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Tarchoun N, Saadaoui W, Hamdi K, Falleh H, Pavli O, Ksouri R, Petropoulos SA. Seed Priming and Biopriming in Two Squash Landraces ( Cucurbita maxima Duchesne) from Tunisia: A Sustainable Strategy to Promote Germination and Alleviate Salt Stress. PLANTS (BASEL, SWITZERLAND) 2024; 13:2464. [PMID: 39273948 PMCID: PMC11397125 DOI: 10.3390/plants13172464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2024] [Revised: 08/21/2024] [Accepted: 08/30/2024] [Indexed: 09/15/2024]
Abstract
In recent years, seed priming has gained interest, with researchers aiming to enhance seed germination and early growth, especially under abiotic stress conditions. In this study, seeds from two squash landraces (Cucurbita maxima Duchesne; i.e., Galaoui large seeds (Galaoui hereafter) and Batati green (Batati hereafter)) were subjected to different priming methods ((a) 0.3% and 0.4% KNO3 (halopriming); (b) 0.1% and 0.2% GA3 (hormopriming); (c) inoculation with Trichoderma spp. (T. harzianum, T. viride, and T. virens), Bacillus subtilis, and Pseudomonas fluorescens (biopriming) in order to promote germination parameters and seedling growth under salinity stress (0, 100, and 200 mM of NaCl). Our findings indicate the better performance of primed seeds compared to the untreated ones in terms of germination and seedling growth traits, although a varied response depending on the priming method and the landrace was observed. The highest germination percentage (GP) and the lowest mean germination time (MGT) were observed in 0.4% KNO3-primed seeds. The positive effects of 0.4% KNO3 were also depicted in all traits related to seedling growth and the seedling vigor index (SVI), indicating its effectiveness as a priming agent in squash seeds. Under salinity stress conditions, priming with 0.4% KNO3 significantly improved the germination and seedling growth traits for both landraces, while the application of 0.2% GA3 at high salinity significantly improved photosynthetic quantum yield (Fv/Fm ratio). Regarding the effects of biopriming in germination and seedling growth traits, our results indicate that T. harzianum and B. subtilis were the most effective bioagents in promoting germination and seedling growth in Galaoui and Batati seeds, respectively. In conclusion, our findings provide important information regarding the practice of using priming and biopriming agents to enhance the germination and seedling growth capacity of squash seeds, as well to mitigate the negative effects of salinity stress at the critical stages of germination and early growth.
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Affiliation(s)
- Néji Tarchoun
- Research Laboratory LR21AGR05, High Agronomic Institute of Chott Mariem, Sousse University, Sousse 4042, Tunisia
| | - Wassim Saadaoui
- Research Laboratory LR21AGR05, High Agronomic Institute of Chott Mariem, Sousse University, Sousse 4042, Tunisia
| | - Khawla Hamdi
- Research Laboratory LR21AGR05, High Agronomic Institute of Chott Mariem, Sousse University, Sousse 4042, Tunisia
| | - Hanen Falleh
- Laboratory of Aromatic and Medicinal Plants, Center of Biotechnology, Technopark of Borj Cedria, BP 901, Hammam-Lif 2050, Tunisia
| | - Ourania Pavli
- Laboratory of Genetics and Plant Breeding, Department of Agriculture, Crop Production and Rural Environment, University of Thessaly, Fytokou Street, 38446 Volos, Greece
| | - Riadh Ksouri
- Laboratory of Aromatic and Medicinal Plants, Center of Biotechnology, Technopark of Borj Cedria, BP 901, Hammam-Lif 2050, Tunisia
| | - Spyridon A Petropoulos
- Laboratory of Vegetable Production, Department of Agriculture, Crop Production and Rural Environment, University of Thessaly, Fytokou Street, 38446 Volos, Greece
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Wang YN, Liu FJ, Liu HD, Zhang Y, Jiao X, Ye ML, Zhao ZBK, Zhang SF. Regulation of autophagy and lipid accumulation under phosphate limitation in Rhodotorula toruloides. Front Microbiol 2023; 13:1046114. [PMID: 36777022 PMCID: PMC9908577 DOI: 10.3389/fmicb.2022.1046114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 12/23/2022] [Indexed: 01/27/2023] Open
Abstract
