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Yakkou L, Houida S, El Baaboua A, Bilen S, Chelkha M, Okyay Kaya L, Aasfar A, Ameen F, Ahmad Bhat S, Raouane M, Amghar S, El Harti A. Unveiling resilience: coelomic fluid bacteria's impact on plant metabolism and abiotic stress tolerance. PLANT SIGNALING & BEHAVIOR 2024; 19:2363126. [PMID: 38832593 DOI: 10.1080/15592324.2024.2363126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Accepted: 05/29/2024] [Indexed: 06/05/2024]
Abstract
Earthworms' coelomic fluid (CF) has been discovered to possess properties that promote plant development. In particular, the earthworm's coelomic fluid-associated bacteria (CFB) are the primary factor influencing the plants' response. To investigate this, we used bacteria isolated from the CF and selected based on different plant growth-promoting traits, in a mesocosm ecosystem that includes plants. This experiment aimed to assess their impact on the metabolism of plants growing under abiotic stress environments (alkaline soil and nitrogen (N), phosphate (P), and potassium (K) deficit) and compare the lipid profiles of plants under the various treatments. We used seven different bacterial species isolated from the CF of Aporrectodea molleri and as a plant model Zea mays L. For the metabolomic analysis method, we used gas chromatography-mass spectrometry lipidomic. After observing the metabolomic profiles, we found that a few molecular pathways are involved in how plants react to bacterial biostimulants. The bacterial isolates belonging to Pantoea vagans, Pseudomonas aeruginosa, Bacillus paramycoides, and Bacillus thuringiensis have led to a significant increase in synthesizing several metabolites belonging to various chemical categories. Contrary to predictions, abiotic stress did not cause a drop in the composition and concentration of lipids in plants treated with the CFB, demonstrating the rigidity of the protective mechanisms. The statistical analysis based on the Pearson method revealed a positive significant correlation between plant growth parameters (length of the aerial part, surface of the leaves, and biomass) and some metabolites belonging to fatty acids, carboxylic acids, benzene derivatives, and alkanes. Moreover, the standard metabolic components of all treatments in much higher concentrations during bacterial treatments than the control treatment suggests that the bacteria have stimulated the overexpression of these metabolic components. According to these results, we could assume that plants treated with CFB exhibit an adaptability of abiotic stress defense mechanisms, which may be attributed to the upregulation of genes involved in lipid biosynthesis pathways.
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Affiliation(s)
- Lamia Yakkou
- Laboratory of Microbial Biotechnologies and Plant Protection (LBVRN), Faculty of Sciences Agadir, University Ibn Zohr, Agadir, Morocco
- Faculty of Applied Sciences- Ait Melloul, University Ibn Zohr, Agadir, Morocco
| | - Sofia Houida
- Laboratory of Mycobacteria and Tuberculosis, Institut Pasteur of Morocco, Casablanca, Morocco
| | - Aicha El Baaboua
- Biotechnology and Applied Microbiology Team, Department of Biology, Faculty of Science, Abdelmalek-Essaadi University, Tetouan, Morocco
| | - Serdar Bilen
- Soil Science and Plant Nutrition Department, Faculty of Agriculture, Ataturk University, Erzurum, Turkey
| | - Maryam Chelkha
- Department of Entomology, Cornell University, Cornell AgriTech, Geneva, NY, USA
| | - Leyla Okyay Kaya
- Soil Science and Plant Nutrition Department, Faculty of Agriculture, Ataturk University, Erzurum, Turkey
| | - Abderrahim Aasfar
- Plant and Microbial Biotechnology Center, Moroccan Foundation for Advanced Science, Innovation and Research (MAScIR), Mohammed VI Polytechnic University, Ben Guerir, Morocco
| | - Fuad Ameen
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | | | - Mohammed Raouane
- Research Team «Lumbricidae, Improving Soil Productivity and Environment (LAPSE)», Center "Water, Natural Resources, Environment and Sustainable Development, Ecole Normale Supérieure (ENS), Mohammed V University, Rabat, Morocco
| | - Souad Amghar
- Research Team «Lumbricidae, Improving Soil Productivity and Environment (LAPSE)», Center "Water, Natural Resources, Environment and Sustainable Development, Ecole Normale Supérieure (ENS), Mohammed V University, Rabat, Morocco
| | - Abdellatif El Harti
- Research Team «Lumbricidae, Improving Soil Productivity and Environment (LAPSE)», Center "Water, Natural Resources, Environment and Sustainable Development, Ecole Normale Supérieure (ENS), Mohammed V University, Rabat, Morocco
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Pan L, Li Y, Zhao W, Sui Y, Yang N, Liu L, Liu Y, Tang Z, Mu L. Metabolomics analysis of different diameter classes of Taxus chinensis reveals that the resource allocation is related to carbon and nitrogen metabolism. BMC PLANT BIOLOGY 2024; 24:383. [PMID: 38724888 PMCID: PMC11080207 DOI: 10.1186/s12870-024-05070-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 04/26/2024] [Indexed: 05/13/2024]
Abstract
Taxus chinensis (Taxus cuspidata Sieb. et Zucc.) is a traditional medicinal plant known for its anticancer substance paclitaxel, and its growth age is also an important factor affecting its medicinal value. However, how age affects the physiological and metabolic characteristics and active substances of T. chinensis is still unclear. In this study, carbon and nitrogen accumulation, contents of active substances and changes in primary metabolites in barks and annual leaves of T. chinensis of different diameter classes were investigated by using diameter classes instead of age. The results showed that leaves and barks of small diameter class (D1) had higher content of non-structural carbohydrates and C, which were effective in enhancing defense capacity, while N content was higher in medium (D2) and large diameter classes (D3). Active substances such as paclitaxel, baccatin III and cephalomannine also accumulated significantly in barks of large diameter classes. Moreover, 21 and 25 differential metabolites were identified in leaves and barks of different diameter classes, respectively. The differential metabolites were enhanced the TCA cycle and amino acid biosynthesis, accumulate metabolites such as organic acids, and promote the synthesis and accumulation of active substances such as paclitaxel in the medium and large diameter classes. These results revealed the carbon and nitrogen allocation mechanism of different diameter classes of T. chinensis, and its relationship with medicinal components, providing a guidance for the harvesting and utilization of wild T. chinensis.
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Affiliation(s)
- Liben Pan
- School of Forestry, Northeast Forestry University, Harbin, 150040, China
- Key Laboratory of Forest Plant Ecology, Ministry of Education, Northeast Forestry University, Harbin, 150040, China
| | - Yi Li
- School of Forestry, Northeast Forestry University, Harbin, 150040, China
| | - Wen Zhao
- School of Forestry, Northeast Forestry University, Harbin, 150040, China
| | - Yushu Sui
- Key Laboratory of Forest Plant Ecology, Ministry of Education, Northeast Forestry University, Harbin, 150040, China
- College of Chemistry, Chemical Engineering and Resource Utilization, Northeast Forestry University, Harbin, 150040, China
| | - Nan Yang
- Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Longjie Liu
- School of Forestry, Northeast Forestry University, Harbin, 150040, China
| | - Yang Liu
- School of Life Sciences, Heilongjiang University, Harbin, 150080, China
| | - Zhonghua Tang
- Key Laboratory of Forest Plant Ecology, Ministry of Education, Northeast Forestry University, Harbin, 150040, China.
