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Klčová B, Balarynová J, Trněný O, Krejčí P, Cechová MZ, Leonova T, Gorbach D, Frolova N, Kysil E, Orlova A, Ihling С, Frolov A, Bednář P, Smýkal P. Domestication has altered gene expression and secondary metabolites in pea seed coat. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:2269-2295. [PMID: 38578789 DOI: 10.1111/tpj.16734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Accepted: 03/09/2024] [Indexed: 04/07/2024]
Abstract
The mature seed in legumes consists of an embryo and seed coat. In contrast to knowledge about the embryo, we know relatively little about the seed coat. We analyzed the gene expression during seed development using a panel of cultivated and wild pea genotypes. Gene co-expression analysis identified gene modules related to seed development, dormancy, and domestication. Oxidoreductase genes were found to be important components of developmental and domestication processes. Proteomic and metabolomic analysis revealed that domestication favored proteins involved in photosynthesis and protein metabolism at the expense of seed defense. Seed coats of wild peas were rich in cell wall-bound metabolites and the protective compounds predominated in their seed coats. Altogether, we have shown that domestication altered pea seed development and modified (mostly reduced) the transcripts along with the protein and metabolite composition of the seed coat, especially the content of the compounds involved in defense. We investigated dynamic profiles of selected identified phenolic and flavonoid metabolites across seed development. These compounds usually deteriorated the palatability and processing of the seeds. Our findings further provide resources to study secondary metabolism and strategies for improving the quality of legume seeds which comprise an important part of the human protein diet.
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Affiliation(s)
- Barbora Klčová
- Department of Botany, Faculty of Sciences, Palacky University, Šlechtitelů 27, Olomouc, 773 71, Czech Republic
| | - Jana Balarynová
- Department of Botany, Faculty of Sciences, Palacky University, Šlechtitelů 27, Olomouc, 773 71, Czech Republic
| | - Oldřich Trněný
- Agricultural Research Ltd., Zemědělská 1, Troubsko, 664 41, Czech Republic
| | - Petra Krejčí
- Department of Analytical Chemistry, Faculty of Sciences, Palacky University, 17. listopadu 1192/12, Olomouc, 771 46, Czech Republic
| | - Monika Zajacová Cechová
- Department of Analytical Chemistry, Faculty of Sciences, Palacky University, 17. listopadu 1192/12, Olomouc, 771 46, Czech Republic
| | - Tatiana Leonova
- Department of Bioorganic Chemistry, Leibniz-Institut für Pflanzenbiochemie, Weinberg 3, Halle (Saale), 06120, Germany
| | - Daria Gorbach
- Department of Bioorganic Chemistry, Leibniz-Institut für Pflanzenbiochemie, Weinberg 3, Halle (Saale), 06120, Germany
| | - Nadezhda Frolova
- Laboratory of Analytical Biochemistry, Timiryazev Institute of Plant Physiology, Botanicheskaja 36, Moscow, 127276, Russia
| | - Elana Kysil
- Department of Bioorganic Chemistry, Leibniz-Institut für Pflanzenbiochemie, Weinberg 3, Halle (Saale), 06120, Germany
| | - Anastasia Orlova
- Laboratory of Analytical Biochemistry, Timiryazev Institute of Plant Physiology, Botanicheskaja 36, Moscow, 127276, Russia
| | - Сhristian Ihling
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Martin-Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3, Halle (Saale), 06120, Germany
| | - Andrej Frolov
- Laboratory of Analytical Biochemistry, Timiryazev Institute of Plant Physiology, Botanicheskaja 36, Moscow, 127276, Russia
| | - Petr Bednář
- Department of Analytical Chemistry, Faculty of Sciences, Palacky University, 17. listopadu 1192/12, Olomouc, 771 46, Czech Republic
| | - Petr Smýkal
- Department of Botany, Faculty of Sciences, Palacky University, Šlechtitelů 27, Olomouc, 773 71, Czech Republic
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Yurkov AP, Afonin AM, Kryukov AA, Gorbunova AO, Kudryashova TR, Kovalchuk AI, Gorenkova AI, Bogdanova EM, Kosulnikov YV, Laktionov YV, Kozhemyakov AP, Romanyuk DA, Zhukov VA, Puzanskiy RK, Mikhailova YV, Yemelyanov VV, Shishova MF. The Effects of Rhizophagus irregularis Inoculation on Transcriptome of Medicago lupulina Leaves at Early Vegetative and Flowering Stages of Plant Development. PLANTS (BASEL, SWITZERLAND) 2023; 12:3580. [PMID: 37896043 PMCID: PMC10610208 DOI: 10.3390/plants12203580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Revised: 10/02/2023] [Accepted: 10/13/2023] [Indexed: 10/29/2023]
Abstract
The study is aimed at revealing the effects of Rhizophagus irregularis inoculation on the transcriptome of Medicago lupulina leaves at the early (second leaf formation) and later (flowering) stages of plant development. A pot experiment was conducted under conditions of low phosphorus (P) level in the substrate. M. lupulina plants were characterized by high mycorrhizal growth response and mycorrhization parameters. Library sequencing was performed on the Illumina HiseqXTen platform. Significant changes in the expression of 4863 (padj < 0.01) genes from 34049 functionally annotated genes were shown by Massive Analysis of cDNA Ends (MACE-Seq). GO enrichment analysis using the Kolmogorov-Smirnov test was performed, and 244 functional GO groups were identified, including genes contributing to the development of effective AM symbiosis. The Mercator online tool was used to assign functional classes of differentially expressed genes (DEGs). The early stage was characterized by the presence of six functional classes that included only upregulated GO groups, such as genes of carbohydrate metabolism, cellular respiration, nutrient uptake, photosynthesis, protein biosynthesis, and solute transport. At the later stage (flowering), the number of stimulated GO groups was reduced to photosynthesis and protein biosynthesis. All DEGs of the GO:0016036 group were downregulated because AM plants had higher resistance to phosphate starvation. For the first time, the upregulation of genes encoding thioredoxin in AM plant leaves was shown. It was supposed to reduce ROS level and thus, consequently, enhance the mechanisms of antioxidant protection in M. lupulina plants under conditions of low phosphorus level. Taken together, the obtained results indicate genes that are the most important for the effective symbiosis with M. lupulina and might be engaged in other plant species.
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Affiliation(s)
- Andrey P. Yurkov
- Laboratory of Ecology of Symbiotic and Associative Rhizobacteria, All-Russia Research Institute for Agricultural Microbiology, Pushkin, St. Petersburg 196608, Russia; (A.M.A.); (A.A.K.); (A.O.G.); (T.R.K.); (A.I.K.); (A.I.G.); (E.M.B.); (Y.V.K.); (Y.V.L.); (A.P.K.)
| | - Alexey M. Afonin
- Laboratory of Ecology of Symbiotic and Associative Rhizobacteria, All-Russia Research Institute for Agricultural Microbiology, Pushkin, St. Petersburg 196608, Russia; (A.M.A.); (A.A.K.); (A.O.G.); (T.R.K.); (A.I.K.); (A.I.G.); (E.M.B.); (Y.V.K.); (Y.V.L.); (A.P.K.)
| | - Alexey A. Kryukov
- Laboratory of Ecology of Symbiotic and Associative Rhizobacteria, All-Russia Research Institute for Agricultural Microbiology, Pushkin, St. Petersburg 196608, Russia; (A.M.A.); (A.A.K.); (A.O.G.); (T.R.K.); (A.I.K.); (A.I.G.); (E.M.B.); (Y.V.K.); (Y.V.L.); (A.P.K.)
| | - Anastasia O. Gorbunova
- Laboratory of Ecology of Symbiotic and Associative Rhizobacteria, All-Russia Research Institute for Agricultural Microbiology, Pushkin, St. Petersburg 196608, Russia; (A.M.A.); (A.A.K.); (A.O.G.); (T.R.K.); (A.I.K.); (A.I.G.); (E.M.B.); (Y.V.K.); (Y.V.L.); (A.P.K.)
| | - Tatyana R. Kudryashova
- Laboratory of Ecology of Symbiotic and Associative Rhizobacteria, All-Russia Research Institute for Agricultural Microbiology, Pushkin, St. Petersburg 196608, Russia; (A.M.A.); (A.A.K.); (A.O.G.); (T.R.K.); (A.I.K.); (A.I.G.); (E.M.B.); (Y.V.K.); (Y.V.L.); (A.P.K.)
- Graduate School of Biotechnology and Food Science, Peter the Great St. Petersburg Polytechnic University, St. Petersburg 194064, Russia
| | - Anastasia I. Kovalchuk
- Laboratory of Ecology of Symbiotic and Associative Rhizobacteria, All-Russia Research Institute for Agricultural Microbiology, Pushkin, St. Petersburg 196608, Russia; (A.M.A.); (A.A.K.); (A.O.G.); (T.R.K.); (A.I.K.); (A.I.G.); (E.M.B.); (Y.V.K.); (Y.V.L.); (A.P.K.)