Background It is known that autophagy is essential for cell survival under stress conditions. Inorganic phosphate (Pi) is an essential nutrient for cell growth and Pi-limitation can trigger autophagy and lipid accumulation in oleaginous yeasts, yet protein (de)-phosphorylation and related signaling events in response to Pi limitation and the molecular basis linking Pi-limitation to autophagy and lipid accumulation remain elusive. Results Here, we compared the proteome and phosphoproteome of Rhodotorula toruloides CGMCC 2.1389 under Pi-limitation and Pi-repletion. In total, proteome analysis identified 3,556 proteins and the phosphoproteome analysis identified 1,649 phosphoproteins contained 5,659 phosphosites including 4,499 pSer, 978 pThr, and 182 pTyr. We found Pi-starvation-induced autophagy was regulated by autophagy-related proteins, but not the PHO pathway. When ATG9 was knocked down, the engineered strains produced significantly less lipids under Pi-limitation, suggesting that autophagy required Atg9 in R. toruloides and that was conducive to lipid accumulation. Conclusion Our results provide new insights into autophagy regulation under Pi-limitation and lipid accumulation in oleaginous yeast, which should be valuable to guide further mechanistic study of oleaginicity and genetic engineering for advanced lipid producing cell factory.
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Affiliation(s)
- Ya-nan Wang
- Laboratory of Biotechnology, Dalian Institute of Chemical Physics, CAS, Dalian, China,State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Fang-jie Liu
- Laboratory of Biotechnology, Dalian Institute of Chemical Physics, CAS, Dalian, China
| | - Hong-di Liu
- Laboratory of Biotechnology, Dalian Institute of Chemical Physics, CAS, Dalian, China
| | - Yue Zhang
- Laboratory of Biotechnology, Dalian Institute of Chemical Physics, CAS, Dalian, China
| | - Xiang Jiao
- Laboratory of Biotechnology, Dalian Institute of Chemical Physics, CAS, Dalian, China
| | - Ming-liang Ye
- Laboratory of Biotechnology, Dalian Institute of Chemical Physics, CAS, Dalian, China,Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, CAS, Dalian, China,Ming-liang Ye,
| | - Zong-bao Kent Zhao
- Laboratory of Biotechnology, Dalian Institute of Chemical Physics, CAS, Dalian, China,Dalian Key Laboratory of Energy Biotechnology, Dalian Institute of Chemical Physics, CAS, Dalian, China,Zong-bao Kent Zhao,
| | - Su-fang Zhang
- Laboratory of Biotechnology, Dalian Institute of Chemical Physics, CAS, Dalian, China,Dalian Key Laboratory of Energy Biotechnology, Dalian Institute of Chemical Physics, CAS, Dalian, China,*Correspondence: Su-fang Zhang, ,
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Wu Y, Li X, Zhang J, Zhao H, Tan S, Xu W, Pan J, Yang F, Pi E. ERF subfamily transcription factors and their function in plant responses to abiotic stresses. FRONTIERS IN PLANT SCIENCE 2022; 13:1042084. [PMID: 36531407 PMCID: PMC9748296 DOI: 10.3389/fpls.2022.1042084] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 11/09/2022] [Indexed: 06/09/2023]
Abstract
Ethylene Responsive Factor (ERF) subfamily comprise the largest number of proteins in the plant AP2/ERF superfamily, and have been most extensively studied on the biological functions. Members of this subfamily have been proven to regulate plant resistances to various abiotic stresses, such as drought, salinity, chilling and some other adversities. Under these stresses, ERFs are usually activated by mitogen-activated protein kinase induced phosphorylation or escape from ubiquitin-ligase enzymes, and then form complex with nucleic proteins before binding to cis-element in promoter regions of stress responsive genes. In this review, we will discuss the phylogenetic relationships among the ERF subfamily proteins, summarize molecular mechanism how the transcriptional activity of ERFs been regulated and how ERFs of different subgroup regulate the transcription of stress responsive genes, such as high-affinity K+ transporter gene PalHKT1;2, reactive oxygen species related genes LcLTP, LcPrx, and LcRP, flavonoids synthesis related genes FtF3H and LhMYBSPLATTER, etc. Though increasing researches demonstrate that ERFs are involved in various abiotic stresses, very few interact proteins and target genes of them have been comprehensively annotated. Hence, future research prospects are described on the mechanisms of how stress signals been transited to ERFs and how ERFs regulate the transcriptional expression of stress responsive genes.