- College of Chemistry, Chemical Engineering and Resource Utilization, Northeast Forestry University, Harbin, 150040, China.
| | - Liqiang Mu
- School of Forestry, Northeast Forestry University, Harbin, 150040, China.
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Wang H, Jia Y, Bai X, Wang J, Liu G, Wang H, Wu Y, Xin J, Ma H, Liu Z, Zou D, Zhao H. Whole-transcriptome profiling and identification of cold tolerance-related ceRNA networks in japonica rice varieties. FRONTIERS IN PLANT SCIENCE 2024; 15:1260591. [PMID: 38567126 PMCID: PMC10985246 DOI: 10.3389/fpls.2024.1260591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 02/02/2024] [Indexed: 04/04/2024]
Abstract
Introduction Low-temperature stress negatively impacts rice yield, posing a significant risk to food security. While previous studies have explored the physiological and linear gene expression alterations in rice under low-temperature conditions, the changes in competing endogenous RNA (ceRNA) networks remain largely unexamined. Methods We conducted RNA sequencing on two japonica rice varieties with differing cold-tolerance capabilities to establish ceRNA networks. This enabled us to investigate the transcriptional regulatory network and molecular mechanisms that rice employs in response to low-temperature stress. Results We identified 364 differentially expressed circular RNAs (circRNAs), 224 differentially expressed microRNAs (miRNAs), and 12,183 differentially expressed messenger RNAs (mRNAs). WRKY family was the most prominent transcription factor family involved in cold tolerance. Based on the expression patterns and targeted relationships of these differentially expressed RNAs, we discerned five potential ceRNA networks related to low-temperature stress in rice: osa-miR166j-5p from the miR166 family was associated with cold tolerance; osa-miR528-3p and osa-miR156j-3p were linked to stress response; and osa-miR156j-3p was involved in the antioxidant system. In addition, Os03g0152000 in the antioxidant system, as well as Os12g0491800 and Os05g0381400, correlated with the corresponding stress response and circRNAs in the network. A gene sequence difference analysis and phenotypic validation of Os11g0685700 (OsWRKY61) within the WRKY family suggested its potential role in regulating cold tolerance in rice. Discussion and conclusion We identified Os11g0685700 (OsWRKY61) as a promising candidate gene for enhancing cold tolerance in japonica rice. The candidate miRNAs, mRNAs, and circRNAs uncovered in this study are valuable targets for researchers and breeders. Our findings will facilitate the development of cold-tolerant rice varieties from multiple angles and provide critical directions for future research into the functions of cold-tolerance-related miRNAs, mRNAs, and circRNAs in rice.
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Affiliation(s)
- Hao Wang
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, China
| | - Yan Jia
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, China
| | - Xu Bai
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, China
| | - Jin Wang
- Bei Da Huang Kenfeng Seed Limited Company, Research and Breeding Center, Harbin, China
| | - Ge Liu
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, China
| | - Haixing Wang
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, China
| | - Yulong Wu
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, China
| | - Junying Xin
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, China
| | - Huimiao Ma
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, China
| | - Zhenyu Liu
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, China
| | - Detang Zou
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, China
| | - Hongwei Zhao
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, China
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Li L, Lu X, Dai P, Ma H. DIA-Based Quantitative Proteomics in the Flower Buds of Two Malus sieversii (Ledeb.) M. Roem Subtypes at Different Overwintering Stages. Int J Mol Sci 2024; 25:2964. [PMID: 38474210 DOI: 10.3390/ijms25052964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 02/29/2024] [Accepted: 02/29/2024] [Indexed: 03/14/2024] Open
Abstract
Malus sieversii is considered the ancestor of the modern cultivated apple, with a high value for apple tolerance breeding. Despite studies on the temperature adaptability of M. sieversii carried out at a physiological response and the genome level, information on the proteome changes of M. sieversii during dormancy is limited, especially about the M. sieversii subtypes. In this study, a DIA-based approach was employed to screen and identify differential proteins involved in three overwintering periods of flower buds in two M. sieversii subtypes (Malus sieversii f. luteolus, GL; Malus sieversii f. aromaticus, HC) with different overwintering adaptabilities. The proteomic analysis revealed that the number of the down-regulated differential expression proteins (DEPs) was obviously higher than that of the up-regulated DEPs in the HC vs. GL groups, especially at the dormancy stage and dormancy-release stage. Through functional classification of those DEPs, the majority of the DEPs in the HC vs. GL groups were associated with protein processing in the endoplasmic reticulum, oxidative phosphorylation, starch and sucrose metabolism and ribosomes. Through WGCNA analysis, tricarboxylic acid cycle and pyruvate metabolism were highly correlated with the overwintering stages; oxidative phosphorylation and starch and sucrose metabolism were highly correlated with the Malus sieversii subtypes. This result suggests that the down-regulation of DEPs, which are predominantly enriched in these pathways, could potentially contribute to the lower cold tolerance observed in HC during overwintering stage.
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Affiliation(s)
- Lijie Li
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China
| | - Xiaochen Lu
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China
| | - Ping Dai
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China
| | - Huaiyu Ma
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China
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Nouraei S, Mia MS, Liu H, Turner NC, Khan JM, Yan G. Proteomic analysis of near-isogenic lines reveals key biomarkers on wheat chromosome 4B conferring drought tolerance. THE PLANT GENOME 2024; 17:e20343. [PMID: 37199103 DOI: 10.1002/tpg2.20343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 02/05/2023] [Accepted: 03/27/2023] [Indexed: 05/19/2023]
Abstract
Drought is a major constraint for wheat production that is receiving increased attention due to global climate change. This study conducted isobaric tags for relative and absolute quantitation proteomic analysis on near-isogenic lines to shed light on the underlying mechanism of qDSI.4B.1 quantitative trait loci (QTL) on the short arm of chromosome 4B conferring drought tolerance in wheat. Comparing tolerant with susceptible isolines, 41 differentially expressed proteins were identified to be responsible for drought tolerance with a p-value of < 0.05 and fold change >1.3 or <0.7. These proteins were mainly enriched in hydrogen peroxide metabolic activity, reactive oxygen species metabolic activity, photosynthetic activity, intracellular protein transport, cellular macromolecule localization, and response to oxidative stress. Prediction of protein interactions and pathways analysis revealed the interaction between transcription, translation, protein export, photosynthesis, and carbohydrate metabolism as the most important pathways responsible for drought tolerance. The five proteins, including 30S ribosomal protein S15, SRP54 domain-containing protein, auxin-repressed protein, serine hydroxymethyltransferase, and an uncharacterized protein with encoding genes on 4BS, were suggested as candidate proteins responsible for drought tolerance in qDSI.4B.1 QTL. The gene coding SRP54 protein was also one of the differentially expressed genes in our previous transcriptomic study.
