1
|
Wang S, Chen L, Li S, Hu F. Uncovering proteome variations and concomitant quality changes of differently drying-treated rape (Brassica napus) bee pollen by label-free quantitative proteomics. Food Chem 2024; 434:137559. [PMID: 37748288 DOI: 10.1016/j.foodchem.2023.137559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 08/31/2023] [Accepted: 09/19/2023] [Indexed: 09/27/2023]
Abstract
High moisture content of fresh bee pollen makes it difficult to preserve and thus makes drying a necessary process during the bee pollen production. Drying treatment will affect its quality and the effects of sun drying, hot-air drying and freeze drying on the proteome of rape (Brassica napus) bee pollen have been evaluated using label-free quantitative proteomics by liquid chromatography-tandem mass spectrometer (LC-MS/MS). A total of 8377 proteins are identified, among which the most abundant differential proteins were found in freeze drying-treated samples. Also freeze-drying treatment maximizes the content of antioxidant, antibacterial and anemic bioactive pollen protein. Besides, rape bee pollen is found to adjust its metabolism to protect itself during the drying process. These results can be favorable to evaluate the effects of drying treatment on the nutrition and function of processed rape bee pollen and insight into how rape bee pollen proteins respond to dehydration.
Collapse
Affiliation(s)
- Shuyue Wang
- Key Laboratory of Silkworm and Bee Resource Utilization and Innovation of Zhejiang Province, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Liang Chen
- Key Laboratory of Silkworm and Bee Resource Utilization and Innovation of Zhejiang Province, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Shanshan Li
- Key Laboratory of Silkworm and Bee Resource Utilization and Innovation of Zhejiang Province, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Fuliang Hu
- Key Laboratory of Silkworm and Bee Resource Utilization and Innovation of Zhejiang Province, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China.
| |
Collapse
|
2
|
Singh V, Gupta K, Singh S, Jain M, Garg R. Unravelling the molecular mechanism underlying drought stress response in chickpea via integrated multi-omics analysis. FRONTIERS IN PLANT SCIENCE 2023; 14:1156606. [PMID: 37287713 PMCID: PMC10242046 DOI: 10.3389/fpls.2023.1156606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 04/18/2023] [Indexed: 06/09/2023]
Abstract
Drought stress affects growth and productivity significantly in chickpea. An integrated multi-omics analysis can provide a better molecular-level understanding of drought stress tolerance. In the present study, comparative transcriptome, proteome and metabolome analyses of two chickpea genotypes with contrasting responses to drought stress, ICC 4958 (drought-tolerant, DT) and ICC 1882 (drought-sensitive, DS), was performed to gain insights into the molecular mechanisms underlying drought stress response/tolerance. Pathway enrichment analysis of differentially abundant transcripts and proteins suggested the involvement of glycolysis/gluconeogenesis, galactose metabolism, and starch and sucrose metabolism in the DT genotype. An integrated multi-omics analysis of transcriptome, proteome and metabolome data revealed co-expressed genes, proteins and metabolites involved in phosphatidylinositol signaling, glutathione metabolism and glycolysis/gluconeogenesis pathways, specifically in the DT genotype under drought. These stress-responsive pathways were coordinately regulated by the differentially abundant transcripts, proteins and metabolites to circumvent the drought stress response/tolerance in the DT genotype. The QTL-hotspot associated genes, proteins and transcription factors may further contribute to improved drought tolerance in the DT genotype. Altogether, the multi-omics approach provided an in-depth understanding of stress-responsive pathways and candidate genes involved in drought tolerance in chickpea.
Collapse
Affiliation(s)
- Vikram Singh
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Khushboo Gupta
- Department of Life Sciences, Shiv Nadar Institution of Eminence, Gautam Buddha Nagar, Uttar Pradesh, India
| | - Shubhangi Singh
- Department of Life Sciences, Shiv Nadar Institution of Eminence, Gautam Buddha Nagar, Uttar Pradesh, India
| | - Mukesh Jain
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Rohini Garg
- Department of Life Sciences, Shiv Nadar Institution of Eminence, Gautam Buddha Nagar, Uttar Pradesh, India
| |
Collapse
|
3
|
Zhang C, Dong Y, Ren Y, Wang S, Yang M. Conjoint Analysis of Genome-Wide lncRNA and mRNA Expression during the Salicylic Acid Response in Populus × euramericana. PLANTS (BASEL, SWITZERLAND) 2023; 12:1377. [PMID: 36987064 PMCID: PMC10058947 DOI: 10.3390/plants12061377] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 03/09/2023] [Accepted: 03/17/2023] [Indexed: 06/19/2023]
Abstract
Long noncoding RNAs (lncRNAs) participate in a wide range of biological processes, but lncRNAs in plants remain largely unknown; in particular, we lack a systematic identification of plant lncRNAs involved in hormone responses. To explore the molecular mechanism of the response of poplar to salicylic acid (SA), the changes in protective enzymes, which are closely related to plant resistance induced by exogenous SA, were studied, and the expression of mRNA and lncRNA were determined by high-throughput RNA sequencing. The results showed that the activities of phenylalanine ammonia lyase (PAL) and polyphenol oxidase (PPO), in the leaves of Populus × euramericana, were significantly increased by exogenous SA application. High-throughput RNA sequencing showed that 26,366 genes and 5690 lncRNAs were detected under the different treatment conditions: SA and H2O application. Among these, 606 genes and 49 lncRNAs were differentially expressed. According to target prediction, lncRNAs and target genes involved in light response, stress response, plant disease resistance, and growth and development, were differentially expressed in SA-treated leaves. Interaction analysis showed that lncRNA-mRNA interactions, following exogenous SA, were involved in the response of poplar leaves to the external environment. Our study provides a comprehensive view of Populus × euramericana lncRNAs and offers insights into the potential functions and regulatory interactions of SA-responsive lncRNAs, thus forming the foundation for future functional analysis of SA-responsive lncRNAs in Populus × euramericana.
Collapse
Affiliation(s)
- Chao Zhang
- Forest Department, Forestry College, Hebei Agricultural University, Baoding 071000, China
- Hebei Key Laboratory for Tree Genetic Resources and Forest Protection, Baoding 071000, China
| | - Yan Dong
- Forest Department, Forestry College, Hebei Agricultural University, Baoding 071000, China
- Hebei Key Laboratory for Tree Genetic Resources and Forest Protection, Baoding 071000, China
| | - Yachao Ren
- Forest Department, Forestry College, Hebei Agricultural University, Baoding 071000, China
- Hebei Key Laboratory for Tree Genetic Resources and Forest Protection, Baoding 071000, China
| | - Shijie Wang
- Forest Department, Forestry College, Hebei Agricultural University, Baoding 071000, China
- Hebei Key Laboratory for Tree Genetic Resources and Forest Protection, Baoding 071000, China
| | - Minsheng Yang
- Forest Department, Forestry College, Hebei Agricultural University, Baoding 071000, China
- Hebei Key Laboratory for Tree Genetic Resources and Forest Protection, Baoding 071000, China
| |
Collapse
|
4
|
Hao Z, Tan Y, Feng J, Lin H, Sun Z, Zhuang JY, Chen Q, Jin X, Sun Y. Integrated metabolomic and transcriptomic analysis reveal the effect of mechanical stress on sugar metabolism in tea leaves ( Camellia sinensis) post-harvest. PeerJ 2023; 11:e14869. [PMID: 36785711 PMCID: PMC9921968 DOI: 10.7717/peerj.14869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 01/18/2023] [Indexed: 02/11/2023] Open
Abstract
Sugar metabolites not only act as the key compounds in tea plant response to stress but are also critical for tea quality formation during the post-harvest processing of tea leaves. However, the mechanisms by which sugar metabolites in post-harvest tea leaves respond to mechanical stress are unclear. In this study, we aimed to investigate the effects of mechanical stress on saccharide metabolites and related post-harvest tea genes. Withered (C15) and mechanically-stressed (V15) for 15 min Oolong tea leaves were used for metabolome and transcriptome sequencing analyses. We identified a total of 19 sugar metabolites, most of which increased in C15 and V15. A total of 69 genes related to sugar metabolism were identified using transcriptome analysis, most of which were down-regulated in C15 and V15. To further understand the relationship between the down-regulated genes and sugar metabolites, we analyzed the sucrose and starch, galactose, and glycolysis metabolic pathways, and found that several key genes of invertase (INV), α-amylase (AMY), β-amylase (BMY), aldose 1-epimerase (AEP), and α-galactosidase (AGAL) were down-regulated. This inhibited the hydrolysis of sugars and might have contributed to the enrichment of galactose and D-mannose in V15. Additionally, galactinol synthase (Gols), raffinose synthase (RS), hexokinase (HXK), 6-phosphofructokinase 1 (PFK-1), and pyruvate kinase (PK) genes were significantly upregulated in V15, promoting the accumulation of D-fructose-6-phosphate (D-Fru-6P), D-glucose-6-phosphate (D-glu-6P), and D-glucose. Transcriptome and metabolome association analysis showed that the glycolysis pathway was enhanced and the hydrolysis rate of sugars related to hemicellulose synthesis slowed in response to mechanical stress. In this study, we explored the role of sugar in the response of post-harvest tea leaves to mechanical stress by analyzing differences in the expression of sugar metabolites and related genes. Our results improve the understanding of post-harvest tea's resistance to mechanical stress and the associated mechanism of sugar metabolism. The resulting treatment may be used to control the quality of Oolong tea.