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Wang F, Das P, Pal N, Bhawal R, Zhang S, Bhattacharyya MK. A Phosphoproteomics Study of the Soybean root necrosis 1 Mutant Revealed Type II Metacaspases Involved in Cell Death Pathway. FRONTIERS IN PLANT SCIENCE 2022; 13:882561. [PMID: 35928708 PMCID: PMC9344878 DOI: 10.3389/fpls.2022.882561] [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: 02/23/2022] [Accepted: 05/17/2022] [Indexed: 06/15/2023]
Abstract
The soybean root necrosis 1 (rn1) mutation causes progressive browning of the roots soon after germination and provides increased tolerance to the soil-borne oomycete pathogen Phytophthora sojae in soybean. Toward understanding the molecular basis of the rn1 mutant phenotypes, we conducted tandem mass tag (TMT)-labeling proteomics and phosphoproteomics analyses of the root tissues of the rn1 mutant and progenitor T322 line to identify potential proteins involved in manifestation of the mutant phenotype. We identified 3,160 proteins. When the p-value was set at ≤0.05 and the fold change of protein accumulation between rn1 and T322 at ≥1.5 or ≤0.67, we detected 118 proteins that showed increased levels and 32 proteins decreased levels in rn1 as compared to that in T322. The differentially accumulated proteins (DAPs) are involved in several pathways including cellular processes for processing environmental and genetic information, metabolism and organismal systems. Five pathogenesis-related proteins were accumulated to higher levels in the mutant as compared to that in T322. Several of the DAPs are involved in hormone signaling, redox reaction, signal transduction, and cell wall modification processes activated in plant-pathogen interactions. The phosphoproteomics analysis identified 22 phosphopeptides, the levels of phosphorylation of which were significantly different between rn1 and T322 lines. The phosphorylation levels of two type II metacaspases were reduced in rn1 as compared to T322. Type II metacaspase has been shown to be a negative regulator of hypersensitive cell death. In absence of the functional Rn1 protein, two type II metacaspases exhibited reduced phosphorylation levels and failed to show negative regulatory cell death function in the soybean rn1 mutant. We hypothesize that Rn1 directly or indirectly phosphorylates type II metacaspases to negatively regulate the cell death process in soybean roots.
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Affiliation(s)
- Feifei Wang
- Department of Agronomy, Iowa State University, Ames, IA, United States
| | - Priyanka Das
- Department of Agronomy, Iowa State University, Ames, IA, United States
| | - Narinder Pal
- Department of Agronomy, Iowa State University, Ames, IA, United States
| | - Ruchika Bhawal
- Proteomics and Metabolomics Facility, Institute of Biotechnology, Cornell University, Ithaca, NY, United States
| | - Sheng Zhang
- Proteomics and Metabolomics Facility, Institute of Biotechnology, Cornell University, Ithaca, NY, United States
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Kosová K, Vítámvás P, Prášil IT, Klíma M, Renaut J. Plant Proteoforms Under Environmental Stress: Functional Proteins Arising From a Single Gene. FRONTIERS IN PLANT SCIENCE 2021; 12:793113. [PMID: 34970290 PMCID: PMC8712444 DOI: 10.3389/fpls.2021.793113] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 11/16/2021] [Indexed: 05/30/2023]
Abstract
Proteins are directly involved in plant phenotypic response to ever changing environmental conditions. The ability to produce multiple mature functional proteins, i.e., proteoforms, from a single gene sequence represents an efficient tool ensuring the diversification of protein biological functions underlying the diversity of plant phenotypic responses to environmental stresses. Basically, two major kinds of proteoforms can be distinguished: protein isoforms, i.e., alterations at protein sequence level arising from posttranscriptional modifications of a single pre-mRNA by alternative splicing or editing, and protein posttranslational modifications (PTMs), i.e., enzymatically catalyzed or spontaneous modifications of certain amino acid residues resulting in altered biological functions (or loss of biological functions, such as in non-functional proteins that raised as a product of spontaneous protein modification by reactive molecular species, RMS). Modulation of protein final sequences resulting in different protein isoforms as well as modulation of chemical properties of key amino acid residues by different PTMs (such as phosphorylation, N- and O-glycosylation, methylation, acylation, S-glutathionylation, ubiquitinylation, sumoylation, and modifications by RMS), thus, represents an efficient means to ensure the flexible modulation of protein biological functions in response to ever changing environmental conditions. The aim of this review is to provide a basic overview of the structural and functional diversity of proteoforms derived from a single gene in the context of plant evolutional adaptations underlying plant responses to the variability of environmental stresses, i.e., adverse cues mobilizing plant adaptive mechanisms to diminish their harmful effects.