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Affiliation(s)
- Sina Nouraei
- UWA School of Agriculture and Environment, The University of Western Australia, Crawley, Western Australia, Australia
- The UWA Institute of Agriculture, The University of Western Australia, Crawley, Western Australia, Australia
| | - Md Sultan Mia
- The UWA Institute of Agriculture, The University of Western Australia, Crawley, Western Australia, Australia
- Department of Primary Industries and Regional Development, South Perth, Western Australia, Australia
| | - Hui Liu
- UWA School of Agriculture and Environment, The University of Western Australia, Crawley, Western Australia, Australia
- The UWA Institute of Agriculture, The University of Western Australia, Crawley, Western Australia, Australia
| | - Neil C Turner
- UWA School of Agriculture and Environment, The University of Western Australia, Crawley, Western Australia, Australia
- The UWA Institute of Agriculture, The University of Western Australia, Crawley, Western Australia, Australia
| | - Javed M Khan
- Proteomics International, Crawley, Western Australia, Australia
- Harry Perkins Institute of Medical Research, QEII Medical Centre, The University of Western Australia, Crawley, Western Australia, Australia
| | - Guijun Yan
- UWA School of Agriculture and Environment, The University of Western Australia, Crawley, Western Australia, Australia
- The UWA Institute of Agriculture, The University of Western Australia, Crawley, Western Australia, Australia
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Omar SA, Ashokhan S, Abdul Majid N, Karsani SA, Lau BYC, Yaacob JS. Enhanced azadirachtin production in neem (Azadirachta indica) callus through NaCl elicitation: Insights into differential protein regulation via shotgun proteomics. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2024; 199:105778. [PMID: 38458685 DOI: 10.1016/j.pestbp.2024.105778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 09/19/2023] [Accepted: 01/09/2024] [Indexed: 03/10/2024]
Abstract
With their remarkable bioactivity and evolving commercial importance, plant secondary metabolites (PSMs) have gained significant research interest in recent years. Plant tissue culture serves as a credible tool to examine how abiotic stresses modulate the production of PSMs, enabling clear insights into plant stress responses and the prospects for controlled synthesis of bioactive compounds. Azadirachta indica, or neem has been recognized as a repository of secondary metabolites for centuries, particularly for the compound named azadirachtin, due to its bio-pesticidal and high antioxidant properties. Introducing salt stress as an elicitor makes it possible to enhance the synthesis of secondary metabolites, specifically azadirachtin. Thus, in this research, in vitro callus cultures of neem were micro-propagated and induced with salinity stress to explore their effects on the production of azadirachtin and identify potential proteins associated with salinity stress through comparative shotgun proteomics (LCMS/MS). To induce salinity stress, 2-month-old calli were subjected to various concentrations of NaCl (0.05-1.5%) for 4 weeks. The results showed that the callus cultures were able to adapt and survive in the salinity treatments, but displayed a reduction in fresh weight as the NaCl concentration increased. Notably, azadirachtin production was significantly enhanced in the salinity treatment compared to control, where 1.5% NaCl-treated calli produced the highest azadirachtin amount (10.847 ± 0.037 mg/g DW). The proteomics analysis showed that key proteins related to primary metabolism, such as defence, energy, cell structure, redox, transcriptional and photosynthesis, were predominantly differentially regulated (36 upregulated and 93 downregulated). While a few proteins were identified as being regulated in secondary metabolism, they were not directly involved in the synthesis of azadirachtin. In conjunction with azadirachtin elicitation, salinity stress treatment could therefore be successfully applied in commercial settings for the controlled synthesis of azadirachtin and other plant-based compounds. Further complementary omics approaches can be employed to enhance molecular-level modifications, to facilitate large-scale production of bioactive compounds in the future.
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Affiliation(s)
- Siti Ainnsyah Omar
- Institute of Biological Sciences, Faculty of Science, Universiti Malaya, 50603 Kuala Lumpur, Malaysia
| | - Sharmilla Ashokhan
- School of Biotechnology, MILA University, Putra Nilai, 71800 Nilai, Negeri Sembilan, Malaysia
| | - Nazia Abdul Majid
- Institute of Biological Sciences, Faculty of Science, Universiti Malaya, 50603 Kuala Lumpur, Malaysia
| | - Saiful Anuar Karsani
- Institute of Biological Sciences, Faculty of Science, Universiti Malaya, 50603 Kuala Lumpur, Malaysia
| | - Benjamin Yii Chung Lau
- Malaysian Palm Oil Board, No. 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia
| | - Jamilah Syafawati Yaacob
- Institute of Biological Sciences, Faculty of Science, Universiti Malaya, 50603 Kuala Lumpur, Malaysia; Centre for Research in Biotechnology for Agriculture (CEBAR), Universiti Malaya, 50603 Kuala Lumpur, Malaysia.
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García Méndez MDC, Encarnación-Guevara S, Martínez Batallar ÁG, Gómez-Caudillo L, Bru-Martínez R, Martínez Márquez A, Selles Marchart S, Tovar-Sánchez E, Álvarez-Berber L, Marquina Bahena S, Perea-Arango I, Arellano-García JDJ. High variability of perezone content in rhizomes of Acourtia cordata wild plants, environmental factors related, and proteomic analysis. PeerJ 2023; 11:e16136. [PMID: 38025722 PMCID: PMC10656900 DOI: 10.7717/peerj.16136] [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: 08/06/2022] [Accepted: 08/29/2023] [Indexed: 12/01/2023] Open
Abstract
With the aim of exploring the source of the high variability observed in the production of perezone, in Acourtia cordata wild plants, we analyze the influence of soil parameters and phenotypic characteristics on its perezone content. Perezone is a sesquiterpene quinone responsible for several pharmacological effects and the A. cordata plants are the natural source of this metabolite. The chemistry of perezone has been widely studied, however, no studies exist related to its production under natural conditions, nor to its biosynthesis and the environmental factors that affect the yield of this compound in wild plants. We also used a proteomic approach to detect differentially expressed proteins in wild plant rhizomes and compare the profiles of high vs. low perezone-producing plants. Our results show that in perezone-producing rhizomes, the presence of high concentrations of this compound could result from a positive response to the effects of some edaphic factors, such as total phosphorus (Pt), total nitrogen (Nt), ammonium (NH4), and organic matter (O. M.), but could also be due to a negative response to the soil pH value. Additionally, we identified 616 differentially expressed proteins between high and low perezone producers. According to the functional annotation of this comparison, the upregulated proteins were grouped in valine biosynthesis, breakdown of leucine and isoleucine, and secondary metabolism such as terpenoid biosynthesis. Downregulated proteins were grouped in basal metabolism processes, such as pyruvate and purine metabolism and glycolysis/gluconeogenesis. Our results suggest that soil parameters can impact the content of perezone in wild plants. Furthermore, we used proteomic resources to obtain data on the pathways expressed when A. cordata plants produce high and low concentrations of perezone. These data may be useful to further explore the possible relationship between perezone production and abiotic or biotic factors and the molecular mechanisms related to high and low perezone production.