Collapse
|
5
|
Morin A, Maurousset L, Vriet C, Lemoine R, Doidy J, Pourtau N. Carbon fluxes and environmental interactions during legume development, with a specific focus on Pisum sativum. PHYSIOLOGIA PLANTARUM 2022; 174:e13729. [PMID: 35662039 PMCID: PMC9328368 DOI: 10.1111/ppl.13729] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 05/25/2022] [Accepted: 06/01/2022] [Indexed: 06/15/2023]
Abstract
Grain legumes are major food crops cultivated worldwide for their seeds with high nutritional content. To answer the growing concern about food safety and protein autonomy, legume cultivation must increase in the coming years. In parallel, current agricultural practices are facing environmental challenges, including global temperature increase and more frequent and severe episodes of drought stress. Crop yield directly relies on carbon allocation and is particularly affected by these global changes. We review the current knowledge on source-sink relationships and carbon resource allocation at all developmental stages, from germination to vegetative growth and seed production in grain legumes, focusing on pea (Pisum sativum). We also discuss how these source-sink relationships and carbon fluxes are influenced by biotic and abiotic factors. Major agronomic traits, including seed yield and quality, are particularly impacted by drought, temperatures, salinity, waterlogging, or pathogens and can be improved through the promotion of beneficial soil microorganisms or through optimized plant carbon resource allocation. Altogether, our review highlights the need for a better understanding of the cellular and molecular mechanisms regulating carbon fluxes from source leaves to sink organs, roots, and seeds. These advancements will further improve our understanding of yield stability and stress tolerance and contribute to the selection of climate-resilient crops.
Collapse
Affiliation(s)
- Amélie Morin
- Université de Poitiers, UMR CNRS 7267, EBI "Ecologie et Biologie des Interactions"PoitiersFrance
| | - Laurence Maurousset
- Université de Poitiers, UMR CNRS 7267, EBI "Ecologie et Biologie des Interactions"PoitiersFrance
| | - Cécile Vriet
- Université de Poitiers, UMR CNRS 7267, EBI "Ecologie et Biologie des Interactions"PoitiersFrance
| | - Rémi Lemoine
- Université de Poitiers, UMR CNRS 7267, EBI "Ecologie et Biologie des Interactions"PoitiersFrance
| | - Joan Doidy
- Université de Poitiers, UMR CNRS 7267, EBI "Ecologie et Biologie des Interactions"PoitiersFrance
| | - Nathalie Pourtau
- Université de Poitiers, UMR CNRS 7267, EBI "Ecologie et Biologie des Interactions"PoitiersFrance
| |
Collapse
|
6
|
Effects of the Chloroplast Fructose-1,6-Bisphosphate Aldolase Gene on Growth and Low-Temperature Tolerance of Tomato. Int J Mol Sci 2022; 23:ijms23020728. [PMID: 35054921 PMCID: PMC8775715 DOI: 10.3390/ijms23020728] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 12/29/2021] [Accepted: 01/05/2022] [Indexed: 01/27/2023] Open
Abstract
Tomato (Solanum lycopersicum) is one of the most important greenhouse vegetables, with a large cultivated area across the world. However, in northern China, tomato plants often suffer from low-temperature stress in solar greenhouse cultivation, which affects plant growth and development and results in economic losses. We previously found that a chloroplast aldolase gene in tomato, SlFBA4, plays an important role in the Calvin-Benson cycle (CBC), and its expression level and activity can be significantly altered when subjected to low-temperature stress. To further study the function of SlFBA4 in the photosynthesis and chilling tolerance of tomato, we obtained transgenic tomato plants by the over-expression and RNA interference (RNAi) of SlFBA4. The over-expression of SlFBA4 led to higher fructose-1,6-bisphosphate aldolase activity, net photosynthetic rate (Pn) and activity of other enzymes in the CBC than wild type. Opposite results were observed in the RNAi lines. Moreover, an increase in thousand-seed weight, plant height, stem diameter and germination rate in optimal and sub-optimal temperatures was observed in the over-expression lines, while opposite effects were observed in the RNAi lines. Furthermore, over-expression of SlFBA4 increased Pn and enzyme activity and decreased malonaldehyde (MDA) content under chilling conditions. On the other hand, Pn and MDA content were more severely influenced by chilling stress in the RNAi lines. These results indicate that SlFBA4 plays an important role in tomato growth and tolerance to chilling stress.
Collapse
|
7
|
San-Eufrasio B, Castillejo MÁ, Labella-Ortega M, Ruiz-Gómez FJ, Navarro-Cerrillo RM, Tienda-Parrilla M, Jorrín-Novo JV, Rey MD. Effect and Response of Quercus ilex subsp. ballota [Desf.] Samp. Seedlings From Three Contrasting Andalusian Populations to Individual and Combined Phytophthora cinnamomi and Drought Stresses. FRONTIERS IN PLANT SCIENCE 2021; 12:722802. [PMID: 34490021 PMCID: PMC8417417 DOI: 10.3389/fpls.2021.722802] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 07/22/2021] [Indexed: 05/09/2023]
Abstract
Quercus ilex L. is the dominant species in the Mediterranean forest and agrosilvopastoral ecosystem "dehesa." Currently, this forest species is threatened by natural and anthropogenic agents, especially by the decline syndrome, which is caused by Phytophthora cinnamomi and drought periods. Although the morphological and physiological responses of Q. ilex to combined stress (P. cinnamomi and drought) have been examined already, little is known at the molecular level. In this study, we studied the effect and response of 8-month seedlings from three contrasting Andalusian populations (Seville [Se], Granada [Gr], and Almeria [Al]) to the individual and combined stresses of P. cinnamomi and drought from morphological, physiological, biochemical, and proteomics data. Whereas, seedling damage (leaf chlorosis and necrosis) and mortality were greater under the combined stresses in the three populations, the effect of each individual stress was population-dependent. Resilient individuals were found in all the populations at different percentages. The decrease in leaf chlorophyll fluorescence, photosynthetic activity, and stomatal conductance observed in undamaged seedlings was greater in the presence of both stresses, the three populations responding similarly to drought and P. cinnamomi. Biochemical and proteomic analyses of undamaged seedlings from the two most markedly contrasting populations (Se and Al) revealed the absence of significant differences in the contents in photosynthetic pigments, amino acids, and phenolics among treatments. The Se and Al populations exhibited changes in protein profile in response to the different treatments, with 83 variable proteins in the former population and 223 in the latter. Variable proteins belonged to 16 different functional groups, the best represented among which were protein folding, sorting and degradation, carbohydrate, amino acid, and secondary metabolism, photosynthesis, and ROS scavenging. While photosynthetic proteins were mainly downaccumulated, those of stress-responsive were upaccumulated. Although no treatment-specific response was observed in any functional group, differences in abundance were especially marked under the combined stresses. The following variable proteins are proposed as putative markers for resilience in Q. ilex, namely, aldehyde dehydrogenase, glucose-6-phosphate isomerase, 50S ribosomal protein L5, and α-1,4-glucan-protein synthase [UDP-forming].
