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Ohm H, Saripella GV, Hofvander P, Grimberg Å. Spatio-temporal transcriptome and storage compound profiles of developing faba bean ( Vicia faba) seed tissues. FRONTIERS IN PLANT SCIENCE 2024; 15:1284997. [PMID: 38379954 PMCID: PMC10877042 DOI: 10.3389/fpls.2024.1284997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 01/18/2024] [Indexed: 02/22/2024]
Abstract
Faba bean (Vicia faba) is a legume grown in diverse climate zones with a high potential for increased cultivation and use in food due to its nutritional seeds. In this study, we characterized seed tissue development in faba bean to identify key developmental processes; from embryo expansion at the expense of the endosperm to the maturing storage stages of the bean seed. A spatio-temporal transcriptome profiling analysis, combined with chemical nutrient analysis of protein, starch, and lipid, of endosperm and embryo tissues at different developmental stages, revealed gene expression patterns, transcriptional networks, and biochemical pathways in faba bean. We identified key players in the LAFL (LEC1, ABI3, FUS3, and LEC2) transcription factor network as well as their major repressors VAL1 and ASIL1. Our results showed that proteins accumulated not only in the embryo but also in the endosperm. Starch accumulated throughout seed development and oil content increased during seed development but at very low levels. The patterns of differentially expressed transcripts encoding proteins with functions in the corresponding metabolic pathways for the synthesis of these storage compounds, to a high extent, aligned with these findings. However, the early expression of transcripts encoding WRI1 combined with the late expression of oil body proteins indicated a not manifested high potential for lipid biosynthesis and oil storage. Altogether, this study contributes to increased knowledge regarding seed developmental processes applicable to future breeding methods and seed quality improvement for faba bean.
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Affiliation(s)
- Hannah Ohm
- Department of Plant Breeding, Swedish University of Agricultural Sciences (SLU), Lomma, Sweden
| | | | | | - Åsa Grimberg
- Department of Plant Breeding, Swedish University of Agricultural Sciences (SLU), Lomma, Sweden
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2
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Morin A, Porcheron B, Kodjovi GC, Moumen B, Vriet C, Maurousset L, Lemoine R, Pourtau N, Doidy J. Genome-wide transcriptional responses to water deficit during seed development in Pisum sativum, focusing on sugar transport and metabolism. PHYSIOLOGIA PLANTARUM 2023; 175:e14062. [PMID: 38148238 DOI: 10.1111/ppl.14062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 10/06/2023] [Accepted: 10/12/2023] [Indexed: 12/28/2023]
Abstract
Agriculture is particularly impacted by global changes, drought being a main limiting factor of crop production. Here, we focus on pea (Pisum sativum), a model legume cultivated for its seed nutritional value. A water deficit (WD) was applied during its early reproductive phase, harvesting plant organs at two key developmental stages, either at the embryonic or the seed-filling stages. We combined phenotypic, physiological and transcriptome analyses to better understand the adaptive response to drought. First, we showed that apical growth arrest is a major phenotypic indicator of water stress. Sugar content was also greatly impacted, especially leaf fructose and starch contents. Our RNA-seq analysis identified 2001 genes regulated by WD in leaf, 3684 genes in root and 2273 genes in embryonic seed, while only 80 genes were regulated during seed-filling. Hence, a large transcriptional reprogramming occurred in response to WD in seeds during early embryonic stage, but no longer during the later stage of nutritional filling. Biological processes involved in transcriptional regulation, carbon transport and metabolism were greatly regulated by WD in both source and sink organs, as illustrated by the expression of genes encoding transcription factors, sugar transporters and enzymes of the starch synthesis pathway. We then looked at the transcriptomic changes during seed development, highlighting a transition from monosaccharide utilization at the embryonic stage to sucrose transport feeding the starch synthesis pathway at the seed-filling stage. Altogether, our study presents an integrative picture of sugar transport and metabolism in response to drought and during seed development at a genome-wide level.