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Affiliation(s)
- Ma del Carmen García Méndez
- Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México
| | | | | | - Leopoldo Gómez-Caudillo
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Roque Bru-Martínez
- Departamento de Agroquímica y Bioquímica, Facultad de Ciencias, Universidad de Alicante, Alicante, Spain
- Instituto de Investigación Sanitaria y Biomédica de Alicante, Instituto de Investigación Sanitaria y Biomédica de Alicante, Alicante, Spain
| | - Ascensión Martínez Márquez
- Departamento de Agroquímica y Bioquímica, Facultad de Ciencias, Universidad de Alicante, Alicante, Spain
| | - Susana Selles Marchart
- Departamento de Agroquímica y Bioquímica, Facultad de Ciencias, Universidad de Alicante, Alicante, Spain
| | - Efraín Tovar-Sánchez
- Centro de Investigación en Biodiversidad y Conservación, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexico
| | - Laura Álvarez-Berber
- Centro de Investigaciones Químicas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexico
| | - Silvia Marquina Bahena
- Centro de Investigaciones Químicas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexico
| | - Irene Perea-Arango
- Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México
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Yadav BG, Aakanksha, Kumar R, Yadava SK, Kumar A, Ramchiary N. Understanding the Proteomes of Plant Development and Stress Responses in Brassica Crops. J Proteome Res 2023; 22:660-680. [PMID: 36786770 DOI: 10.1021/acs.jproteome.2c00684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
Brassica crops have great economic value due to their rich nutritional content and are therefore grown worldwide as oilseeds, vegetables, and condiments. Deciphering the molecular mechanisms associated with the advantageous phenotype is the major objective of various Brassica improvement programs. As large technological advancements have been achieved in the past decade, the methods to understand molecular mechanisms underlying the traits of interest have also taken a sharp upturn in plant breeding practices. Proteomics has emerged as one of the preferred choices nowadays along with genomics and other molecular approaches, as proteins are the ultimate effector molecules responsible for phenotypic changes in living systems, and allow plants to resist variable environmental stresses. In the last two decades, rapid progress has been made in the field of proteomics research in Brassica crops, but a comprehensive review that collates the different studies is lacking. This review provides an inclusive summary of different proteomic studies undertaken in Brassica crops for cytoplasmic male sterility, oil content, and proteomics of floral organs and seeds, under different biotic and abiotic stresses including post-translational modifications of proteins. This comprehensive review will help in understanding the role of different proteins in controlling plant phenotypes, and provides information for initiating future studies on Brassica breeding and improvement programs.
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Affiliation(s)
- Bal Govind Yadav
- International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, Delhi, India
| | - Aakanksha
- Department of Genetics, University of Delhi South Campus, New Delhi 110021, Delhi, India
| | - Rahul Kumar
- International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, Delhi, India
| | - Satish Kumar Yadava
- Centre for Genetic Manipulation of Crop Plants, University of Delhi South Campus, New Delhi 110021, Delhi, India
| | - Ajay Kumar
- Department of Plant Science, School of Biological Sciences, Central University of Kerala, Kasaragod 671316, Kerala, India
| | - Nirala Ramchiary
- School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, Delhi, India
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Integrative Omics Analysis of Three Oil Palm Varieties Reveals (Tanzania × Ekona) TE as a Cold-Resistant Variety in Response to Low-Temperature Stress. Int J Mol Sci 2022; 23:ijms232314926. [PMID: 36499255 PMCID: PMC9740226 DOI: 10.3390/ijms232314926] [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: 10/28/2022] [Revised: 11/21/2022] [Accepted: 11/24/2022] [Indexed: 12/05/2022] Open
Abstract
Oil palm (Elaeis guineensis Jacq.) is an economically important tropical oil crop widely cultivated in tropical zones worldwide. Being a tropical crop, low-temperature stress adversely affects the oil palm. However, integrative leaf transcriptomic and proteomic analyses have not yet been conducted on an oil palm crop under cold stress. In this study, integrative omics transcriptomic and iTRAQ-based proteomic approaches were employed for three oil palm varieties, i.e., B × E (Bamenda × Ekona), O × G (E. oleifera × Elaeis guineensis), and T × E (Tanzania × Ekona), in response to low-temperature stress. In response to low-temperature stress at (8 °C) for 5 days, a total of 5175 up- and 2941 downregulated DEGs in BE-0_VS_BE-5, and a total of 3468 up- and 2443 downregulated DEGs for OG-0_VS_OG-5, and 3667 up- and 2151 downregulated DEGs for TE-0_VS_TE-5 were identified. iTRAQ-based proteomic analysis showed 349 up- and 657 downregulated DEPs for BE-0_VS_BE-5, 372 up- and 264 downregulated DEPs for OG-0_VS_OG-5, and 500 up- and 321 downregulated DEPs for TE-0_VS_TE-5 compared to control samples treated at 28 °C and 8 °C, respectively. The KEGG pathway correlation of oil palm has shown that the metabolic synthesis and biosynthesis of secondary metabolites pathways were significantly enriched in the transcriptome and proteome of the oil palm varieties. The correlation expression pattern revealed that TE-0_VS_TE-5 is highly expressed and BE-0_VS_BE-5 is suppressed in both the transcriptome and proteome in response to low temperature. Furthermore, numerous transcription factors (TFs) were found that may regulate cold acclimation in three oil palm varieties at low temperatures. Moreover, this study identified proteins involved in stresses (abiotic, biotic, oxidative, and heat shock), photosynthesis, and respiration in iTRAQ-based proteomic analysis of three oil palm varieties. The increased abundance of stress-responsive proteins and decreased abundance of photosynthesis-related proteins suggest that the TE variety may become cold-resistant in response to low-temperature stress. This study may provide a basis for understanding the molecular mechanism for the adaptation of oil palm varieties in response to low-temperature stress in China.
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Alhajhoj MR, Munir M, Sudhakar B, Ali-Dinar HM, Iqbal Z. Common and novel metabolic pathways related ESTs were upregulated in three date palm cultivars to ameliorate drought stress. Sci Rep 2022; 12:15027. [PMID: 36056140 PMCID: PMC9440037 DOI: 10.1038/s41598-022-19399-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 08/29/2022] [Indexed: 11/16/2022] Open
Abstract
Date palm is an important staple crop in Saudi Arabia, and about 400 different date palm cultivars grown here, only 50-60 of them are used commercially. The most popular and commercially consumed cultivars of these are Khalas, Reziz, and Sheshi, which are also widely cultivated across the country. Date palm is high water-demanding crop in oasis agriculture, with an inherent ability to tolerate drought stress. However, the mechanisms by which it tolerates drought stress, especially at the transcriptomic level, are still elusive. This study appraised the physiological and molecular response of three commercial date palm cultivars Khalas, Reziz, and Sheshi at two different field capacities (FC; 100% and 25%) levels. At 25% FC (drought stress), leaf relative water content, chlorophyll, photosynthesis, stomatal conductance, and transpiration were significantly reduced. However, leaf intercellular CO2 concentration and water use efficiency increased under drought stress. In comparison to cvs. Khalas and Reziz, date palm cv. Sheshi showed less tolerance to drought stress. A total of 1118 drought-responsive expressed sequence tags (ESTs) were sequenced, 345 from Khalas, 391 from Reziz, and 382 from Sheshi and subjected to functional characterization, gene ontology classification, KEGG pathways elucidation, and enzyme codes dissemination. Three date palm cultivars deployed a multivariate approach to ameliorate drought stress by leveraging common and indigenous molecular, cellular, biological, structural, transcriptional and reproductive mechanisms. Approximately 50% of the annotated ESTs were related to photosynthesis regulation, photosynthetic structure, signal transduction, auxin biosynthesis, osmoregulation, stomatal conductance, protein synthesis/turnover, active transport of solutes, and cell structure modulation. Along with the annotated ESTs, ca. 45% of ESTs were novel. Conclusively, the study provides novel clues and opens the myriads of genetic resources to understand the fine-tuned drought amelioration mechanisms in date palm.
