allowed us to obtain a complete picture of the sulfur-deficiency response and quantify the contributions of these two transcription factors. We confirmed the key role of SLIM1/EIL3 in controlling the response, particularly in the roots, but showed that in leaves more than 50% of the response is independent of SLIM1/EIL3 and EIL1. RNA sequencing showed an additive contribution of EIL1 to the regulation of the sulfur-deficiency response but also identified genes specifically regulated through EIL1. SLIM1/EIL3 seems to have further functions (e.g. in the regulation of genes responsive to hypoxia or mediating defense at both low and normal sulfur supply). These results contribute to the dissection of mechanisms of the sulfur-deficiency response and provide additional possibilities to improve adaptation to sulfur-deficiency conditions.
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Affiliation(s)
- Christof Dietzen
- Institute for Plant Sciences, Cluster of Excellence on Plant Sciences, University of Cologne, 50674 Cologne, Germany
| | - Anna Koprivova
- Institute for Plant Sciences, Cluster of Excellence on Plant Sciences, University of Cologne, 50674 Cologne, Germany
| | - Sarah J Whitcomb
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Gregor Langen
- Institute for Plant Sciences, Cluster of Excellence on Plant Sciences, University of Cologne, 50674 Cologne, Germany
| | - Timothy O Jobe
- Institute for Plant Sciences, Cluster of Excellence on Plant Sciences, University of Cologne, 50674 Cologne, Germany
| | - Rainer Hoefgen
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Stanislav Kopriva
- Institute for Plant Sciences, Cluster of Excellence on Plant Sciences, University of Cologne, 50674 Cologne, Germany
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22
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Abstract
Sulfur (S) is an essential macronutrient for plant growth and development. S is majorly absorbed as sulfate from soil, and is then translocated to plastids in leaves, where it is assimilated into organic products. Cysteine (Cys) is the first organic product generated from S, and it is used as a precursor to synthesize many S-containing metabolites with important biological functions, such as glutathione (GSH) and methionine (Met). The reduction of sulfate takes place in a two-step reaction involving a variety of enzymes. Sulfate transporters (SULTRs) are responsible for the absorption of SO42- from the soil and the transport of SO42- in plants. There are 12-16 members in the S transporter family, which is divided into five categories based on coding sequence homology and biochemical functions. When exposed to S deficiency, plants will alter a series of morphological and physiological processes. Adaptive strategies, including cis-acting elements, transcription factors, non-coding microRNAs, and phytohormones, have evolved in plants to respond to S deficiency. In addition, there is crosstalk between S and other nutrients in plants. In this review, we summarize the recent progress in understanding the mechanisms underlying S homeostasis in plants.
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Affiliation(s)
| | | | - An Yang
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, The Chinese Academy of Sciences, Beijing 100093, China; (Q.L.); (Y.G.)
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Shi W, Liu W, Ma C, Zhang Y, Ding S, Yu W, Deng S, Zhou J, Li H, Luo ZB. Dissecting MicroRNA-mRNA Regulatory Networks Underlying Sulfur Assimilation and Cadmium Accumulation in Poplar Leaves. Plant Cell Physiol 2020; 61:1614-1630. [PMID: 32678905 DOI: 10.1093/pcp/pcaa084] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 06/15/2020] [Indexed: 05/22/2023]
Abstract
The process of cadmium (Cd) accumulation and detoxification under different sulfur levels remains largely unknown in woody plants. To investigate the physiological and transcriptomic regulation mechanisms of poplars in response to different sulfate (S) supply levels and Cd exposure, we exposed Populus deltoides saplings to one of the low, moderate and high S levels together with either 0 or 50 µM Cd. Cd accumulation was decreased in low S-treated poplar leaves, and it tended to be increased in high S-supplied leaves under the Cd exposure condition. Sulfur nutrition was deficient in low S-supplied poplars, and it was improved in high S-treated leaves. Cd exposure resulted in lower sulfur level in the leaves supplied with moderate S, it exacerbated a Cd-induced sulfur decrease in low S-treated leaves and it caused a higher sulfur concentration in high S-supplied leaves. In line with the physiological changes, a number of mRNAs and microRNAs (miRNAs) involved in Cd accumulation and sulfur assimilation were identified and the miRNA-mRNA networks were dissected. In the networks, miR395 and miR399 members were identified as hub miRNAs and their targets were ATP sulfurylase 3 (ATPS3) and phosphate 2 (PHO2), respectively. These results suggest that Cd accumulation and sulfur assimilation are constrained by low and enhanced by high S supply, and Cd toxicity is aggravated by low and relieved by high S in poplar leaves, and that miRNA-mRNA regulatory networks play pivotal roles in sulfur-mediated Cd accumulation and detoxification in Cd-exposed poplars.
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Affiliation(s)
- Wenguang Shi
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Silviculture of the State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Wenzhe Liu
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Silviculture of the State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Chaofeng Ma
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Silviculture of the State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
- College of Forestry, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yuhong Zhang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Silviculture of the State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
- Annoroad Gene Technology Co., Ltd, 6 Kechuang Road, Beijing 100176, China
| | - Shen Ding
- College of Forestry, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Wenjian Yu
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Silviculture of the State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Shurong Deng
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Silviculture of the State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Jing Zhou
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Silviculture of the State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Hong Li
- Postgraduate School, Chinese Academy of Forestry, Beijing 100091, China
| | - Zhi-Bin Luo
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Silviculture of the State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
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Canales J, Uribe F, Henríquez-Valencia C, Lovazzano C, Medina J, Vidal EA. Transcriptomic analysis at organ and time scale reveals gene regulatory networks controlling the sulfate starvation response of Solanum lycopersicum. BMC Plant Biol 2020; 20:385. [PMID: 32831040 PMCID: PMC7444261 DOI: 10.1186/s12870-020-02590-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 08/10/2020] [Indexed: 05/17/2023]
Abstract
BACKGROUND Sulfur is a major component of biological molecules and thus an essential element for plants. Deficiency of sulfate, the main source of sulfur in soils, negatively influences plant growth and crop yield. The effect of sulfate deficiency on plants has been well characterized at the physiological, transcriptomic and metabolomic levels in Arabidopsis thaliana and a limited number of crop plants. However, we still lack a thorough understanding of the molecular mechanisms and regulatory networks underlying sulfate deficiency in most plants. In this work we analyzed the impact of sulfate starvation on the transcriptome of tomato plants to identify regulatory networks and key transcriptional regulators at a temporal and organ scale. RESULTS Sulfate starvation reduces the growth of roots and leaves which is accompanied by major changes in the organ transcriptome, with the response being temporally earlier in roots than leaves. Comparative analysis showed that a major part of the Arabidopsis and tomato transcriptomic response to sulfate starvation is conserved between these plants and allowed for the identification of processes specifically regulated in tomato at the transcript level, including the control of internal phosphate levels. Integrative gene network analysis uncovered key transcription factors controlling the temporal expression of genes involved in sulfate assimilation, as well as cell cycle, cell division and photosynthesis during sulfate starvation in tomato roots and leaves. Interestingly, one of these transcription factors presents a high identity with SULFUR LIMITATION1, a central component of the sulfate starvation response in Arabidopsis. CONCLUSIONS Together, our results provide the first comprehensive catalog of sulfate-responsive genes in tomato, as well as novel regulatory targets for future functional analyses in tomato and other crops.
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Affiliation(s)
- Javier Canales
- Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile.
- Millennium Institute for Integrative Biology (iBio), Santiago, Chile.
| | - Felipe Uribe
- Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
- Millennium Institute for Integrative Biology (iBio), Santiago, Chile
| | - Carlos Henríquez-Valencia
- Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
- Millennium Institute for Integrative Biology (iBio), Santiago, Chile
| | - Carlos Lovazzano
- Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
- Millennium Institute for Integrative Biology (iBio), Santiago, Chile
| | - Joaquín Medina
- Centro de Biotecnología y Genómica de Plantas (CBGP), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Universidad Politécnica de Madrid (UPM), Madrid, Spain
| | - Elena A Vidal
- Millennium Institute for Integrative Biology (iBio), Santiago, Chile.
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Santiago, Chile.
- Escuela de Biotecnología, Facultad de Ciencias, Universidad Mayor, Santiago, Chile.