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Affiliation(s)
- Klára Kosová
- Division of Crop Genetics and Plant Breeding, Crop Research Institute, Prague, Czechia
| | - Pavel Vítámvás
- Division of Crop Genetics and Plant Breeding, Crop Research Institute, Prague, Czechia
| | - Ilja Tom Prášil
- Division of Crop Genetics and Plant Breeding, Crop Research Institute, Prague, Czechia
| | - Miroslav Klíma
- Division of Crop Genetics and Plant Breeding, Crop Research Institute, Prague, Czechia
| | - Jenny Renaut
- Biotechnologies and Environmental Analytics Platform (BEAP), Environmental Research and Innovation (ERIN) Department, Luxembourg Institute of Science and Technology (LIST), Esch-Sur-Alzette, Luxembourg
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Mustafa G, Komatsu S. Plant proteomic research for improvement of food crops under stresses: a review. Mol Omics 2021; 17:860-880. [PMID: 34870299 DOI: 10.1039/d1mo00151e] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Crop improvement approaches have been changed due to technological advancements in traditional plant-breeding methods. Abiotic and biotic stresses limit plant growth and development, which ultimately lead to reduced crop yield. Proteins encoded by genomes have a considerable role in the endurance and adaptation of plants to different environmental conditions. Biotechnological applications in plant breeding depend upon the information generated from proteomic studies. Proteomics has a specific advantage to contemplate post-translational modifications, which indicate the functional effects of protein modifications on crop production. Subcellular proteomics helps in exploring the precise cellular responses and investigating the networking among subcellular compartments during plant development and biotic/abiotic stress responses. Large-scale mass spectrometry-based plant proteomic studies with a more comprehensive overview are now possible due to dramatic improvements in mass spectrometry, sample preparation procedures, analytical software, and strengthened availability of genomes for numerous plant species. Development of stress-tolerant or resilient crops is essential to improve crop productivity and growth. Use of high throughput techniques with advanced instrumentation giving efficient results made this possible. In this review, the role of proteomic studies in identifying the stress-response processes in different crops is summarized. Advanced techniques and their possible utilization on plants are discussed in detail. Proteomic studies accelerate marker-assisted genetic augmentation studies on crops for developing high yielding stress-tolerant lines or varieties under stresses.
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Affiliation(s)
- Ghazala Mustafa
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Setsuko Komatsu
- Faculty of Environment and Information Sciences, Fukui University of Technology, Fukui 910-8505, Japan.
