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Su L, Xu C, Zeng S, Su L, Joshi T, Stacey G, Xu D. Large-Scale Integrative Analysis of Soybean Transcriptome Using an Unsupervised Autoencoder Model. FRONTIERS IN PLANT SCIENCE 2022; 13:831204. [PMID: 35310659 PMCID: PMC8927983 DOI: 10.3389/fpls.2022.831204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 02/09/2022] [Indexed: 06/14/2023]
Abstract
Plant tissues are distinguished by their gene expression patterns, which can help identify tissue-specific highly expressed genes and their differential functional modules. For this purpose, large-scale soybean transcriptome samples were collected and processed starting from raw sequencing reads in a uniform analysis pipeline. To address the gene expression heterogeneity in different tissues, we utilized an adversarial deconfounding autoencoder (AD-AE) model to map gene expressions into a latent space and adapted a standard unsupervised autoencoder (AE) model to help effectively extract meaningful biological signals from the noisy data. As a result, four groups of 1,743, 914, 2,107, and 1,451 genes were found highly expressed specifically in leaf, root, seed and nodule tissues, respectively. To obtain key transcription factors (TFs), hub genes and their functional modules in each tissue, we constructed tissue-specific gene regulatory networks (GRNs), and differential correlation networks by using corrected and compressed gene expression data. We validated our results from the literature and gene enrichment analysis, which confirmed many identified tissue-specific genes. Our study represents the largest gene expression analysis in soybean tissues to date. It provides valuable targets for tissue-specific research and helps uncover broader biological patterns. Code is publicly available with open source at https://github.com/LingtaoSu/SoyMeta.
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Affiliation(s)
- Lingtao Su
- Department of Electrical Engineering and Computer Science and Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
| | - Chunhui Xu
- Institute for Data Science and Informatics, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
| | - Shuai Zeng
- Department of Electrical Engineering and Computer Science and Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
| | - Li Su
- Institute for Data Science and Informatics, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
| | - Trupti Joshi
- Department of Electrical Engineering and Computer Science and Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
- Institute for Data Science and Informatics, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
- Department of Health Management and Informatics and Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
| | - Gary Stacey
- Division of Plant Sciences and Technology and Biochemistry Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
| | - Dong Xu
- Department of Electrical Engineering and Computer Science and Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
- Institute for Data Science and Informatics, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
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2
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Gu B, Chen Y, Xie F, Murray JD, Miller AJ. Inorganic Nitrogen Transport and Assimilation in Pea ( Pisum sativum). Genes (Basel) 2022; 13:158. [PMID: 35052498 PMCID: PMC8774688 DOI: 10.3390/genes13010158] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 01/04/2022] [Accepted: 01/06/2022] [Indexed: 12/22/2022] Open
Abstract
The genome sequences of several legume species are now available allowing the comparison of the nitrogen (N) transporter inventories with non-legume species. A survey of the genes encoding inorganic N transporters and the sensing and assimilatory families in pea, revealed similar numbers of genes encoding the primary N assimilatory enzymes to those in other types of plants. Interestingly, we find that pea and Medicago truncatula have fewer members of the NRT2 nitrate transporter family. We suggest that this difference may result from a decreased dependency on soil nitrate acquisition, as legumes have the capacity to derive N from a symbiotic relationship with diazotrophs. Comparison with M. truncatula, indicates that only one of three NRT2s in pea is likely to be functional, possibly indicating less N uptake before nodule formation and N-fixation starts. Pea seeds are large, containing generous amounts of N-rich storage proteins providing a reserve that helps seedling establishment and this may also explain why fewer high affinity nitrate transporters are required. The capacity for nitrate accumulation in the vacuole is another component of assimilation, as it can provide a storage reservoir that supplies the plant when soil N is depleted. Comparing published pea tissue nitrate concentrations with other plants, we find that there is less accumulation of nitrate, even in non-nodulated plants, and that suggests a lower capacity for vacuolar storage. The long-distance transported form of organic N in the phloem is known to be specialized in legumes, with increased amounts of organic N molecules transported, like ureides, allantoin, asparagine and amides in pea. We suggest that, in general, the lower tissue and phloem nitrate levels compared with non-legumes may also result in less requirement for high affinity nitrate transporters. The pattern of N transporter and assimilatory enzyme distribution in pea is discussed and compared with non-legumes with the aim of identifying future breeding targets.
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Affiliation(s)
- Benguo Gu
- Biochemistry & Metabolism Department, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK; (B.G.); (Y.C.)
- CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences (CAS), Shanghai 200032, China;
| | - Yi Chen
- Biochemistry & Metabolism Department, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK; (B.G.); (Y.C.)
- CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences (CAS), Shanghai 200032, China;
| | - Fang Xie
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences (CAS), Shanghai 200032, China;
| | - Jeremy D. Murray
- CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences (CAS), Shanghai 200032, China;
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences (CAS), Shanghai 200032, China;
| | - Anthony J. Miller
- Biochemistry & Metabolism Department, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK; (B.G.); (Y.C.)
- CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences (CAS), Shanghai 200032, China;
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3
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Chen Y, Xu W, Yu S, Ni K, She G, Ye X, Xing Q, Zhao J, Huang C. Assembly status transition offers an avenue for activity modulation of a supramolecular enzyme. eLife 2021; 10:72535. [PMID: 34898426 PMCID: PMC8668187 DOI: 10.7554/elife.72535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 11/30/2021] [Indexed: 11/13/2022] Open
Abstract
Nature has evolved many supramolecular proteins assembled in certain, sometimes even seemingly oversophisticated, morphological manners. The rationale behind such evolutionary efforts is often poorly understood. Here, we provide atomic-resolution insights into how the dynamic building of a structurally complex enzyme with higher order symmetry offers amenability to intricate regulation. We have established the functional coupling between enzymatic activity and protein morphological states of glutamine synthetase (GS), an old multi-subunit enzyme essential for cellular nitrogen metabolism. Cryo-EM structure determination of GS in both the catalytically active and inactive assembly states allows us to reveal an unanticipated self-assembly-induced disorder-order transition paradigm, in which the remote interactions between two subcomplex entities significantly rigidify the otherwise structurally fluctuating active sites, thereby regulating activity. We further show in vivo evidences that how the enzyme morphology transitions could be modulated by cellular factors on demand. Collectively, our data present an example of how assembly status transition offers an avenue for activity modulation, and sharpens our mechanistic understanding of the complex functional and regulatory properties of supramolecular enzymes.
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Affiliation(s)
- Yao Chen
- Ministry of Education Key Laboratory for Membrane-less Organelles & Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Weiya Xu
- Ministry of Education Key Laboratory for Membrane-less Organelles & Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Shuwei Yu
- State Key Laboratory of Tea Plant Biology and Utilization, College of Tea and Food Science and Technology, Anhui Agricultural University, Hefei, China
| | - Kang Ni
- Hefei National Laboratory for Physical Sciences at the Microscale, Department of Chemical Physics, University of Science and Technology of China, Hefei, China
| | - Guangbiao She
- State Key Laboratory of Tea Plant Biology and Utilization, College of Tea and Food Science and Technology, Anhui Agricultural University, Hefei, China
| | - Xiaodong Ye
- Hefei National Laboratory for Physical Sciences at the Microscale, Department of Chemical Physics, University of Science and Technology of China, Hefei, China
| | - Qiong Xing
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, China
| | - Jian Zhao
- State Key Laboratory of Tea Plant Biology and Utilization, College of Tea and Food Science and Technology, Anhui Agricultural University, Hefei, China
| | - Chengdong Huang
- Ministry of Education Key Laboratory for Membrane-less Organelles & Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
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4
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Mondal R, Kumar A, Chattopadhyay SK. Structural property, molecular regulation, and functional diversity of glutamine synthetase in higher plants: a data-mining bioinformatics approach. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 108:1565-1584. [PMID: 34628690 DOI: 10.1111/tpj.15536] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 09/24/2021] [Accepted: 10/01/2021] [Indexed: 05/26/2023]
Abstract
Glutamine synthetase (GS; E.C.6.3.1.2) is a key enzyme in higher plants with two isozymes, cytosolic GS1 and plastidic GS2, and involves in the assimilation and recycling of NH4+ ions and maintenance of complex traits such as crop nitrogen-use efficiency and yield. Our present understanding of crop nitrogen-use efficiency and its correlation with the functional role of the GS family genes is inadequate, which delays harnessing the benefit of this key enzyme in crop improvement. In this report, we performed a comprehensive investigation on the phylogenetic relationship, structural properties, complex multilevel gene regulation, and expression patterns of the GS genes to enrich present understanding about the enzyme. Our Gene Ontology and protein-protein interactions analysis revealed the functional aspects of GS isozymes in stress mitigation, aging, nucleotide biosynthesis/transport, DNA repair and response to metals. The insight gained here contributes to the future research strategies in developing climate-smart crops for global sustainability.