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25
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Meng X, Zhao X, Ding X, Li Y, Cao G, Chu Z, Su X, Liu Y, Chen X, Guo J, Cai Z, Ding X. Integrated Functional Omics Analysis of Flavonoid-Related Metabolism in AtMYB12 Transcript Factor Overexpressed Tomato. J Agric Food Chem 2020; 68:6776-6787. [PMID: 32396374 DOI: 10.1021/acs.jafc.0c01894] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Genetic engineering (GE) technology is widely used in plant modification. However, the results of modification may not exactly meet the expectations. Herein, we propose a new multi-omics method for GE plant evaluation based on the optimized use of the metID algorithm. Using this method, we found that flavonoid accumulation was at the expense of the great sacrifice of l-phenylalanine in GE tomatoes for the first time. Meanwhile, the ceramide series of sphingolipid is synthesized de novo from l-serine, and ceramides are the primary source of vesicles coated with flavonoids and secreted from the endoplasmic reticulum. Therefore, the accumulation of the ceramide series of sphingolipid changed the cell component of intracellular organelles. Furthermore, the improvement of the method allows us to identify more metabolites related to dysregulated pathways.
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Affiliation(s)
- Xuanlin Meng
- College of Plant Protection, State Key Laboratory of Crop Biology, Shandong Agricultural University, Taian, Shandong 271000, People's Republic of China
- Department of Chemistry and State Key Laboratory of Environmental and Biological Analysis, Hong Kong Baptist University, Kowloon Tong, Kowloon, Hong Kong Special Administrative Region of the People's Republic of China
| | - Xingchen Zhao
- Department of Chemistry and State Key Laboratory of Environmental and Biological Analysis, Hong Kong Baptist University, Kowloon Tong, Kowloon, Hong Kong Special Administrative Region of the People's Republic of China
| | - Xiangyu Ding
- College of Plant Protection, State Key Laboratory of Crop Biology, Shandong Agricultural University, Taian, Shandong 271000, People's Republic of China
| | - Yang Li
- College of Plant Protection, State Key Laboratory of Crop Biology, Shandong Agricultural University, Taian, Shandong 271000, People's Republic of China
| | - Guodong Cao
- Department of Chemistry and State Key Laboratory of Environmental and Biological Analysis, Hong Kong Baptist University, Kowloon Tong, Kowloon, Hong Kong Special Administrative Region of the People's Republic of China
| | - Zhaohui Chu
- College of Plant Protection, State Key Laboratory of Crop Biology, Shandong Agricultural University, Taian, Shandong 271000, People's Republic of China
| | - Xiuli Su
- Department of Chemistry and State Key Laboratory of Environmental and Biological Analysis, Hong Kong Baptist University, Kowloon Tong, Kowloon, Hong Kong Special Administrative Region of the People's Republic of China
| | - Yuanchen Liu
- Department of Chemistry and State Key Laboratory of Environmental and Biological Analysis, Hong Kong Baptist University, Kowloon Tong, Kowloon, Hong Kong Special Administrative Region of the People's Republic of China
| | - Xiangfeng Chen
- Key Laboratory for Applied Technology of Sophisticated Analytic Instrument, Qilu University of Technology (Shandong Academy of Science), Jinan, Shandong 250014, People's Republic of China
| | - Jinggong Guo
- Center for Multi-Omics Research, State Key Laboratory of Cotton Biology, Institute of Plant Stress Biology, Henan University, Kaifeng, Henan 475004, People's Republic of China
| | - Zongwei Cai
- Department of Chemistry and State Key Laboratory of Environmental and Biological Analysis, Hong Kong Baptist University, Kowloon Tong, Kowloon, Hong Kong Special Administrative Region of the People's Republic of China
| | - Xinhua Ding
- College of Plant Protection, State Key Laboratory of Crop Biology, Shandong Agricultural University, Taian, Shandong 271000, People's Republic of China
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Asim M, Ullah Z, Xu F, An L, Aluko OO, Wang Q, Liu H. Nitrate Signaling, Functions, and Regulation of Root System Architecture: Insights from Arabidopsis thaliana. Genes (Basel) 2020; 11:E633. [PMID: 32526869 DOI: 10.3390/genes11060633] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Revised: 05/22/2020] [Accepted: 05/28/2020] [Indexed: 01/07/2023] Open
Abstract
Root system architecture (RSA) is required for the acquisition of water and mineral nutrients from the soil. One of the essential nutrients, nitrate (NO3−), is sensed and transported by nitrate transporters NRT1.1 and NRT2.1 in the plants. Nitrate transporter 1.1 (NRT1.1) is a dual-affinity nitrate transporter phosphorylated at the T101 residue by calcineurin B-like interacting protein kinase (CIPKs); it also regulates the expression of other key nitrate assimilatory genes. The differential phosphorylation (phosphorylation and dephosphorylation) strategies and underlying Ca2+ signaling mechanism of NRT1.1 stimulate lateral root growth by activating the auxin transport activity and Ca2+-ANR1 signaling at the plasma membrane and the endosomes, respectively. NO3− additionally functions as a signal molecule that forms a signaling system, which consists of a vast array of transcription factors that control root system architecture that either stimulate or inhibit lateral and primary root development in response to localized and high nitrate (NO3−), respectively. This review elucidates the so-far identified nitrate transporters, nitrate sensing, signal transduction, and the key roles of nitrate transporters and its downstream transcriptional regulatory network in the primary and lateral root development in Arabidopsis thaliana under stress conditions.
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27
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Armbruster L, Uslu VV, Wirtz M, Hell R. The Recovery from Sulfur Starvation Is Independent from the mRNA Degradation Initiation Enzyme PARN in Arabidopsis. Plants (Basel) 2019; 8:E380. [PMID: 31569782 DOI: 10.3390/plants8100380] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 09/23/2019] [Accepted: 09/26/2019] [Indexed: 11/23/2022]
Abstract
When plants are exposed to sulfur limitation, they upregulate the sulfate assimilation pathway at the expense of growth-promoting measures. Upon cessation of the stress, however, protective measures are deactivated, and growth is restored. In accordance with these findings, transcripts of sulfur-deficiency marker genes are rapidly degraded when starved plants are resupplied with sulfur. Yet it remains unclear which enzymes are responsible for the degradation of transcripts during the recovery from starvation. In eukaryotes, mRNA decay is often initiated by the cleavage of poly(A) tails via deadenylases. As mutations in the poly(A) ribonuclease PARN have been linked to altered abiotic stress responses in Arabidopsis thaliana, we investigated the role of PARN in the recovery from sulfur starvation. Despite the presence of putative PARN-recruiting AU-rich elements in sulfur-responsive transcripts, sulfur-depleted PARN hypomorphic mutants were able to reset their transcriptome to pre-starvation conditions just as readily as wildtype plants. Currently, the subcellular localization of PARN is disputed, with studies reporting both nuclear and cytosolic localization. We detected PARN in cytoplasmic speckles and reconciled the diverging views in literature by identifying two PARN splice variants whose predicted localization is in agreement with those observations.
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28
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Abstract
Systems biology approaches have been applied over the last two decades to study plant sulphur metabolism. These 'sulphur-omics' approaches have been developed in parallel with the advancing field of systems biology, which is characterized by permanent improvements of high-throughput methods to obtain system-wide data. The aim is to obtain a holistic view of sulphur metabolism and to generate models that allow predictions of metabolic and physiological responses. Besides known sulphur-responsive genes derived from previous studies, numerous genes have been identified in transcriptomics studies. This has not only increased our knowledge of sulphur metabolism but has also revealed links between metabolic processes, thus indicating a previously unexpected complex interconnectivity. The identification of response and control networks has been supported through metabolomics and proteomics studies. Due to the complex interlacing nature of biological processes, experimental validation using targeted or systems approaches is ongoing. There is still room for improvement in integrating the findings from studies of metabolomes, proteomes, and metabolic fluxes into a single unifying concept and to generate consistent models. We therefore suggest a joint effort of the sulphur research community to standardize data acquisition. Furthermore, focusing on a few different model plant systems would help overcome the problem of fragmented data, and would allow us to provide a standard data set against which future experiments can be designed and compared.
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Affiliation(s)
- Mutsumi Watanabe
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
- Nara Institute of Science and Technology, Ikoma, Japan
| | - Rainer Hoefgen
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
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29
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Anoman AD, Flores-Tornero M, Benstein RM, Blau S, Rosa-Téllez S, Bräutigam A, Fernie AR, Muñoz-Bertomeu J, Schilasky S, Meyer AJ, Kopriva S, Segura J, Krueger S, Ros R. Deficiency in the Phosphorylated Pathway of Serine Biosynthesis Perturbs Sulfur Assimilation. Plant Physiol 2019; 180:153-170. [PMID: 30787133 PMCID: PMC6501105 DOI: 10.1104/pp.18.01549] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 02/05/2019] [Indexed: 05/19/2023]
Abstract
Although the plant Phosphorylated Pathway of l-Ser Biosynthesis (PPSB) is essential for embryo and pollen development, and for root growth, its metabolic implications have not been fully investigated. A transcriptomics analysis of Arabidopsis (Arabidopsis thaliana) PPSB-deficient mutants at night, when PPSB activity is thought to be more important, suggested interaction with the sulfate assimilation process. Because sulfate assimilation occurs mainly in the light, we also investigated it in PPSB-deficient lines in the day. Key genes in the sulfate starvation response, such as the adenosine 5'phosphosulfate reductase genes, along with sulfate transporters, especially those involved in sulfate translocation in the plant, were induced in the PPSB-deficient lines. However, sulfate content was not reduced in these lines as compared with wild-type plants; besides the glutathione (GSH) steady-state levels in roots of PPSB-deficient lines were even higher than in wild type. This suggested that PPSB deficiency perturbs the sulfate assimilation process between tissues/organs. Alteration of thiol distribution in leaves from different developmental stages, and between aerial parts and roots in plants with reduced PPSB activity, provided evidence supporting this idea. Diminished PPSB activity caused an enhanced flux of 35S into thiol biosynthesis, especially in roots. GSH turnover also accelerated in the PPSB-deficient lines, supporting the notion that not only biosynthesis, but also transport and allocation, of thiols were perturbed in the PPSB mutants. Our results suggest that PPSB is required for sulfide assimilation in specific heterotrophic tissues and that a lack of PPSB activity perturbs sulfur homeostasis between photosynthetic and nonphotosynthetic tissues.