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Affiliation(s)
- Amélie Morin
- Université de Poitiers, UMR CNRS 7267, EBI "Ecologie et Biologie des Interactions", Poitiers, France
- Team "Environment, Bioenergies, Microalgae and Plants", BiAM DRF, CEA Cadarache, France
| | - Benoit Porcheron
- Université de Poitiers, UMR CNRS 7267, EBI "Ecologie et Biologie des Interactions", Poitiers, France
| | - Gatepe Cedoine Kodjovi
- Université de Poitiers, UMR CNRS 7267, EBI "Ecologie et Biologie des Interactions", Poitiers, France
| | - Bouziane Moumen
- Université de Poitiers, UMR CNRS 7267, EBI "Ecologie et Biologie des Interactions", Poitiers, France
| | - Cécile Vriet
- Université de Poitiers, UMR CNRS 7267, EBI "Ecologie et Biologie des Interactions", Poitiers, France
| | - Laurence Maurousset
- Université de Poitiers, UMR CNRS 7267, EBI "Ecologie et Biologie des Interactions", Poitiers, France
| | - Rémi Lemoine
- Université de Poitiers, UMR CNRS 7267, EBI "Ecologie et Biologie des Interactions", Poitiers, France
| | - Nathalie Pourtau
- Université de Poitiers, UMR CNRS 7267, EBI "Ecologie et Biologie des Interactions", Poitiers, France
| | - Joan Doidy
- Université de Poitiers, UMR CNRS 7267, EBI "Ecologie et Biologie des Interactions", Poitiers, France
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Kosolapova AO, Belousov MV, Sulatsky MI, Tsyganova AV, Sulatskaya AI, Bobylev AG, Shtark OY, Tsyganov VE, Volkov KV, Zhukov VA, Tikhonovich IA, Nizhnikov AA. RopB protein of Rhizobium leguminosarum bv. viciae adopts amyloid state during symbiotic interactions with pea ( Pisum sativum L.). FRONTIERS IN PLANT SCIENCE 2022; 13:1014699. [PMID: 36388578 PMCID: PMC9650718 DOI: 10.3389/fpls.2022.1014699] [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: 08/08/2022] [Accepted: 10/06/2022] [Indexed: 06/16/2023]
Abstract
Amyloids represent protein aggregates with highly ordered fibrillar structure associated with the development of various disorders in humans and animals and involved in implementation of different vital functions in all three domains of life. In prokaryotes, amyloids perform a wide repertoire of functions mostly attributed to their interactions with other organisms including interspecies interactions within bacterial communities and host-pathogen interactions. Recently, we demonstrated that free-living cells of Rhizobium leguminosarum, a nitrogen-fixing symbiont of legumes, produce RopA and RopB which form amyloid fibrils at cell surface during the stationary growth phase thus connecting amyloid formation and host-symbiont interactions. Here we focused on a more detailed analysis of the RopB amyloid state in vitro and in vivo, during the symbiotic interaction between R. leguminosarum bv. viciae with its macrosymbiont, garden pea (Pisum sativum L.). We confirmed that RopB is the bona fide amyloid protein since its fibrils exhibit circular x-ray reflections indicating its cross-β structure specific for amyloids. We found that fibrils containing RopB and exhibiting amyloid properties are formed in vivo at the surface of bacteroids of R. leguminosarum extracted from pea nodules. Moreover, using pea sym31 mutant we demonstrated that formation of extracellular RopB amyloid state occurs at different stages of bacteroid development but is enhanced in juvenile symbiosomes. Proteomic screening of potentially amyloidogenic proteins in the nodules revealed the presence of detergent-resistant aggregates of different plant and bacterial proteins including pea amyloid vicilin. We demonstrated that preformed vicilin amyloids can cross-seed RopB amyloid formation suggesting for probable interaction between bacterial and plant amyloidogenic proteins in the nodules. Taken together, we demonstrate that R. leguminosarum bacteroids produce extracellular RopB amyloids in pea nodules in vivo and these nodules also contain aggregates of pea vicilin amyloid protein, which is able to cross-seed RopB fibrillogenesis in vitro. Thus, we hypothesize that plant nodules contain a complex amyloid network consisting of plant and bacterial amyloids and probably modulating host-symbiont interactions.