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Affiliation(s)
- Raju Mondal
- Mulberry Tissue Culture Lab, Central Sericultural Germplasm Resources Centre (CSGRC), Central Silk Board, Ministry of Textile, Govt. of India, Hosur, 635109, India
| | - Amit Kumar
- Host Plant Section, Central Muga Eri Research & Training Institute, Central Silk Board, Ministry of Textile, Govt. of India, Lahdoigarh, Jorhat, Assam, 785700, India
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5
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Wang W, Li A, Zhang Z, Chu C. Posttranslational Modifications: Regulation of Nitrogen Utilization and Signaling. PLANT & CELL PHYSIOLOGY 2021; 62:543-552. [PMID: 33493288 PMCID: PMC8462382 DOI: 10.1093/pcp/pcab008] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 01/07/2021] [Indexed: 05/08/2023]
Abstract
Nitrogen is the most important macroelement required for the composition of key molecules, such as nucleic acids, proteins and other organic compounds. As sessile organisms, plants have evolved sophisticated mechanisms to acquire nitrogen for their normal growth and development. Besides the transcriptional and translational regulation of nitrogen uptake, assimilation, remobilization and signal transduction, posttranslational modifications (PTMs) are shown to participate in these processes in plants. In addition to alterations in protein abundance, PTMs may dramatically increase the complexity of the proteome without the concomitant changes in gene transcription and have emerged as an important type of protein regulation in terms of protein function, subcellular localization and protein activity and stability. Herein, we briefly summarize recent advances on the posttranslational regulation of nitrogen uptake, assimilation, remobilization and nitrogen signaling and discuss the underlying mechanisms of PTMs as well as the signal output of such PTMs. Understanding these regulation mechanisms will provide novel insights for improving the nitrogen use efficiency of plants.
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Affiliation(s)
- Wei Wang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Aifu Li
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhihua Zhang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
- School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Chengcai Chu
- * Corresponding author: E-mail, ; Fax, +86-10-64806608
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6
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Berger N, Vignols F, Przybyla-Toscano J, Roland M, Rofidal V, Touraine B, Zienkiewicz K, Couturier J, Feussner I, Santoni V, Rouhier N, Gaymard F, Dubos C. Identification of client iron-sulfur proteins of the chloroplastic NFU2 transfer protein in Arabidopsis thaliana. JOURNAL OF EXPERIMENTAL BOTANY 2020; 72:873-884. [PMID: 32240305 DOI: 10.1093/jxb/eraa403] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 09/01/2020] [Indexed: 05/15/2023]
Abstract
Iron-sulfur (Fe-S) proteins have critical functions in plastids, notably participating in photosynthetic electron transfer, sulfur and nitrogen assimilation, chlorophyll metabolism, and vitamin or amino acid biosynthesis. Their maturation relies on the so-called SUF (sulfur mobilization) assembly machinery. Fe-S clusters are synthesized de novo on a scaffold protein complex and then delivered to client proteins via several transfer proteins. However, the maturation pathways of most client proteins and their specificities for transfer proteins are mostly unknown. In order to decipher the proteins interacting with the Fe-S cluster transfer protein NFU2, one of the three plastidial representatives found in Arabidopsis thaliana, we performed a quantitative proteomic analysis of shoots, roots, and seedlings of nfu2 plants, combined with NFU2 co-immunoprecipitation and binary yeast two-hybrid experiments. We identified 14 new targets, among which nine were validated in planta using a binary bimolecular fluorescence complementation assay. These analyses also revealed a possible role for NFU2 in the plant response to desiccation. Altogether, this study better delineates the maturation pathways of many chloroplast Fe-S proteins, considerably extending the number of NFU2 clients. It also helps to clarify the respective roles of the three NFU paralogs NFU1, NFU2, and NFU3.
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Affiliation(s)
- Nathalie Berger
- BPMP, Université de Montpellier, CNRS, INRAE, SupAgro, Montpellier, France
| | - Florence Vignols
- BPMP, Université de Montpellier, CNRS, INRAE, SupAgro, Montpellier, France
| | | | | | - Valérie Rofidal
- BPMP, Université de Montpellier, CNRS, INRAE, SupAgro, Montpellier, France
| | - Brigitte Touraine
- BPMP, Université de Montpellier, CNRS, INRAE, SupAgro, Montpellier, France
| | - Krzysztof Zienkiewicz
- Department of Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences and Göttingen Center for Molecular Biosciences (GZMB), University of Göttingen, Göttingen, Germany
| | | | - Ivo Feussner
- Department of Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences and Göttingen Center for Molecular Biosciences (GZMB), University of Göttingen, Göttingen, Germany
- Service unit for Metabolomics and Lipidomics, Göttingen Center for Molecular Biosciences (GZMB), University of Göttingen, Göttingen, Germany