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Affiliation(s)
- Mohammed Refdan Alhajhoj
- Department of Arid Land Agriculture, College of Agriculture and Food Sciences, King Faisal University, PO Box 31982, Al-Ahsa, Saudi Arabia
| | - Muhammad Munir
- Date Palm Research Center of Excellence, King Faisal University, PO Box 31982, Al-Ahsa, Saudi Arabia
| | - Balakrishnan Sudhakar
- Date Palm Research Center of Excellence, King Faisal University, PO Box 31982, Al-Ahsa, Saudi Arabia
| | - Hassan Muzzamil Ali-Dinar
- Date Palm Research Center of Excellence, King Faisal University, PO Box 31982, Al-Ahsa, Saudi Arabia
| | - Zafar Iqbal
- Central Laboratories, King Faisal University, PO Box 31982, Al-Ahsa, Saudi Arabia.
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Wei J, Shen Y, Dong X, Zhu Y, Cui J, Li H, Zheng G, Tian H, Wang Y, Liu Z. DNA methylation affects freezing tolerance in winter rapeseed by mediating the expression of genes related to JA and CK pathways. Front Genet 2022; 13:968494. [PMID: 36061187 PMCID: PMC9432081 DOI: 10.3389/fgene.2022.968494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 07/29/2022] [Indexed: 11/13/2022] Open
Abstract
Winter rapeseed is the largest source of edible oil in China and is especially sensitive to low temperature, which causes tremendous agricultural yield reduction and economic losses. It is still unclear how DNA methylation regulates the formation of freezing tolerance in winter rapeseed under freezing stress. Therefore, in this study, the whole-genome DNA methylation map and transcriptome expression profiles of freezing-resistant cultivar NTS57 (NS) under freezing stress were obtained. The genome-wide methylation assay exhibited lower levels of methylation in gene-rich regions. DNA methylation was identified in three genomic sequence contexts including CG, CHG and CHH, of which CG contexts exhibited the highest methylation levels (66.8%), followed by CHG (28.6%) and CHH (9.5%). Higher levels of the methylation were found in upstream 2 k and downstream 2 k of gene regions, whereas lowest levels were in the gene body regions. In addition, 331, 437, and 1720 unique differentially methylated genes (DMGs) were identified in three genomic sequence contexts in 17NS under freezing stress compared to the control. Function enrichment analysis suggested that most of enriched DMGs were involved in plant hormones signal transduction, phenylpropanoid biosynthesis and protein processing pathways. Changes of genes expression in signal transduction pathways for cytokinin (CK) and jasmonic acid (JA) implied their involvement in freezing stress responses. Collectively, these results suggested a critical role of DNA methylation in their transcriptional regulation in winter rapeseed under freezing stress.
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Affiliation(s)
- Jiaping Wei
- State Key Laboratory of Aridland Crop Science, Lanzhou, China
| | - Yingzi Shen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Xiaoyun Dong
- College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Yajing Zhu
- Economic Crop Research Institute, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Junmei Cui
- State Key Laboratory of Aridland Crop Science, Lanzhou, China
| | - Hui Li
- College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Guoqiang Zheng
- College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Haiyan Tian
- College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Ying Wang
- College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Zigang Liu
- State Key Laboratory of Aridland Crop Science, Lanzhou, China
- College of Agronomy, Gansu Agricultural University, Lanzhou, China
- *Correspondence: Zigang Liu,
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Liu Y, Pan J, Ni S, Xing B, Cheng K, Peng X. Transcriptome and Metabonomics Combined Analysis Revealed the Defense Mechanism Involved in Hydrogen-Rich Water-Regulated Cold Stress Response of Tetrastigma hemsleyanum. FRONTIERS IN PLANT SCIENCE 2022; 13:889726. [PMID: 35812920 PMCID: PMC9260428 DOI: 10.3389/fpls.2022.889726] [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: 03/04/2022] [Accepted: 05/18/2022] [Indexed: 06/15/2023]
Abstract
The poor resistance to cold stress conditions has become the bottleneck problem in Tetrastigma hemsleyanum (T. hemsleyanum) planting industry. Exogenous hydrogen (H2) plays an important role in improving stress resistance in plants. However, the key factors and regulatory network of plants in response to hydrogen-rich water (HRW) treatment under environmental stress are not clear. Here, we conducted integrative analyses of metabolome and transcriptome profiles to reveal the defense mechanism involved in the HRW-regulated cold stress response of T. hemsleyanum. The application of 75% HRW could alleviate stress damage by decreasing stomatal apparatus density and significantly increasing photosynthetic efficiency and mitigating physiological indexes of resistance, such as Pn, Cond, MDA, SOD, etc., which were changed by cold stress conditions. A total of 7,883 DEGs and 439 DEMs were identified. DEGs were the most relevant to phenylpropanoid, isoflavonoid, monoterpenoid, and flavonoid biosynthesis pathways. Using gene co-expression analysis (WGCNA), we identified one gene module that showed a strong correlation between total antioxidant capacity and transpiration rate. Trend analysis indicated that the phenylpropanoid biosynthesis pathway played a major role in the transcription and metabolism process of HRW treatment under cold stress. Based on the integrated analysis of genes and metabolites, the results showed cold stress upregulated the expression of PAL, CHS, COMT, CCR, AtBG1, etc., resulting in the accumulation of coniferyl alcohol and eriodictyol contents in T. hemsleyanum under cold stress, but the 75% HRW treatment could attenuate the enhancement. The study not only identified the main strategy of HRW protection against cold stress but also provided candidate genes for flavonoid biosynthesis, so as to better improve cold tolerance through molecular breeding techniques.