Collapse
Affiliation(s)
- Bonoso San-Eufrasio
- Agroforestry and Plant Biochemistry, Proteomics and Systems Biology, Department of Biochemistry and Molecular Biology, University of Córdoba, Córdoba, Spain
| | - María Ángeles Castillejo
- Agroforestry and Plant Biochemistry, Proteomics and Systems Biology, Department of Biochemistry and Molecular Biology, University of Córdoba, Córdoba, Spain
| | - Mónica Labella-Ortega
- Agroforestry and Plant Biochemistry, Proteomics and Systems Biology, Department of Biochemistry and Molecular Biology, University of Córdoba, Córdoba, Spain
| | - Francisco J. Ruiz-Gómez
- Evaluation and Restoration of Agronomic and Forest Systems ERSAF, Department of Forest Engineering, University of Córdoba, Córdoba, Spain
| | - Rafael M. Navarro-Cerrillo
- Evaluation and Restoration of Agronomic and Forest Systems ERSAF, Department of Forest Engineering, University of Córdoba, Córdoba, Spain
| | - Marta Tienda-Parrilla
- Agroforestry and Plant Biochemistry, Proteomics and Systems Biology, Department of Biochemistry and Molecular Biology, University of Córdoba, Córdoba, Spain
| | - Jesús V. Jorrín-Novo
- Agroforestry and Plant Biochemistry, Proteomics and Systems Biology, Department of Biochemistry and Molecular Biology, University of Córdoba, Córdoba, Spain
| | - María-Dolores Rey
- Agroforestry and Plant Biochemistry, Proteomics and Systems Biology, Department of Biochemistry and Molecular Biology, University of Córdoba, Córdoba, Spain
| |
Collapse
|
8
|
Li ZQ, Zhang Y, Li H, Su TT, Liu CG, Han ZC, Wang AY, Zhu JB. Genome-Wide Characterization and Expression Analysis Provide Basis to the Biological Function of Cotton FBA Genes. FRONTIERS IN PLANT SCIENCE 2021; 12:696698. [PMID: 34490001 PMCID: PMC8416763 DOI: 10.3389/fpls.2021.696698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 07/30/2021] [Indexed: 06/13/2023]
Abstract
Fructose-1,6-biphosphate aldolase (FBA) is a multifunctional enzyme in plants, which participates in the process of Calvin-Benson cycle, glycolysis and gluconeogenesis. Despite the importance of FBA genes in regulating plant growth, development and abiotic stress responses, little is known about their roles in cotton. In the present study, we performed a genome-wide identification and characterization of FBAs in Gossypium hirsutum. Totally seventeen GhFBA genes were identified. According to the analysis of functional domain, phylogenetic relationship, and gene structure, GhFBA genes were classified into two subgroups. Furthermore, nine GhFBAs were predicted to be in chloroplast and eight were located in cytoplasm. Moreover, the promoter prediction showed a variety of abiotic stresses and phytohormone related cis-acting elements exist in the 2k up-stream region of GhFBA. And the evolutionary characteristics of cotton FBA genes were clearly presented by synteny analysis. Moreover, the results of transcriptome and qRT-PCR analysis showed that the expression of GhFBAs were related to the tissue distribution, and further analysis suggested that GhFBAs could respond to various abiotic stress and phytohormonal treatments. Overall, our systematic analysis of GhFBA genes would not only provide a basis for the understanding of the evolution of GhFBAs, but also found a foundation for the further function analysis of GhFBAs to improve cotton yield and environmental adaptability.
Collapse
|
9
|
Ling N, Li W, Xu G, Qi Z, Ji C, Liu X, Cui D, Sun Y. Transcriptomic sequencing reveals the response of Dunaliella salina to copper stress via the increased photosynthesis and carbon mechanism. Mol Omics 2021; 17:769-782. [PMID: 34254634 DOI: 10.1039/d1mo00125f] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Copper (Cu) is one of the essential microelements for plants and algae. It can stimulate growth and photosynthesis at low concentration but inhibit them at higher concentration. The knowledge of molecular response mechanisms to copper stress in green algae is still limited. The responses of the green algae Dunaliella salina to Cu stress were studied using the physiochemical indexes and RNA-seq analysis. The physiochemical indexes such as growth rate, the content of chlorophyll and soluble sugar, photosynthesis and peroxidase activity were all changed in D. salina under Cu stress. In addition, a total of 3799 differentially expressed genes (DEGs) were identified between the control and Cu-treated group. Among these, 2350 unigenes were up-regulated whereas 1449 were down-regulated. Here, the DEGs encoding proteins relevant to photosynthesis, carbon assimilation and carbohydrate mechanism were significantly up-regulated in the Cu-treated group. In addition, the unigenes encoding proteins involved in the antioxidant system and heat shock proteins were also up-regulated, and these were consistent with the expression patterns based on TPM (transcripts per million) values. This study shows that the enhanced growth and photosynthesis and carbon mechanism in D. salina can be triggered by copper, which will lay a firm foundation for future breeding and carotenoid production, further highlighting the underlying application of D. salina as a functional food.
Collapse
Affiliation(s)
- Na Ling
- Engineering Research Center for Natural Anticancer Drugs, Ministry of Education, Harbin University of Commerce, Harbin, Heilongjiang 150076, China. and Engineering Research Center for Medicines, Harbin University of Commerce, Harbin, Heilongjiang 150076, China.
| | - Weilu Li
- Engineering Research Center for Natural Anticancer Drugs, Ministry of Education, Harbin University of Commerce, Harbin, Heilongjiang 150076, China.
| | - Guiguo Xu
- Engineering Research Center for Natural Anticancer Drugs, Ministry of Education, Harbin University of Commerce, Harbin, Heilongjiang 150076, China.
| | - Zheng Qi
- Engineering Research Center for Natural Anticancer Drugs, Ministry of Education, Harbin University of Commerce, Harbin, Heilongjiang 150076, China. and Engineering Research Center for Medicines, Harbin University of Commerce, Harbin, Heilongjiang 150076, China.
| | - Chenfeng Ji
- Engineering Research Center for Natural Anticancer Drugs, Ministry of Education, Harbin University of Commerce, Harbin, Heilongjiang 150076, China. and Engineering Research Center for Medicines, Harbin University of Commerce, Harbin, Heilongjiang 150076, China.
| | - Xiaorui Liu
- Engineering Research Center for Natural Anticancer Drugs, Ministry of Education, Harbin University of Commerce, Harbin, Heilongjiang 150076, China.
| | - Di Cui
- Engineering Research Center for Natural Anticancer Drugs, Ministry of Education, Harbin University of Commerce, Harbin, Heilongjiang 150076, China.
| | - Yuan Sun
- Engineering Research Center for Natural Anticancer Drugs, Ministry of Education, Harbin University of Commerce, Harbin, Heilongjiang 150076, China. and Engineering Research Center for Medicines, Harbin University of Commerce, Harbin, Heilongjiang 150076, China.
| |
Collapse
|
10
|
Moosavi SS, Abdi F, Abdollahi MR, Tahmasebi-Enferadi S, Maleki M. Phenological, morpho-physiological and proteomic responses of Triticum boeoticum to drought stress. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2020; 156:95-104. [PMID: 32920225 DOI: 10.1016/j.plaphy.2020.08.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Revised: 07/27/2020] [Accepted: 08/05/2020] [Indexed: 06/11/2023]
Abstract
Drought is the most important abiotic stress limiting wheat production worldwide. Triticum boeoticum, as wild wheat, is a rich gene pool for breeding for drought stress tolerance. In this study, to identify the most drought-tolerant and susceptible genotypes, ten T. boeoticum accessions were evaluated under non-stress and drought-stress conditions for two years. Among the studied traits, water-use efficiency (WUE) was suggested as the most important trait to identify drought-tolerant genotypes. According to the desirable and undesirable areas of the bi-plot, Tb5 and Tb6 genotypes were less and more affected by drought stress, respectively. Therefore, their flag-leaves proteins were used for two-dimensional gel electrophoresis. While, Tb5 contained a high amount of yield, yield components, and WUE, Tb6 had higher levels of water use, phenological related traits, and root related characters. Of the 235 spots found in the studied accessions, 14 spots (11 and 3 spots of Tb5 and Tb6, respectively) were selected for sequencing. Of these 14 spots, 9 and 5 spots were upregulated and downregulated, respectively. The identified proteins were grouped into six functional protein clusters, which were mainly involved in photosynthesis (36%), carbohydrate metabolism (29%), chaperone (7%), oxidation and reduction (7%), lipid metabolism and biological properties of the membrane (7%) and unknown function (14%). We report for the first time that MICP, in the group of lipid metabolism proteins, was significantly changed into wild wheat in response to drought stress. Maybe, the present-identified proteins could play an important role to understand the molecular pathways of wheat drought tolerance. We believe comparing and evaluating the similarity-identified proteins of T. boeoticum with the previously identified proteins of Aegilops tauschii, can provide a new direction to improve wheat tolerance to drought stress.