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Affiliation(s)
- Armand D Anoman
- Departament de Biologia Vegetal, Facultat de Farmàcia, Universitat de València, 46010 València, Spain
- Estructura de Recerca Interdisciplinar en Biotecnologia i Biomedicina (ERI BIOTECMED), Universitat de València, 46100 Burjassot, Spain
| | - María Flores-Tornero
- Departament de Biologia Vegetal, Facultat de Farmàcia, Universitat de València, 46010 València, Spain
- Estructura de Recerca Interdisciplinar en Biotecnologia i Biomedicina (ERI BIOTECMED), Universitat de València, 46100 Burjassot, Spain
| | - Ruben M Benstein
- Biocenter - Botanical Institute II, University of Cologne, 50674 Cologne, Germany
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, SE-901 87 Umeå, Sweden
| | - Samira Blau
- Biocenter - Botanical Institute II, University of Cologne, 50674 Cologne, Germany
| | - Sara Rosa-Téllez
- Departament de Biologia Vegetal, Facultat de Farmàcia, Universitat de València, 46010 València, Spain
- Estructura de Recerca Interdisciplinar en Biotecnologia i Biomedicina (ERI BIOTECMED), Universitat de València, 46100 Burjassot, Spain
| | - Andrea Bräutigam
- Fakultät für Biologie Gebäude G (CebiTec), Bielefeld University, 33615 Bielefeld, Germany
| | - Alisdair R Fernie
- Max Planck Institut für Molekulare Pflanzenphysiologie, 14476 Potsdam-Golm, Germany
| | - Jesús Muñoz-Bertomeu
- Departament de Biologia Vegetal, Facultat de Farmàcia, Universitat de València, 46010 València, Spain
| | - Sören Schilasky
- INRES-Chemical Signalling, University Bonn, 53113 Bonn, Germany
| | - Andreas J Meyer
- INRES-Chemical Signalling, University Bonn, 53113 Bonn, Germany
| | - Stanislav Kopriva
- Biocenter - Botanical Institute II, University of Cologne, 50674 Cologne, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, 50674 Cologne, Germany
| | - Juan Segura
- Departament de Biologia Vegetal, Facultat de Farmàcia, Universitat de València, 46010 València, Spain
- Estructura de Recerca Interdisciplinar en Biotecnologia i Biomedicina (ERI BIOTECMED), Universitat de València, 46100 Burjassot, Spain
| | - Stephan Krueger
- Biocenter - Botanical Institute II, University of Cologne, 50674 Cologne, Germany
| | - Roc Ros
- Departament de Biologia Vegetal, Facultat de Farmàcia, Universitat de València, 46010 València, Spain
- Estructura de Recerca Interdisciplinar en Biotecnologia i Biomedicina (ERI BIOTECMED), Universitat de València, 46100 Burjassot, Spain
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30
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White PJ. Selenium metabolism in plants. Biochim Biophys Acta Gen Subj 2018; 1862:2333-2342. [DOI: 10.1016/j.bbagen.2018.05.006] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2018] [Revised: 05/01/2018] [Accepted: 05/04/2018] [Indexed: 10/16/2022]
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31
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da Fonseca-Pereira P, Neri-Silva R, Cavalcanti JHF, Brito DS, Weber APM, Araújo WL, Nunes-Nesi A. Data-Mining Bioinformatics: Connecting Adenylate Transport and Metabolic Responses to Stress. Trends Plant Sci 2018; 23:961-974. [PMID: 30287161 DOI: 10.1016/j.tplants.2018.09.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Revised: 08/30/2018] [Accepted: 09/07/2018] [Indexed: 06/08/2023]
Abstract
Adenine nucleotides are essential in countless processes within the cellular metabolism. In plants, ATP is mainly produced in chloroplasts and mitochondria through photophosphorylation and oxidative phosphorylation, respectively. Thus, efficient adenylate transport systems are required for intracellular energy partitioning between the cell organelles. Adenylate carriers present in different subcellular compartments have been previously identified and biochemically characterized in plants. Here, by using data-mining bioinformatics tools, we propose how, and to what extent, these carriers integrate energy metabolism within a plant cell under different environmental conditions. We demonstrate that the expression pattern of the corresponding genes is variable under different environmental conditions, suggesting that specific adenylate carriers have distinct and nonredundant functions in plants.
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Affiliation(s)
- Paula da Fonseca-Pereira
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil; These authors contributed equally to this work
| | - Roberto Neri-Silva
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil; These authors contributed equally to this work
| | - João Henrique F Cavalcanti
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil; Max-Panck Partner Group at the Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil
| | - Danielle S Brito
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil
| | - Andreas P M Weber
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Science (CEPLAS), Heinrich-Heine-Universität, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Wagner L Araújo
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil; Max-Panck Partner Group at the Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil
| | - Adriano Nunes-Nesi
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil.
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Pavlů J, Novák J, Koukalová V, Luklová M, Brzobohatý B, Černý M. Cytokinin at the Crossroads of Abiotic Stress Signalling Pathways. Int J Mol Sci 2018; 19:ijms19082450. [PMID: 30126242 PMCID: PMC6121657 DOI: 10.3390/ijms19082450] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 08/14/2018] [Accepted: 08/17/2018] [Indexed: 01/13/2023] Open
Abstract
Cytokinin is a multifaceted plant hormone that plays major roles not only in diverse plant growth and development processes, but also stress responses. We summarize knowledge of the roles of its metabolism, transport, and signalling in responses to changes in levels of both macronutrients (nitrogen, phosphorus, potassium, sulphur) and micronutrients (boron, iron, silicon, selenium). We comment on cytokinin's effects on plants' xenobiotic resistance, and its interactions with light, temperature, drought, and salinity signals. Further, we have compiled a list of abiotic stress-related genes and demonstrate that their expression patterns overlap with those of cytokinin metabolism and signalling genes.
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Affiliation(s)
- Jaroslav Pavlů
- Department of Molecular Biology and Radiobiology, Faculty of AgriSciences, Mendel University in Brno, 613 00 Brno, Czech Republic.
- CEITEC-Central European Institute of Technology, Faculty of AgriSciences, Mendel University in Brno, 613 00 Brno, Czech Republic.
| | - Jan Novák
- Department of Molecular Biology and Radiobiology, Faculty of AgriSciences, Mendel University in Brno, 613 00 Brno, Czech Republic.
| | - Vladěna Koukalová
- Department of Molecular Biology and Radiobiology, Faculty of AgriSciences, Mendel University in Brno, 613 00 Brno, Czech Republic.
| | - Markéta Luklová
- Department of Molecular Biology and Radiobiology, Faculty of AgriSciences, Mendel University in Brno, 613 00 Brno, Czech Republic.
- CEITEC-Central European Institute of Technology, Faculty of AgriSciences, Mendel University in Brno, 613 00 Brno, Czech Republic.
| | - Břetislav Brzobohatý
- Department of Molecular Biology and Radiobiology, Faculty of AgriSciences, Mendel University in Brno, 613 00 Brno, Czech Republic.
- CEITEC-Central European Institute of Technology, Faculty of AgriSciences, Mendel University in Brno, 613 00 Brno, Czech Republic.
- Institute of Biophysics AS CR, 612 00 Brno, Czech Republic.
| | - Martin Černý
- Department of Molecular Biology and Radiobiology, Faculty of AgriSciences, Mendel University in Brno, 613 00 Brno, Czech Republic.
- Phytophthora Research Centre, Faculty of AgriSciences, Mendel University in Brno, 613 00 Brno, Czech Republic.