- Graduate School of Biotechnology and Food Science, Peter the Great St. Petersburg Polytechnic University, St. Petersburg 194064, Russia
| | - Anastasia I. Gorenkova
- Laboratory of Ecology of Symbiotic and Associative Rhizobacteria, All-Russia Research Institute for Agricultural Microbiology, Pushkin, St. Petersburg 196608, Russia; (A.M.A.); (A.A.K.); (A.O.G.); (T.R.K.); (A.I.K.); (A.I.G.); (E.M.B.); (Y.V.K.); (Y.V.L.); (A.P.K.)
- Faculty of Biology, St. Petersburg State University, St. Petersburg 199034, Russia; (R.K.P.); (V.V.Y.); (M.F.S.)
| | - Ekaterina M. Bogdanova
- Laboratory of Ecology of Symbiotic and Associative Rhizobacteria, All-Russia Research Institute for Agricultural Microbiology, Pushkin, St. Petersburg 196608, Russia; (A.M.A.); (A.A.K.); (A.O.G.); (T.R.K.); (A.I.K.); (A.I.G.); (E.M.B.); (Y.V.K.); (Y.V.L.); (A.P.K.)
- Faculty of Biology, St. Petersburg State University, St. Petersburg 199034, Russia; (R.K.P.); (V.V.Y.); (M.F.S.)
| | - Yuri V. Kosulnikov
- Laboratory of Ecology of Symbiotic and Associative Rhizobacteria, All-Russia Research Institute for Agricultural Microbiology, Pushkin, St. Petersburg 196608, Russia; (A.M.A.); (A.A.K.); (A.O.G.); (T.R.K.); (A.I.K.); (A.I.G.); (E.M.B.); (Y.V.K.); (Y.V.L.); (A.P.K.)
| | - Yuri V. Laktionov
- Laboratory of Ecology of Symbiotic and Associative Rhizobacteria, All-Russia Research Institute for Agricultural Microbiology, Pushkin, St. Petersburg 196608, Russia; (A.M.A.); (A.A.K.); (A.O.G.); (T.R.K.); (A.I.K.); (A.I.G.); (E.M.B.); (Y.V.K.); (Y.V.L.); (A.P.K.)
| | - Andrey P. Kozhemyakov
- Laboratory of Ecology of Symbiotic and Associative Rhizobacteria, All-Russia Research Institute for Agricultural Microbiology, Pushkin, St. Petersburg 196608, Russia; (A.M.A.); (A.A.K.); (A.O.G.); (T.R.K.); (A.I.K.); (A.I.G.); (E.M.B.); (Y.V.K.); (Y.V.L.); (A.P.K.)
| | - Daria A. Romanyuk
- Laboratory of Genetics of Plant-Microbe Interactions, All-Russia Research Institute for Agricultural Microbiology, Pushkin, St. Petersburg 196608, Russia; (D.A.R.); (V.A.Z.)
| | - Vladimir A. Zhukov
- Laboratory of Genetics of Plant-Microbe Interactions, All-Russia Research Institute for Agricultural Microbiology, Pushkin, St. Petersburg 196608, Russia; (D.A.R.); (V.A.Z.)
| | - Roman K. Puzanskiy
- Faculty of Biology, St. Petersburg State University, St. Petersburg 199034, Russia; (R.K.P.); (V.V.Y.); (M.F.S.)
- Laboratory of Analytical Phytochemistry, Komarov Botanical Institute of the Russian Academy of Sciences, St. Petersburg 197022, Russia
| | - Yulia V. Mikhailova
- Laboratory of Biosystematics and Cytology, Komarov Botanical Institute of the Russian Academy of Sciences, St. Petersburg 197022, Russia;
| | - Vladislav V. Yemelyanov
- Faculty of Biology, St. Petersburg State University, St. Petersburg 199034, Russia; (R.K.P.); (V.V.Y.); (M.F.S.)
| | - Maria F. Shishova
- Faculty of Biology, St. Petersburg State University, St. Petersburg 199034, Russia; (R.K.P.); (V.V.Y.); (M.F.S.)
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3
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Rodrigues L, Nogales A, Nunes J, Rodrigues L, Hansen LD, Cardoso H. Germination of Pisum sativum L. Seeds Is Associated with the Alternative Respiratory Pathway. BIOLOGY 2023; 12:1318. [PMID: 37887028 PMCID: PMC10604721 DOI: 10.3390/biology12101318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 10/04/2023] [Accepted: 10/05/2023] [Indexed: 10/28/2023]
Abstract
The alternative oxidase (AOX) is a ubiquinol oxidase with a crucial role in the mitochondrial alternative respiratory pathway, which is associated with various processes in plants. In this study, the activity of AOX in pea seed germination was determined in two pea cultivars, 'Maravilha d'América' (MA) and 'Torta de Quebrar' (TQ), during a germination trial using cytochrome oxidase (COX) and AOX inhibitors [rotenone (RT) and salicylic hydroxamic acid (SHAM), respectively]. Calorespirometry was used to assess respiratory changes during germination. In both cultivars, SHAM had a greater inhibitory effect on germination than RT, demonstrating the involvement of AOX in germination. Although calorespirometry did not provide direct information on the involvement of the alternative pathway in seed germination, this methodology was valuable for distinguishing cultivars. To gain deeper insights into the role of AOX in seed germination, the AOX gene family was characterized, and the gene expression pattern was evaluated. Three PsAOX members were identified-PsAOX1, PsAOX2a and PsAOX2b-and their expression revealed a marked genotype effect. This study emphasizes the importance of AOX in seed germination, contributing to the understanding of the role of the alternative respiratory pathway in plants.
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Affiliation(s)
- Lénia Rodrigues
- MED—Mediterranean Institute for Agriculture, Environment and Development & CHANGE—Global Change and Sustainability Institute, Institute for Advanced Studies and Research, University of Évora, Pólo da Mitra, Ap. 94, 7006-554 Évora, Portugal;
| | - Amaia Nogales
- IRTA Institute of Agrifood Research and Technology, Sustainable Plant Protection Programme, Centre Cabrils, Ctra. Cabrils Km 2, 08348 Cabrils, Spain;
| | - João Nunes
- School of Sciences and Technology, University of Évora, Pólo da Mitra, Ap. 94, 7006-554 Évora, Portugal; (J.N.); (L.R.)
| | - Leonardo Rodrigues
- School of Sciences and Technology, University of Évora, Pólo da Mitra, Ap. 94, 7006-554 Évora, Portugal; (J.N.); (L.R.)
| | - Lee D. Hansen
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602, USA;
| | - Hélia Cardoso
- MED—Mediterranean Institute for Agriculture, Environment and Development & CHANGE—Global Change and Sustainability Institute, School of Science and Technology, Department of Biology, University of Évora, Pólo da Mitra, Ap. 94, 7006-554 Évora, Portugal
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4
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Rodríguez-Vázquez R, Mesa-Marín J. Plant responses to plant growth promoting bacteria: Insights from proteomics. JOURNAL OF PLANT PHYSIOLOGY 2023; 287:154031. [PMID: 37321049 DOI: 10.1016/j.jplph.2023.154031] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 06/05/2023] [Accepted: 06/07/2023] [Indexed: 06/17/2023]
Affiliation(s)
| | - Jennifer Mesa-Marín
- Department of Plant Biology and Ecology, Faculty of Biology, University of Seville, Seville, Spain.
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5
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Xavier GR, Jesus EDC, Dias A, Coelho MRR, Molina YC, Rumjanek NG. Contribution of Biofertilizers to Pulse Crops: From Single-Strain Inoculants to New Technologies Based on Microbiomes Strategies. PLANTS (BASEL, SWITZERLAND) 2023; 12:954. [PMID: 36840302 PMCID: PMC9962295 DOI: 10.3390/plants12040954] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 02/14/2023] [Accepted: 02/16/2023] [Indexed: 06/18/2023]
Abstract
Pulses provide distinct health benefits due to their low fat content and high protein and fiber contents. Their grain production reaches approximately 93,210 × 103 tons per year. Pulses benefit from the symbiosis with atmospheric N2-fixing bacteria, which increases productivity and reduces the need for N fertilizers, thus contributing to mitigation of environmental impact mitigation. Additionally, the root region harbors a rich microbial community with multiple traits related to plant growth promotion, such as nutrient increase and tolerance enhancement to abiotic or biotic stresses. We reviewed the eight most common pulses accounting for almost 90% of world production: common beans, chickpeas, peas, cowpeas, mung beans, lentils, broad beans, and pigeon peas. We focused on updated information considering both single-rhizobial inoculation and co-inoculation with plant growth-promoting rhizobacteria. We found approximately 80 microbial taxa with PGPR traits, mainly Bacillus sp., B. subtilis, Pseudomonas sp., P. fluorescens, and arbuscular mycorrhizal fungi, and that contributed to improve plant growth and yield under different conditions. In addition, new data on root, nodule, rhizosphere, and seed microbiomes point to strategies that can be used to design new generations of biofertilizers, highlighting the importance of microorganisms for productive pulse systems.