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Affiliation(s)
- Yuxiu Liu
- Ningbo Municipal Hospital of TCM, Affiliated Hospital of Zhejiang Chinese Medical University, Ningbo, China
- School of Marine Sciences, Ningbo University, Ningbo, China
| | - Junjie Pan
- Chemical Biology Center, Lishui Institute of Agriculture and Forestry Sciences, Lishui, China
| | - Sui Ni
- School of Marine Sciences, Ningbo University, Ningbo, China
| | - Bincong Xing
- Zhejiang Provincial Key Laboratory of Resources Protection and Innovation of Traditional Chinese Medicine, Zhejiang A&F University, Hangzhou, China
| | - Kejun Cheng
- Chemical Biology Center, Lishui Institute of Agriculture and Forestry Sciences, Lishui, China
| | - Xin Peng
- Ningbo Municipal Hospital of TCM, Affiliated Hospital of Zhejiang Chinese Medical University, Ningbo, China
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Wu W, Yang H, Xing P, Dong Y, Shen J, Wu G, Zheng S, Da L, He J, Wu Y. Comparative Transcriptome Analysis Revealed the Freezing Tolerance Signaling Events in Winter Rapeseed ( Brassica rapa L.). Front Genet 2022; 13:871825. [PMID: 35559032 PMCID: PMC9086196 DOI: 10.3389/fgene.2022.871825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 04/01/2022] [Indexed: 11/13/2022] Open
Abstract
Winter rapeseed (Brassica rapa L.) is an important oilseed crop in northwest China. Freezing stress severely limits its production and geographical distribution, and frequent extreme freezing events caused by climate change are increasing the chances of winter freeze-injury. However, the underlying mechanism of B. rapa response to freezing stress remains elusive. Here, B. rapa genome (v3.0) was used as a reference for the comparative transcriptomic analysis of Longyou 6 and Tianyou 2 (strong and weak cold tolerance, respectively) under different freezing stress. Before and after freezing stress, 5,982 and 11,630 unique differentially expressed genes (DEGs) between two cultivars were identified, respectively. After freezing stress, the GO terms in Tianyou 2 were mainly involved in "macromolecule biosynthetic process", and those in Longyou 6 were involved in "response to stimulus" and "oxidoreductase activity". Morphological and physiological results indicated that Longyou 6 retained a higher basal freezing resistance than Tinayou 2, and that cold acclimation could strengthen the basal freezing resistance. Freezing stress could activate the MAPK signal cascades, and the phosphorylation level of Longyou 6 showed a higher increase in response to freezing treatment than Tianyou 2. Based on our findings, it was speculated that the cell membrane of B. rapa perceives external signals under freezing stress, which are then transmitted to the nucleus through the cold-activated MAPK cascades and Ca2+-related protein kinase pathway, thus leading to activation of downstream target genes to enhance the freezing resistance of B. rapa.
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Affiliation(s)
- Wangze Wu
- College of Life Sciences, Northwest Normal University, Lanzhou, China
| | - Haobo Yang
- College of Life Sciences, Northwest Normal University, Lanzhou, China
| | - Peng Xing
- College of Life Sciences, Northwest Normal University, Lanzhou, China
| | - Yun Dong
- Crop Research Institute, Gansu Academy of Agriculture Sciences, Lanzhou, China
| | - Juan Shen
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Guofan Wu
- College of Life Sciences, Northwest Normal University, Lanzhou, China
| | - Sheng Zheng
- College of Life Sciences, Northwest Normal University, Lanzhou, China
| | - Lingling Da
- College of Life Sciences, Northwest Normal University, Lanzhou, China
| | - Jiangtao He
- College of Life Sciences, Northwest Normal University, Lanzhou, China
| | - Yujun Wu
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, China
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Zenda T, Liu S, Dong A, Li J, Wang Y, Liu X, Wang N, Duan H. Omics-Facilitated Crop Improvement for Climate Resilience and Superior Nutritive Value. FRONTIERS IN PLANT SCIENCE 2021; 12:774994. [PMID: 34925418 PMCID: PMC8672198 DOI: 10.3389/fpls.2021.774994] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 11/08/2021] [Indexed: 05/17/2023]
Abstract
Novel crop improvement approaches, including those that facilitate for the exploitation of crop wild relatives and underutilized species harboring the much-needed natural allelic variation are indispensable if we are to develop climate-smart crops with enhanced abiotic and biotic stress tolerance, higher nutritive value, and superior traits of agronomic importance. Top among these approaches are the "omics" technologies, including genomics, transcriptomics, proteomics, metabolomics, phenomics, and their integration, whose deployment has been vital in revealing several key genes, proteins and metabolic pathways underlying numerous traits of agronomic importance, and aiding marker-assisted breeding in major crop species. Here, citing several relevant examples, we appraise our understanding on the recent developments in omics technologies and how they are driving our quest to breed climate resilient crops. Large-scale genome resequencing, pan-genomes and genome-wide association studies are aiding the identification and analysis of species-level genome variations, whilst RNA-sequencing driven transcriptomics has provided unprecedented opportunities for conducting crop abiotic and biotic stress response studies. Meanwhile, single cell transcriptomics is slowly becoming an indispensable tool for decoding cell-specific stress responses, although several technical and experimental design challenges still need to be resolved. Additionally, the refinement of the conventional techniques and advent of modern, high-resolution proteomics technologies necessitated a gradual shift from the general descriptive studies of plant protein abundances to large scale analysis of protein-metabolite interactions. Especially, metabolomics is currently receiving special attention, owing to the role metabolites play as metabolic intermediates and close links to the phenotypic expression. Further, high throughput phenomics applications are driving the targeting of new research domains such as root system architecture analysis, and exploration of plant root-associated microbes for improved crop health and climate resilience. Overall, coupling these multi-omics technologies to modern plant breeding and genetic engineering methods ensures an all-encompassing approach to developing nutritionally-rich and climate-smart crops whose productivity can sustainably and sufficiently meet the current and future food, nutrition and energy demands.
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Affiliation(s)
- Tinashe Zenda
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, China
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding, China
- Department of Crop Science, Faculty of Agriculture and Environmental Science, Bindura University of Science Education, Bindura, Zimbabwe
| | - Songtao Liu
- Academy of Agriculture and Forestry Sciences, Hebei North University, Zhangjiakou, China
| | - Anyi Dong
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, China
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding, China
| | - Jiao Li
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, China
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding, China
| | - Yafei Wang
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, China
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding, China
| | - Xinyue Liu
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, China
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding, China
| | - Nan Wang
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, China
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding, China
| | - Huijun Duan
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, China
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding, China
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15
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Neto JCR, Vieira LR, de Aquino Ribeiro JA, de Sousa CAF, Júnior MTS, Abdelnur PV. Metabolic effect of drought stress on the leaves of young oil palm (Elaeis guineensis) plants using UHPLC-MS and multivariate analysis. Sci Rep 2021; 11:18271. [PMID: 34521943 PMCID: PMC8440612 DOI: 10.1038/s41598-021-97835-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 08/30/2021] [Indexed: 01/14/2023] Open
Abstract
The expansion of the oil palm in marginal areas can face challenges, such as water deficit, leading to an impact on palm oil production. A better understanding of the biological consequences of abiotic stresses on this crop can result from joint metabolic profiling and multivariate analysis. Metabolic profiling of leaves was performed from control and stressed plants (7 and 14 days of stress). Samples were extracted and analyzed on a UHPLC-ESI-Q-TOF-HRMS system. Acquired data were processed using XCMS Online and MetaboAnalyst for multivariate and pathway activity analysis. Metabolism was affected by drought stress through clear segregation between control and stressed groups. More importantly, metabolism changed through time, gradually from 7 to 14 days. The pathways most affected by drought stress were: starch and sucrose metabolism, glyoxylate and dicarboxylate metabolism, alanine, aspartate and glutamate metabolism, arginine and proline metabolism, and glycine, serine and threonine metabolism. The analysis of the metabolic profile were efficient to correlate and differentiate groups of oil palm plants submitted to different levels of drought stress. Putative compounds and their affected pathways can be used in future multiomics analysis.