| | - Véronique Santoni
- BPMP, Université de Montpellier, CNRS, INRAE, SupAgro, Montpellier, France
| | | | - Frédéric Gaymard
- BPMP, Université de Montpellier, CNRS, INRAE, SupAgro, Montpellier, France
| | - Christian Dubos
- BPMP, Université de Montpellier, CNRS, INRAE, SupAgro, Montpellier, France
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7
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Berger A, Boscari A, Horta Araújo N, Maucourt M, Hanchi M, Bernillon S, Rolin D, Puppo A, Brouquisse R. Plant Nitrate Reductases Regulate Nitric Oxide Production and Nitrogen-Fixing Metabolism During the Medicago truncatula-Sinorhizobium meliloti Symbiosis. FRONTIERS IN PLANT SCIENCE 2020; 11:1313. [PMID: 33013954 PMCID: PMC7500168 DOI: 10.3389/fpls.2020.01313] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 08/11/2020] [Indexed: 05/08/2023]
Abstract
Nitrate reductase (NR) is the first enzyme of the nitrogen reduction pathway in plants, leading to the production of ammonia. However, in the nitrogen-fixing symbiosis between legumes and rhizobia, atmospheric nitrogen (N2) is directly reduced to ammonia by the bacterial nitrogenase, which questions the role of NR in symbiosis. Next to that, NR is the best-characterized source of nitric oxide (NO) in plants, and NO is known to be produced during the symbiosis. In the present study, we first surveyed the three NR genes (MtNR1, MtNR2, and MtNR3) present in the Medicago truncatula genome and addressed their expression, activity, and potential involvement in NO production during the symbiosis between M. truncatula and Sinorhizobium meliloti. Our results show that MtNR1 and MtNR2 gene expression and activity are correlated with NO production throughout the symbiotic process and that MtNR1 is particularly involved in NO production in mature nodules. Moreover, NRs are involved together with the mitochondrial electron transfer chain in NO production throughout the symbiotic process and energy regeneration in N2-fixing nodules. Using an in vivo NMR spectrometric approach, we show that, in mature nodules, NRs participate also in the regulation of energy state, cytosolic pH, carbon and nitrogen metabolism under both normoxia and hypoxia. These data point to the importance of NR activity for the N2-fixing symbiosis and provide a first explanation of its role in this process.
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Affiliation(s)
- Antoine Berger
- Institut Sophia Agrobiotech, UMR INRAE 1355, Université Côte d’Azur, CNRS, Sophia Antipolis, France
- Department of Horticultural Science, University of Florida, Gainesville, FL, United States
| | - Alexandre Boscari
- Institut Sophia Agrobiotech, UMR INRAE 1355, Université Côte d’Azur, CNRS, Sophia Antipolis, France
| | - Natasha Horta Araújo
- Institut Sophia Agrobiotech, UMR INRAE 1355, Université Côte d’Azur, CNRS, Sophia Antipolis, France
| | - Mickaël Maucourt
- Univ. Bordeaux INRAE, UMR Biologie du Fruit et Pathologie, Villenave d’Ornon, France
| | - Mohamed Hanchi
- Institut Sophia Agrobiotech, UMR INRAE 1355, Université Côte d’Azur, CNRS, Sophia Antipolis, France
| | - Stéphane Bernillon
- PMB-Metabolome, INRAE, Bordeaux Metabolome Facility, Villenave d’Ornon, France
| | - Dominique Rolin
- Univ. Bordeaux INRAE, UMR Biologie du Fruit et Pathologie, Villenave d’Ornon, France
- PMB-Metabolome, INRAE, Bordeaux Metabolome Facility, Villenave d’Ornon, France
| | - Alain Puppo
- Institut Sophia Agrobiotech, UMR INRAE 1355, Université Côte d’Azur, CNRS, Sophia Antipolis, France
| | - Renaud Brouquisse
- Institut Sophia Agrobiotech, UMR INRAE 1355, Université Côte d’Azur, CNRS, Sophia Antipolis, France
- *Correspondence: Renaud Brouquisse,
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8
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Gao Y, de Bang TC, Schjoerring JK. Cisgenic overexpression of cytosolic glutamine synthetase improves nitrogen utilization efficiency in barley and prevents grain protein decline under elevated CO 2. PLANT BIOTECHNOLOGY JOURNAL 2019; 17:1209-1221. [PMID: 30525274 PMCID: PMC6576097 DOI: 10.1111/pbi.13046] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 10/23/2018] [Accepted: 11/09/2018] [Indexed: 05/23/2023]
Abstract
Cytosolic glutamine synthetase (GS1) plays a central role in nitrogen (N) metabolism. The importance of GS1 in N remobilization during reproductive growth has been reported in cereal species but attempts to improve N utilization efficiency (NUE) by overexpressing GS1 have yielded inconsistent results. Here, we demonstrate that transformation of barley (Hordeum vulgare L.) plants using a cisgenic strategy to express an extra copy of native HvGS1-1 lead to increased HvGS1.1 expression and GS1 enzyme activity. GS1 overexpressing lines exhibited higher grain yields and NUE than wild-type plants when grown under three different N supplies and two levels of atmospheric CO2 . In contrast with the wild-type, the grain protein concentration in the GS1 overexpressing lines did not decline when plants were exposed to elevated (800-900 μL/L) atmospheric CO2 . We conclude that an increase in GS1 activity obtained through cisgenic overexpression of HvGS1-1 can improve grain yield and NUE in barley. The extra capacity for N assimilation obtained by GS1 overexpression may also provide a means to prevent declining grain protein levels under elevated atmospheric CO2 .