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Affiliation(s)
| | | | - Anelise Dias
- Departamento de Fitotecnia, Instituto de Agronomia, Universidade Federal Rural do Rio de Janeiro, UFRRJ, Rodovia BR-465, Km 7, Seropédica 23890-000, RJ, Brazil
| | | | - Yulimar Castro Molina
- Programa de Pós-graduação em Microbiologia Agrícola, Universidade Federal de Lavras, UFLA, Trevo Rotatório Professor Edmir Sá Santos, Lavras 37203-202, MG, Brazil
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6
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Leonova T, Ihling C, Saoud M, Frolova N, Rennert R, Wessjohann LA, Frolov A. Does filter-aided sample preparation provide sufficient method linearity for quantitative plant shotgun proteomics? FRONTIERS IN PLANT SCIENCE 2022; 13:874761. [PMID: 36507396 PMCID: PMC9728026 DOI: 10.3389/fpls.2022.874761] [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: 02/12/2022] [Accepted: 10/26/2022] [Indexed: 06/17/2023]
Abstract
Due to its outstanding throughput and analytical resolution, gel-free LC-based shotgun proteomics represents the gold standard of proteome analysis. Thereby, the efficiency of sample preparation dramatically affects the correctness and reliability of protein quantification. Thus, the steps of protein isolation, solubilization, and proteolysis represent the principal bottleneck of shotgun proteomics. The desired performance of the sample preparation protocols can be achieved by the application of detergents. However, these compounds ultimately compromise reverse-phase chromatographic separation and disrupt electrospray ionization. Filter-aided sample preparation (FASP) represents an elegant approach to overcome these limitations. Although this method is comprehensively validated for cell proteomics, its applicability to plants and compatibility with plant-specific protein isolation protocols remain to be confirmed. Thereby, the most important gap is the absence of the data on the linearity of underlying protein quantification methods for plant matrices. To fill this gap, we address here the potential of FASP in combination with two protein isolation protocols for quantitative analysis of pea (Pisum sativum) seed and Arabidopsis thaliana leaf proteomes by the shotgun approach. For this aim, in comprehensive spiking experiments with bovine serum albumin (BSA), we evaluated the linear dynamic range (LDR) of protein quantification in the presence of plant matrices. Furthermore, we addressed the interference of two different plant matrices in quantitative experiments, accomplished with two alternative sample preparation workflows in comparison to conventional FASP-based digestion of cell lysates, considered here as a reference. The spiking experiments revealed high sensitivities (LODs of up to 4 fmol) for spiked BSA and LDRs of at least 0.6 × 102. Thereby, phenol extraction yielded slightly better recoveries, whereas the detergent-based method showed better linearity. Thus, our results indicate the very good applicability of FASP to quantitative plant proteomics with only limited impact of the protein isolation technique on the method's overall performance.
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Affiliation(s)
- Tatiana Leonova
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, Halle (Saale), Germany
- Department of Biochemistry, St Petersburg State University, St Petersburg, Russia
| | - Christian Ihling
- Institute of Pharmacy, Department of Pharmaceutical Chemistry and Bioanalytics, Martin-Luther Universität Halle-Wittenberg, Halle (Saale), Germany
| | - Mohamad Saoud
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, Halle (Saale), Germany
| | - Nadezhda Frolova
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, Halle (Saale), Germany
- Department of Biochemistry, St Petersburg State University, St Petersburg, Russia
| | - Robert Rennert
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, Halle (Saale), Germany
| | - Ludger A. Wessjohann
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, Halle (Saale), Germany
| | - Andrej Frolov
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, Halle (Saale), Germany
- Department of Biochemistry, St Petersburg State University, St Petersburg, Russia
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Danko K, Lukasheva E, Zhukov VA, Zgoda V, Frolov A. Detergent-Assisted Protein Digestion-On the Way to Avoid the Key Bottleneck of Shotgun Bottom-Up Proteomics. Int J Mol Sci 2022; 23:13903. [PMID: 36430380 PMCID: PMC9695859 DOI: 10.3390/ijms232213903] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 11/02/2022] [Accepted: 11/05/2022] [Indexed: 11/16/2022] Open
Abstract
Gel-free bottom-up shotgun proteomics is the principal methodological platform for the state-of-the-art proteome research. This methodology assumes quantitative isolation of the total protein fraction from a complex biological sample, its limited proteolysis with site-specific proteases, analysis of the resulted peptides with nanoscaled reversed-phase high-performance liquid chromatography-(tandem) mass spectrometry (nanoRP-HPLC-MS and MS/MS), protein identification by sequence database search and peptide-based quantitative analysis. The most critical steps of this workflow are protein reconstitution and digestion; therefore, detergents and chaotropic agents are strongly mandatory to ensure complete solubilization of complex protein isolates and to achieve accessibility of all protease cleavage sites. However, detergents are incompatible with both RP separation and electrospray ionization (ESI). Therefore, to make LC-MS analysis possible, several strategies were implemented in the shotgun proteomics workflow. These techniques rely either on enzymatic digestion in centrifugal filters with subsequent evacuation of the detergent, or employment of MS-compatible surfactants, which can be degraded upon the digestion. In this review we comprehensively address all currently available strategies for the detergent-assisted proteolysis in respect of their relative efficiency when applied to different biological matrices. We critically discuss the current progress and the further perspectives of these technologies in the context of its advances and gaps.
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Affiliation(s)
- Katerina Danko
- Department of Biochemistry, St. Petersburg State University, 199034 St. Petersburg, Russia
| | - Elena Lukasheva
- Department of Biochemistry, St. Petersburg State University, 199034 St. Petersburg, Russia
| | - Vladimir A. Zhukov
- All-Russia Research Institute for Agricultural Microbiology, Podbelsky Chaussee 3, Pushkin, 196608 St. Petersburg, Russia
| | - Viktor Zgoda
- Institute of Biomedical Chemistry, 119121 Moscow, Russia
| | - Andrej Frolov
- K.A. Timiryazev Institute of Plant Physiology RAS, 127276 Moscow, Russia
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Balarynová J, Klčová B, Sekaninová J, Kobrlová L, Cechová MZ, Krejčí P, Leonova T, Gorbach D, Ihling C, Smržová L, Trněný O, Frolov A, Bednář P, Smýkal P. The loss of polyphenol oxidase function is associated with hilum pigmentation and has been selected during pea domestication. THE NEW PHYTOLOGIST 2022; 235:1807-1821. [PMID: 35585778 DOI: 10.1111/nph.18256] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 05/12/2022] [Indexed: 06/15/2023]
Abstract
Seed coats serve as protective tissue to the enclosed embryo. As well as mechanical there are also chemical defence functions. During domestication, the property of the seed coat was altered including the removal of the seed dormancy. We used a range of genetic, transcriptomic, proteomic and metabolomic approaches to determine the function of the pea seed polyphenol oxidase (PPO) gene. Sequencing analysis revealed one nucleotide insertion or deletion in the PPO gene, with the functional PPO allele found in all wild pea samples, while most cultivated peas have one of the three nonfunctional ppo alleles. PPO functionality cosegregates with hilum pigmentation. PPO gene and protein expression, as well as enzymatic activity, was downregulated in the seed coats of cultivated peas. The functionality of the PPO gene relates to the oxidation and polymerisation of gallocatechin in the seed coat. Additionally, imaging mass spectrometry supports the hypothesis that hilum pigmentation is conditioned by the presence of both phenolic precursors and sufficient PPO activity. Taken together these results indicate that the nonfunctional polyphenol oxidase gene has been selected during pea domestication, possibly due to better seed palatability or seed coat visual appearance.