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Wang X, Deng X, Zhu D, Duan W, Zhang J, Yan Y. N-linked glycoproteome analysis reveals central glycosylated proteins involved in wheat early seedling growth. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 163:327-337. [PMID: 33906120 DOI: 10.1016/j.plaphy.2021.04.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 04/07/2021] [Indexed: 06/12/2023]
Abstract
Glycosylation is an important protein post-translational modification in eukaryotic organisms. It is involved in many important life processes, such as cell recognition, differentiation, development, signal transduction and immune response. This study carried out the first N-linked glycosylation proteome analysis of wheat seedling leaves using HILIC glycosylation enrichment, chemical deglycosylation, HPLC separation and tandem mass spectrometric identification. In total, we detected 308 glycosylated peptides and 316 glycosylated sites corresponding to 248 unique glycoproteins. The identified glycoproteins were mainly concentrated in plasma membranes (25.6%), cell wall (16.8%) and extracellular area (16%). In terms of molecular function, 65% glycoproteins belonged to various enzymes with catalytic activity such as kinase, carboxypeptidase, peroxidase and phosphatase, and, particularly, 25% of glycoproteins were related to binding functions. These glycoproteins are involved in cell wall reconstruction, biomacromolecular metabolism, signal transduction, endoplasmic reticulum quality control and stress response. Analysis indicated that 57.66% of glycoproteins were highly conserved in other plant species while 42.34% of glycoproteins went unidentified among the conserved glycosylated homologous proteins in other plant species; these may be the new N-linked glycosylated proteins first identified in wheat. The glycosylation sites generally occurred on the random coil, which could play roles in maintaining the structural stability of proteins. PNGase F digestion and glycosylation site mutations further verified the glycosylation modification and glycosylation sites of LRR receptor-like serine/threonine-protein kinase (LRR-RLK) and Beta-D-glucan exohydrolase (β-D-GEH). Our results indicated that N-linked glycosylated proteins could play important roles in the early seedling growth of wheat.
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Affiliation(s)
- Xueqian Wang
- College of Life Science, Capital Normal University, 100048, Beijing, China.
| | - Xiong Deng
- College of Life Science, Capital Normal University, 100048, Beijing, China.
| | - Dong Zhu
- College of Life Science, Capital Normal University, 100048, Beijing, China.
| | - Wenjing Duan
- College of Life Science, Capital Normal University, 100048, Beijing, China.
| | - Junwei Zhang
- College of Life Science, Capital Normal University, 100048, Beijing, China.
| | - Yueming Yan
- College of Life Science, Capital Normal University, 100048, Beijing, China.
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Arefian M, Bhagya N, Prasad TSK. Phosphorylation-mediated signalling in flowering: prospects and retrospects of phosphoproteomics in crops. Biol Rev Camb Philos Soc 2021; 96:2164-2191. [PMID: 34047006 DOI: 10.1111/brv.12748] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 05/11/2021] [Accepted: 05/13/2021] [Indexed: 12/18/2022]
Abstract
Protein phosphorylation is a major post-translational modification, regulating protein function, stability, and subcellular localization. To date, annotated phosphorylation data are available mainly for model organisms and humans, despite the economic importance of crop species and their large kinomes. Our understanding of the phospho-regulation of flowering in relation to the biology and interaction between the pollen and pistil is still significantly lagging, limiting our knowledge on kinase signalling and its potential applications to crop production. To address this gap, we bring together relevant literature that were previously disconnected to present an overview of the roles of phosphoproteomic signalling pathways in modulating molecular and cellular regulation within specific tissues at different morphological stages of flowering. This review is intended to stimulate research, with the potential to increase crop productivity by providing a platform for novel molecular tools.
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Affiliation(s)
- Mohammad Arefian
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Center, Yenepoya (Deemed to be University), Mangalore, 575018, India
| | - N Bhagya
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Center, Yenepoya (Deemed to be University), Mangalore, 575018, India
| | - T S Keshava Prasad
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Center, Yenepoya (Deemed to be University), Mangalore, 575018, India
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Zhang X, Zhuang L, Liu Y, Yang Z, Huang B. Protein phosphorylation associated with drought priming-enhanced heat tolerance in a temperate grass species. HORTICULTURE RESEARCH 2020; 7:207. [PMID: 33328446 PMCID: PMC7705721 DOI: 10.1038/s41438-020-00440-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 10/12/2020] [Accepted: 10/20/2020] [Indexed: 05/24/2023]
Abstract
Protein phosphorylation is known to play crucial roles in plant tolerance to individual stresses, but how protein phosphorylation is associated with cross-stress tolerance, particularly drought priming-enhanced heat tolerance is largely unknown. The objectives of the present study were to identify phosphorylated proteins and phosphorylation sites that were responsive to drought priming and to determine whether drought priming-enhanced heat tolerance in temperate grass species involves changes in protein phosphorylation. Comparative analysis of phosphoproteomic profiles was performed on leaves of tall fescue (Festuca arundinacea) exposed to heat stress (38/33 °C, day/night) with or without drought priming. A total of 569 differentially regulated phosphoproteins (DRPs) with 1098 phosphorylation sites were identified in response to drought priming or heat stress individually or sequentially. Most DRPs were nuclear-localized and cytosolic proteins. Motif analysis detected [GS], [DSD], and [S..E] as major phosphorylation sites in casein kinase-II and mitogen-activated protein kinases regulated by drought priming and heat stress. Functional annotation and gene ontology analysis demonstrated that DRPs in response to drought priming and in drought-primed plants subsequently exposed to heat stress were mostly enriched in four major biological processes, including RNA splicing, transcription control, stress protection/defense, and stress perception/signaling. These results suggest the involvement of post-translational regulation of the aforementioned biological processes and signaling pathways in drought priming memory and cross-tolerance with heat stress in a temperate grass species.