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Affiliation(s)
- Anastasiia O. Kosolapova
- All-Russia Research Institute for Agricultural Microbiology, St. Petersburg, Russia
- St. Petersburg State University, St. Petersburg, Russia
| | - Mikhail V. Belousov
- All-Russia Research Institute for Agricultural Microbiology, St. Petersburg, Russia
- St. Petersburg State University, St. Petersburg, Russia
| | - Maksim I. Sulatsky
- Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russia
| | - Anna V. Tsyganova
- All-Russia Research Institute for Agricultural Microbiology, St. Petersburg, Russia
| | - Anna I. Sulatskaya
- Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russia
| | - Alexander G. Bobylev
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino, Russia
| | - Oksana Y. Shtark
- All-Russia Research Institute for Agricultural Microbiology, St. Petersburg, Russia
| | - Viktor E. Tsyganov
- All-Russia Research Institute for Agricultural Microbiology, St. Petersburg, Russia
| | | | - Vladimir A. Zhukov
- All-Russia Research Institute for Agricultural Microbiology, St. Petersburg, Russia
| | - Igor A. Tikhonovich
- All-Russia Research Institute for Agricultural Microbiology, St. Petersburg, Russia
- St. Petersburg State University, St. Petersburg, Russia
| | - Anton A. Nizhnikov
- All-Russia Research Institute for Agricultural Microbiology, St. Petersburg, Russia
- St. Petersburg State University, St. Petersburg, Russia
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Wu L, Fredua-Agyeman R, Strelkov SE, Chang KF, Hwang SF. Identification of Novel Genes Associated with Partial Resistance to Aphanomyces Root Rot in Field Pea by BSR-Seq Analysis. Int J Mol Sci 2022; 23:9744. [PMID: 36077139 PMCID: PMC9456226 DOI: 10.3390/ijms23179744] [Citation(s) in RCA: 6] [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: 07/28/2022] [Revised: 08/26/2022] [Accepted: 08/26/2022] [Indexed: 12/04/2022] Open
Abstract
Aphanomyces root rot, caused by Aphanomyces euteiches, causes severe yield loss in field pea (Pisum sativum). The identification of a pea germplasm resistant to this disease is an important breeding objective. Polygenetic resistance has been reported in the field pea cultivar '00-2067'. To facilitate marker-assisted selection (MAS), bulked segregant RNA-seq (BSR-seq) analysis was conducted using an F8 RIL population derived from the cross of 'Carman' × '00-2067'. Root rot development was assessed under controlled conditions in replicated experiments. Resistant (R) and susceptible (S) bulks were constructed based on the root rot severity in a greenhouse study. The BSR-seq analysis of the R bulks generated 44,595,510~51,658,688 reads, of which the aligned sequences were linked to 44,757 genes in a reference genome. In total, 2356 differentially expressed genes were identified, of which 44 were used for gene annotation, including defense-related pathways (jasmonate, ethylene and salicylate) and the GO biological process. A total of 344.1 K SNPs were identified between the R and S bulks, of which 395 variants were located in 31 candidate genes. The identification of novel genes associated with partial resistance to Aphanomyces root rot in field pea by BSR-seq may facilitate efforts to improve management of this important disease.