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Affiliation(s)
- Jana Balarynová
- Department of Botany, Faculty of Sciences, Palacky University, Olomouc, 783 71, Czech Republic
| | - Barbora Klčová
- Department of Botany, Faculty of Sciences, Palacky University, Olomouc, 783 71, Czech Republic
| | - Jana Sekaninová
- Department of Biochemistry, Faculty of Sciences, Palacky University, Olomouc, 783 71, Czech Republic
| | - Lucie Kobrlová
- Department of Botany, Faculty of Sciences, Palacky University, Olomouc, 783 71, Czech Republic
| | - Monika Zajacová Cechová
- Department of Analytical Chemistry, Faculty of Sciences, Palacky University, Olomouc, 771 46, Czech Republic
| | - Petra Krejčí
- Department of Analytical Chemistry, Faculty of Sciences, Palacky University, Olomouc, 771 46, Czech Republic
| | - Tatiana Leonova
- Department of Bioorganic Chemistry, Leibniz-Institut für Pflanzenbiochemie, Halle (Saale), 06120, Germany
- Department of Biochemistry, St Petersburg State University, St Petersburg, 199004, Russia
| | - Daria Gorbach
- Department of Biochemistry, St Petersburg State University, St Petersburg, 199004, Russia
| | - Christian Ihling
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Martin-Luther University, Halle-Wittenberg, 06120, Germany
| | - Lucie Smržová
- Department of Botany, Faculty of Sciences, Palacky University, Olomouc, 783 71, Czech Republic
| | - Oldřich Trněný
- Agricultural Research Ltd, Troubsko, 664 41, Czech Republic
| | - Andrej Frolov
- Department of Bioorganic Chemistry, Leibniz-Institut für Pflanzenbiochemie, Halle (Saale), 06120, Germany
- Department of Biochemistry, St Petersburg State University, St Petersburg, 199004, Russia
| | - Petr Bednář
- Department of Analytical Chemistry, Faculty of Sciences, Palacky University, Olomouc, 771 46, Czech Republic
| | - Petr Smýkal
- Department of Botany, Faculty of Sciences, Palacky University, Olomouc, 783 71, Czech Republic
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Yadav R, Chakraborty S, Ramakrishna W. Wheat grain proteomic and protein-metabolite interactions analyses provide insights into plant growth promoting bacteria-arbuscular mycorrhizal fungi-wheat interactions. PLANT CELL REPORTS 2022; 41:1417-1437. [PMID: 35396966 DOI: 10.1007/s00299-022-02866-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 03/18/2022] [Indexed: 06/14/2023]
Abstract
Proteomic, protein-protein and protein-metabolite interaction analyses in wheat inoculated with PGPB and AMF identified key proteins and metabolites that may have a role in enhancing yield and biofortification. Plant growth-promoting bacteria (PGPB) and arbuscular mycorrhizal fungi (AMF) have an impact on grain yield and nutrition. This dynamic yet complex interaction implies a broad reprogramming of the plant's metabolic and proteomic activities. However, little information is available regarding the role of native PGPB and AMF and how they affect the plant proteome, especially under field conditions. Here, proteomic, protein-protein and protein-metabolite interaction studies in wheat triggered by PGPB, Bacillus subtilis CP4 either alone or together with AMF under field conditions was carried out. The dual inoculation with native PGPB (CP4) and AMF promoted the differential abundance of many proteins, such as histones, glutenin, avenin and ATP synthase compared to the control and single inoculation. Interaction study of these differentially expressed proteins using STRING revealed that they interact with other proteins involved in seed development and abiotic stress tolerance. Furthermore, these interacting proteins are involved in carbon fixation, sugar metabolism and biosynthesis of amino acids. Molecular docking predicted that wheat seed storage proteins, avenin and glutenin interact with secondary metabolites, such as trehalose, and sugars, such as xylitol. Mapping of differentially expressed proteins to KEGG pathways showed their involvement in sugar metabolism, biosynthesis of secondary metabolites and modulation of histones. These proteins and metabolites can serve as markers for improving wheat-PGPB-AMF interactions leading to higher yield and biofortification.
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Affiliation(s)
- Radheshyam Yadav
- Department of Biochemistry, Central University of Punjab, VPO Ghudda, Punjab, India
| | - Sudip Chakraborty
- Department of Computational Sciences, Central University of Punjab, VPO Ghudda, Punjab, India
| | - Wusirika Ramakrishna
- Department of Biochemistry, Central University of Punjab, VPO Ghudda, Punjab, India.
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10
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Ajilogba CF, Olanrewaju OS, Babalola OO. Improving Bambara Groundnut Production: Insight Into the Role of Omics and Beneficial Bacteria. FRONTIERS IN PLANT SCIENCE 2022; 13:836133. [PMID: 35310649 PMCID: PMC8929175 DOI: 10.3389/fpls.2022.836133] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 02/04/2022] [Indexed: 05/05/2023]
Abstract
With the rise in the world population, environmental hazards caused by chemical fertilizers, and a decrease in food supply due to global climate change, food security has become very pertinent. In addition, considerable parts of agriculture lands have been lost to urbanization. It has therefore been projected that at the present rate of population increase coupled with the other mentioned factors, available food will not be enough to feed the world. Hence, drastic approach is needed to improve agriculture output as well as human sustainability. Application of environmentally sustainable approach, such as the use of beneficial microbes, and improved breeding of underutilized legumes are one of the proposed sustainable ways of achieving food security. Microbiome-assisted breeding in underutilized legumes is an untapped area with great capabilities to improve food security. Furthermore, revolution in genomics adaptation to crop improvement has changed the approach from conventional breeding to more advanced genomic-assisted breeding on the host plant and its microbiome. The use of rhizobacteria is very important to improving crop yield, especially rhizobacteria from legumes like Bambara groundnut (BGN). BGN is an important legume in sub-Saharan Africa with high ability to tolerate drought and thrive well in marginalized soils. BGN and its interaction with various rhizobacteria in the soil could play a vital role in crop production and protection. This review focus on the importance of genomics application to BGN and its microbiome with the view of setting a potential blueprint for improved BGN breeding through integration of beneficial bacteria.
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Affiliation(s)
- Caroline Fadeke Ajilogba
- Food Security and Safety Focus Area, Faculty of Natural and Agricultural Science, North-West University, Mafikeng, South Africa
- Division of Agrometeorology, Agricultural Research Council, Natural Resources and Engineering, Pretoria, South Africa
| | - Oluwaseyi Samuel Olanrewaju
- Food Security and Safety Focus Area, Faculty of Natural and Agricultural Science, North-West University, Mafikeng, South Africa
| | - Olubukola Oluranti Babalola
- Food Security and Safety Focus Area, Faculty of Natural and Agricultural Science, North-West University, Mafikeng, South Africa
- *Correspondence: Olubukola Oluranti Babalola,
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11
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Malovichko YV, Shikov AE, Nizhnikov AA, Antonets KS. Temporal Control of Seed Development in Dicots: Molecular Bases, Ecological Impact and Possible Evolutionary Ramifications. Int J Mol Sci 2021; 22:ijms22179252. [PMID: 34502157 PMCID: PMC8430901 DOI: 10.3390/ijms22179252] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 08/20/2021] [Accepted: 08/23/2021] [Indexed: 12/21/2022] Open
Abstract
In flowering plants, seeds serve as organs of both propagation and dispersal. The developing seed passes through several consecutive stages, following a conserved general outline. The overall time needed for a seed to develop, however, may vary both within and between plant species, and these temporal developmental properties remain poorly understood. In the present paper, we summarize the existing data for seed development alterations in dicot plants. For genetic mutations, the reported cases were grouped in respect of the key processes distorted in the mutant specimens. Similar phenotypes arising from the environmental influence, either biotic or abiotic, were also considered. Based on these data, we suggest several general trends of timing alterations and how respective mechanisms might add to the ecological plasticity of the families considered. We also propose that the developmental timing alterations may be perceived as an evolutionary substrate for heterochronic events. Given the current lack of plausible models describing timing control in plant seeds, the presented suggestions might provide certain insights for future studies in this field.
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Affiliation(s)
- Yury V. Malovichko
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608 St. Petersburg, Russia; (Y.V.M.); (A.E.S.); (A.A.N.)
- Faculty of Biology, St. Petersburg State University, 199034 St. Petersburg, Russia
| | - Anton E. Shikov
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608 St. Petersburg, Russia; (Y.V.M.); (A.E.S.); (A.A.N.)
- Faculty of Biology, St. Petersburg State University, 199034 St. Petersburg, Russia
| | - Anton A. Nizhnikov
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608 St. Petersburg, Russia; (Y.V.M.); (A.E.S.); (A.A.N.)
- Faculty of Biology, St. Petersburg State University, 199034 St. Petersburg, Russia
| | - Kirill S. Antonets
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608 St. Petersburg, Russia; (Y.V.M.); (A.E.S.); (A.A.N.)
- Faculty of Biology, St. Petersburg State University, 199034 St. Petersburg, Russia
- Correspondence:
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12
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Shtark O, Puzanskiy R, Avdeeva G, Yemelyanov V, Shavarda A, Romanyuk D, Kliukova M, Kirpichnikova A, Tikhonovich I, Zhukov V, Shishova M. Metabolic Alterations in Pisum sativum Roots during Plant Growth and Arbuscular Mycorrhiza Development. PLANTS 2021; 10:plants10061033. [PMID: 34063836 PMCID: PMC8224052 DOI: 10.3390/plants10061033] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 05/17/2021] [Accepted: 05/18/2021] [Indexed: 01/04/2023]
Abstract
Intensive exchange of nutrients is a crucial part of the complex interaction between a host plant and fungi within arbuscular mycorrhizal (AM) symbiosis. For the first time, the present study demonstrates how inoculation with AMF Rhizophagus irregularis affects the pea (Pisum sativum L.) root metabolism at key stages of plant development. These correspond to days 21 (vegetation), 42 (flowering initiation), and 56 (fruiting-green pod). Metabolome profiling was carried out by means of a state-of-the-art GC-MS technique. The content shifts revealed include lipophilic compounds, sugars, carboxylates, and amino acids. The metabolic alterations were principally dependent on the stage of plant development but were also affected by the development of AM fungi, a fact which highlights interaction between symbiotic partners. The comparison of the present data with the results of leaf metabolome profiling earlier obtained did not reveal common signatures of metabolic response to mycorrhization in leaves and roots. We supposed that the feedback for the development and symbiotic interaction on the part of the supraorganismic system (root + AM fungi) was the cause of the difference between the metabolic profile shift in leaf and root cells that our examination revealed. New investigations are required to expand our knowledge of metabolome plasticity of the whole organism and/or system of organisms, and such results might be put to use for the intensification of sustainable agriculture.