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Affiliation(s)
- Jorge Candido Rodrigues Neto
- Institute of Chemistry, Federal University of Goiás, Campus Samambaia, Goiânia, GO, 74690-900, Brazil.,Brazilian Agricultural Research Corporation, Embrapa Agroenergy, Brasília, DF, 70770-901, Brazil
| | - Letícia Rios Vieira
- Graduate Program of Plant Biotechnology, Federal University of Lavras, CP 3037, Lavras, MG, 37200-000, Brazil.,Brazilian Agricultural Research Corporation, Embrapa Agroenergy, Brasília, DF, 70770-901, Brazil
| | | | | | - Manoel Teixeira Souza Júnior
- Graduate Program of Plant Biotechnology, Federal University of Lavras, CP 3037, Lavras, MG, 37200-000, Brazil.,Brazilian Agricultural Research Corporation, Embrapa Agroenergy, Brasília, DF, 70770-901, Brazil
| | - Patrícia Verardi Abdelnur
- Institute of Chemistry, Federal University of Goiás, Campus Samambaia, Goiânia, GO, 74690-900, Brazil. .,Brazilian Agricultural Research Corporation, Embrapa Agroenergy, Brasília, DF, 70770-901, Brazil.
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Wei J, Zheng G, Yu X, Liu S, Dong X, Cao X, Fang X, Li H, Jin J, Mi W, Liu Z. Comparative Transcriptomics and Proteomics Analyses of Leaves Reveals a Freezing Stress-Responsive Molecular Network in Winter Rapeseed ( Brassica rapa L.). FRONTIERS IN PLANT SCIENCE 2021; 12:664311. [PMID: 33995460 PMCID: PMC8113625 DOI: 10.3389/fpls.2021.664311] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 03/19/2021] [Indexed: 06/12/2023]
Abstract
Winter rapeseed is susceptible to low temperature during winter in Northwest China, which could lead to a severe reduction of crop production. The freezing temperature could stress the whole plant, especially the leaf, and ultimately harm the survival rate of winter rapeseed. However, the molecular mechanism underlying freezing tolerance is still unclear in winter rapeseed. In this study, a comprehensive investigation of winter rapeseed freezing tolerance was conducted at the levels of transcript, protein, and physiology and biochemistry, using a pair of freezing-sensitive and freezing-resistant cultivars NQF24 and 17NTS57. There were 4,319 unique differentially expressed genes (DEGs) and 137 unique differentially abundant proteins (DAPs) between two cultivars identified in leaf under freezing stress. Function enrichment analysis showed that most of the enriched DEGs and DAPs were involved in plant hormone signal transduction, alpha-linolenic/linoleic acid metabolism, peroxisome, glutathione metabolism, fatty acid degradation, and secondary metabolite biosynthesis pathways. Based on our findings, it was speculated that freezing tolerance formation is caused by increased signal transduction, enhanced biosynthesis of protein, secondary metabolites, and plant hormones, elevated energy supply, greater reactive oxygen species scavenging, and lower lipid peroxidation as well as stronger cell stability in leaf under freezing stress. These results provide a comprehensive profile of leaf response under freezing stress, which have potential to be used as selection indicators of breeding programs to improve freezing tolerance in rapeseed.
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Affiliation(s)
- Jiaping Wei
- Gansu Province Key Laboratory of Aridland Crop Sciences, Lanzhou, China
| | - Guoqiang Zheng
- College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Xingwang Yu
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC, United States
| | - Sushuang Liu
- Department of Life Sciences and Health, Huzhou University, Huzhou, China
| | - Xiaoyun Dong
- College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Xiaodong Cao
- College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Xinling Fang
- College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Hui Li
- College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Jiaojiao Jin
- College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Wenbo Mi
- College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Zigang Liu
- Gansu Province Key Laboratory of Aridland Crop Sciences, Lanzhou, China
- College of Agronomy, Gansu Agricultural University, Lanzhou, China
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Mi W, Liu Z, Jin J, Dong X, Xu C, Zou Y, Xu M, Zheng G, Cao X, Fang X, Zhao C, Mi C. Comparative proteomics analysis reveals the molecular mechanism of enhanced cold tolerance through ROS scavenging in winter rapeseed (Brassica napus L.). PLoS One 2021; 16:e0243292. [PMID: 33434207 PMCID: PMC7802968 DOI: 10.1371/journal.pone.0243292] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 11/19/2020] [Indexed: 02/05/2023] Open
Abstract
Two winter rapeseed cultivars, "NS" (cold tolerant) and "NF" (cold sensitive), were used to reveal the morphological, physiological, and proteomic characteristics in leaves of plants after treatment at -4°C for 12 h(T1) and 24 h(T2), and at room temperature(T0), to understand the molecular mechanisms of cold tolerance. Antioxidant activity and osmotic adjustment ability were higher, and plasma membrane injury was less obvious, in NS than in NF under cold stress. We detected different abundant proteins (DAPs) related to cold tolerance in winter rapeseed through data-independent acquisition (DIA). Compared with NF, A total of 1,235 and 1,543 DAPs were identified in the NSs under T1 and T2, respectively. Compared with NF, 911 proteins were more abundant in NS only after cold treatment. Some of these proteins were related to ROS scavenging through four metabolic pathways: lysine degradation; phenylalanine, tyrosine, and tryptophan; flavonoid biosynthesis; and ubiquinone and other terpenoid-quinone biosynthesis. Analysis of these proteins in the four candidate pathways revealed that they were rapidly accumulated to quickly enhance ROS scavenging and improve the cold tolerance of NS. These proteins were noticeably more abundant during the early stage of cold stress, which was critical for avoiding ROS damage.