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Affiliation(s)
- Yajie Gao
- Department of Plant and Environmental SciencesFaculty of ScienceCopenhagen UniversityFrederiksbergDenmark
| | - Thomas C. de Bang
- Department of Plant and Environmental SciencesFaculty of ScienceCopenhagen UniversityFrederiksbergDenmark
| | - Jan K. Schjoerring
- Department of Plant and Environmental SciencesFaculty of ScienceCopenhagen UniversityFrederiksbergDenmark
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9
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Silva LS, Alves MQ, Seabra AR, Carvalho HG. Characterization of plant glutamine synthetase S-nitrosation. Nitric Oxide 2019; 88:73-86. [PMID: 31026500 DOI: 10.1016/j.niox.2019.04.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 04/05/2019] [Accepted: 04/13/2019] [Indexed: 10/27/2022]
Abstract
The identification of S-nitrosated substrates and their target cysteine residues is a crucial step to understand the signaling functions of nitric oxide (NO) inside the cells. Here, we show that the key nitrogen metabolic enzyme glutamine synthetase (GS) is a S-nitrosation target in Medicago truncatula and characterize the molecular determinants and the effects of this NO-induced modification on different GS isoenzymes. We found that all the four M. truncatula GS isoforms are S-nitrosated, but despite the high percentage of amino acid identity between the four proteins, S-nitrosation only affects the activity of the plastid-located enzymes, leading to inactivation. A biotin-switch/mass spectrometry approach revealed that cytosolic and plastid-located GSs share an S-nitrosation site at a conserved cysteine residue, but the plastidic enzymes contain additional S-nitrosation sites at non-conserved cysteines, which are accountable for enzyme inactivation. By site-directed mutagenesis, we identified Cys369 as the regulatory S-nitrosation site relevant for the catalytic function of the plastid-located GS and an analysis of the structural environment of the SNO-targeted cysteines in cytosolic and plastid-located isoenzymes explains their differential regulation by S-nitrosation and elucidates the mechanistic by which S-nitrosation of Cys369 leads to enzyme inactivation. We also provide evidence that both the cytosolic and plastid-located GSs are endogenously S-nitrosated in leaves and root nodules of M. truncatula, supporting a physiological meaning for S-nitrosation. Taken together, these results provide new insights into the molecular details of the differential regulation of individual GS isoenzymes by NO-derived molecules and open new paths to explore the biological significance of the NO-mediated regulation of this essential metabolic enzyme.
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Affiliation(s)
- Liliana S Silva
- IBMC, Instituto de Biologia Molecular e Celular da Universidade do Porto; i3S, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen, 4200-135 Porto, Portugal; Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal; Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto, Campus de Vairão, Rua Padre Armando Quintas, No 7, 4485-661, Vairão, Portugal
| | - Mariana Q Alves
- IBMC, Instituto de Biologia Molecular e Celular da Universidade do Porto; i3S, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen, 4200-135 Porto, Portugal
| | - Ana R Seabra
- Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto, Campus de Vairão, Rua Padre Armando Quintas, No 7, 4485-661, Vairão, Portugal
| | - Helena G Carvalho
- IBMC, Instituto de Biologia Molecular e Celular da Universidade do Porto; i3S, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen, 4200-135 Porto, Portugal; Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal; Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto, Campus de Vairão, Rua Padre Armando Quintas, No 7, 4485-661, Vairão, Portugal.
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10
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Balotf S, Islam S, Kavoosi G, Kholdebarin B, Juhasz A, Ma W. How exogenous nitric oxide regulates nitrogen assimilation in wheat seedlings under different nitrogen sources and levels. PLoS One 2018; 13:e0190269. [PMID: 29320529 PMCID: PMC5761883 DOI: 10.1371/journal.pone.0190269] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2017] [Accepted: 12/11/2017] [Indexed: 12/17/2022] Open
Abstract
Nitrogen (N) is one of the most important nutrients for plants and nitric oxide (NO) as a signaling plant growth regulator involved in nitrogen assimilation. Understanding the influence of exogenous NO on nitrogen metabolism at the gene expression and enzyme activity levels under different sources of nitrogen is vitally important for increasing nitrogen use efficiency (NUE). This study investigated the expression of key genes and enzymes in relation to nitrogen assimilation in two Australian wheat cultivars, a popular high NUE cv. Spitfire and a normal NUE cv. Westonia, under different combinations of nitrogen and sodium nitroprusside (SNP) as the NO donor. Application of NO increased the gene expressions and activities of nitrogen assimilation pathway enzymes in both cultivars at low levels of nitrogen. At high nitrogen supplies, the expressions and activities of N assimilation genes increased in response to exogenous NO only in cv. Spitfire but not in cv. Westonia. Exogenous NO caused an increase in leaf NO content at low N supplies in both cultivars, while under high nitrogen treatments, cv. Spitfire showed an increase under ammonium nitrate (NH4NO3) treatment but cv. Westonia was not affected. N assimilation gene expression and enzyme activity showed a clear relationship between exogenous NO, N concentration and N forms in primary plant nitrogen assimilation. Results reveal the possible role of NO and different nitrogen sources on nitrogen assimilation in Triticum aestivum plants.