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Affiliation(s)
- Oksana Shtark
- Department of Biotechnology, All-Russia Research Institute for Agricultural Microbiology, Pushkin, 196608 St. Petersburg, Russia; (D.R.); (M.K.); (I.T.); (V.Z.)
- Correspondence: (O.S.); (M.S.); Tel.: +7-812-470-5183 (O.S.); +7-812-328-9695 (M.S.)
| | - Roman Puzanskiy
- Laboratory of Analytical Phytochemistry, Komarov Botanical Institute of the Russian Academy of Sciences, 193022 St. Petersburg, Russia; (R.P.); (A.S.)
- Faculty of Biology, St. Petersburg State University, 199034 St. Petersburg, Russia; (G.A.); (V.Y.); (A.K.)
| | - Galina Avdeeva
- Faculty of Biology, St. Petersburg State University, 199034 St. Petersburg, Russia; (G.A.); (V.Y.); (A.K.)
| | - Vladislav Yemelyanov
- Faculty of Biology, St. Petersburg State University, 199034 St. Petersburg, Russia; (G.A.); (V.Y.); (A.K.)
| | - Alexey Shavarda
- Laboratory of Analytical Phytochemistry, Komarov Botanical Institute of the Russian Academy of Sciences, 193022 St. Petersburg, Russia; (R.P.); (A.S.)
- Center for Molecular and Cell Technologies, St. Petersburg State University, 199034 St. Petersburg, Russia
| | - Daria Romanyuk
- Department of Biotechnology, All-Russia Research Institute for Agricultural Microbiology, Pushkin, 196608 St. Petersburg, Russia; (D.R.); (M.K.); (I.T.); (V.Z.)
| | - Marina Kliukova
- Department of Biotechnology, All-Russia Research Institute for Agricultural Microbiology, Pushkin, 196608 St. Petersburg, Russia; (D.R.); (M.K.); (I.T.); (V.Z.)
| | - Anastasia Kirpichnikova
- Faculty of Biology, St. Petersburg State University, 199034 St. Petersburg, Russia; (G.A.); (V.Y.); (A.K.)
| | - Igor Tikhonovich
- Department of Biotechnology, All-Russia Research Institute for Agricultural Microbiology, Pushkin, 196608 St. Petersburg, Russia; (D.R.); (M.K.); (I.T.); (V.Z.)
- Faculty of Biology, St. Petersburg State University, 199034 St. Petersburg, Russia; (G.A.); (V.Y.); (A.K.)
| | - Vladimir Zhukov
- Department of Biotechnology, All-Russia Research Institute for Agricultural Microbiology, Pushkin, 196608 St. Petersburg, Russia; (D.R.); (M.K.); (I.T.); (V.Z.)
| | - Maria Shishova
- Faculty of Biology, St. Petersburg State University, 199034 St. Petersburg, Russia; (G.A.); (V.Y.); (A.K.)
- Correspondence: (O.S.); (M.S.); Tel.: +7-812-470-5183 (O.S.); +7-812-328-9695 (M.S.)
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13
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Nunes RDO, Domiciano Abrahão G, de Sousa Alves W, Aparecida de Oliveira J, César Sousa Nogueira F, Pasqualoto Canellas L, Lopes Olivares F, Benedeta Zingali R, Soares MR. Quantitative proteomic analysis reveals altered enzyme expression profile in Zea mays roots during the early stages of colonization by Herbaspirillum seropedicae. Proteomics 2021; 21:e2000129. [PMID: 33570822 DOI: 10.1002/pmic.202000129] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 01/29/2021] [Accepted: 02/01/2021] [Indexed: 11/09/2022]
Abstract
The use of plant growth-promoting bacteria as agricultural inoculants of plants should be encouraged because of their prominent role in biological nitrogen fixation, the increase of nutrient uptake by roots, abiotic stress mitigation, and disease control. The complex mechanisms underlying the association between plant and beneficial bacteria have been increasingly studied, and proteomic tools can expand our perception regarding the fundamental molecular processes modulated by the interaction. In this study, we investigated the changes in protein expression in maize roots in response to treatment with the endophytic diazotrophic Herbaspirillum seropedicae and the activities of enzymes related to nitrogen metabolism. To identify maize proteins whose expression levels were altered in the presence of bacteria, a label-free quantitative proteomic approach was employed. Using this approach, we identified 123 differentially expressed proteins, of which 34 were upregulated enzymes, in maize roots cultivated with H. seropedicae. The maize root colonization of H. seropedicae modulated the differential expression of enzymes involved in the stress response, such as peroxidases, phenylalanine ammonia-lyase, and glutathione transferase. The differential protein profile obtained in the inoculated roots reflects the effect of colonization on plant growth and development compared with control plants.
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Affiliation(s)
- Rosane de Oliveira Nunes
- Departamento de Bioquímica/Instituto de Química, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Giselli Domiciano Abrahão
- Departamento de Bioquímica/Instituto de Química, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Wilber de Sousa Alves
- Departamento de Ensino Médio e Técnico, Centro Federal de Educação Tecnológica Celso Suckow da Fonseca, Rio de Janeiro, Brazil
| | - Jaqueline Aparecida de Oliveira
- Núcleo de Desenvolvimento de Insumos Biológicos para Agricultura, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Brazil
| | - Fábio César Sousa Nogueira
- Laboratório de Proteômica/LADETEC, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.,Unidade de Proteômica, Instituto de Química, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Luciano Pasqualoto Canellas
- Núcleo de Desenvolvimento de Insumos Biológicos para Agricultura, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Brazil
| | - Fábio Lopes Olivares
- Núcleo de Desenvolvimento de Insumos Biológicos para Agricultura, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Brazil
| | - Russolina Benedeta Zingali
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Márcia Regina Soares
- Departamento de Bioquímica/Instituto de Química, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
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14
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Afonin AM, Leppyanen IV, Kulaeva OA, Shtark OY, Tikhonovich IA, Dolgikh EA, Zhukov VA. A high coverage reference transcriptome assembly of pea (Pisum sativum L.) mycorrhizal roots. Vavilovskii Zhurnal Genet Selektsii 2021; 24:331-339. [PMID: 33659815 PMCID: PMC7716550 DOI: 10.18699/vj20.625] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Arbuscular mycorrhiza (AM) is an ancient mutualistic symbiosis formed by 80–90 % of land plant species with
the obligatorily biotrophic fungi that belong to the phylum Glomeromycota. This symbiosis is mutually beneficial, as
AM fungi feed on plant photosynthesis products, in turn improving the efficiency of nutrient uptake from the environment. The garden pea (Pisum sativum L.), a widely cultivated crop and an important model for genetics, is capable of
forming triple symbiotic systems consisting of the plant, AM fungi and nodule bacteria. As transcriptomic and proteomic approaches are being implemented for studying the mutualistic symbioses of pea, a need for a reference transcriptome of genes expressed under these specific conditions for increasing the resolution and the accuracy of other
methods arose. Numerous transcriptome assemblies constructed for pea did not include mycorrhizal roots, hence the
aim of the study to construct a reference transcriptome assembly of pea mycorrhizal roots. The combined transcriptome of mycorrhizal roots of Pisum sativum cv. Frisson inoculated with Rhizophagus irregularis BEG144 was investigated,
and for both the organisms independent transcriptomes were assembled (coverage 177x for pea and 45x for fungus).
Genes specific to mycorrhizal roots were found in the assembly, their expression patterns were examined with qPCR on
two pea cultivars, Frisson and Finale. The gene expression depended on the inoculation stage and on the pea cultivar.
The investigated genes may serve as markers for early stages of inoculation in genetically diverse pea cultivars.