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Yue Y, Tian S, Wang Y, Ma H, Liu S, Wang Y, Hu H. Transcriptomic and GC-MS Metabolomic Analyses Reveal the Sink Strength Changes during Petunia Anther Development. Int J Mol Sci 2018; 19:ijms19040955. [PMID: 29570614 PMCID: PMC5979359 DOI: 10.3390/ijms19040955] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 03/10/2018] [Accepted: 03/18/2018] [Indexed: 12/17/2022] Open
Abstract
Petunia, which has been prevalently cultivated in landscaping, is a dicotyledonous herbaceous flower of high ornamental value. Annually, there is a massive worldwide market demand for petunia seeds. The normal development of anther is the necessary prerequisite for the plants to generate seeds. However, the knowledge of petunia anther development processes is still limited. To better understand the mechanisms of petunia anther development, the transcriptomes and metabolomes of petunia anthers at three typical development stages were constructed and then used to detect the gene expression patterns and primary metabolite profiles during the anther development processes. Results suggested that there were many differentially-expressed genes (DEGs) that mainly participated in photosynthesis and starch and sucrose metabolism when DEGs were compared between the different development stages of anthers. In this study, fructose and glucose, which were involved in starch and sucrose metabolism, were taken as the most important metabolites by partial least-squares discriminate analysis (PLS-DA). Additionally, the qRT-PCR analysis of the photosynthetic-related genes all showed decreased expression trends along with the anther development. These pieces of evidence indicated that the activities of energy and carbohydrate metabolic pathways were gradually reduced during all the development stages of anther, which affects the sink strength. Overall, this work provides a novel and comprehensive understanding of the metabolic processes in petunia anthers.
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Affiliation(s)
- Yuanzheng Yue
- Key Laboratory of Urban Agriculture in Central China, Ministry of Agriculture, Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China.
- Key Laboratory of Landscape Architecture, Jiangsu Province, College of Landscape Architecture, Nanjing Forestry University, Nanjing 210037, China.
| | - Shaoze Tian
- Key Laboratory of Urban Agriculture in Central China, Ministry of Agriculture, Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China.
| | - Yu Wang
- Key Laboratory of Urban Agriculture in Central China, Ministry of Agriculture, Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China.
| | - Hui Ma
- Key Laboratory of Urban Agriculture in Central China, Ministry of Agriculture, Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China.
| | - Siyu Liu
- Key Laboratory of Urban Agriculture in Central China, Ministry of Agriculture, Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China.
| | - Yuqiao Wang
- Key Laboratory of Urban Agriculture in Central China, Ministry of Agriculture, Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China.
| | - Huirong Hu
- Key Laboratory of Urban Agriculture in Central China, Ministry of Agriculture, Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China.
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Wei T, Deng K, Wang H, Zhang L, Wang C, Song W, Zhang Y, Chen C. Comparative Transcriptome Analyses Reveal Potential Mechanisms of Enhanced Drought Tolerance in Transgenic Salvia Miltiorrhiza Plants Expressing AtDREB1A from Arabidopsis. Int J Mol Sci 2018. [PMID: 29534548 PMCID: PMC5877688 DOI: 10.3390/ijms19030827] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
In our previous study, drought-resistant transgenic plants of Salvia miltiorrhiza were produced via overexpression of the transcription factor AtDREB1A. To unravel the molecular mechanisms underpinning elevated drought tolerance in transgenic plants, in the present study we compared the global transcriptional profiles of wild-type (WT) and AtDREB1A-expressing transgenic plants using RNA-sequencing (RNA-seq). Using cluster analysis, we identified 3904 differentially expressed genes (DEGs). Compared with WT plants, 423 unigenes were up-regulated in pRD29A::AtDREB1A-31 before drought treatment, while 936 were down-regulated and 1580 and 1313 unigenes were up- and down-regulated after six days of drought. COG analysis revealed that the 'signal transduction mechanisms' category was highly enriched among these DEGs both before and after drought stress. Based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) annotation, DEGs associated with "ribosome", "plant hormone signal transduction", photosynthesis", "plant-pathogen interaction", "glycolysis/gluconeogenesis" and "carbon fixation" are hypothesized to perform major functions in drought resistance in AtDREB1A-expressing transgenic plants. Furthermore, the number of DEGs associated with different transcription factors increased significantly after drought stress, especially the AP2/ERF, bZIP and MYB protein families. Taken together, this study substantially expands the transcriptomic information for S. miltiorrhiza and provides valuable clues for elucidating the mechanism of AtDREB1A-mediated drought tolerance in transgenic plants.
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Affiliation(s)
- Tao Wei
- National Engineering Research Center of Pesticide (Tianjin), Nankai University, Tianjin 300071, China.
- College of Life Sciences, Nankai University, Tianjin 300071, China.
- School of Life Sciences and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China.
| | - Kejun Deng
- School of Life Sciences and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China.
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China.
| | - Hongbin Wang
- College of Life Sciences, Nankai University, Tianjin 300071, China.
| | - Lipeng Zhang
- College of Life Sciences, Nankai University, Tianjin 300071, China.
| | - Chunguo Wang
- College of Life Sciences, Nankai University, Tianjin 300071, China.
| | - Wenqin Song
- College of Life Sciences, Nankai University, Tianjin 300071, China.
| | - Yong Zhang
- School of Life Sciences and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China.
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China.
| | - Chengbin Chen
- College of Life Sciences, Nankai University, Tianjin 300071, China.
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Li Z, Xu H, Li Y, Wan X, Ma Z, Cao J, Li Z, He F, Wang Y, Wan L, Tong Z, Li X. Analysis of physiological and miRNA responses to Pi deficiency in alfalfa (Medicago sativa L.). Plant Mol Biol 2018; 96:473-492. [PMID: 29532290 DOI: 10.1007/s11103-018-0711-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2017] [Accepted: 02/19/2018] [Indexed: 05/18/2023]
Abstract
The induction of miR399 and miR398 and the inhibition of miR156, miR159, miR160, miR171, miR2111, and miR2643 were observed under Pi deficiency in alfalfa. The miRNA-mediated genes involved in basic metabolic process, root and shoot development, stress response and Pi uptake. Inorganic phosphate (Pi) deficiency is known to be a limiting factor in plant development and growth. However, the underlying miRNAs associated with the Pi deficiency-responsive mechanism in alfalfa are unclear. To elucidate the molecular mechanism at the miRNA level, we constructed four small RNA (sRNA) libraries from the roots and shoots of alfalfa grown under normal or Pi-deficient conditions. In the present study, alfalfa plants showed reductions in biomass, photosynthesis, and Pi content and increases in their root-to-shoot ratio and citric, malic, and succinic acid contents under Pi limitation. Sequencing results identified 47 and 44 differentially expressed miRNAs in the roots and shoots, respectively. Furthermore, 909 potential target genes were predicted, and some targets were validated by RLM-RACE assays. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses showed prominent enrichment in signal transducer activity, binding and basic metabolic pathways for carbohydrates, fatty acids and amino acids; cellular response to hormone stimulus and response to auxin pathways were also enriched. qPCR results verified that the differentially expressed miRNA profile was consistent with sequencing results, and putative target genes exhibited opposite expression patterns. In this study, the miRNAs associated with the response to Pi limitation in alfalfa were identified. In addition, there was an enrichment of miRNA-targeted genes involved in biological regulatory processes such as basic metabolic pathways, root and shoot development, stress response, Pi transportation and citric acid secretion.
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Affiliation(s)
- Zhenyi Li
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Hongyu Xu
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Yue Li
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Xiufu Wan
- State Key Laboratory of Dao-Di Herbs, National Resource Center for Chinese Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Zhao Ma
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Jing Cao
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Zhensong Li
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Feng He
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Yufei Wang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Liqiang Wan
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Zongyong Tong
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Xianglin Li
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
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Liu C, Su J, Stephen GK, Wang H, Song A, Chen F, Zhu Y, Chen S, Jiang J. Overexpression of Phosphate Transporter Gene CmPht1;2 Facilitated Pi Uptake and Alternated the Metabolic Profiles of Chrysanthemum Under Phosphate Deficiency. Front Plant Sci 2018; 9:686. [PMID: 30079072 PMCID: PMC6062769 DOI: 10.3389/fpls.2018.00686] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 05/04/2018] [Indexed: 05/21/2023]
Abstract
Low availability of phosphorus (P) in the soil is the principal limiting factor for the growth of cut chrysanthemum. Plant phosphate transporters (PTs) facilitate acquisition of inorganic phosphate (Pi) and its homeostasis within the plant. In the present study, CmPht1;2 of the Pht1 family was cloned from chrysanthemum. CmPht1;2 is composed of 12 transmembrane domains and localized to the plasma membrane. Expression of CmPht1;2 in roots was induced by Pi starvation. Chrysanthemum plants with overexpression of CmPht1;2 (Oe) showed higher Pi uptake, as compared to the wild type (WT), both under Pi-starvation and Pi-sufficient conditions, and also showed a higher root biomass compared to WT in the Pi-starvation conditions. Seven days after the P-deficiency treatment, 85 distinct analytes were identified in the roots and 27 in the shoots between the Oe1 plant and WT, in which sophorose, sorbitol (sugars), hydroxybutyric acid (organic acids), and ornithine (amino acid) of CmPht1;2 overexpressing chrysanthemum are specific responses to P-starvation.