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Affiliation(s)
- Sadegh Balotf
- School of Veterinary and Life Science, Murdoch University, Perth, Western Australia, Australia
- Institute of Biotechnology, Shiraz University, Shiraz, Iran
| | - Shahidul Islam
- School of Veterinary and Life Science, Murdoch University, Perth, Western Australia, Australia
| | | | - Bahman Kholdebarin
- Department of Biology, Faculty of Sciences, Shiraz University, Shiraz, Iran
| | - Angela Juhasz
- School of Veterinary and Life Science, Murdoch University, Perth, Western Australia, Australia
| | - Wujun Ma
- School of Veterinary and Life Science, Murdoch University, Perth, Western Australia, Australia
- * E-mail:
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11
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Dal Cortivo C, Conselvan GB, Carletti P, Barion G, Sella L, Vamerali T. Biostimulant Effects of Seed-Applied Sedaxane Fungicide: Morphological and Physiological Changes in Maize Seedlings. FRONTIERS IN PLANT SCIENCE 2017; 8:2072. [PMID: 29270181 PMCID: PMC5723653 DOI: 10.3389/fpls.2017.02072] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 11/20/2017] [Indexed: 05/23/2023]
Abstract
Most crops are routinely protected against seed-born and soil-borne fungal pathogens through seed-applied fungicides. The recently released succinate dehydrogenase inhibitor (SDHI), sedaxane®, is a broad-spectrum fungicide, used particularly to control Rhizoctonia spp., but also has documented growth-enhancement effects on wheat. This study investigates the potential biostimulant effects of sedaxane and related physiological changes in disease-free maize seedlings (3-leaf stage) at increasing application doses (25, 75 and 150 μg a.i. seed-1) under controlled sterilized conditions. We show sedaxane to have significant auxin-like and gibberellin-like effects, which effect marked morphological and physiological changes according to an approximate saturation dose-response model. Maximum benefits were attained at the intermediate dose, which significantly increased root length (+60%), area (+45%) and forks (+51%), and reduced root diameter as compared to untreated controls. Sedaxane enhanced leaf and root glutamine synthetase (GS) activity resulting in greater protein accumulation, particularly in the above-ground compartment, while glutamate synthase (GOGAT) activity remained almost unchanged. Sedaxane also improved leaf phenylalanine ammonia-lyase (PAL) activity, which may be responsible for the increase in shoot antioxidant activity (phenolic acids), mainly represented by p-coumaric and caffeic acids. We conclude that, in addition to its protective effect, sedaxane can facilitate root establishment and intensify nitrogen and phenylpropanoid metabolism in young maize plants, and may be beneficial in overcoming biotic and abiotic stresses in early growth stages.