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Affiliation(s)
- A M Afonin
- All-Russia Research Institute for Agricultural Microbiology, Pushkin, St. Petersburg, Russia
| | - I V Leppyanen
- All-Russia Research Institute for Agricultural Microbiology, Pushkin, St. Petersburg, Russia
| | - O A Kulaeva
- All-Russia Research Institute for Agricultural Microbiology, Pushkin, St. Petersburg, Russia
| | - O Y Shtark
- All-Russia Research Institute for Agricultural Microbiology, Pushkin, St. Petersburg, Russia
| | - I A Tikhonovich
- All-Russia Research Institute for Agricultural Microbiology, Pushkin, St. Petersburg, Russia Faculty of Biology, St. Petersburg State University, St. Petersburg, Russia
| | - E A Dolgikh
- All-Russia Research Institute for Agricultural Microbiology, Pushkin, St. Petersburg, Russia
| | - V A Zhukov
- All-Russia Research Institute for Agricultural Microbiology, Pushkin, St. Petersburg, Russia
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15
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Bai B, van der Horst N, Cordewener JH, America AHP, Nijveen H, Bentsink L. Delayed Protein Changes During Seed Germination. FRONTIERS IN PLANT SCIENCE 2021; 12:735719. [PMID: 34603360 PMCID: PMC8480309 DOI: 10.3389/fpls.2021.735719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Accepted: 08/05/2021] [Indexed: 05/12/2023]
Abstract
Over the past decade, ample transcriptome data have been generated at different stages during seed germination; however, far less is known about protein synthesis during this important physiological process. Generally, the correlation between transcript levels and protein abundance is low, which strongly limits the use of transcriptome data to accurately estimate protein expression. Polysomal profiling has emerged as a tool to identify mRNAs that are actively translated. The association of the mRNA to the polysome, also referred to as translatome, provides a proxy for mRNA translation. In this study, the correlation between the changes in total mRNA, polysome-associated mRNA, and protein levels across seed germination was investigated. The direct correlation between polysomal mRNA and protein abundance at a single time-point during seed germination is low. However, once the polysomal mRNA of a time-point is compared to the proteome of the next time-point, the correlation is much higher. 35% of the investigated proteome has delayed changes at the protein level. Genes have been classified based on their delayed protein changes, and specific motifs in these genes have been identified. Moreover, mRNA and protein stability and mRNA length have been found as important predictors for changes in protein abundance. In conclusion, polysome association and/or dissociation predicts future changes in protein abundance in germinating seeds.
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Affiliation(s)
- Bing Bai
- Wageningen Seed Science Centre, Laboratory of Plant Physiology, Wageningen University, Wageningen, Netherlands
- *Correspondence: Bing Bai,
| | | | - Jan H. Cordewener
- BU Bioscience, Wageningen Plant Research, Wageningen, Netherlands
- Centre for BioSystems Genomics, Wageningen, Netherlands
- Netherlands Proteomics Centre, Utrecht, Netherlands
| | - Antoine H. P. America
- BU Bioscience, Wageningen Plant Research, Wageningen, Netherlands
- Centre for BioSystems Genomics, Wageningen, Netherlands
- Netherlands Proteomics Centre, Utrecht, Netherlands
| | - Harm Nijveen
- Bioinformatics Group, Wageningen University, Wageningen, Netherlands
| | - Leónie Bentsink
- Wageningen Seed Science Centre, Laboratory of Plant Physiology, Wageningen University, Wageningen, Netherlands
- Leónie Bentsink,
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16
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Frolova N, Soboleva A, Nguyen VD, Kim A, Ihling C, Eisenschmidt-Bönn D, Mamontova T, Herfurth UM, Wessjohann LA, Sinz A, Birkemeyer C, Frolov A. Probing glycation potential of dietary sugars in human blood by an integrated in vitro approach. Food Chem 2020; 347:128951. [PMID: 33493836 DOI: 10.1016/j.foodchem.2020.128951] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 12/11/2020] [Accepted: 12/22/2020] [Indexed: 01/12/2023]
Abstract
Glycation is referred to as the interaction of protein amino and guanidino groups with reducing sugars and carbonyl products of their degradation. Resulting advanced glycation end-products (AGEs) contribute to pathogenesis of diabetes mellitus and neurodegenerative disorders. Upon their intestinal absorption, dietary sugars and α-dicarbonyl compounds interact with blood proteins yielding AGEs. Although the differences in glycation potential of monosaccharides are well characterized, the underlying mechanisms are poorly understood. To address this question, d-glucose, d-fructose and l-ascorbic acid were incubated with human serum albumin (HSA). The sugars and α-dicarbonyl intermediates of their degradation were analyzed in parallel to protein glycation patterns (exemplified with hydroimidazolone modifications of arginine residues and products of their hydrolysis) by bottom-up proteomics and computational chemistry. Glycation of HSA with sugars revealed 9 glyoxal- and 14 methylglyoxal-derived modification sites. Their dynamics was sugar-specific and depended on concentrations of α-dicarbonyls, their formation kinetics, and presence of stabilizing residues in close proximity to the glycation sites.
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Affiliation(s)
- Nadezhda Frolova
- Institute of Analytical Chemistry, Faculty of Chemistry and Mineralogy, University of Leipzig, Germany
| | - Alena Soboleva
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, Germany; Department of Biochemistry, St. Petersburg State University, Russia.
| | - Viet Duc Nguyen
- Institute of Analytical Chemistry, Faculty of Chemistry and Mineralogy, University of Leipzig, Germany; Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, Germany
| | - Ahyoung Kim
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, Germany
| | - Christian Ihling
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Martin-Luther Universität Halle-Wittenberg, Germany
| | | | - Tatiana Mamontova
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, Germany; Department of Biochemistry, St. Petersburg State University, Russia
| | - Uta M Herfurth
- Department of Food Safety, German Federal Institute for Risk Assessment, Germany
| | - Ludger A Wessjohann
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, Germany
| | - Andrea Sinz
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Martin-Luther Universität Halle-Wittenberg, Germany
| | - Claudia Birkemeyer
- Institute of Analytical Chemistry, Faculty of Chemistry and Mineralogy, University of Leipzig, Germany
| | - Andrej Frolov
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, Germany; Department of Biochemistry, St. Petersburg State University, Russia.
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17
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Smolikova G, Gorbach D, Lukasheva E, Mavropolo-Stolyarenko G, Bilova T, Soboleva A, Tsarev A, Romanovskaya E, Podolskaya E, Zhukov V, Tikhonovich I, Medvedev S, Hoehenwarter W, Frolov A. Bringing New Methods to the Seed Proteomics Platform: Challenges and Perspectives. Int J Mol Sci 2020; 21:E9162. [PMID: 33271881 PMCID: PMC7729594 DOI: 10.3390/ijms21239162] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 11/26/2020] [Accepted: 11/27/2020] [Indexed: 12/14/2022] Open
Abstract
For centuries, crop plants have represented the basis of the daily human diet. Among them, cereals and legumes, accumulating oils, proteins, and carbohydrates in their seeds, distinctly dominate modern agriculture, thus play an essential role in food industry and fuel production. Therefore, seeds of crop plants are intensively studied by food chemists, biologists, biochemists, and nutritional physiologists. Accordingly, seed development and germination as well as age- and stress-related alterations in seed vigor, longevity, nutritional value, and safety can be addressed by a broad panel of analytical, biochemical, and physiological methods. Currently, functional genomics is one of the most powerful tools, giving direct access to characteristic metabolic changes accompanying plant development, senescence, and response to biotic or abiotic stress. Among individual post-genomic methodological platforms, proteomics represents one of the most effective ones, giving access to cellular metabolism at the level of proteins. During the recent decades, multiple methodological advances were introduced in different branches of life science, although only some of them were established in seed proteomics so far. Therefore, here we discuss main methodological approaches already employed in seed proteomics, as well as those still waiting for implementation in this field of plant research, with a special emphasis on sample preparation, data acquisition, processing, and post-processing. Thereby, the overall goal of this review is to bring new methodologies emerging in different areas of proteomics research (clinical, food, ecological, microbial, and plant proteomics) to the broad society of seed biologists.
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Affiliation(s)
- Galina Smolikova
- Department of Plant Physiology and Biochemistry, St. Petersburg State University; 199034 St. Petersburg, Russia; (G.S.); (T.B.); (S.M.)
| | - Daria Gorbach
- Department of Biochemistry, St. Petersburg State University; 199178 St. Petersburg, Russia; (D.G.); (E.L.); (G.M.-S.); (A.S.); (A.T.); (E.R.)
| | - Elena Lukasheva
- Department of Biochemistry, St. Petersburg State University; 199178 St. Petersburg, Russia; (D.G.); (E.L.); (G.M.-S.); (A.S.); (A.T.); (E.R.)
| | - Gregory Mavropolo-Stolyarenko
- Department of Biochemistry, St. Petersburg State University; 199178 St. Petersburg, Russia; (D.G.); (E.L.); (G.M.-S.); (A.S.); (A.T.); (E.R.)
| | - Tatiana Bilova
- Department of Plant Physiology and Biochemistry, St. Petersburg State University; 199034 St. Petersburg, Russia; (G.S.); (T.B.); (S.M.)