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Affiliation(s)
- Xiaxiang Zhang
- College of Agro-grassland Science, Nanjing Agricultural University, 210095, Nanjing, China
- Department of Plant Biology, Rutgers University, New Brunswick, NJ, 08901, USA
| | - Lili Zhuang
- College of Agro-grassland Science, Nanjing Agricultural University, 210095, Nanjing, China
| | - Yu Liu
- College of Agro-grassland Science, Nanjing Agricultural University, 210095, Nanjing, China
| | - Zhimin Yang
- College of Agro-grassland Science, Nanjing Agricultural University, 210095, Nanjing, China.
| | - Bingru Huang
- Department of Plant Biology, Rutgers University, New Brunswick, NJ, 08901, USA.
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Amand J, Fehlmann T, Backes C, Keller A. DynaVenn: web-based computation of the most significant overlap between ordered sets. BMC Bioinformatics 2019; 20:743. [PMID: 31888436 PMCID: PMC6937821 DOI: 10.1186/s12859-019-3320-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 12/16/2019] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND In many research disciplines, ordered lists are compared. One example is to compare a subset of all significant genes or proteins in a primary study to those in a replication study. Often, the top of the lists are compared using Venn diagrams, ore more precisely Euler diagrams (set diagrams showing logical relations between a finite collection of different sets). If different cohort sizes, different techniques or algorithms for evaluation were applied, a direct comparison of significant genes with a fixed threshold can however be misleading and approaches comparing lists would be more appropriate. RESULTS We developed DynaVenn, a web-based tool that incrementally creates all possible subsets from two or three ordered lists and computes for each combination a p-value for the overlap. Respectively, dynamic Venn diagrams are generated as graphical representations. Additionally an animation is generated showing how the most significant overlap is reached by backtracking. We demonstrate the improved performance of DynaVenn over an arbitrary cut-off approach on an Alzheimer's Disease biomarker set. CONCLUSION DynaVenn combines the calculation of the most significant overlap of different cohorts with an intuitive visualization of the results. It is freely available as a web service at http://www.ccb.uni-saarland.de/dynavenn.
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Affiliation(s)
- Jérémy Amand
- Chair for Clinical Bioinformatics, Saarland University, Saarbrücken, 66123, DE, Germany
| | - Tobias Fehlmann
- Chair for Clinical Bioinformatics, Saarland University, Saarbrücken, 66123, DE, Germany
| | - Christina Backes
- Chair for Clinical Bioinformatics, Saarland University, Saarbrücken, 66123, DE, Germany
| | - Andreas Keller
- Chair for Clinical Bioinformatics, Saarland University, Saarbrücken, 66123, DE, Germany.
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Zhang B, Chen J, Zong J, Yan X, Liu J. Unbiased phosphoproteome profiling uncovers novel phosphoproteins and phosphorylation motifs in bermudagrass stolons. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2019; 144:92-99. [PMID: 31561202 DOI: 10.1016/j.plaphy.2019.09.036] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 09/06/2019] [Accepted: 09/21/2019] [Indexed: 05/20/2023]
Abstract
As a widely used turfgrass species, bermudagrass (Cynodon dactylon L.) can be easily propagated through colonial growth of stolons. Previous studies collectively revealed that exotic environmental factors and intrinsic hormones and genes are all involved in the differentiation, development, and diageotropical growth of stolons. However, the detailed molecular mechanism how environmental and hormone signals regulate the gene expression and biochemical activities in bermudagrass stolons remains unclear. In this study, we observed that reversible phosphorylation modification plays important roles in normal growth and physiological functions of bermudagrass stolons. LC-MS/MS analyses of the total protein extracts of bermudagrass stolons without preliminary phosphopeptide-enrichment successfully identified 646 nonredundant phosphorylation sites and 485 phosphoproteins. The phosphoproteins were significantly enriched in protein phosphorylation regulation and starch metabolism processes. Motif-X analyses further revealed that phosphoproteins containing novel phosphorylation motifs might be involved in transcription regulation of bermudagrass stolons. These results greatly expanded our understanding of the growth and development of bermudagrass stolons at the post-translational level.