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Affiliation(s)
- Chen Liu
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
- Key Laboratory of Landscape Agriculture, Ministry of Agriculture, Nanjing, China
| | - Jiangshuo Su
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
- Key Laboratory of Landscape Agriculture, Ministry of Agriculture, Nanjing, China
| | - Githeng’u K. Stephen
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
- Key Laboratory of Landscape Agriculture, Ministry of Agriculture, Nanjing, China
| | - Haibin Wang
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
- Key Laboratory of Landscape Agriculture, Ministry of Agriculture, Nanjing, China
| | - Aiping Song
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
- Key Laboratory of Landscape Agriculture, Ministry of Agriculture, Nanjing, China
| | - Fadi Chen
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
- Key Laboratory of Landscape Agriculture, Ministry of Agriculture, Nanjing, China
| | - Yiyong Zhu
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Sumei Chen
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
- Key Laboratory of Landscape Agriculture, Ministry of Agriculture, Nanjing, China
- *Correspondence: Sumei Chen, Jiafu Jiang,
| | - Jiafu Jiang
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
- Key Laboratory of Landscape Agriculture, Ministry of Agriculture, Nanjing, China
- *Correspondence: Sumei Chen, Jiafu Jiang,
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Watanabe M, Tohge T, Fernie AR, Hoefgen R. The Effect of Single and Multiple SERAT Mutants on Serine and Sulfur Metabolism. Front Plant Sci 2018; 9:702. [PMID: 29892307 PMCID: PMC5985473 DOI: 10.3389/fpls.2018.00702] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 05/07/2018] [Indexed: 05/08/2023]
Abstract
The gene family of serine acetyltransferases (SERATs) constitutes an interface between the plant pathways of serine and sulfur metabolism. SERATs provide the activated precursor, O-acetylserine for the fixation of reduced sulfur into cysteine by exchanging the serine hydroxyl moiety by a sulfhydryl moiety, and subsequently all organic compounds containing reduced sulfur moieties. We investigate here, how manipulation of the SERAT interface results in metabolic alterations upstream or downstream of this boundary and the extent to which the five SERAT isoforms exert an effect on the coupled system, respectively. Serine is synthesized through three distinct pathways while cysteine biosynthesis is distributed over the three compartments cytosol, mitochondria, and plastids. As the respective mutants are viable, all necessary metabolites can obviously cross various membrane systems to compensate what would otherwise constitute a lethal failure in cysteine biosynthesis. Furthermore, given that cysteine serves as precursor for multiple pathways, cysteine biosynthesis is highly regulated at both, the enzyme and the expression level. In this study, metabolite profiles of a mutant series of the SERAT gene family displayed that levels of the downstream metabolites in sulfur metabolism were affected in correlation with the reduction levels of SERAT activities and the growth phenotypes, while levels of the upstream metabolites in serine metabolism were unchanged in the serat mutants compared to wild-type plants. These results suggest that despite of the fact that the two metabolic pathways are directly connected, there seems to be no causal link in metabolic alterations. This might be caused by the difference of their pool sizes or the tight regulation by homeostatic mechanisms that control the metabolite concentration in plant cells. Additionally, growth conditions exerted an influence on metabolic compositions.
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Affiliation(s)
- Mutsumi Watanabe
- Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
- Nara Institute of Science and Technology, Ikoma, Japan
- *Correspondence: Mutsumi Watanabe, Rainer Hoefgen,
| | - Takayuki Tohge
- Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
- Nara Institute of Science and Technology, Ikoma, Japan
| | | | - Rainer Hoefgen
- Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
- *Correspondence: Mutsumi Watanabe, Rainer Hoefgen,
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Henríquez-Valencia C, Arenas-M A, Medina J, Canales J. Integrative Transcriptomic Analysis Uncovers Novel Gene Modules That Underlie the Sulfate Response in Arabidopsis thaliana. Front Plant Sci 2018; 9:470. [PMID: 29692794 PMCID: PMC5902692 DOI: 10.3389/fpls.2018.00470] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Accepted: 03/26/2018] [Indexed: 05/10/2023]
Abstract
Sulfur is an essential nutrient for plant growth and development. Sulfur is a constituent of proteins, the plasma membrane and cell walls, among other important cellular components. To obtain new insights into the gene regulatory networks underlying the sulfate response, we performed an integrative meta-analysis of transcriptomic data from five different sulfate experiments available in public databases. This bioinformatic approach allowed us to identify a robust set of genes whose expression depends only on sulfate availability, indicating that those genes play an important role in the sulfate response. In relation to sulfate metabolism, the biological function of approximately 45% of these genes is currently unknown. Moreover, we found several consistent Gene Ontology terms related to biological processes that have not been extensively studied in the context of the sulfate response; these processes include cell wall organization, carbohydrate metabolism, nitrogen compound transport, and the regulation of proteolysis. Gene co-expression network analyses revealed relationships between the sulfate-responsive genes that were distributed among seven function-specific co-expression modules. The most connected genes in the sulfate co-expression network belong to a module related to the carbon response, suggesting that this biological function plays an important role in the control of the sulfate response. Temporal analyses of the network suggest that sulfate starvation generates a biphasic response, which involves that major changes in gene expression occur during both the early and late responses. Network analyses predicted that the sulfate response is regulated by a limited number of transcription factors, including MYBs, bZIPs, and NF-YAs. In conclusion, our analysis identified new candidate genes and provided new hypotheses to advance our understanding of the transcriptional regulation of sulfate metabolism in plants.
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Affiliation(s)
- Carlos Henríquez-Valencia
- Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | - Anita Arenas-M
- Instituto de Producción y Sanidad Vegetal, Facultad de Ciencias Agrarias, Universidad Austral de Chile, Valdivia, Chile
| | - Joaquín Medina
- Centro de Biotecnología y Genómica de Plantas, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Universidad Politécnica de Madrid, Madrid, Spain
| | - Javier Canales
- Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
- Millennium Institute for Integrative Systems and Synthetic Biology (MIISSB), Santiago, Chile
- *Correspondence: Javier Canales,
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Jin J, Zhang H, Zhang J, Liu P, Chen X, Li Z, Xu Y, Lu P, Cao P. Integrated transcriptomics and metabolomics analysis to characterize cold stress responses in Nicotiana tabacum. BMC Genomics 2017; 18:496. [PMID: 28662642 PMCID: PMC5492280 DOI: 10.1186/s12864-017-3871-7] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Accepted: 06/19/2017] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND CB-1 and K326 are closely related tobacco cultivars; however, their cold tolerance capacities are different. K326 is much more cold tolerant than CB-1. RESULTS We studied the transcriptomes and metabolomes of CB-1 and K326 leaf samples treated with cold stress. Totally, we have identified 14,590 differentially expressed genes (DEGs) in CB-1 and 14,605 DEGs in K326; there was also 200 differentially expressed metabolites in CB-1 and 194 in K326. Moreover, there were many overlapping genes (around 50%) that were cold-responsive in both plant cultivars, although there were also many differences in the cold responsive genes between the two cultivars. Importantly, for most of the overlapping cold responsive genes, the extent of the changes in expression were typically much more pronounced in K326 than in CB-1, which may help explain the superior cold tolerance of K326. Similar results were found in the metabolome analysis, particularly with the analysis of primary metabolites, including amino acids, organic acids, and sugars. The large number of specific responsive genes and metabolites highlight the complex regulatory mechanisms associated with cold stress in tobacco. In addition, our work implies that the energy metabolism and hormones may function distinctly between CB-1 and K326. CONCLUSIONS Differences in gene expression and metabolite levels following cold stress treatment seem likely to have contributed to the observed difference in the cold tolerance phenotype of these two tobacco cultivars.