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry; 06120 Halle (Saale), Germany
| | - Alena Soboleva
- Department of Biochemistry, St. Petersburg State University; 199178 St. Petersburg, Russia; (D.G.); (E.L.); (G.M.-S.); (A.S.); (A.T.); (E.R.)
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry; 06120 Halle (Saale), Germany
| | - Alexander Tsarev
- Department of Biochemistry, St. Petersburg State University; 199178 St. Petersburg, Russia; (D.G.); (E.L.); (G.M.-S.); (A.S.); (A.T.); (E.R.)
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry; 06120 Halle (Saale), Germany
| | - Ekaterina Romanovskaya
- Department of Biochemistry, St. Petersburg State University; 199178 St. Petersburg, Russia; (D.G.); (E.L.); (G.M.-S.); (A.S.); (A.T.); (E.R.)
| | - Ekaterina Podolskaya
- Institute of Analytical Instrumentation, Russian Academy of Science; 190103 St. Petersburg, Russia;
- Institute of Toxicology, Russian Federal Medical Agency; 192019 St. Petersburg, Russia
| | - Vladimir Zhukov
- All-Russia Research Institute for Agricultural Microbiology; 196608 St. Petersburg, Russia; (V.Z.); (I.T.)
| | - Igor Tikhonovich
- All-Russia Research Institute for Agricultural Microbiology; 196608 St. Petersburg, Russia; (V.Z.); (I.T.)
- Department of Genetics and Biotechnology, St. Petersburg State University; 199034 St. Petersburg, Russia
| | - Sergei Medvedev
- Department of Plant Physiology and Biochemistry, St. Petersburg State University; 199034 St. Petersburg, Russia; (G.S.); (T.B.); (S.M.)
| | - Wolfgang Hoehenwarter
- Proteome Analytics Research Group, Leibniz Institute of Plant Biochemistry, 06120 Halle (Saale), Germany;
| | - Andrej Frolov
- Department of Biochemistry, St. Petersburg State University; 199178 St. Petersburg, Russia; (D.G.); (E.L.); (G.M.-S.); (A.S.); (A.T.); (E.R.)
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry; 06120 Halle (Saale), Germany
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18
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Proteomic Profiling of Emiliania huxleyi Using a Three-Dimensional Separation Method Combined with Tandem Mass Spectrometry. Molecules 2020; 25:molecules25133028. [PMID: 32630776 PMCID: PMC7411631 DOI: 10.3390/molecules25133028] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 06/30/2020] [Accepted: 06/30/2020] [Indexed: 12/31/2022] Open
Abstract
Emiliania huxleyi is one of the most abundant marine planktons, and it has a crucial feature in the carbon cycle. However, proteomic analyses of Emiliania huxleyi have not been done extensively. In this study, a three-dimensional liquid chromatography (3D-LC) system consisting of strong cation exchange, high- and low-pH reversed-phase liquid chromatography was established for in-depth proteomic profiling of Emiliania huxleyi. From tryptic proteome digest, 70 fractions were generated and analyzed using liquid chromatography-tandem mass spectrometry. In total, more than 84,000 unique peptides and 10,000 proteins groups were identified with a false discovery rate of ≤0.01. The physicochemical properties of the identified peptides were evaluated. Using ClueGO, approximately 700 gene ontology terms and 15 pathways were defined from the identified protein groups with p-value ≤0.05, covering a wide range of biological processes, cellular components, and molecular functions. Many biological processes associated with CO2 fixation, photosynthesis, biosynthesis, and metabolic process were identified. Various molecular functions relating to protein binding and enzyme activities were also found. The 3D-LC strategy is a powerful approach for comparative proteomic studies on Emiliania huxleyi to reveal changes in its protein level and related mechanism.
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Malovichko YV, Shtark OY, Vasileva EN, Nizhnikov AA, Antonets KS. Transcriptomic Insights into Mechanisms of Early Seed Maturation in the Garden Pea ( Pisum sativum L.). Cells 2020; 9:E779. [PMID: 32210065 PMCID: PMC7140803 DOI: 10.3390/cells9030779] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 03/20/2020] [Accepted: 03/21/2020] [Indexed: 02/07/2023] Open
Abstract
The garden pea (Pisum sativum L.) is a legume crop of immense economic value. Extensive breeding has led to the emergence of numerous pea varieties, of which some are distinguished by accelerated development in various stages of ontogenesis. One such trait is rapid seed maturation, which, despite novel insights into the genetic control of seed development in legumes, remains poorly studied. This article presents an attempt to dissect mechanisms of early maturation in the pea line Sprint-2 by means of whole transcriptome RNA sequencing in two developmental stages. By using a de novo assembly approach, we have obtained a reference transcriptome of 25,756 non-redundant entries expressed in pea seeds at either 10 or 20 days after pollination. Differential expression in Sprint-2 seeds has affected 13,056 transcripts. A comparison of the two pea lines with a common maturation rate demonstrates that while at 10 days after pollination, Sprint-2 seeds show development retardation linked to intensive photosynthesis, morphogenesis, and cell division, and those at 20 days show a rapid onset of desiccation marked by the cessation of translation and cell anabolism and accumulation of dehydration-protective and -storage moieties. Further inspection of certain transcript functional categories, including the chromatin constituent, transcription regulation, protein turnover, and hormonal regulation, has revealed transcriptomic trends unique to specific stages and cultivars. Among other remarkable features, Sprint-2 demonstrated an enhanced expression of transposable element-associated open reading frames and an altered expression of major maturation regulators and DNA methyltransferase genes. To the best of our knowledge, this is the first comparative transcriptomic study in which the issue of the seed maturation rate is addressed.
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Affiliation(s)
- Yury V. Malovichko
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), Podbelskogo sh., 3, Pushkin, 196608 St. Petersburg, Russia;
- Faculty of Biology, St. Petersburg State University, 199034 St. Petersburg, Russia;
| | - Oksana Y. Shtark
- Department of Biotechnology, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), Podbelskogo sh., 3, Pushkin, 196608 St. Petersburg, Russia;
| | - Ekaterina N. Vasileva
- Faculty of Biology, St. Petersburg State University, 199034 St. Petersburg, Russia;
- Department of Biotechnology, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), Podbelskogo sh., 3, Pushkin, 196608 St. Petersburg, Russia;
| | - Anton A. Nizhnikov
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), Podbelskogo sh., 3, Pushkin, 196608 St. Petersburg, Russia;
- Faculty of Biology, St. Petersburg State University, 199034 St. Petersburg, Russia;
| | - Kirill S. Antonets
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), Podbelskogo sh., 3, Pushkin, 196608 St. Petersburg, Russia;
- Faculty of Biology, St. Petersburg State University, 199034 St. Petersburg, Russia;
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20
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Leonova T, Popova V, Tsarev A, Henning C, Antonova K, Rogovskaya N, Vikhnina M, Baldensperger T, Soboleva A, Dinastia E, Dorn M, Shiroglasova O, Grishina T, Balcke GU, Ihling C, Smolikova G, Medvedev S, Zhukov VA, Babakov V, Tikhonovich IA, Glomb MA, Bilova T, Frolov A. Does Protein Glycation Impact on the Drought-Related Changes in Metabolism and Nutritional Properties of Mature Pea ( Pisum sativum L.) Seeds? Int J Mol Sci 2020; 21:E567. [PMID: 31952342 PMCID: PMC7013545 DOI: 10.3390/ijms21020567] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 01/01/2020] [Accepted: 01/03/2020] [Indexed: 12/24/2022] Open
Abstract
Protein glycation is usually referred to as an array of non-enzymatic post-translational modifications formed by reducing sugars and carbonyl products of their degradation. The resulting advanced glycation end products (AGEs) represent a heterogeneous group of covalent adducts, known for their pro-inflammatory effects in mammals, and impacting on pathogenesis of metabolic diseases and ageing. In plants, AGEs are the markers of tissue ageing and response to environmental stressors, the most prominent of which is drought. Although water deficit enhances protein glycation in leaves, its effect on seed glycation profiles is still unknown. Moreover, the effect of drought on biological activities of seed protein in mammalian systems is still unstudied with respect to glycation. Therefore, here we address the effects of a short-term drought on the patterns of seed protein-bound AGEs and accompanying alterations in pro-inflammatory properties of seed protein in the context of seed metabolome dynamics. A short-term drought, simulated as polyethylene glycol-induced osmotic stress and applied at the stage of seed filling, resulted in the dramatic suppression of primary seed metabolism, although the secondary metabolome was minimally affected. This was accompanied with significant suppression of NF-kB activation in human SH-SY5Y neuroblastoma cells after a treatment with protein hydrolyzates, isolated from the mature seeds of drought-treated plants. This effect could not be attributed to formation of known AGEs. Most likely, the prospective anti-inflammatory effect of short-term drought is related to antioxidant effect of unknown secondary metabolite protein adducts, or down-regulation of unknown plant-specific AGEs due to suppression of energy metabolism during seed filling.