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Affiliation(s)
- Bing Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China.
| | - Jingbo Chen
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China
| | - Junqin Zong
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China
| | - Xuebing Yan
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China
| | - Jianxiu Liu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China
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12
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Geng F, Liu X, Wang J, He R, Zhao J, Xiang D, Zou L, Peng L, Zhao G. In-depth mapping of the seed phosphoproteome and N-glycoproteome of Tartary buckwheat (Fagopyrum tataricum) using off-line high pH RPLC fractionation and nLC-MS/MS. Int J Biol Macromol 2019; 137:688-696. [DOI: 10.1016/j.ijbiomac.2019.07.026] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 03/21/2019] [Accepted: 07/03/2019] [Indexed: 12/18/2022]
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Yu C, Wu Q, Sun C, Tang M, Sun J, Zhan Y. The Phosphoproteomic Response of Okra ( Abelmoschus esculentus L.) Seedlings to Salt Stress. Int J Mol Sci 2019; 20:ijms20061262. [PMID: 30871161 PMCID: PMC6470868 DOI: 10.3390/ijms20061262] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2019] [Revised: 03/05/2019] [Accepted: 03/09/2019] [Indexed: 01/30/2023] Open
Abstract
Soil salinization is a major environmental stresses that seriously threatens land use efficiency and crop yields worldwide. Although the overall response of plants to NaCl has been well studied, the contribution of protein phosphorylation to the detoxification and tolerance of NaCl in okra (Abelmoschus esculentus L.) seedlings is unclear. The molecular bases of okra seedlings’ responses to 300 mM NaCl stress are discussed in this study. Using a combination of affinity enrichment, tandem mass tag (TMT) labeling and high-performance liquid chromatography–tandem mass spectrometry analysis, a large-scale phosphoproteome analysis was performed in okra. A total of 4341 phosphorylation sites were identified on 2550 proteins, of which 3453 sites of 2268 proteins provided quantitative information. We found that 91 sites were upregulated and 307 sites were downregulated in the NaCl/control comparison group. Subsequently, we performed a systematic bioinformatics analysis including gene ontology annotation, domain annotation, subcellular localization, and Kyoto Encyclopedia of Genes and Genomes pathway annotation. The latter revealed that the differentially expressed proteins were most strongly associated with ‘photosynthesis antenna proteins’ and ‘RNA degradation’. These differentially expressed proteins probably play important roles in salt stress responses in okra. The results should help to increase our understanding of the molecular mechanisms of plant post-translational modifications in response to salt stress.
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Affiliation(s)
- Chenliang Yu
- Institute of Agricultural Equipment, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China.
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China.
| | - Qinqfei Wu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China.
| | - Chendong Sun
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, School of Agriculture and Food Science, Zhejiang A&F University, Linan, Hangzhou 311300, China.
| | - Mengling Tang
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, School of Agriculture and Food Science, Zhejiang A&F University, Linan, Hangzhou 311300, China.
| | - Junwei Sun
- College of modern science and technology, China Jiliang University, Hangzhou 310018, China.
| | - Yihua Zhan
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China.