Collapse
Affiliation(s)
- Sayyed Saeed Moosavi
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, Bu-Ali Sina University, Hamedan, Iran.
| | - Fatemeh Abdi
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, Bu-Ali Sina University, Hamedan, Iran
| | - Mohammad Reza Abdollahi
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, Bu-Ali Sina University, Hamedan, Iran
| | - Sattar Tahmasebi-Enferadi
- Department of Molecular Plant Biotechnology, Faculty of Agricultural Biotechnology, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran
| | - Mahmood Maleki
- Department of Biotechnology, Institute of Science and High Technology and Environmental Science, Graduate University of Advanced Technology, Kerman, Iran
| |
Collapse
|
11
|
Grabsztunowicz M, Rokka A, Farooq I, Aro EM, Mulo P. Gel-based proteomic map of Arabidopsis thaliana root plastids and mitochondria. BMC PLANT BIOLOGY 2020; 20:413. [PMID: 32887556 PMCID: PMC7650296 DOI: 10.1186/s12870-020-02635-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 08/30/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND Non-photosynthetic plastids of plants are known to be involved in a range of metabolic and biosynthetic reactions, even if they have been difficult to study due to their small size and lack of color. The morphology of root plastids is heterogeneous and also the plastid size, density and subcellular distribution varies depending on the cell type and developmental stage, and therefore the functional features have remained obscure. Although the root plastid proteome is likely to reveal specific functional features, Arabidopsis thaliana root plastid proteome has not been studied to date. RESULTS In the present study, we separated Arabidopsis root protein fraction enriched with plastids and mitochondria by 2D-PAGE and identified 84 plastid-targeted and 77 mitochondrion-targeted proteins using LC-MS/MS. The most prevalent root plastid protein categories represented amino acid biosynthesis, carbohydrate metabolism and lipid biosynthesis pathways, while the enzymes involved in starch and sucrose metabolism were not detected. Mitochondrion-targeted proteins were classified mainly into the energetics category. CONCLUSIONS This is the first study presenting gel-based map of Arabidopsis thaliana root plastid and mitochondrial proteome. Our findings suggest that Arabidopsis root plastids have broad biosynthetic capacity, and that they do not play a major role in a long-term storage of carbohydrates. The proteomic map provides a tool for further studies to compare changes in the proteome, e.g. in response to environmental cues, and emphasizes the role of root plastids in nitrogen and sulfur metabolism as well as in amino acid and fatty acid biosynthesis. The results enable taking a first step towards an integrated view of root plastid/mitochondrial proteome and metabolic functions in Arabidopsis thaliana roots.
Collapse
Affiliation(s)
| | - Anne Rokka
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520, Turku, Finland
| | - Irum Farooq
- Molecular Plant Biology, University of Turku, 20520, Turku, Finland
| | - Eva-Mari Aro
- Molecular Plant Biology, University of Turku, 20520, Turku, Finland
| | - Paula Mulo
- Molecular Plant Biology, University of Turku, 20520, Turku, Finland.
| |
Collapse
|
12
|
Shokat S, Großkinsky DK, Roitsch T, Liu F. Activities of leaf and spike carbohydrate-metabolic and antioxidant enzymes are linked with yield performance in three spring wheat genotypes grown under well-watered and drought conditions. BMC PLANT BIOLOGY 2020; 20:400. [PMID: 32867688 PMCID: PMC7457523 DOI: 10.1186/s12870-020-02581-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 07/27/2020] [Indexed: 05/08/2023]
Abstract
BACKGROUND To improve our understanding about the physiological mechanism of grain yield reduction at anthesis, three spring wheat genotypes [L1 (advanced line), L2 (Vorobey) and L3 (Punjab-11)] having contrasting yield potential under drought in field were investigated under controlled greenhouse conditions, drought stress was imposed at anthesis stage by withholding irrigation until all plant available water was depleted, while well-watered control plants were kept at 95% pot water holding capacity. RESULTS Compared to genotype L1 and L2, pronounced decrease in grain number (NGS), grain yield (GY) and harvest index (HI) were found in genotype L3, mainly due to its greater kernel abortion (KA) under drought. A significant positive correlation of leaf monodehydroascorbate reductase (MDHAR) with both NGS and HI was observed. In contrast, significant negative correlations of glutathione S-transferase (GST) and vacuolar invertase (vacInv) both within source and sink were found with NGS and HI. Likewise, a significant negative correlation of leaf abscisic acid (ABA) with NGS was noticed. Moreover, leaf aldolase and cell wall peroxidase (cwPOX) activities were significantly and positively associated with thousand kernel weight (TKW). CONCLUSION Distinct physiological markers correlating with yield traits and higher activity of leaf aldolase and cwPOX may be chosen as predictive biomarkers for higher TKW. Also, higher activity of MDHAR within the leaf can be selected as a predictive biomarker for higher NGS in wheat under drought. Whereas, lower activity of vacInv and GST both within leaf and spike can be selected as biomarkers for higher NGS and HI. The results highlighted the role of antioxidant and carbohydrate-metabolic enzymes in the modulation of source-sink balance in wheat crops, which could be used as bio-signatures for breeding and selection of drought-resilient wheat genotypes for a future drier climate.
Collapse
Affiliation(s)
- Sajid Shokat
- Crop Science, Department of Plant and Environmental Sciences, University of Copenhagen, Højbakkegård Allé 13, 2630, Taastrup, Denmark.
- Wheat Breeding Group, Plant Breeding and Genetic Division, Nuclear Institute for Agriculture and Biology, Faisalabad, 38000, Pakistan.
| | - Dominik K Großkinsky
- Transport Biology, Department of Plant and Environmental Sciences, Copenhagen Plant Science Centre, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark
- AIT Austrian Institute of Technology GmbH, Center for Health and Bioresources, Bioresources Unit, Konrad-Lorenz-Straße 24, 3430, Tulln, Austria
| | - Thomas Roitsch
- Crop Science, Department of Plant and Environmental Sciences, University of Copenhagen, Højbakkegård Allé 13, 2630, Taastrup, Denmark
| | - Fulai Liu
- Crop Science, Department of Plant and Environmental Sciences, University of Copenhagen, Højbakkegård Allé 13, 2630, Taastrup, Denmark
| |
Collapse
|
13
|
Olalde-Portugal V, Cabrera-Ponce JL, Gastelum-Arellanez A, Guerrero-Rangel A, Winkler R, Valdés-Rodríguez S. Proteomic analysis and interactions network in leaves of mycorrhizal and nonmycorrhizal sorghum plants under water deficit. PeerJ 2020; 8:e8991. [PMID: 32351787 PMCID: PMC7183753 DOI: 10.7717/peerj.8991] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 03/26/2020] [Indexed: 11/21/2022] Open
Abstract
For understanding the water deficit stress mechanism in sorghum, we conducted a physiological and proteomic analysis in the leaves of Sorghum bicolor L. Moench (a drought tolerant crop model) of non-colonized and colonized plants with a consortium of arbuscular mycorrhizal fungi. Physiological results indicate that mycorrhizal fungi association enhances growth and photosynthesis in plants, under normal and water deficit conditions. 2D-electrophoresis profiles revealed 51 differentially accumulated proteins in response to water deficit, of which HPLC/MS successfully identified 49. Bioinformatics analysis of protein–protein interactions revealed the participation of different metabolic pathways in nonmycorrhizal compared to mycorrhizal sorghum plants under water deficit. In noninoculated plants, the altered proteins are related to protein synthesis and folding (50S ribosomal protein L1, 30S ribosomal protein S10, Nascent polypeptide-associated complex subunit alpha), coupled with multiple signal transduction pathways, guanine nucleotide-binding beta subunit (Rack1) and peptidyl-prolyl-cis-trans isomerase (ROC4). In contrast, in mycorrhizal plants, proteins related to energy metabolism (ATP synthase-24kDa, ATP synthase β), carbon metabolism (malate dehydrogenase, triosephosphate isomerase, sucrose-phosphatase), oxidative phosphorylation (mitochondrial-processing peptidase) and sulfur metabolism (thiosulfate/3-mercaptopyruvate sulfurtransferase) were found. Our results provide a set of proteins of different metabolic pathways involved in water deficit produced by sorghum plants alone or associated with a consortium of arbuscular mycorrhizal fungi isolated from the tropical rain forest Los Tuxtlas Veracruz, México.