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Affiliation(s)
- Tatiana Leonova
- Department of Biochemistry, St. Petersburg State University, 199004 St. Petersburg, Russia
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, 06120 Halle, Germany
| | - Veronika Popova
- Department of Biochemistry, St. Petersburg State University, 199004 St. Petersburg, Russia
- Department of Plant Physiology and Biochemistry, St. Petersburg State University, 199034 St. Petersburg, Russia
| | - Alexander Tsarev
- Department of Biochemistry, St. Petersburg State University, 199004 St. Petersburg, Russia
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, 06120 Halle, Germany
| | - Christian Henning
- Institute of Chemistry - Food Chemistry, Martin-Luther University Halle-Wittenberg, 06120 Halle, Germany
| | - Kristina Antonova
- Department of Biochemistry, St. Petersburg State University, 199004 St. Petersburg, Russia
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, 06120 Halle, Germany
| | - Nadezhda Rogovskaya
- Research Institute of Hygiene, Occupational Pathology and Human Ecology, 188663 Leningrad Oblast, Russia
| | - Maria Vikhnina
- Department of Biochemistry, St. Petersburg State University, 199004 St. Petersburg, Russia
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, 06120 Halle, Germany
| | - Tim Baldensperger
- Institute of Chemistry - Food Chemistry, Martin-Luther University Halle-Wittenberg, 06120 Halle, Germany
| | - Alena Soboleva
- Department of Biochemistry, St. Petersburg State University, 199004 St. Petersburg, Russia
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, 06120 Halle, Germany
| | - Ekaterina Dinastia
- Department of Biochemistry, St. Petersburg State University, 199004 St. Petersburg, Russia
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, 06120 Halle, Germany
- Postovsky Institute of Organic Synthesis of Ural Division of Russian Academy of Sciences, 620137 Yekaterinburg, Russia
| | - Mandy Dorn
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, 06120 Halle, Germany
| | - Olga Shiroglasova
- Department of Plant Physiology and Biochemistry, St. Petersburg State University, 199034 St. Petersburg, Russia
| | - Tatiana Grishina
- Department of Biochemistry, St. Petersburg State University, 199004 St. Petersburg, Russia
| | - Gerd U Balcke
- Department of Metabolic and Cell Biology, Leibniz Institute of Plant Biochemistry, 06120 Halle, Germany
| | - Christian Ihling
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Martin-Luther University Halle-Wittenberg, 06120 Halle, Germany
| | - Galina Smolikova
- Department of Plant Physiology and Biochemistry, St. Petersburg State University, 199034 St. Petersburg, Russia
| | - Sergei Medvedev
- Department of Plant Physiology and Biochemistry, St. Petersburg State University, 199034 St. Petersburg, Russia
| | - Vladimir A Zhukov
- All-Russia Research Institute for Agricultural Microbiology, 196608 St. Petersburg, Russia
| | - Vladimir Babakov
- Research Institute of Hygiene, Occupational Pathology and Human Ecology, 188663 Leningrad Oblast, Russia
| | - Igor A Tikhonovich
- All-Russia Research Institute for Agricultural Microbiology, 196608 St. Petersburg, Russia
- Department of Genetics and Biotechnology, St. Petersburg State University, 199034 St. Petersburg, Russia
| | - Marcus A Glomb
- Institute of Chemistry - Food Chemistry, Martin-Luther University Halle-Wittenberg, 06120 Halle, Germany
| | - Tatiana Bilova
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, 06120 Halle, Germany
- Department of Plant Physiology and Biochemistry, St. Petersburg State University, 199034 St. Petersburg, Russia
| | - Andrej Frolov
- Department of Biochemistry, St. Petersburg State University, 199004 St. Petersburg, Russia
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, 06120 Halle, Germany
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21
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Shtark OY, Puzanskiy RK, Avdeeva GS, Yurkov AP, Smolikova GN, Yemelyanov VV, Kliukova MS, Shavarda AL, Kirpichnikova AA, Zhernakov AI, Afonin AM, Tikhonovich IA, Zhukov VA, Shishova MF. Metabolic alterations in pea leaves during arbuscular mycorrhiza development. PeerJ 2019; 7:e7495. [PMID: 31497392 PMCID: PMC6709666 DOI: 10.7717/peerj.7495] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 07/16/2019] [Indexed: 12/20/2022] Open
Abstract
Arbuscular mycorrhiza (AM) is known to be a mutually beneficial plant-fungal symbiosis; however, the effect of mycorrhization is heavily dependent on multiple biotic and abiotic factors. Therefore, for the proper employment of such plant-fungal symbiotic systems in agriculture, a detailed understanding of the molecular basis of the plant developmental response to mycorrhization is needed. The aim of this work was to uncover the physiological and metabolic alterations in pea (Pisum sativum L.) leaves associated with mycorrhization at key plant developmental stages. Plants of pea cv. Finale were grown in constant environmental conditions under phosphate deficiency. The plants were analyzed at six distinct time points, which corresponded to certain developmental stages of the pea: I: 7 days post inoculation (DPI) when the second leaf is fully unfolded with one pair of leaflets and a simple tendril; II: 21 DPI at first leaf with two pairs of leaflets and a complex tendril; III: 32 DPI when the floral bud is enclosed; IV: 42 DPI at the first open flower; V: 56 DPI when the pod is filled with green seeds; and VI: 90-110 DPI at the dry harvest stage. Inoculation with Rhizophagus irregularis had no effect on the fresh or dry shoot weight, the leaf photochemical activity, accumulation of chlorophyll a, b or carotenoids. However, at stage III (corresponding to the most active phase of mycorrhiza development), the number of internodes between cotyledons and the youngest completely developed leaf was lower in the inoculated plants than in those without inoculation. Moreover, inoculation extended the vegetation period of the host plants, and resulted in increase of the average dry weight per seed at stage VI. The leaf metabolome, as analyzed with GC-MS, included about three hundred distinct metabolites and showed a strong correlation with plant age, and, to a lesser extent, was influenced by mycorrhization. Metabolic shifts influenced the levels of sugars, amino acids and other intermediates of nitrogen and phosphorus metabolism. The use of unsupervised dimension reduction methods showed that (i) at stage II, the metabolite spectra of inoculated plants were similar to those of the control, and (ii) at stages IV and V, the leaf metabolic profiles of inoculated plants shifted towards the profiles of the control plants at earlier developmental stages. At stage IV the inoculated plants exhibited a higher level of metabolism of nitrogen, organic acids, and lipophilic compounds in comparison to control plants. Thus, mycorrhization led to the retardation of plant development, which was also associated with higher seed biomass accumulation in plants with an extended vegetation period. The symbiotic crosstalk between host plant and AM fungi leads to alterations in several biochemical pathways the details of which need to be elucidated in further studies.
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Affiliation(s)
- Oksana Y. Shtark
- Department of Biotechnology, All-Russia Research Institute for Agricultural Microbiology, Pushkin, St. Petersburg, Russia
- Faculty of Biology, St. Petersburg State University, St. Petersburg, Russia
| | - Roman K. Puzanskiy
- Faculty of Biology, St. Petersburg State University, St. Petersburg, Russia
- Laboratory of Dynamics of Arctic Vegetation, Komarov Botanical Institute of the Russian Academy of Sciences, St. Petersburg, Russia
| | - Galina S. Avdeeva
- Faculty of Biology, St. Petersburg State University, St. Petersburg, Russia
| | - Andrey P. Yurkov
- Department of Biotechnology, All-Russia Research Institute for Agricultural Microbiology, Pushkin, St. Petersburg, Russia
- Faculty of Biology, St. Petersburg State University, St. Petersburg, Russia
| | | | | | - Marina S. Kliukova
- Department of Biotechnology, All-Russia Research Institute for Agricultural Microbiology, Pushkin, St. Petersburg, Russia
- Faculty of Biology, St. Petersburg State University, St. Petersburg, Russia
| | - Alexey L. Shavarda
- Center for Molecular and Cell Technologies, St. Petersburg State University, St. Petersburg, Russia
| | | | - Aleksandr I. Zhernakov
- Department of Biotechnology, All-Russia Research Institute for Agricultural Microbiology, Pushkin, St. Petersburg, Russia
| | - Alexey M. Afonin
- Department of Biotechnology, All-Russia Research Institute for Agricultural Microbiology, Pushkin, St. Petersburg, Russia
| | - Igor A. Tikhonovich
- Department of Biotechnology, All-Russia Research Institute for Agricultural Microbiology, Pushkin, St. Petersburg, Russia
- Faculty of Biology, St. Petersburg State University, St. Petersburg, Russia
| | - Vladimir A. Zhukov
- Department of Biotechnology, All-Russia Research Institute for Agricultural Microbiology, Pushkin, St. Petersburg, Russia
| | - Maria F. Shishova
- Faculty of Biology, St. Petersburg State University, St. Petersburg, Russia
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