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Affiliation(s)
| | | | | | | | - Sheau-Fang Hwang
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada
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Garmendia I, Rashidi S, Quezada-Salirrosas MR, Goicoechea N. Atmospheric CO 2 concentration affects the life cycle, yield, and fruit quality of early maturing edible legume cultivars. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2022; 102:3964-3971. [PMID: 34952971 DOI: 10.1002/jsfa.11743] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 12/07/2021] [Accepted: 12/25/2021] [Indexed: 06/14/2023]
Abstract
BACKGROUND Elevated CO2 usually reduces levels of proteins and essential micronutrients in crops. The adoption of early maturing varieties may minimize the deleterious effect of climate change on farming activities. Legumes stand out for their high nutritional quality, so the objective was to study whether the atmospheric CO2 concentration affected the growth, yield, and food quality of early maturing cultivars of peas, snap beans, and faba beans. Plants grew in greenhouses either at ambient (ACO2 , 392 μmol mol-1 ) or under elevated (ECO2 , 700 μmol mol-1 ) CO2 levels. Minerals, proteins, sugars, and phenolic compounds were measured in grains of peas and faba beans, and in pods of snap beans. RESULTS The effect of ECO2 depended on legume species, being more evident for food quality than for vegetative growth and yield. The ECO2 increased Fe and P in faba bean grains, and Ca in snap bean pods. Under ECO2 , grains of pea and faba bean increased levels of proteins and phenolics, respectively, and the sugars-to-protein ratio decreased in pods of snap beans. CONCLUSION Early maturing varieties of legumes appear to be an interesting tool to cope with the negative effects that a long exposure to rising CO2 can exert on food quality. © 2021 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
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Affiliation(s)
- Idoia Garmendia
- Department of Environment and Earth Sciences, University of Alicante, Alicante, Spain
| | - Sakineh Rashidi
- Department of Environmental Biology, Plant Stress Physiology Group, Associated to CSIC (EEAD, Zaragoza), University of Navarra, Pamplona, Spain
| | - Marilyn Ra Quezada-Salirrosas
- Department of Environmental Biology, Plant Stress Physiology Group, Associated to CSIC (EEAD, Zaragoza), University of Navarra, Pamplona, Spain
| | - Nieves Goicoechea
- Department of Environmental Biology, Plant Stress Physiology Group, Associated to CSIC (EEAD, Zaragoza), University of Navarra, Pamplona, Spain
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6
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The Seed Coat’s Impact on Crop Performance in Pea (Pisum sativum L.). PLANTS 2022; 11:plants11152056. [PMID: 35956534 PMCID: PMC9370168 DOI: 10.3390/plants11152056] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 08/03/2022] [Accepted: 08/05/2022] [Indexed: 11/17/2022]
Abstract
Seed development in angiosperms produces three genetically and developmentally distinct sub-compartments: the embryo, endosperm, and seed coat. The maternally derived seed coat protects the embryo and interacts closely with the external environment especially during germination and seedling establishment. Seed coat is a key contributor to seed composition and an important determinant of nutritional value for humans and livestock. In this review, we examined pea crop productivity through the lens of the seed coat, its contribution to several valued nutritional traits of the pea crop, and its potential as a breeding target. Key discoveries made in advancing the knowledge base for sensing and transmission of external signals, the architecture and chemistry of the pea seed coat, and relevant insights from other important legumes were discussed. Furthermore, for selected seed coat traits, known mechanisms of genetic regulation and efforts to modulate these mechanisms to facilitate composition and productivity improvements in pea were discussed, alongside opportunities to support the continued development and improvement of this underutilized crop. This review describes the most important features of seed coat development in legumes and highlights the key roles played by the seed coat in pea seed development, with a focus on advances made in the genetic and molecular characterization of pea and other legumes and the potential of this key seed tissue for targeted improvement and crop optimization.
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Transcriptomic Insight into Viviparous Growth in Water Lily. BIOMED RESEARCH INTERNATIONAL 2022; 2022:8445484. [PMID: 35845943 PMCID: PMC9283058 DOI: 10.1155/2022/8445484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 04/30/2022] [Accepted: 05/18/2022] [Indexed: 11/17/2022]
Abstract
Water lily is an important ornamental flower plant which is capable of viviparous plantlet development. But no study has been reported on the molecular basis of viviparity in water lily. Hence, we performed a comparative transcriptome study between viviparous water lily Nymphaea micrantha and a nonviviparous species Nymphaea colorata at four developmental stages. The higher expression of highly conserved AUX/IAA, ARF, GH3, and SAUR gene families in N. micrantha compared to N. colorata is predicted to have a major impact on the development and evolution of viviparity in water lily. Likewise, differential regulation of hormone signaling, brassinosteroid, photosynthesis, and energy-related pathways in the two species provide clues of their involvement in viviparity phenomenon. This study revealed the complex mechanism of viviparity trait in water lily. The transcriptomic signatures identified are important basis for future breeding and research of viviparity in water lily and other plant species.