Collapse
Affiliation(s)
- Víctor Olalde-Portugal
- Departamento de Biotecnología y Bioquímica, Centro de Investigación y de Estudios Avanzados del IPN-Unidad Irapuato, Irapuato, Guanajuato, México
| | - José Luis Cabrera-Ponce
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del IPN-Unidad Irapuato, Irapuato, Guanajuato, México
| | - Argel Gastelum-Arellanez
- Área de Medio Ambiente y Biotecnología, Cátedra CONACYT. Centro de Innovación Aplicada en Tecnologías Competitivas A.C. (CIATEC AC), León, Guanajuato, México
| | - Armando Guerrero-Rangel
- Departamento de Biotecnología y Bioquímica, Centro de Investigación y de Estudios Avanzados del IPN-Unidad Irapuato, Irapuato, Guanajuato, México
| | - Robert Winkler
- Departamento de Biotecnología y Bioquímica, Centro de Investigación y de Estudios Avanzados del IPN-Unidad Irapuato, Irapuato, Guanajuato, México
| | - Silvia Valdés-Rodríguez
- Departamento de Biotecnología y Bioquímica, Centro de Investigación y de Estudios Avanzados del IPN-Unidad Irapuato, Irapuato, Guanajuato, México
| |
Collapse
|
14
|
Li Q, Jin C, Wang G, Ji J, Guan C, Li X. Enhancement of endogenous SA accumulation improves poor-nutrition stress tolerance in transgenic tobacco plants overexpressing a SA-binding protein gene. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 292:110384. [PMID: 32005389 DOI: 10.1016/j.plantsci.2019.110384] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 12/13/2019] [Accepted: 12/16/2019] [Indexed: 05/12/2023]
Abstract
Salicylic acid (SA) plays an important role in the response of plants to abiotic stresses. Starvation stress affects plant cell metabolic activities, which further limits the normal growth and development of plants. It was reported that SA might play a regulatory role in the process of plant against starvation stress, but the mechanism involved in this process is still unclear. Thus, in this study, the transgenic plants overexpressing a SA binding protein 2 (SABP2) gene were exposed to starvation stress and the transgenic lines showed starvation-tolerant phenotype. Compared with wild-type (WT) plants, transgenic plants showed better growth status under poor-nutrition stress. Transgenic plants also showed more vigorous roots than WT plants. Physiological tests indicated that the transgenic plants showed higher relative water content (RWC), chlorophyll content, photosynthetic capacity, endogenous SA content, and lower ROS level compared to WT plants. Transcriptome analysis of tobacco plants identified 3, 748 differentially expressed genes (DEGs) between transgenic and WT plants under starvation stress. These DEGs are mainly involved in glycolysis/gluconeogenesis pathway group, MAPK signaling pathway group and plant hormone signal transduction pathway group. As determined by qPCR, up-regulated expression of fifteen genes such as abscisic acid receptor PYR1-like gene (NtPYR1-like), bidirectional sugar transporter N3-like gene (NtSWEETN3-like) and superoxide dismutase [Fe] chloroplastic-like gene (NtFeSOD-like), etc., was observed in transgenic plants under poor-nutrition stress which was in accordance with RNA-sequencing results. The modified pathways involved in plant hormone signaling are thought to be at least one of the main causes of the increased starvation tolerance of transgenic tobacco plants with altered SA homeostasis.
Collapse
Affiliation(s)
- Qian Li
- School of Environmental Science and Engineering, Tianjin University, Tianjin, 300072, China
| | - Chao Jin
- School of Environmental Science and Engineering, Tianjin University, Tianjin, 300072, China
| | - Gang Wang
- School of Environmental Science and Engineering, Tianjin University, Tianjin, 300072, China
| | - Jing Ji
- School of Environmental Science and Engineering, Tianjin University, Tianjin, 300072, China
| | - Chunfeng Guan
- School of Environmental Science and Engineering, Tianjin University, Tianjin, 300072, China.
| | - Xiaozhou Li
- Tianjin Prenatal Diagnosis Center, Department of Gynecology and Obstetrics, Tianjin Medical University General Hospital, Tianjin, 300070, China.
| |
Collapse
|
15
|
Liu ZJ, Zhang YH, Ma XF, Ye P, Gao F, Li XF, Zhou YJ, Shi ZH, Cheng HM, Zheng CX, Li HJ, Zhang GF. Biological functions of Arabidopsis thaliana MBP-1-like protein encoded by ENO2 in the response to drought and salt stresses. PHYSIOLOGIA PLANTARUM 2020; 168:660-674. [PMID: 31343741 DOI: 10.1111/ppl.13013] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Revised: 06/21/2019] [Accepted: 07/16/2019] [Indexed: 06/10/2023]
Abstract
Arabidopsis thaliana ENO2 (AtENO2) plays an important role in plant growth and development. It encodes two proteins, a full-length AtENO2 and a truncated version, AtMBP-1, alternatively translated from the second start codon of the mRNA. The AtENO2 mutant (eno2- ) exhibited reduced leaf size, shortened siliques, a dwarf phenotype and higher sensitivity to abiotic stress. The objectives of this study were to analyze the regulatory network of the ENO2 gene in plant growth development and understand the function of AtENO2/AtMBP-1 to abiotic stresses. An eno2- /35S:AtENO2-GFP line and an eno2- /35S:AtMBP-1-GFP line of Arabidopsis were obtained. Results of sequencing by 454 GS FLX identified 578 upregulated and 720 downregulated differential expressed genes (DEGs) in a pairwise comparison (WT-VS-eno2- ). All the high-quality reads were annotated using the Gene Ontology (GO) terms. The DEGs with KEGG pathway annotations occurred in 110 pathways. The metabolic pathways and biosynthesis of secondary metabolites contained more DEGs. Moreover, the eno2- /35S:AtENO2-GFP line returned to the wild-type (WT) phenotype and was tolerant to drought and salt stresses. However, the eno2- /35S:AtMBP-1-GFP line was not able to recover the WT phenotype but it has a higher tolerance to drought and salt stresses. Results from this study demonstrate that AtENO2 is critical for the growth and development, and the AtMBP-1 coded by AtENO2 is important in tolerance of Arabidopsis to abiotic stresses.
Collapse
Affiliation(s)
- Zi-Jin Liu
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Yong-Hua Zhang
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Xiao-Feng Ma
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Pan Ye
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Fei Gao
- College of Life and Environmental Sciences, Minzu University of China, Beijing, 100081, China
| | - Xiao-Feng Li
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Yi-Jun Zhou
- College of Life and Environmental Sciences, Minzu University of China, Beijing, 100081, China
| | - Zi-Han Shi
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Hui-Mei Cheng
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Chao-Xing Zheng
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Hong-Jie Li
- The National Engineering Laboratory of Crop Molecular Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Gen-Fa Zhang
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| |
Collapse
|
16
|
A TMT-Based Quantitative Proteome Analysis to Elucidate the TSWV Induced Signaling Cascade in Susceptible and Resistant Cultivars of Solanum lycopersicum. PLANTS 2020; 9:plants9030290. [PMID: 32110948 PMCID: PMC7154910 DOI: 10.3390/plants9030290] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Revised: 02/22/2020] [Accepted: 02/22/2020] [Indexed: 01/12/2023]
Abstract
Tomato spotted wilt virus (TSWV), transmitted by small insects known as thrips, is one of the major threats to tomato productivity across the globe. In addition to tomato, this virus infects more than 1000 other plants belonging to 85 families and is a cause of serious concern. Very little, however, is known about the molecular mechanism of TSWV induced signaling in plants. Here, we used a tandem mass tags (TMT)-based quantitative proteome approach to investigate the protein profiles of tomato leaves of two cultivars (cv 2621 and 2689; susceptible and resistant to TSWV infection, respectively) following TSWV inoculation. This approach resulted in the identification of 5112 proteins of which 1022 showed significant changes in response to TSWV. While the proteome of resistant cultivar majorly remains unaltered, the proteome of susceptible cultivar showed distinct differences following TSWV inoculation. TSWV modulated proteins in tomato included those with functions previously implicated in plant defense including secondary metabolism, reactive oxygen species (ROS) detoxification, mitogen-activated protein (MAP) kinase signaling, calcium signaling and jasmonate biosynthesis, among others. Taken together, results reported here provide new insights into the TSWV induced signaling in tomato leaves and may be useful in the future to manage this deadly disease of plants.