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Affiliation(s)
- Wenbo Mi
- Gansu Provincial Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Zigang Liu
- Gansu Provincial Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou, China
- * E-mail:
| | - Jiaojiao Jin
- Gansu Provincial Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Xiaoyun Dong
- Gansu Provincial Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Chunmei Xu
- Gansu Provincial Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Ya Zou
- Gansu Provincial Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Mingxia Xu
- Gansu Provincial Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Guoqiang Zheng
- Gansu Provincial Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Xiaodong Cao
- Gansu Provincial Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Xinling Fang
- Gansu Provincial Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Caixia Zhao
- Gansu Provincial Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Chao Mi
- Gansu Provincial Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou, China
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18
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Yang Y, Saand MA, Abdelaal WB, Zhang J, Wu Y, Li J, Fan H, Wang F. iTRAQ-based comparative proteomic analysis of two coconut varieties reveals aromatic coconut cold-sensitive in response to low temperature. J Proteomics 2020; 220:103766. [DOI: 10.1016/j.jprot.2020.103766] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 03/02/2020] [Accepted: 03/28/2020] [Indexed: 11/28/2022]
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Temperature Stress and Responses in Plants. Int J Mol Sci 2019; 20:ijms20082001. [PMID: 31022827 PMCID: PMC6514902 DOI: 10.3390/ijms20082001] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 04/22/2019] [Indexed: 02/07/2023] Open
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Transcriptome Analysis Reveals Key Cold-Stress-Responsive Genes in Winter Rapeseed ( Brassica rapa L.). Int J Mol Sci 2019; 20:ijms20051071. [PMID: 30832221 PMCID: PMC6429191 DOI: 10.3390/ijms20051071] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 02/22/2019] [Accepted: 02/25/2019] [Indexed: 12/31/2022] Open
Abstract
Low ambient air temperature limits the growth and selection of crops in cold regions, and cold tolerance is a survival strategy for overwintering plants in cold winters. Studies of differences in transcriptional levels of winter rapeseed (Brassica rapa L.) under cold stress can improve our understanding of transcript-mediated cold stress responses. In this study, two winter rapeseed varieties, Longyou-7 (cold-tolerant) and Lenox (cold-sensitive), were used to reveal morphological, physiological, and transcriptome levels after 24 h of cold stress, and 24 h at room temperature, to identify the mechanism of tolerance to cold stress. Compared to Lenox, Longyou-7 has a shorter growth period and greater belowground mass, and exhibits stronger physiological activity after cold stress. Subsequently, more complete genomic annotation was obtained by sequencing. A total of 10,251 and 10,972 differentially expressed genes (DEG) were identified in Longyou-7 and Lenox, respectively. Six terms closely related to cold stress were found by the Gene Ontology (GO) function annotation. Some of these terms had greater upregulated expression in Longyou-7, and the expression of these genes was verified by qRT-PCR. Most of these DEGs are involved in phenylpropanoid biosynthesis, plant hormone signal transduction, ribosome biogenesis, MAPK signaling pathway, basal transcription factors, and photosynthesis. Analysis of the genes involved in the peroxisome pathway revealed that Longyou-7 and Lenox may have different metabolic patterns. Some transcription factors may play an important role in winter rapeseed tolerance to cold stress, and Longyou-7 is slightly slower than Lenox. Our results provide a transcriptome database and candidate genes for further study of winter rapeseed cold stress.
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Wang X, Li M, Liu X, Zhang L, Duan Q, Zhang J. Quantitative Proteomic Analysis of Castor ( Ricinus communis L.) Seeds During Early Imbibition Provided Novel Insights into Cold Stress Response. Int J Mol Sci 2019; 20:E355. [PMID: 30654474 PMCID: PMC6359183 DOI: 10.3390/ijms20020355] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 01/08/2019] [Accepted: 01/08/2019] [Indexed: 12/23/2022] Open
Abstract
Early planting is one of the strategies used to increase grain yield in temperate regions. However, poor cold tolerance in castor inhibits seed germination, resulting in lower seedling emergence and biomass. Here, the elite castor variety Tongbi 5 was used to identify the differential abundance protein species (DAPS) between cold stress (4 °C) and control conditions (30 °C) imbibed seeds. As a result, 127 DAPS were identified according to isobaric tag for relative and absolute quantification (iTRAQ) strategy. These DAPS were mainly involved in carbohydrate and energy metabolism, translation and posttranslational modification, stress response, lipid transport and metabolism, and signal transduction. Enzyme-linked immunosorbent assays (ELISA) demonstrated that the quantitative proteomics data collected here were reliable. This study provided some invaluable insights into the cold stress responses of early imbibed castor seeds: (1) up-accumulation of all DAPS involved in translation might confer cold tolerance by promoting protein synthesis; (2) stress-related proteins probably protect the cell against damage caused by cold stress; (3) up-accumulation of key DAPS associated with fatty acid biosynthesis might facilitate resistance or adaptation of imbibed castor seeds to cold stress by the increased content of unsaturated fatty acid (UFA). The data has been deposited to the ProteomeXchange with identifier PXD010043.
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Affiliation(s)
- Xiaoyu Wang
- College of Life Science, Inner Mongolia University for Nationalities, Tongliao 028000, China.
- Inner Mongolia Key Laboratory for Castor, Tongliao 028000, China.
- Inner Mongolia Industrial Engineering Research Center of Universities for Castor, Tongliao 028000, China.
- Inner Mongolia Collaborate Innovation Cultivate Center for Castor, Tongliao 028000, China.
- Horqin Plant Stress Biology Research Institute of Inner Mongolia University for Nationalities, Tongliao 028000, China.
| | - Min Li
- College of Agriculture, Inner Mongolia University for Nationalities, Tongliao 028000, China.
| | - Xuming Liu
- College of Life Science, Inner Mongolia University for Nationalities, Tongliao 028000, China.
- Inner Mongolia Key Laboratory for Castor, Tongliao 028000, China.
- Inner Mongolia Industrial Engineering Research Center of Universities for Castor, Tongliao 028000, China.
- Inner Mongolia Collaborate Innovation Cultivate Center for Castor, Tongliao 028000, China.
- Horqin Plant Stress Biology Research Institute of Inner Mongolia University for Nationalities, Tongliao 028000, China.
| | - Lixue Zhang
- College of Life Science, Inner Mongolia University for Nationalities, Tongliao 028000, China.
- Inner Mongolia Key Laboratory for Castor, Tongliao 028000, China.
- Inner Mongolia Industrial Engineering Research Center of Universities for Castor, Tongliao 028000, China.
- Inner Mongolia Collaborate Innovation Cultivate Center for Castor, Tongliao 028000, China.
- Horqin Plant Stress Biology Research Institute of Inner Mongolia University for Nationalities, Tongliao 028000, China.
| | - Qiong Duan
- College of Life Science, Inner Mongolia University for Nationalities, Tongliao 028000, China.
- Inner Mongolia Key Laboratory for Castor, Tongliao 028000, China.
- Inner Mongolia Industrial Engineering Research Center of Universities for Castor, Tongliao 028000, China.
- Inner Mongolia Collaborate Innovation Cultivate Center for Castor, Tongliao 028000, China.
- Horqin Plant Stress Biology Research Institute of Inner Mongolia University for Nationalities, Tongliao 028000, China.
| | - Jixing Zhang
- College of Life Science, Inner Mongolia University for Nationalities, Tongliao 028000, China.
- Inner Mongolia Key Laboratory for Castor, Tongliao 028000, China.
- Inner Mongolia Industrial Engineering Research Center of Universities for Castor, Tongliao 028000, China.
- Inner Mongolia Collaborate Innovation Cultivate Center for Castor, Tongliao 028000, China.
- Horqin Plant Stress Biology Research Institute of Inner Mongolia University for Nationalities, Tongliao 028000, China.
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