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Huang R, Snedden WA, diCenzo GC. Reference nodule transcriptomes for Melilotus officinalis and Medicago sativa cv. Algonquin. PLANT DIRECT 2022; 6:e408. [PMID: 35774624 PMCID: PMC9219011 DOI: 10.1002/pld3.408] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 05/14/2022] [Accepted: 05/19/2022] [Indexed: 05/10/2023]
Abstract
Host/symbiont compatibility is a hallmark of the symbiotic nitrogen-fixing interaction between rhizobia and legumes, mediated in part by plant-produced nodule-specific cysteine-rich (NCR) peptides and the bacterial BacA membrane protein that can act as a NCR peptide transporter. In addition, the genetic and metabolic properties supporting symbiotic nitrogen fixation often differ between compatible partners, including those sharing a common partner, highlighting the need for multiple study systems. Here, we report high-quality nodule transcriptome assemblies for Medicago sativa cv. Algonquin and Melilotus officinalis, two legumes able to form compatible symbioses with Sinorhizobium meliloti. The compressed M. sativa and M. officinalis assemblies consisted of 79,978 and 64,593 contigs, respectively, of which 33,341 and 28,278 were assigned putative annotations, respectively. As expected, the two transcriptomes showed broad similarity at a global level. We were particularly interested in the NCR peptide profiles of these plants, as these peptides drive bacterial differentiation during the symbiosis. A total of 412 and 308 NCR peptides were predicted from the M. sativa and M. officinalis transcriptomes, respectively, with approximately 9% of the transcriptome of both species consisting of NCR transcripts. Notably, transcripts encoding highly cationic NCR peptides (isoelectric point > 9.5), which are known to have antimicrobial properties, were ∼2-fold more abundant in M. sativa than in M. officinalis, and ∼27-fold more abundant when considering only NCR peptides in the six-cysteine class. We hypothesize that the difference in abundance of highly cationic NCR peptides explains our previous observation that some rhizobial bacA alleles which can support symbiosis with M. officinalis are unable to support symbiosis with M. sativa.
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Affiliation(s)
- Rui Huang
- Department of BiologyQueen's UniversityKingstonOntarioCanada
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9
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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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Pradhan S, Verma S, Chakraborty A, Bhatia S. Identification and molecular characterization of miRNAs and their target genes associated with seed development through small RNA sequencing in chickpea. Funct Integr Genomics 2021; 21:283-298. [PMID: 33630193 DOI: 10.1007/s10142-021-00777-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 01/12/2021] [Accepted: 02/09/2021] [Indexed: 11/30/2022]
Abstract
Multiple studies have attempted to dissect the molecular mechanism underlying seed development in chickpea (Cicer arietinum L.). These studies highlight the need to focus on the role of miRNAs in regulating storage protein accumulation in seeds. Therefore, a total of 8,856,691 short-read sequences were generated from a small RNA library of developing chickpea seeds and were analyzed using miRDeep-P to identify 74 known and 26 novel miRNA sequences. Known miRNAs were classified into 22 miRNA families with miRNA156 family being most abundant. Of the 26 putative novel miRNAs identified, only 22 could be experimentally validated using stem loop end point PCR. Differential expression analyses led to the identification of known as well as novel miRNAs that could regulate various stages of chickpea seed development. In silico target prediction revealed several important target genes and transcription factors like SPL, mediator of RNA Polymerase II transcription subunit 12, aspartic proteinase and NACs, which were further validated by real-time PCR analysis. A comparative expression analysis in chickpea genotypes with contrasting seed protein content revealed one known (Car-miR156h) and two novel miRNA (Car-novmiR7 and Car-novmiR23) candidates to be highly expressed in the LPC (low protein content) chickpea genotypes, targets of which are known to regulate seed storage protein accumulation. Therefore, this study provides a useful resource in the form of miRNA and their targets which can be further utilized to understand and manipulate various regulatory mechanisms involved in seed development with the overall aim of improving yield and nutrition attributes in chickpea.