Collapse
|
17
|
Lu Q, Meng X, Yang F, Liu X, Cui J. Characterization of LcGAPC and its transcriptional response to salt and alkali stress in two ecotypes of Leymus chinensis (Trin.) Tzvelev. BIOTECHNOL BIOTEC EQ 2020. [DOI: 10.1080/13102818.2020.1719020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Affiliation(s)
- Qian Lu
- College of Life Science and Technology, Harbin Normal University, Harbin, PR China
| | - Xue Meng
- College of Life Science and Technology, Harbin Normal University, Harbin, PR China
| | - Fanghui Yang
- College of Life Science and Technology, Harbin Normal University, Harbin, PR China
| | - Xin Liu
- College of Life Science and Technology, Harbin Normal University, Harbin, PR China
| | - Jizhe Cui
- College of Life Science and Technology, Harbin Normal University, Harbin, PR China
| |
Collapse
|
18
|
Zhao W, Liu H, Zhang L, Hu Z, Liu J, Hua W, Xu S, Liu J. Genome-Wide Identification and Characterization of FBA Gene Family in Polyploid Crop Brassica napus. Int J Mol Sci 2019; 20:E5749. [PMID: 31731804 PMCID: PMC6888112 DOI: 10.3390/ijms20225749] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 11/14/2019] [Accepted: 11/14/2019] [Indexed: 12/31/2022] Open
Abstract
Fructose-1,6-bisphosphate aldolase (FBA) is a versatile metabolic enzyme involved in multiple important processes of glycolysis, gluconeogenesis, and Calvin cycle. Despite its significance in plant biology, the identity of this gene family in oil crops is lacking. Here, we performed genome-wide identification and characterization of FBAs in an allotetraploid species, oilseed rape Brassica napus. Twenty-two BnaFBA genes were identified and divided into two groups based on integrative analyses of functional domains, phylogenetic relationships, and gene structures. Twelve and ten B. napus FBAs (BnaFBAs) were predicted to be localized in the chloroplast and cytoplasm, respectively. Notably, synteny analysis revealed that Brassica-specific triplication contributed to the expansion of the BnaFBA gene family during the evolution of B. napus. Various cis-acting regulatory elements pertinent to abiotic and biotic stresses, as well as phytohormone responses, were detected. Intriguingly, each of the BnaFBA genes exhibited distinct sequence polymorphisms. Among them, six contained signatures of selection, likely having experienced breeding selection during adaptation and domestication. Importantly, BnaFBAs showed diverse expression patterns at different developmental stages and were preferentially highly expressed in photosynthetic tissues. Our data thus provided the foundation for further elucidating the functional roles of individual BnaFBA and also potential targets for engineering to improve photosynthetic productivity in B. napus.
Collapse
Affiliation(s)
- Wei Zhao
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan 430062, China; (W.Z.); (H.L.); (L.Z.); (Z.H.); (J.L.); (W.H.)
| | - Hongfang Liu
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan 430062, China; (W.Z.); (H.L.); (L.Z.); (Z.H.); (J.L.); (W.H.)
| | - Liang Zhang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan 430062, China; (W.Z.); (H.L.); (L.Z.); (Z.H.); (J.L.); (W.H.)
| | - Zhiyong Hu
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan 430062, China; (W.Z.); (H.L.); (L.Z.); (Z.H.); (J.L.); (W.H.)
| | - Jun Liu
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan 430062, China; (W.Z.); (H.L.); (L.Z.); (Z.H.); (J.L.); (W.H.)
| | - Wei Hua
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan 430062, China; (W.Z.); (H.L.); (L.Z.); (Z.H.); (J.L.); (W.H.)
| | - Shouming Xu
- Henan key laboratory of Plant Stress Biology, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Jing Liu
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan 430062, China; (W.Z.); (H.L.); (L.Z.); (Z.H.); (J.L.); (W.H.)
| |
Collapse
|
19
|
Chang L, Wang L, Peng C, Tong Z, Wang D, Ding G, Xiao J, Guo A, Wang X. The chloroplast proteome response to drought stress in cassava leaves. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2019; 142:351-362. [PMID: 31422174 DOI: 10.1016/j.plaphy.2019.07.025] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2019] [Revised: 07/30/2019] [Accepted: 07/30/2019] [Indexed: 06/10/2023]
Abstract
Cassava is an important tropical crop with strong resistance to drought stress. The chloroplast, the site of photosynthesis, is sensitive to stress, and the drought-response proteins in cassava chloroplasts are worthy of investigation. In this study, cassava leaves were collected for ultra-structure observation from plants subjected to different drought stress conditions. Our results showed that drought stress can promote starch accumulation in cassava chloroplasts. To evaluate changes in chloroplast proteins under different drought conditions, two-dimensional electrophoresis was performed using purified chloroplasts, which resulted in the identification of 26 unique chloroplast proteins responsive to drought stress. These drought-responsive proteins are predominantly related to photosynthesis, carbon and nitrogen metabolism, and amino acid metabolism. Among them, most photosynthesis-related proteins are downregulated, with decreases in photosynthetic parameters upon drought stress. Several proteins associated with carbon and nitrogen metabolism, including rubisco and carbonic anhydrase, were upregulated, which might promote drought tolerance in cassava by enhancing the carbohydrate conversion efficiency and protecting the plant from oxidative stress. Our proteomic data not only provide insight into the complement of proteins in cassava chloroplasts but also further our overall understanding of drought-responsive proteins in cassava chloroplasts.
Collapse
Affiliation(s)
- Lili Chang
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, 571101, China
| | - Limin Wang
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, 571101, China; College of Agriculture, Ludong University, Yantai, Shandong, 264025, China
| | - Cunzhi Peng
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, 571101, China
| | - Zheng Tong
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, 571101, China
| | - Dan Wang
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, 571101, China
| | - Guohua Ding
- College of Life Sciences, Key Laboratory for Ecology of Tropical Islands, Ministry of Education, Hainan Normal University, Haikou, Hainan, 571158, China
| | - Junhan Xiao
- College of Life Sciences, Key Laboratory for Ecology of Tropical Islands, Ministry of Education, Hainan Normal University, Haikou, Hainan, 571158, China
| | - Anping Guo
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, 571101, China
| | - Xuchu Wang
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, 571101, China; College of Life Sciences, Key Laboratory for Ecology of Tropical Islands, Ministry of Education, Hainan Normal University, Haikou, Hainan, 571158, China.
| |
Collapse
|
20
|
Genome wide characterization, evolution and expression analysis of FBA gene family under salt stress in Gossypium species. Biologia (Bratisl) 2019. [DOI: 10.2478/s11756-019-00296-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
|
21
|
Xin L, Zheng H, Yang Z, Guo J, Liu T, Sun L, Xiao Y, Yang J, Yang Q, Guo L. Physiological and proteomic analysis of maize seedling response to water deficiency stress. JOURNAL OF PLANT PHYSIOLOGY 2018; 228:29-38. [PMID: 29852332 DOI: 10.1016/j.jplph.2018.05.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 05/14/2018] [Accepted: 05/14/2018] [Indexed: 05/10/2023]
Abstract
Low water availability is a major abiotic factor limiting photosynthesis and the growth and yield of crops. Maize (Zea mays) is among the most drought-sensitive cereal crops. Herein, the physiological and proteomic changes of maize seedlings caused by polyethylene-glycol-induced water deficit were analyzed. The results showed that malondialdehyde and proline contents increased continuously in the treated seedlings. Soluble sugar content and superoxide dismutase activity were upregulated initially but became downregulated under prolonged water deficit. A total of 104 proteins were found to be differentially accumulated under water stress. The identified proteins were mainly involved in photosynthesis, carbohydrate metabolism, stress defense, energy production, and protein metabolism. Interestingly, substantial incongruence between protein and transcript levels was observed, indicating that gene expression in water-stressed maize seedlings is controlled by complex mechanisms. Finally, we propose a hypothetical model that includes the different molecular, physiological, and biochemical changes that occurred during the response and tolerance of maize seedlings to water deficiency. Our study provides valuable insight for further research into the overall mechanisms underlying drought response and tolerance in maize and other plants.