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Affiliation(s)
- Jingjing Jin
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, 450001 China
| | - Hui Zhang
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, 450001 China
| | - Jianfeng Zhang
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, 450001 China
| | - Pingping Liu
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, 450001 China
| | - Xia Chen
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, 450001 China
| | - Zefeng Li
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, 450001 China
| | - Yalong Xu
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, 450001 China
| | - Peng Lu
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, 450001 China
| | - Peijian Cao
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, 450001 China
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Schiavon M, Lima LW, Jiang Y, Hawkesford MJ. Effects of Selenium on Plant Metabolism and Implications for Crops and Consumers. In: Pilon-smits EA, Winkel LH, Lin Z, editors. Selenium in plants. Cham: Springer International Publishing; 2017. pp. 257-75. [DOI: 10.1007/978-3-319-56249-0_15] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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Lee WK, Namasivayam P, Ong Abdullah J, Ho CL. Transcriptome profiling of sulfate deprivation responses in two agarophytes Gracilaria changii and Gracilaria salicornia (Rhodophyta). Sci Rep 2017; 7:46563. [PMID: 28436444 DOI: 10.1038/srep46563] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 03/22/2017] [Indexed: 12/11/2022] Open
Abstract
Seaweeds survive in marine waters with high sulfate concentration compared to those living at freshwater habitats. The cell wall polymer of Gracilaria spp. which supplies more than 50% of the world agar is heavily sulfated. Since sulfation reduces the agar quality, it is interesting to investigate the effects of sulfate deprivation on the sulfate contents of seaweed and agar, as well as the metabolic pathways of these seaweeds. In this study, two agarophytes G. changii and G. salicornia were treated under sulfate deprivation for 5 days. The sulfate contents in the seaweed/agar were generally lower in sulfate-deprivated samples compared to those in the controls, but the differences were only statistically significant for seaweed sample of G. changii and agar sample of G. salicornia. RNA sequencing (RNA-Seq) of sulfate-deprivated and untreated seaweed samples revealed 1,292 and 3,439 differentially expressed genes (DEGs; ≥1.5-fold) in sulfate-deprivated G. changii and G. salicornia, respectively, compared to their respective controls. Among the annotated DEGs were genes involved in putative agar biosynthesis, sulfur metabolism, metabolism of sulfur-containing amino acids, carbon metabolism and oxidative stress. These findings shed light on the sulfate deprivation responses in agarophytes and help to identify candidate genes involved in agar biosynthesis.
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Heyneke E, Watanabe M, Erban A, Duan G, Buchner P, Walther D, Kopka J, Hawkesford MJ, Hoefgen R. Characterization of the Wheat Leaf Metabolome during Grain Filling and under Varied N-Supply. Front Plant Sci 2017; 8:2048. [PMID: 29238358 PMCID: PMC5712589 DOI: 10.3389/fpls.2017.02048] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 11/15/2017] [Indexed: 05/20/2023]
Abstract
Progress in improving crop growth is an absolute goal despite the influence multifactorial components have on crop yield and quality. An Avalon × Cadenza doubled-haploid wheat mapping population was used to study the leaf metabolome of field grown wheat at weekly intervals during the time in which the canopy contributes to grain filling, i.e., from anthesis to 5 weeks post-anthesis. Wheat was grown under four different nitrogen supplies reaching from residual soil N to a luxury over-fertilization (0, 100, 200, and 350 kg N ha-1). Four lines from a segregating doubled haploid population derived of a cross of the wheat elite cvs. Avalon and Cadenza were chosen as they showed pairwise differences in either N utilization efficiency (NUtE) or senescence timing. 108 annotated metabolites of primary metabolism and ions were determined. The analysis did not provide genotype specific markers because of a remarkable stability of the metabolome between lines. We speculate that the reason for failing to identify genotypic markers might be due to insufficient genetic diversity of the wheat parents and/or the known tendency of plants to keep metabolome homeostasis even under adverse conditions through multiple adaptations and rescue mechanism. The data, however, provided a consistent catalogue of metabolites and their respective responses to environmental and developmental factors and may bode well for future systems biology approaches, and support plant breeding and crop improvement.
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Affiliation(s)
- Elmien Heyneke
- Department Willmitzer, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Mutsumi Watanabe
- Department Willmitzer, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Alexander Erban
- Department Willmitzer, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Guangyou Duan
- Department Willmitzer, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
- European Molecular Biology Laboratory, European Bioinformatics Institute, Heidelberg, Germany
| | - Peter Buchner
- Plant Sciences, Rothamsted Research, Harpenden, United Kingdom
| | - Dirk Walther
- Department Willmitzer, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Joachim Kopka
- Department Willmitzer, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | | | - Rainer Hoefgen
- Department Willmitzer, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
- *Correspondence: Rainer Hoefgen
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Yue X, Li XG, Gao XQ, Zhao XY, Dong YX, Zhou C. The Arabidopsis phytohormone crosstalk network involves a consecutive metabolic route and circular control units of transcription factors that regulate enzyme-encoding genes. BMC Syst Biol 2016; 10:87. [PMID: 27590055 PMCID: PMC5009710 DOI: 10.1186/s12918-016-0333-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 08/25/2016] [Indexed: 01/26/2023]
Abstract
Background Phytohormone synergies and signaling interdependency are important topics in plant developmental biology. Physiological and genetic experimental evidence for phytohormone crosstalk has been accumulating and a genome-scale enzyme correlation model representing the Arabidopsis metabolic pathway has been published. However, an integrated molecular characterization of phytohormone crosstalk is still not available. Results A novel modeling methodology and advanced computational approaches were used to construct an enzyme-based Arabidopsis phytohormone crosstalk network (EAPCN) at the biosynthesis level. The EAPCN provided the structural connectivity architecture of phytohormone biosynthesis pathways and revealed a surprising result; that enzymes localized at the highly connected nodes formed a consecutive metabolic route. Furthermore, our analysis revealed that the transcription factors (TFs) that regulate enzyme-encoding genes in the consecutive metabolic route formed structures, which we describe as circular control units operating at the transcriptional level. Furthermore, the downstream TFs in phytohormone signal transduction pathways were found to be involved in the circular control units that included the TFs regulating enzyme-encoding genes. In addition, multiple functional enzymes in the EAPCN were found to be involved in ion and pH homeostasis, environmental signal perception, cellular redox homeostasis, and circadian clocks. Last, publicly available transcriptional profiles and a protein expression map of the Arabidopsis root apical meristem were used as a case study to validate the proposed framework. Conclusions Our results revealed multiple scales of coupled mechanisms in that hormonal crosstalk networks that play a central role in coordinating internal developmental processes with environmental signals, and give a broader view of Arabidopsis phytohormone crosstalk. We also uncovered potential key regulators that can be further analyzed in future studies. Electronic supplementary material The online version of this article (doi:10.1186/s12918-016-0333-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xun Yue
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, 271018, China. .,State Key Laboratory of Crop Biology, College of Information Sciences and Engineering, Shandong Agricultural University, Tai'an, Shandong, 271018, China.
| | - Xing Guo Li
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Xin-Qi Gao
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Xiang Yu Zhao
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Yu Xiu Dong
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Chao Zhou
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, 271018, China
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Zhao H, Frank T, Tan Y, Zhou C, Jabnoune M, Arpat AB, Cui H, Huang J, He Z, Poirier Y, Engel KH, Shu Q. Disruption of OsSULTR3;3 reduces phytate and phosphorus concentrations and alters the metabolite profile in rice grains. New Phytol 2016; 211:926-939. [PMID: 27110682 DOI: 10.1111/nph.13969] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2016] [Accepted: 03/09/2016] [Indexed: 06/05/2023]
Abstract
Two low phytic acid (lpa) mutants have been developed previously with the aim to improve the nutritional value of rice (Oryza sativa) grains. In the present study, the impacts of lpa mutations on grain composition and underlying molecular mechanisms were investigated. Comparative compositional analyses and metabolite profiling demonstrated that concentrations of both phytic acid (PA) and total phosphorus (P) were significantly reduced in lpa brown rice, accompanied by changes in other metabolites and increased concentrations of nutritionally relevant compounds. The lpa mutations modified the expression of a number of genes involved in PA metabolism, as well as in sulfate and phosphate homeostasis and metabolism. Map-based cloning and complementation identified the underlying lpa gene to be OsSULTR3;3. The promoter of OsSULTR3;3 is highly active in the vascular bundles of leaves, stems and seeds, and its protein is localized in the endoplasmic reticulum. No activity of OsSULTR3;3 was revealed for the transport of phosphate, sulfate, inositol or inositol 1,4,5 triphosphate by heterologous expression in either yeast or Xenopus oocytes. The findings reveal that OsSULTR3;3 plays an important role in grain metabolism, pointing to a new route to generate value-added grains in rice and other cereal crops.