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Affiliation(s)
- Seema Pradhan
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Subodh Verma
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Anirban Chakraborty
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Sabhyata Bhatia
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India.
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Nikoghosyan M, Schmidt M, Margaryan K, Loeffler-Wirth H, Arakelyan A, Binder H. SOMmelier-Intuitive Visualization of the Topology of Grapevine Genome Landscapes Using Artificial Neural Networks. Genes (Basel) 2020; 11:genes11070817. [PMID: 32709105 PMCID: PMC7397337 DOI: 10.3390/genes11070817] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 06/26/2020] [Accepted: 07/15/2020] [Indexed: 01/02/2023] Open
Abstract
Background: Whole-genome studies of vine cultivars have brought novel knowledge about the diversity, geographical relatedness, historical origin and dissemination, phenotype associations and genetic markers. Method: We applied SOM (self-organizing maps) portrayal, a neural network-based machine learning method, to re-analyze the genome-wide Single Nucleotide Polymorphism (SNP) data of nearly eight hundred grapevine cultivars. The method generates genome-specific data landscapes. Their topology reflects the geographical distribution of cultivars, indicates paths of cultivar dissemination in history and genome-phenotype associations about grape utilization. Results: The landscape of vine genomes resembles the geographic map of the Mediterranean world, reflecting two major dissemination paths from South Caucasus along a northern route via Balkan towards Western Europe and along a southern route via Palestine and Maghreb towards Iberian Peninsula. The Mediterranean and Black Sea, as well as the Pyrenees, constitute barriers for genetic exchange. On the coarsest level of stratification, cultivars divide into three major groups: Western Europe and Italian grapes, Iberian grapes and vine cultivars from Near East and Maghreb regions. Genetic landmarks were associated with agronomic traits, referring to their utilization as table and wine grapes. Pseudotime analysis describes the dissemination of grapevines in an East to West direction in different waves of cultivation. Conclusion: In analogy to the tasks of the wine waiter in gastronomy, the sommelier, our ‘SOMmelier’-approach supports understanding the diversity of grapevine genomes in the context of their geographic and historical background, using SOM portrayal. It offers an option to supplement vine cultivar passports by genome fingerprint portraits.
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Affiliation(s)
- Maria Nikoghosyan
- Research Group of Bioinformatics, Institute of Molecular Biology of National Academy of Sciences RA, Yerevan 0014, Armenia; (M.N.); (A.A.)
- Institute of Biomedicine and Pharmacy, Russian-Armenian University, Yerevan 0051, Armenia
| | - Maria Schmidt
- Interdisciplinary Centre for Bioinformatics, University of Leipzig, 04107 Leipzig, Germany; (M.S.); (H.L.-W.)
| | - Kristina Margaryan
- Research Group of Plant Genetics and Immunology, Institute of Molecular Biology of National Academy of Sciences RA, Yerevan 0014, Armenia;
- Department of Genetics and Cytology, Yerevan State University, Yerevan 0025, Armenia
| | - Henry Loeffler-Wirth
- Interdisciplinary Centre for Bioinformatics, University of Leipzig, 04107 Leipzig, Germany; (M.S.); (H.L.-W.)
| | - Arsen Arakelyan
- Research Group of Bioinformatics, Institute of Molecular Biology of National Academy of Sciences RA, Yerevan 0014, Armenia; (M.N.); (A.A.)
- Institute of Biomedicine and Pharmacy, Russian-Armenian University, Yerevan 0051, Armenia
| | - Hans Binder
- Interdisciplinary Centre for Bioinformatics, University of Leipzig, 04107 Leipzig, Germany; (M.S.); (H.L.-W.)