Collapse
Affiliation(s)
- Longfei Xin
- Collaborative Innovation Center of Henan Grain Crops/State Key Laboratory of Wheat and Maize Crop Science/College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Huifang Zheng
- Collaborative Innovation Center of Henan Grain Crops/State Key Laboratory of Wheat and Maize Crop Science/College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Zongju Yang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; Graduate School, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jiameng Guo
- Collaborative Innovation Center of Henan Grain Crops/State Key Laboratory of Wheat and Maize Crop Science/College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Tianxue Liu
- Collaborative Innovation Center of Henan Grain Crops/State Key Laboratory of Wheat and Maize Crop Science/College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Lei Sun
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; Graduate School, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yang Xiao
- Graduate School, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jianping Yang
- Collaborative Innovation Center of Henan Grain Crops/State Key Laboratory of Wheat and Maize Crop Science/College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China; Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Qinghua Yang
- Collaborative Innovation Center of Henan Grain Crops/State Key Laboratory of Wheat and Maize Crop Science/College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China.
| | - Lin Guo
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| |
Collapse
|
22
|
Responses of the marine diatom Thalassiosira pseudonana to changes in CO 2 concentration: a proteomic approach. Sci Rep 2017; 7:42333. [PMID: 28181560 PMCID: PMC5299434 DOI: 10.1038/srep42333] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 01/10/2017] [Indexed: 12/18/2022] Open
Abstract
The concentration of CO2 in many aquatic systems is variable, often lower than the KM of the primary carboxylating enzyme Rubisco, and in order to photosynthesize efficiently, many algae operate a facultative CO2 concentrating mechanism (CCM). Here we measured the responses of a marine diatom, Thalassiosira pseudonana, to high and low concentrations of CO2 at the level of transcripts, proteins and enzyme activity. Low CO2 caused many metabolic pathways to be remodeled. Carbon acquisition enzymes, primarily carbonic anhydrase, stress, degradation and signaling proteins were more abundant while proteins associated with nitrogen metabolism, energy production and chaperones were less abundant. A protein with similarities to the Ca2+/ calmodulin dependent protein kinase II_association domain, having a chloroplast targeting sequence, was only present at low CO2. This protein might be a specific response to CO2 limitation since a previous study showed that other stresses caused its reduction. The protein sequence was found in other marine diatoms and may play an important role in their response to low CO2 concentration.
Collapse
|
23
|
Lv GY, Guo XG, Xie LP, Xie CG, Zhang XH, Yang Y, Xiao L, Tang YY, Pan XL, Guo AG, Xu H. Molecular Characterization, Gene Evolution, and Expression Analysis of the Fructose-1, 6-bisphosphate Aldolase (FBA) Gene Family in Wheat ( Triticum aestivum L.). FRONTIERS IN PLANT SCIENCE 2017; 8:1030. [PMID: 28659962 PMCID: PMC5470051 DOI: 10.3389/fpls.2017.01030] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 05/29/2017] [Indexed: 05/17/2023]
Abstract
Fructose-1, 6-bisphosphate aldolase (FBA) is a key plant enzyme that is involved in glycolysis, gluconeogenesis, and the Calvin cycle. It plays significant roles in biotic and abiotic stress responses, as well as in regulating growth and development processes. In the present paper, 21 genes encoding TaFBA isoenzymes were identified, characterized, and categorized into three groups: class I chloroplast/plastid FBA (CpFBA), class I cytosol FBA (cFBA), and class II chloroplast/plastid FBA. By using a prediction online database and genomic PCR analysis of Chinese Spring nulli-tetrasomic lines, we have confirmed the chromosomal location of these genes in 12 chromosomes of four homologous groups. Sequence and genomic structure analysis revealed the high identity of the allelic TaFBA genes and the origin of different TaFBA genes. Numerous putative environment stimulus-responsive cis-elements have been identified in 1,500-bp regions of TaFBA gene promoters, of which the most abundant are the light-regulated elements (LREs). Phylogenetic reconstruction using the deduced protein sequence of 245 FBA genes indicated an independent evolutionary pathway for the class I and class II groups. Although, earlier studies have indicated that class II FBA only occurs in prokaryote and fungi, our results have demonstrated that a few class II CpFBAs exist in wheat and other closely related species. Class I TaFBA was predicted to be tetramers and class II to be dimers. Gene expression analysis based on microarray and transcriptome databases suggested the distinct role of TaFBAs in different tissues and developmental stages. The TaFBA 4-9 genes were highly expressed in leaves and might play important roles in wheat development. The differential expression patterns of the TaFBA genes in light/dark and a few abiotic stress conditions were also analyzed. The results suggested that LRE cis-elements of TaFBA gene promoters were not directly related to light responses. Most TaFBA genes had higher expression levels in the roots than in the shoots when under various stresses. Class I cytosol TaFBA genes, particularly TaFBA10/12/18 and TaFBA13/16, and three class II TaFBA genes are involved in responses to various abiotic stresses. Class I CpFBA genes in wheat are apparently sensitive to different stress conditions.
Collapse
Affiliation(s)
- Geng-Yin Lv
- College of Life Sciences, Northwest A & F UniversityYangling, China
| | - Xiao-Guang Guo
- College of Life Sciences, Northwest A & F UniversityYangling, China
| | - Li-Ping Xie
- College of Life Sciences, Northwest A & F UniversityYangling, China
| | - Chang-Gen Xie
- College of Life Sciences, Northwest A & F UniversityYangling, China
- State Key Laboratory of Crop Stress Biology for Arid AreasYangling, China
| | - Xiao-Hong Zhang
- College of Life Sciences, Northwest A & F UniversityYangling, China
| | - Yuan Yang
- College of Life Sciences, Northwest A & F UniversityYangling, China
| | - Lei Xiao
- College of Life Sciences, Northwest A & F UniversityYangling, China
| | - Yu-Ying Tang
- College of Life Sciences, Northwest A & F UniversityYangling, China
| | - Xing-Lai Pan
- Department of Food Crop Science, Cotton Research Institute, Shanxi Academy of Agricultural Sciences (CAAS)Yuncheng, China
| | - Ai-Guang Guo
- College of Life Sciences, Northwest A & F UniversityYangling, China
- State Key Laboratory of Crop Stress Biology for Arid AreasYangling, China
| | - Hong Xu
- College of Life Sciences, Northwest A & F UniversityYangling, China
- State Key Laboratory of Crop Stress Biology for Arid AreasYangling, China
- *Correspondence: Hong Xu
| |
Collapse
|
24
|
Chien HJ, Chu YW, Chen CW, Juang YM, Chien MW, Liu CW, Wu CC, Tzen JT, Lai CC. 2-DE combined with two-layer feature selection accurately establishes the origin of oolong tea. Food Chem 2016; 211:392-9. [DOI: 10.1016/j.foodchem.2016.05.043] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 05/05/2016] [Accepted: 05/08/2016] [Indexed: 12/01/2022]
|
25
|
Cai B, Li Q, Xu Y, Yang L, Bi H, Ai X. Genome-wide analysis of the fructose 1,6-bisphosphate aldolase (FBA) gene family and functional characterization of FBA7 in tomato. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2016; 108:251-265. [PMID: 27474933 DOI: 10.1016/j.plaphy.2016.07.019] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Revised: 07/15/2016] [Accepted: 07/18/2016] [Indexed: 05/01/2023]
Abstract
Fructose 1,6-bisphosphate aldolase (FBA) is a key enzyme in plants that is involved in glycolysis, gluconeogenesis, and the Calvin cycle. FBA genes play significant roles in biotic and abiotic stress responses and also regulate growth and development. Despite the importance of FBA genes, little is known about it in tomato. In this study, we identified 8 FBA genes in tomato and classified them into 2 subgroups based on a phylogenetic tree, gene structures, and conserved motifs. Five (SlFBA1, 2, 3, 4 and 5) and three (SlFBA6, 7, and 8) SlFBA proteins were predicted to be localized in chloroplasts and cytoplasm, respectively. The phylogenetic analysis of FBAs from tomato, Arabidopsis, rice, and other organisms suggested that SlFBA shared the highest protein homology with FBAs from other plants. Synteny analysis indicated that segmental duplication events contributed to the expansion of the tomato FBA family. The expression profiles revealed that all SlFBAs were involved in the response to low and high temperature stresses. SlFBA7 overexpression increased the expression and activities of other main enzymes in Calvin cycle, net photosynthetic rate (Pn), seed size and stem diameter. SlFBA7 overexpression enhanced tolerances in seed germination under suboptimal temperature stresses. Taken together, comprehensive analyses of SlFBAs would provide a basis for understanding of evolution and function of SlFBA family.