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Luo F, Deng X, Liu Y, Yan Y. Identification of phosphorylation proteins in response to water deficit during wheat flag leaf and grain development. BOTANICAL STUDIES 2018; 59:28. [PMID: 30535879 PMCID: PMC6286713 DOI: 10.1186/s40529-018-0245-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 12/03/2018] [Indexed: 05/04/2023]
Abstract
BACKGROUND Wheat (Triticum aestivum L.) serves as important grain crop widely cultivated in the world, which is often suffered by drought stress in natural conditions. As one of the most important post translation modifications, protein phosphorylation widely participates in plant abiotic stress regulation. In this study, we performed the first comparative analysis of phosphorylated protein characterization in flag leaves and developing grains of elite Chinese bread wheat cultivar Zhongmai 175 under water deficit by combining with proteomic approach and Pro-Q Diamond gel staining. RESULTS Field experiment showed that water deficit caused significant reduction of plant height, tiller number, ear length and grain yield. 2-DE and Pro-Q Diamond gel staining analysis showed that 58 proteins were phosphorylated among 112 differentially accumulated proteins in response to water deficit, including 20 in the flag leaves and 38 in the developing grains. The phosphorylated proteins from flag leaves mainly involved in photosynthesis, carbohydrate and energy metabolism, while those from developing grains were closely related with detoxification and defense, protein, carbohydrate and energy metabolism. Particularly, water deficit resulted in significant downregulation of phosphorylated modification level in the flag leaves, which could affect photosynthesis and grain yield. However, some important phosphorylated proteins involved in stress defense, energy metabolism and starch biosynthesis were upregulated under water deficit, which could benefit drought tolerance, accelerate grain filling and shorten grain developing time. CONCLUSIONS The modification level of those identified proteins from flag leaves and grains had great changes when wheat was suffered from water deficit, indicating that phosphoproteins played a key role in response to drought stress. Our results provide new insights into the molecular mechanisms how phosphoproteins respond to drought stress and thus reduce production.
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Affiliation(s)
- Fei Luo
- College of Life Science, Capital Normal University, Beijing, 100048, China
| | - Xiong Deng
- College of Life Science, Capital Normal University, Beijing, 100048, China
| | - Yue Liu
- College of Life Science, Capital Normal University, Beijing, 100048, China
| | - Yueming Yan
- College of Life Science, Capital Normal University, Beijing, 100048, China.
- Hubei Collaborative Innovation Center for Grain Industry (HCICGI), Yangtze University, Jingzhou, 434025, China.
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15
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Zhu GR, Yan X, Zhu D, Deng X, Wu JS, Xia J, Yan YM. Lysine acetylproteome profiling under water deficit reveals key acetylated proteins involved in wheat grain development and starch biosynthesis. J Proteomics 2018; 185:8-24. [DOI: 10.1016/j.jprot.2018.06.019] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 06/06/2018] [Accepted: 06/18/2018] [Indexed: 01/17/2023]
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16
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Quantitative Phosphoproteomic Analysis Provides Insight into the Response to Short-Term Drought Stress in Ammopiptanthus mongolicus Roots. Int J Mol Sci 2017; 18:ijms18102158. [PMID: 29039783 PMCID: PMC5666839 DOI: 10.3390/ijms18102158] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 10/11/2017] [Accepted: 10/14/2017] [Indexed: 01/12/2023] Open
Abstract
Drought is one of the major abiotic stresses that negatively affects plant growth and development. Ammopiptanthus mongolicus is an ecologically important shrub in the mid-Asia desert region and used as a model for abiotic tolerance research in trees. Protein phosphorylation participates in the regulation of various biological processes, however, phosphorylation events associated with drought stress signaling and response in plants is still limited. Here, we conducted a quantitative phosphoproteomic analysis of the response of A. mongolicus roots to short-term drought stress. Data are available via the iProx database with project ID IPX0000971000. In total, 7841 phosphorylation sites were found from the 2019 identified phosphopeptides, corresponding to 1060 phosphoproteins. Drought stress results in significant changes in the abundance of 103 phosphopeptides, corresponding to 90 differentially-phosphorylated phosphoproteins (DPPs). Motif-x analysis identified two motifs, including [pSP] and [RXXpS], from these DPPs. Functional enrichment and protein-protein interaction analysis showed that the DPPs were mainly involved in signal transduction and transcriptional regulation, osmotic adjustment, stress response and defense, RNA splicing and transport, protein synthesis, folding and degradation, and epigenetic regulation. These drought-corresponsive phosphoproteins, and the related signaling and metabolic pathways probably play important roles in drought stress signaling and response in A. mongolicus roots. Our results provide new information for understanding the molecular mechanism of the abiotic stress response in plants at the posttranslational level.
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