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Affiliation(s)
- Cristian Dal Cortivo
- Department of Agronomy, Food, Natural Resources, Animals and the Environment, University of Padua, Padua, Italy
| | - Giovanni Battista Conselvan
- Department of Agronomy, Food, Natural Resources, Animals and the Environment, University of Padua, Padua, Italy
| | - Paolo Carletti
- Department of Agronomy, Food, Natural Resources, Animals and the Environment, University of Padua, Padua, Italy
| | - Giuseppe Barion
- Department of Agronomy, Food, Natural Resources, Animals and the Environment, University of Padua, Padua, Italy
| | - Luca Sella
- Department of Land, Environment, Agriculture and Forestry, University of Padua, Padua, Italy
| | - Teofilo Vamerali
- Department of Agronomy, Food, Natural Resources, Animals and the Environment, University of Padua, Padua, Italy
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12
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Furlan AL, Bianucci E, Castro S, Dietz KJ. Metabolic features involved in drought stress tolerance mechanisms in peanut nodules and their contribution to biological nitrogen fixation. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2017; 263:12-22. [PMID: 28818367 DOI: 10.1016/j.plantsci.2017.06.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Revised: 06/22/2017] [Accepted: 06/23/2017] [Indexed: 05/04/2023]
Abstract
Legumes belong to the most important crops worldwide. They increase soil fertility due their ability to establish symbiotic associations with soil microorganisms, known as rhizobia, capable of fixing nitrogen from the atmosphere. However, they are frequently exposed to abiotic stress conditions in particular drought. Such adverse conditions impair the biological nitrogen fixation (BNF) and depend largely on the legume. Therefore, two peanut cultivars with contrasting tolerance to drought, namely the more tolerant EC-98 and the sensitive Granoleico, were investigated to elucidate the relative contribution of BNF to the tolerance to drought. The tolerant cultivar EC-98 sustained growth and BNF similar to the control condition despite the reduced water potential and photosynthesis, suggesting the functioning of distinct metabolic pathways that contributed to enhance the tolerance. The biochemical and metabolomics approaches revealed that nodules from the tolerant cultivar accumulated trehalose, proline and gamma-aminobutyric acid (GABA), metabolites with known function in protecting against drought stress. The amide metabolism was severely affected in nodules from the sensitive cultivar Granoleico as revealed by the low content of asparagine and glutamine in the drought stressed plants. The sensitive cultivar upon rehydration was unable to re-establish a metabolism similar to well-watered plants. This was evidenced by the low level of metabolites and, transcripts and specific activities of enzymes from the carbon (sucrose synthase) and nitrogen (glutamine synthetase) metabolism which decreased below the values of control plants. Therefore, the increased content of metabolites with protective functions under drought stress likely is crucial for the full restoration upon rehydration. Smaller changes of drought stress-related metabolites in nodule are another trait that contributes to the effective control of BNF in the tolerant peanut cultivar (EC-98).
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Affiliation(s)
- Ana Laura Furlan
- Departamento de Ciencias Naturales, Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto, Ruta 36, Km 601, 5800 Río Cuarto, Córdoba, Argentina; Biochemistry and Physiology of Plants, Bielefeld University, D-33501 Bielefeld, Germany.
| | - Eliana Bianucci
- Departamento de Ciencias Naturales, Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto, Ruta 36, Km 601, 5800 Río Cuarto, Córdoba, Argentina
| | - Stella Castro
- Departamento de Ciencias Naturales, Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto, Ruta 36, Km 601, 5800 Río Cuarto, Córdoba, Argentina
| | - Karl-Josef Dietz
- Biochemistry and Physiology of Plants, Bielefeld University, D-33501 Bielefeld, Germany
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13
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Aybeke M. Fusarium Infection Causes Phenolic Accumulations and Hormonal Disorders in Orobanche spp. Indian J Microbiol 2017; 57:416-421. [PMID: 29151642 DOI: 10.1007/s12088-017-0669-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 08/08/2017] [Indexed: 12/20/2022] Open
Abstract
The physiological effects of Fusarium oxysporum on in-root parasitic weed, Orobanche spp. (broomrape) with references to change in plant hormones and secondary plant constituents were investigated. The levels of IAA, GA, ABA and JA in the experimental group were significantly lower than those in the control group, while the level of SA was higher in the experimental group. In secondary metabolic studies, the quantities of various phenols were measured in the two groups and catechin, syringic acid and p-coumaric acid amounts were significantly higher in the experimental group than in the control group, unlike gallic acid which have a lower amount. Consequently, in the light of all data, it was concluded that Fusarium oxysporum (1) causes heavy hormonal disorder, (2) triggered only SA-mediated defense and (3) induced intensively accumulation of phenolic substances in orobanche. Fusarium oxysporum causes lethal physiological damage on Orobanche spp.
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Affiliation(s)
- Mehmet Aybeke
- Department of Biology, Faculty of Science, Trakya University, Balkan Campus, 22030 Edirne, Turkey
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14
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Fusarium infection causes genotoxic disorders and antioxidant-based damages in Orobanche spp. Microbiol Res 2017; 201:46-51. [PMID: 28602401 DOI: 10.1016/j.micres.2017.05.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Revised: 04/24/2017] [Accepted: 05/04/2017] [Indexed: 12/21/2022]
Abstract
This study aims to evaluate the toxic effects of Fusarium oxysporum on root parasitic weed, Orobanche spp. Comparative genetic and gene expression studies were conducted on uninfected and fungus-infected orobanches. In genetic studies, isolated total DNA was amplified by RAPD PCR. Fragment properties were analysed by GTS test. According to the results, the fragment properties of control and Fusarium infected (experimental) groups varied widely; and it has been observed that Fusarium has genotoxic effects on the DNA of orobanches. In gene expression studies, the expression levels of genes encoding enzymes or proteins were associated with ROS damage and toxic effects, therefore, gene expressions of Mn-superoxide dismutase (SOD), Zn-superoxide dismutase (=SOD2, mitochondrial), glutamine synthetase (GS), heat shock protein gene (HSP70), BAX, Caspase-3 and BCL2 were significantly higher in the experimental group. In the light of obtained data, it was concluded that F. oxysporum (1) caused heavy ROS damage in Orobanche (2) induced significant irrevocable genotoxic effects on the DNA of Orobanche, (3) degraded protein metabolism and synthesis, and finally (4) triggered apoptosis. The results of this study can be a ground for further research on reducing the toxic effects of Fusarium on agricultural products, so that advancements in bio-herbicide technology may provide a sustainable agricultural production.