Collapse
Affiliation(s)
- Bingbing Cai
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, Shandong 271018, PR China.
| | - Qiang Li
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, Shandong 271018, PR China.
| | - Yongchao Xu
- College of Plant Protection, Shandong Agricultural University, Tai'an, Shandong 271018, PR China.
| | - Long Yang
- College of Plant Protection, Shandong Agricultural University, Tai'an, Shandong 271018, PR China.
| | - Huangai Bi
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, Shandong 271018, PR China.
| | - Xizhen Ai
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, Shandong 271018, PR China.
| |
Collapse
|
26
|
Yasmeen F, Raja NI, Razzaq A, Komatsu S. Proteomic and physiological analyses of wheat seeds exposed to copper and iron nanoparticles. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1865:28-42. [PMID: 27717896 DOI: 10.1016/j.bbapap.2016.10.001] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Revised: 09/29/2016] [Accepted: 10/03/2016] [Indexed: 10/20/2022]
Abstract
To elucidate the role of Cu and Fe NPs on the yield of wheat varieties, a gel-free proteomic technique was used. NPs were synthesized and characterized through zeta potential, EDX, and SEM. Spike length, number of grains per spike, and 1000 grain weight were increased in wheat varieties treated with 25ppm Cu and Fe NPs. On treatment with 25ppm Cu and Fe NPs, a total of 58, 121, and 25 proteins were changed in abundance in wheat seeds of galaxy-13, Pakistan-13, and NARC-11, respectively. In galaxy-13, exposure to Cu NPs increased proteins involved in starch degradation and glycolysis. Furthermore, the number of proteins related to starch degradation, glycolysis, and tricarboxylic acid cycle was increased in galaxy-13 on Fe NPs exposure. Proteins related to glycolysis and the tricarboxylic acid cycle was increased in Pakistan-13 and NARC-11 by Fe NPs exposure. The sugar content and SOD activity was increased in wheat seeds treated with Cu and Fe NPs. The Cu content was increased at 25ppm Cu NPs exposure in seeds of wheat varieties. These results suggest that Cu NPs improved stress tolerance in wheat varieties by mediating the process of starch degradation, glycolysis, and tricarboxylic acid cycle through NPs uptake.
Collapse
Affiliation(s)
- Farhat Yasmeen
- Department of Botany, PMAS Arid Agriculture University, Rawalpindi 46300, Pakistan; National Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba 305-8518, Japan
| | - Naveed Iqbal Raja
- Department of Botany, PMAS Arid Agriculture University, Rawalpindi 46300, Pakistan.
| | - Abdul Razzaq
- Department of Agronomy, PMAS Arid Agriculture University, Rawalpindi 46300, Pakistan
| | - Setsuko Komatsu
- National Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba 305-8518, Japan.
| |
Collapse
|
27
|
Chen W, Yao Q, Patil GB, Agarwal G, Deshmukh RK, Lin L, Wang B, Wang Y, Prince SJ, Song L, Xu D, An YC, Valliyodan B, Varshney RK, Nguyen HT. Identification and Comparative Analysis of Differential Gene Expression in Soybean Leaf Tissue under Drought and Flooding Stress Revealed by RNA-Seq. FRONTIERS IN PLANT SCIENCE 2016; 7:1044. [PMID: 27486466 PMCID: PMC4950259 DOI: 10.3389/fpls.2016.01044] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 07/04/2016] [Indexed: 05/18/2023]
Abstract
Drought and flooding are two major causes of severe yield loss in soybean worldwide. A lack of knowledge of the molecular mechanisms involved in drought and flood stress has been a limiting factor for the effective management of soybeans; therefore, it is imperative to assess the expression of genes involved in response to flood and drought stress. In this study, differentially expressed genes (DEGs) under drought and flooding conditions were investigated using Illumina RNA-Seq transcriptome profiling. A total of 2724 and 3498 DEGs were identified under drought and flooding treatments, respectively. These genes comprise 289 Transcription Factors (TFs) representing Basic Helix-loop Helix (bHLH), Ethylene Response Factors (ERFs), myeloblastosis (MYB), No apical meristem (NAC), and WRKY amino acid motif (WRKY) type major families known to be involved in the mechanism of stress tolerance. The expression of photosynthesis and chlorophyll synthesis related genes were significantly reduced under both types of stresses, which limit the metabolic processes and thus help prolong survival under extreme conditions. However, cell wall synthesis related genes were up-regulated under drought stress and down-regulated under flooding stress. Transcript profiles involved in the starch and sugar metabolism pathways were also affected under both stress conditions. The changes in expression of genes involved in regulating the flux of cell wall precursors and starch/sugar content can serve as an adaptive mechanism for soybean survival under stress conditions. This study has revealed the involvement of TFs, transporters, and photosynthetic genes, and has also given a glimpse of hormonal cross talk under the extreme water regimes, which will aid as an important resource for soybean crop improvement.
Collapse
Affiliation(s)
- Wei Chen
- Division of Plant Sciences, University of MissouriColumbia, MO, USA
| | - Qiuming Yao
- Department of Computer Science and Christopher S. Bond Life Sciences Center, University of MissouriColumbia, MO, USA
| | - Gunvant B. Patil
- Division of Plant Sciences, University of MissouriColumbia, MO, USA
| | - Gaurav Agarwal
- Division of Plant Sciences, University of MissouriColumbia, MO, USA
- Center of Excellence in Genomics, International Crops Research Institute for the Semi-Arid TropicsHyderabad, India
| | | | - Li Lin
- Division of Plant Sciences, University of MissouriColumbia, MO, USA
| | - Biao Wang
- Division of Plant Sciences, University of MissouriColumbia, MO, USA
- Legume Biotechnology Laboratory, School of Agriculture and Biology, Shanghai Jiao Tong UniversityShanghai, China
| | - Yongqin Wang
- Division of Plant Sciences, University of MissouriColumbia, MO, USA
| | - Silvas J. Prince
- Division of Plant Sciences, University of MissouriColumbia, MO, USA
| | - Li Song
- Division of Plant Sciences, University of MissouriColumbia, MO, USA
| | - Dong Xu
- Department of Computer Science and Christopher S. Bond Life Sciences Center, University of MissouriColumbia, MO, USA
| | - Yongqiang C. An
- Plant Genetics Research Unit, Donald Danforth Plant Science Center, US Department of Agriculture, Agricultural Research Service, Midwest AreaSt. Louis, MO, USA
| | - Babu Valliyodan
- Division of Plant Sciences, University of MissouriColumbia, MO, USA
| | - Rajeev K. Varshney
- Center of Excellence in Genomics, International Crops Research Institute for the Semi-Arid TropicsHyderabad, India
| | - Henry T. Nguyen
- Division of Plant Sciences, University of MissouriColumbia, MO, USA
- *Correspondence: Henry T. Nguyen
| |
Collapse
|
28
|
Yi F, Chen J, Yu J. Global analysis of uncapped mRNA changes under drought stress and microRNA-dependent endonucleolytic cleavages in foxtail millet. BMC PLANT BIOLOGY 2015; 15:241. [PMID: 26444665 PMCID: PMC4594888 DOI: 10.1186/s12870-015-0632-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2015] [Accepted: 09/30/2015] [Indexed: 05/20/2023]
Abstract
BACKGROUND mRNA degradation plays an important role in the determination of mRNA abundance and can quickly regulate gene expression. The production of uncapped mRNAs, an important mechanism of mRNA degradation, can be initiated by decapping enzymes, endonucleases or small RNAs such as microRNAs (miRNAs). Little is known, however, about the role of uncapped mRNAs in plants under environmental stress. RESULTS Using a novel approach called parallel analysis of RNA ends (PARE), we performed a global study of uncapped mRNAs under drought stress in foxtail millet (Setaria italica [L.] P. Beauv.). When both gene degradation (PARE) and gene transcription (RNA-sequencing) data were considered, four types of mRNA decay patterns were identified under drought stress. In addition, 385 miRNA-target interactions were identified in the PARE data using PAREsnip. The PARE analysis also suggested that two miRNA hairpin processing mechanisms--loop-last and loop-first processing--operate in foxtail millet, with both miR319 and miR156 gene families undergoing precise processing via the unusual loop-first mechanism. Finally, we found 11 C4 photosynthesis-related enzymes encoded by drought-responsive genes. CONCLUSIONS We performed a global analysis of mRNA degradation under drought stress and uncovered diverse drought-response mechanisms in foxtail millet. This information will deepen our understanding of mRNA expression under stressful environmental conditions in gramineous plants. In addition, PARE analysis identified many miRNA targets and revealed miRNA-precursor processing modes in foxtail millet.
Collapse
Affiliation(s)
- Fei Yi
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China.
| | - Jian Chen
- State Key Laboratory of Agrobiotechnology, College of Agriculture and Biotechnology, China Agricultural University, Beijing, 100193, China.
| | - Jingjuan Yu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China.
| |
Collapse
|