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Affiliation(s)
- Haijun Zhao
- State Key Laboratory of Rice Biology, Institute of Crop Sciences, Zhejiang University, Hangzhou, 310058, China
- Hubei Collaborative Innovation Center for Grain Industry, Jingzhou, 434025, China
| | - Thomas Frank
- Lehrstuhl für Allgemeine Lebensmitteltechnologie, Technische Universität München, Maximum-von-Imhof-Forum 2, Freising-Weihenstephan, D-85354, Germany
| | - Yuanyuan Tan
- State Key Laboratory of Rice Biology, Institute of Crop Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Chenguang Zhou
- Lehrstuhl für Allgemeine Lebensmitteltechnologie, Technische Universität München, Maximum-von-Imhof-Forum 2, Freising-Weihenstephan, D-85354, Germany
| | - Mehdi Jabnoune
- Department of Plant Molecular Biology, Biophore, University of Lausanne, Lausanne, CH-1015, Switzerland
| | - A Bulak Arpat
- Department of Plant Molecular Biology, Biophore, University of Lausanne, Lausanne, CH-1015, Switzerland
| | - Hairui Cui
- Institute of Nuclear Agricultural Sciences, Zhejiang University, Hangzhou, 310029, China
| | - Jianzhong Huang
- Institute of Nuclear Agricultural Sciences, Zhejiang University, Hangzhou, 310029, China
| | - Zuhua He
- Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Yves Poirier
- Department of Plant Molecular Biology, Biophore, University of Lausanne, Lausanne, CH-1015, Switzerland
| | - Karl-Heinz Engel
- Lehrstuhl für Allgemeine Lebensmitteltechnologie, Technische Universität München, Maximum-von-Imhof-Forum 2, Freising-Weihenstephan, D-85354, Germany
| | - Qingyao Shu
- State Key Laboratory of Rice Biology, Institute of Crop Sciences, Zhejiang University, Hangzhou, 310058, China
- Hubei Collaborative Innovation Center for Grain Industry, Jingzhou, 434025, China
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Lu N, Chen JH, Wei D, Chen F, Chen G. Global Metabolic Regulation of the Snow Alga Chlamydomonas nivalis in Response to Nitrate or Phosphate Deprivation by a Metabolome Profile Analysis. Int J Mol Sci 2016; 17:ijms17050694. [PMID: 27171077 PMCID: PMC4881520 DOI: 10.3390/ijms17050694] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Revised: 04/29/2016] [Accepted: 04/29/2016] [Indexed: 01/27/2023] Open
Abstract
In the present work, Chlamydomonas nivalis, a model species of snow algae, was used to illustrate the metabolic regulation mechanism of microalgae under nutrient deprivation stress. The seed culture was inoculated into the medium without nitrate or phosphate to reveal the cell responses by a metabolome profile analysis using gas chromatography time-of-flight mass spectrometry (GC/TOF-MS). One hundred and seventy-one of the identified metabolites clustered into five groups by the orthogonal partial least squares discriminant analysis (OPLS-DA) model. Among them, thirty of the metabolites in the nitrate-deprived group and thirty-nine of the metabolites in the phosphate-deprived group were selected and identified as “responding biomarkers” by this metabolomic approach. A significant change in the abundance of biomarkers indicated that the enhanced biosynthesis of carbohydrates and fatty acids coupled with the decreased biosynthesis of amino acids, N-compounds and organic acids in all the stress groups. The up- or down-regulation of these biomarkers in the metabolic network provides new insights into the global metabolic regulation and internal relationships within amino acid and fatty acid synthesis, glycolysis, the tricarboxylic acid cycle (TCA) and the Calvin cycle in the snow alga under nitrate or phosphate deprivation stress.
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Affiliation(s)
- Na Lu
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510641, China.
| | - Jun-Hui Chen
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510641, China.
| | - Dong Wei
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510641, China.
| | - Feng Chen
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510641, China.
- Institute for Food and Bioresource Engineering, College of Engineering, Peking University, Beijing 100871, China.
| | - Gu Chen
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510641, China.
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Yıldız M, Terzi H. Proteomic analysis of chromium stress and sulfur deficiency responses in leaves of two canola (Brassica napus L.) cultivars differing in Cr(VI) tolerance. Ecotoxicol Environ Saf 2016; 124:255-266. [PMID: 26546907 DOI: 10.1016/j.ecoenv.2015.10.023] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Revised: 09/17/2015] [Accepted: 10/20/2015] [Indexed: 05/19/2023]
Abstract
Sulfur (S) is an essential macronutrient for plant growth and development, and it plays an essential role in response to environmental stresses. Plants suffer with combined stress of S deficiency and hexavalent chromium [Cr(VI)] in the rhizosphere. Little is known about the impact of S deficiency on leaf metabolism of canola (Brassica napus L.) under Cr(VI) stress. Therefore, this study is the first to examine the effects of Cr(VI) stress and S deficiency in canola at a molecular level. A comparative proteomic approach was used to investigate the differences in protein abundance between Cr-tolerant NK Petrol and Cr-sensitive Sary cultivars. The germinated seeds were grown hydroponically in S-sufficient (+S) nutrient solution for 7 days and then subjected to S-deficiency (-S) for 7 days. S-deficient and +S seedlings were then exposed to 100μM Cr(VI) for 3 days. Protein patterns analyzed by two-dimensional electrophoresis (2-DE) revealed that 58 protein spots were differentially regulated by Cr(VI) stress (+S/+Cr), S-deficiency (-S/-Cr) and combined stress (-S/+Cr). Of these, 39 protein spots were identified by MALDI-TOF/TOF mass spectrometry. Differentially regulated proteins predominantly had functions not only in photosynthesis, but also in energy metabolism, stress defense, protein folding and stabilization, signal transduction, redox regulation and sulfur metabolism. Six stress defense related proteins including 2-Cys peroxiredoxin BAS1, glutathione S-transferase, ferritin-1, l-ascorbate peroxidase, thiazole biosynthetic enzyme and myrosinase-binding protein-like At3g16470 exhibited a greater increase in NK Petrol. The stress-related proteins play an important role in the detoxification of Cr(VI) and maintaining cellular homeostasis under variable S nutrition.
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Affiliation(s)
- Mustafa Yıldız
- Department of Molecular Biology and Genetics, Faculty of Science and Literature, Afyon Kocatepe University, 03200 Afyonkarahisar, Turkey.
| | - Hakan Terzi
- Department of Molecular Biology and Genetics, Faculty of Science and Literature, Afyon Kocatepe University, 03200 Afyonkarahisar, Turkey
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Zuchi S, Watanabe M, Hubberten HM, Bromke M, Osorio S, Fernie AR, Celletti S, Paolacci AR, Catarcione G, Ciaffi M, Hoefgen R, Astolfi S. The Interplay between Sulfur and Iron Nutrition in Tomato. Plant Physiol 2015; 169:2624-39. [PMID: 26438787 PMCID: PMC4677893 DOI: 10.1104/pp.15.00995] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 10/02/2015] [Indexed: 05/20/2023]
Abstract
Plant response mechanisms to deficiency of a single nutrient, such as sulfur (S) or iron (Fe), have been described at agronomic, physiological, biochemical, metabolomics, and transcriptomic levels. However, agroecosystems are often characterized by different scenarios, in which combined nutrient deficiencies are likely to occur. Soils are becoming depleted for S, whereas Fe, although highly abundant in the soil, is poorly available for uptake because of its insolubility in the soil matrix. To this end, earlier reports showed that a limited S availability reduces Fe uptake and that Fe deficiency results in the modulation of sulfate uptake and assimilation. However, the mechanistic basis of this interaction remains largely unknown. Metabolite profiling of tomato (Solanum lycopersicum) shoots and roots from plants exposed to Fe, S, and combined Fe and S deficiency was performed to improve the understanding of the S-Fe interaction through the identification of the main players in the considered pathways. Distinct changes were revealed under the different nutritional conditions. Furthermore, we investigated the development of the Fe deficiency response through the analysis of expression of ferric chelate reductase, iron-regulated transporter, and putative transcription factor genes and plant sulfate uptake and mobilization capacity by analyzing the expression of genes encoding sulfate transporters (STs) of groups 1, 2, and 4 (SlST1.1, SlST1.2, SlST2.1, SlST2.2, and SlST4.1). We identified a high degree of common and even synergistic response patterns as well as nutrient-specific responses. The results are discussed in the context of current models of nutrient deficiency responses in crop plants.