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15
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Afkhami ME, Stinchcombe JR. Multiple mutualist effects on genomewide expression in the tripartite association between
Medicago truncatula,
nitrogen‐fixing bacteria and mycorrhizal fungi. Mol Ecol 2016; 25:4946-62. [DOI: 10.1111/mec.13809] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Revised: 08/05/2016] [Accepted: 08/11/2016] [Indexed: 01/25/2023]
Affiliation(s)
- Michelle E. Afkhami
- Department of Biology University of Miami 1301 Memorial Dr. #215 Coral Gables FL 33146 USA
- Department of Ecology and Evolutionary Biology University of Toronto 25 Willcocks St. Toronto ON Canada M5S 3B2
| | - John R. Stinchcombe
- Department of Ecology and Evolutionary Biology University of Toronto 25 Willcocks St. Toronto ON Canada M5S 3B2
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16
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Yu DY, Noh SM, Lee GM. Limitations to the development of recombinant human embryonic kidney 293E cells using glutamine synthetase-mediated gene amplification: Methionine sulfoximine resistance. J Biotechnol 2016; 231:136-140. [DOI: 10.1016/j.jbiotec.2016.06.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Revised: 05/16/2016] [Accepted: 06/06/2016] [Indexed: 10/21/2022]
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17
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Guan M, de Bang TC, Pedersen C, Schjoerring JK. Cytosolic Glutamine Synthetase Gln1;2 Is the Main Isozyme Contributing to GS1 Activity and Can Be Up-Regulated to Relieve Ammonium Toxicity. PLANT PHYSIOLOGY 2016; 171:1921-33. [PMID: 27231101 PMCID: PMC4936538 DOI: 10.1104/pp.16.01195] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Accepted: 05/25/2016] [Indexed: 05/19/2023]
Abstract
Cytosolic GS1 (Gln synthetase) is central for ammonium assimilation in plants. High ammonium treatment enhanced the expression of the GS1 isogene Gln-1;2 encoding a low-affinity high-capacity GS1 protein in Arabidopsis (Arabidopsis thaliana) shoots. Under the same conditions, the expression of the high-affinity low-capacity isoform Gln-1;1 was reduced. The expression of Gln-1;3 did not respond to ammonium treatment while Gln-1;4 and Gln-1;5 isogenes in all cases were expressed at a very low level. Gln-2 was highly expressed in shoots but only at a very low level in roots. To investigate the specific functions of the two isogenes Gln-1;1 and Gln-1;2 in shoots for ammonium detoxification, single and double knock-out mutants were grown under standard N supply or with high ammonium provision. Phenotypes of the single mutant gln1;1 were similar to the wild type, while growth of the gln1;2 single mutant and the gln1;1:gln1;2 double mutant was significantly impaired irrespective of N regime. GS1 activity was significantly reduced in both gln1;2 and gln1;1:gln1;2 Along with this, the ammonium content increased while that of Gln decreased, showing that Gln-1;2 was essential for ammonium assimilation and amino acid synthesis. We conclude that Gln-1;2 is the main isozyme contributing to shoot GS1 activity in vegetative growth stages and can be up-regulated to relieve ammonium toxicity. This reveals, to our knowledge, a novel shoot function of Gln-1;2 in Arabidopsis shoots.
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Affiliation(s)
- Miao Guan
- Department of Plant and Environmental Sciences and Copenhagen Plant Science Center, Faculty of Science, University of Copenhagen, DK-1871 Frederiksberg C, Denmark
| | - Thomas C de Bang
- Department of Plant and Environmental Sciences and Copenhagen Plant Science Center, Faculty of Science, University of Copenhagen, DK-1871 Frederiksberg C, Denmark
| | - Carsten Pedersen
- Department of Plant and Environmental Sciences and Copenhagen Plant Science Center, Faculty of Science, University of Copenhagen, DK-1871 Frederiksberg C, Denmark
| | - Jan K Schjoerring
- Department of Plant and Environmental Sciences and Copenhagen Plant Science Center, Faculty of Science, University of Copenhagen, DK-1871 Frederiksberg C, Denmark
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