- Correspondence:
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12
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Antonets KS, Belousov MV, Sulatskaya AI, Belousova ME, Kosolapova AO, Sulatsky MI, Andreeva EA, Zykin PA, Malovichko YV, Shtark OY, Lykholay AN, Volkov KV, Kuznetsova IM, Turoverov KK, Kochetkova EY, Bobylev AG, Usachev KS, Demidov ON, Tikhonovich IA, Nizhnikov AA. Accumulation of storage proteins in plant seeds is mediated by amyloid formation. PLoS Biol 2020; 18:e3000564. [PMID: 32701952 PMCID: PMC7377382 DOI: 10.1371/journal.pbio.3000564] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Accepted: 06/19/2020] [Indexed: 02/04/2023] Open
Abstract
Amyloids are protein aggregates with a highly ordered spatial structure giving them unique physicochemical properties. Different amyloids not only participate in the development of numerous incurable diseases but control vital functions in archaea, bacteria and eukarya. Plants are a poorly studied systematic group in the field of amyloid biology. Amyloid properties have not yet been demonstrated for plant proteins under native conditions in vivo. Here we show that seeds of garden pea Pisum sativum L. contain amyloid-like aggregates of storage proteins, the most abundant one, 7S globulin Vicilin, forms bona fide amyloids in vivo and in vitro. Full-length Vicilin contains 2 evolutionary conserved β-barrel domains, Cupin-1.1 and Cupin-1.2, that self-assemble in vitro into amyloid fibrils with similar physicochemical properties. However, Cupin-1.2 fibrils unlike Cupin-1.1 can seed Vicilin fibrillation. In vivo, Vicilin forms amyloids in the cotyledon cells that bind amyloid-specific dyes and possess resistance to detergents and proteases. The Vicilin amyloid accumulation increases during seed maturation and wanes at germination. Amyloids of Vicilin resist digestion by gastrointestinal enzymes, persist in canned peas, and exhibit toxicity for yeast and mammalian cells. Our finding for the first time reveals involvement of amyloid formation in the accumulation of storage proteins in plant seeds.
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Affiliation(s)
- Kirill S. Antonets
- All-Russia Research Institute for Agricultural Microbiology (ARRIAM), St. Petersburg, Russia
- St. Petersburg State University, St. Petersburg, Russia
| | - Mikhail V. Belousov
- All-Russia Research Institute for Agricultural Microbiology (ARRIAM), St. Petersburg, Russia
- St. Petersburg State University, St. Petersburg, Russia
| | - Anna I. Sulatskaya
- Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russia
| | - Maria E. Belousova
- All-Russia Research Institute for Agricultural Microbiology (ARRIAM), St. Petersburg, Russia
| | - Anastasiia O. Kosolapova
- All-Russia Research Institute for Agricultural Microbiology (ARRIAM), St. Petersburg, Russia
- St. Petersburg State University, St. Petersburg, Russia
| | - Maksim I. Sulatsky
- Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russia
| | | | | | - Yury V. Malovichko
- All-Russia Research Institute for Agricultural Microbiology (ARRIAM), St. Petersburg, Russia
- St. Petersburg State University, St. Petersburg, Russia
| | - Oksana Y. Shtark
- All-Russia Research Institute for Agricultural Microbiology (ARRIAM), St. Petersburg, Russia
| | | | | | | | | | | | - Alexander G. Bobylev
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - Konstantin S. Usachev
- Laboratory of Structural Biology, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russia
| | - Oleg. N. Demidov
- Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russia
- INSERM UMR1231, UBFC, Dijon, France
| | - Igor A. Tikhonovich
- All-Russia Research Institute for Agricultural Microbiology (ARRIAM), St. Petersburg, Russia
- St. Petersburg State University, St. Petersburg, Russia
| | - Anton A. Nizhnikov
- All-Russia Research Institute for Agricultural Microbiology (ARRIAM), St. Petersburg, Russia
- St. Petersburg State University, St. Petersburg, Russia
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