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Affiliation(s)
- Sabrina Zuchi
- Department of Agricultural and Forestry Sciences (S.Z., S.C., A.R.P., S.A.) and Department for Innovation in Biological, Agrofood, and Forest Systems (G.C., M.C.), University of Tuscia, 01100 Viterbo, Italy;Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14424 Potsdam, Germany (M.W., H.-M.H., M.B., A.R.F., R.H.); andDepartment of Molecular Biology and Biochemistry, Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora," University of Malaga, Consejo Superior de Investigaciones Científicas, 29071 Malaga, Spain (S.O.)
| | - Mutsumi Watanabe
- Department of Agricultural and Forestry Sciences (S.Z., S.C., A.R.P., S.A.) and Department for Innovation in Biological, Agrofood, and Forest Systems (G.C., M.C.), University of Tuscia, 01100 Viterbo, Italy;Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14424 Potsdam, Germany (M.W., H.-M.H., M.B., A.R.F., R.H.); andDepartment of Molecular Biology and Biochemistry, Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora," University of Malaga, Consejo Superior de Investigaciones Científicas, 29071 Malaga, Spain (S.O.)
| | - Hans-Michael Hubberten
- Department of Agricultural and Forestry Sciences (S.Z., S.C., A.R.P., S.A.) and Department for Innovation in Biological, Agrofood, and Forest Systems (G.C., M.C.), University of Tuscia, 01100 Viterbo, Italy;Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14424 Potsdam, Germany (M.W., H.-M.H., M.B., A.R.F., R.H.); andDepartment of Molecular Biology and Biochemistry, Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora," University of Malaga, Consejo Superior de Investigaciones Científicas, 29071 Malaga, Spain (S.O.)
| | - Mariusz Bromke
- Department of Agricultural and Forestry Sciences (S.Z., S.C., A.R.P., S.A.) and Department for Innovation in Biological, Agrofood, and Forest Systems (G.C., M.C.), University of Tuscia, 01100 Viterbo, Italy;Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14424 Potsdam, Germany (M.W., H.-M.H., M.B., A.R.F., R.H.); andDepartment of Molecular Biology and Biochemistry, Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora," University of Malaga, Consejo Superior de Investigaciones Científicas, 29071 Malaga, Spain (S.O.)
| | - Sonia Osorio
- Department of Agricultural and Forestry Sciences (S.Z., S.C., A.R.P., S.A.) and Department for Innovation in Biological, Agrofood, and Forest Systems (G.C., M.C.), University of Tuscia, 01100 Viterbo, Italy;Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14424 Potsdam, Germany (M.W., H.-M.H., M.B., A.R.F., R.H.); andDepartment of Molecular Biology and Biochemistry, Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora," University of Malaga, Consejo Superior de Investigaciones Científicas, 29071 Malaga, Spain (S.O.)
| | - Alisdair R Fernie
- Department of Agricultural and Forestry Sciences (S.Z., S.C., A.R.P., S.A.) and Department for Innovation in Biological, Agrofood, and Forest Systems (G.C., M.C.), University of Tuscia, 01100 Viterbo, Italy;Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14424 Potsdam, Germany (M.W., H.-M.H., M.B., A.R.F., R.H.); andDepartment of Molecular Biology and Biochemistry, Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora," University of Malaga, Consejo Superior de Investigaciones Científicas, 29071 Malaga, Spain (S.O.)
| | - Silvia Celletti
- Department of Agricultural and Forestry Sciences (S.Z., S.C., A.R.P., S.A.) and Department for Innovation in Biological, Agrofood, and Forest Systems (G.C., M.C.), University of Tuscia, 01100 Viterbo, Italy;Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14424 Potsdam, Germany (M.W., H.-M.H., M.B., A.R.F., R.H.); andDepartment of Molecular Biology and Biochemistry, Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora," University of Malaga, Consejo Superior de Investigaciones Científicas, 29071 Malaga, Spain (S.O.)
| | - Anna Rita Paolacci
- Department of Agricultural and Forestry Sciences (S.Z., S.C., A.R.P., S.A.) and Department for Innovation in Biological, Agrofood, and Forest Systems (G.C., M.C.), University of Tuscia, 01100 Viterbo, Italy;Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14424 Potsdam, Germany (M.W., H.-M.H., M.B., A.R.F., R.H.); andDepartment of Molecular Biology and Biochemistry, Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora," University of Malaga, Consejo Superior de Investigaciones Científicas, 29071 Malaga, Spain (S.O.)
| | - Giulio Catarcione
- Department of Agricultural and Forestry Sciences (S.Z., S.C., A.R.P., S.A.) and Department for Innovation in Biological, Agrofood, and Forest Systems (G.C., M.C.), University of Tuscia, 01100 Viterbo, Italy;Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14424 Potsdam, Germany (M.W., H.-M.H., M.B., A.R.F., R.H.); andDepartment of Molecular Biology and Biochemistry, Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora," University of Malaga, Consejo Superior de Investigaciones Científicas, 29071 Malaga, Spain (S.O.)
| | - Mario Ciaffi
- Department of Agricultural and Forestry Sciences (S.Z., S.C., A.R.P., S.A.) and Department for Innovation in Biological, Agrofood, and Forest Systems (G.C., M.C.), University of Tuscia, 01100 Viterbo, Italy;Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14424 Potsdam, Germany (M.W., H.-M.H., M.B., A.R.F., R.H.); andDepartment of Molecular Biology and Biochemistry, Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora," University of Malaga, Consejo Superior de Investigaciones Científicas, 29071 Malaga, Spain (S.O.)
| | - Rainer Hoefgen
- Department of Agricultural and Forestry Sciences (S.Z., S.C., A.R.P., S.A.) and Department for Innovation in Biological, Agrofood, and Forest Systems (G.C., M.C.), University of Tuscia, 01100 Viterbo, Italy;Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14424 Potsdam, Germany (M.W., H.-M.H., M.B., A.R.F., R.H.); andDepartment of Molecular Biology and Biochemistry, Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora," University of Malaga, Consejo Superior de Investigaciones Científicas, 29071 Malaga, Spain (S.O.)
| | - Stefania Astolfi
- Department of Agricultural and Forestry Sciences (S.Z., S.C., A.R.P., S.A.) and Department for Innovation in Biological, Agrofood, and Forest Systems (G.C., M.C.), University of Tuscia, 01100 Viterbo, Italy;Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14424 Potsdam, Germany (M.W., H.-M.H., M.B., A.R.F., R.H.); andDepartment of Molecular Biology and Biochemistry, Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora," University of Malaga, Consejo Superior de Investigaciones Científicas, 29071 Malaga, Spain (S.O.)
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Tohge T, Scossa F, Fernie AR. Integrative Approaches to Enhance Understanding of Plant Metabolic Pathway Structure and Regulation. Plant Physiol 2015; 169:1499-511. [PMID: 26371234 PMCID: PMC4634077 DOI: 10.1104/pp.15.01006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Accepted: 09/10/2015] [Indexed: 05/05/2023]
Abstract
Huge insight into molecular mechanisms and biological network coordination have been achieved following the application of various profiling technologies. Our knowledge of how the different molecular entities of the cell interact with one another suggests that, nevertheless, integration of data from different techniques could drive a more comprehensive understanding of the data emanating from different techniques. Here, we provide an overview of how such data integration is being used to aid the understanding of metabolic pathway structure and regulation. We choose to focus on the pairwise integration of large-scale metabolite data with that of the transcriptomic, proteomics, whole-genome sequence, growth- and yield-associated phenotypes, and archival functional genomic data sets. In doing so, we attempt to provide an update on approaches that integrate data obtained at different levels to reach a better understanding of either single gene function or metabolic pathway structure and regulation within the context of a broader biological process.
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Affiliation(s)
- Takayuki Tohge
- Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany (T.T., A.R.F.); andConsiglio per la Ricerca e Analisi dell'Economia Agraria, Centro di Ricerca per la Frutticoltura, 00134 Rome, Italy (F.S.)
| | - Federico Scossa
- Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany (T.T., A.R.F.); andConsiglio per la Ricerca e Analisi dell'Economia Agraria, Centro di Ricerca per la Frutticoltura, 00134 Rome, Italy (F.S.)
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany (T.T., A.R.F.); andConsiglio per la Ricerca e Analisi dell'Economia Agraria, Centro di Ricerca per la Frutticoltura, 00134 Rome, Italy (F.S.)
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Peng B, Li H, Peng XX. Functional metabolomics: from biomarker discovery to metabolome reprogramming. Protein Cell 2015; 6:628-37. [PMID: 26135925 DOI: 10.1007/s13238-015-0185-x] [Citation(s) in RCA: 204] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 05/28/2015] [Indexed: 12/14/2022] Open
Abstract
Metabolomics is emerging as a powerful tool for studying metabolic processes, identifying crucial biomarkers responsible for metabolic characteristics and revealing metabolic mechanisms, which construct the content of discovery metabolomics. The crucial biomarkers can be used to reprogram a metabolome, leading to an aimed metabolic strategy to cope with alteration of internal and external environments, naming reprogramming metabolomics here. The striking feature on the similarity of the basic metabolic pathways and components among vastly different species makes the reprogramming metabolomics possible when the engineered metabolites play biological roles in cellular activity as a substrate of enzymes and a regulator to other molecules including proteins. The reprogramming metabolomics approach can be used to clarify metabolic mechanisms of responding to changed internal and external environmental factors and to establish a framework to develop targeted tools for dealing with the changes such as controlling and/or preventing infection with pathogens and enhancing host immunity against pathogens. This review introduces the current state and trends of discovery metabolomics and reprogramming metabolomics and highlights the importance of reprogramming metabolomics.
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