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Galindo-Luján R, Pont L, Quispe F, Sanz-Nebot V, Benavente F. Matrix-Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry Combined with Chemometrics for Protein Profiling and Classification of Boiled and Extruded Quinoa from Conventional and Organic Crops. Foods 2024; 13:1906. [PMID: 38928847 PMCID: PMC11203106 DOI: 10.3390/foods13121906] [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: 05/14/2024] [Revised: 06/03/2024] [Accepted: 06/11/2024] [Indexed: 06/28/2024] Open
Abstract
Quinoa is an Andean crop that stands out as a high-quality protein-rich and gluten-free food. However, its increasing popularity exposes quinoa products to the potential risk of adulteration with cheaper cereals. Consequently, there is a need for novel methodologies to accurately characterize the composition of quinoa, which is influenced not only by the variety type but also by the farming and processing conditions. In this study, we present a rapid and straightforward method based on matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF-MS) to generate global fingerprints of quinoa proteins from white quinoa varieties, which were cultivated under conventional and organic farming and processed through boiling and extrusion. The mass spectra of the different protein extracts were processed using the MALDIquant software (version 1.19.3), detecting 49 proteins (with 31 tentatively identified). Intensity values from these proteins were then considered protein fingerprints for multivariate data analysis. Our results revealed reliable partial least squares-discriminant analysis (PLS-DA) classification models for distinguishing between farming and processing conditions, and the detected proteins that were critical for differentiation. They confirm the effectiveness of tracing the agricultural origins and technological treatments of quinoa grains through protein fingerprinting by MALDI-TOF-MS and chemometrics. This untargeted approach offers promising applications in food control and the food-processing industry.
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Affiliation(s)
- Rocío Galindo-Luján
- Department of Chemical Engineering and Analytical Chemistry, Institute for Research on Nutrition and Food Safety (INSA·UB), University of Barcelona, 08028 Barcelona, Spain; (R.G.-L.); (L.P.); (V.S.-N.)
| | - Laura Pont
- Department of Chemical Engineering and Analytical Chemistry, Institute for Research on Nutrition and Food Safety (INSA·UB), University of Barcelona, 08028 Barcelona, Spain; (R.G.-L.); (L.P.); (V.S.-N.)
- Serra Húnter Program, Generalitat de Catalunya, 08007 Barcelona, Spain
| | - Fredy Quispe
- National Institute of Agricultural Innovation (INIA), Lima 15024, Peru;
| | - Victoria Sanz-Nebot
- Department of Chemical Engineering and Analytical Chemistry, Institute for Research on Nutrition and Food Safety (INSA·UB), University of Barcelona, 08028 Barcelona, Spain; (R.G.-L.); (L.P.); (V.S.-N.)
| | - Fernando Benavente
- Department of Chemical Engineering and Analytical Chemistry, Institute for Research on Nutrition and Food Safety (INSA·UB), University of Barcelona, 08028 Barcelona, Spain; (R.G.-L.); (L.P.); (V.S.-N.)
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2
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Rey E, Maughan PJ, Maumus F, Lewis D, Wilson L, Fuller J, Schmöckel SM, Jellen EN, Tester M, Jarvis DE. A chromosome-scale assembly of the quinoa genome provides insights into the structure and dynamics of its subgenomes. Commun Biol 2023; 6:1263. [PMID: 38092895 PMCID: PMC10719370 DOI: 10.1038/s42003-023-05613-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 11/20/2023] [Indexed: 12/17/2023] Open
Abstract
Quinoa (Chenopodium quinoa Willd.) is an allotetraploid seed crop with the potential to help address global food security concerns. Genomes have been assembled for four accessions of quinoa; however, all assemblies are fragmented and do not reflect known chromosome biology. Here, we use in vitro and in vivo Hi-C data to produce a chromosome-scale assembly of the Chilean accession PI 614886 (QQ74). The final assembly spans 1.326 Gb, of which 90.5% is assembled into 18 chromosome-scale scaffolds. The genome is annotated with 54,499 protein-coding genes, 96.9% of which are located on the 18 largest scaffolds. We also report an updated genome assembly for the B-genome diploid C. suecicum and use it, together with the A-genome diploid C. pallidicaule, to identify genomic rearrangements within the quinoa genome, including a large pericentromeric inversion representing 71.7% of chromosome Cq3B. Repetitive sequences comprise 65.2%, 48.6%, and 57.9% of the quinoa, C. pallidicaule, and C. suecicum genomes, respectively. Evidence suggests that the B subgenome is more dynamic and has expanded more than the A subgenome. These genomic resources will enable more accurate assessments of genome evolution within the Amaranthaceae and will facilitate future efforts to identify variation in genes underlying important agronomic traits in quinoa.
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Affiliation(s)
- Elodie Rey
- 1King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences & Engineering Division (BESE), Thuwal, 23955-6900, Saudi Arabia
| | - Peter J Maughan
- Brigham Young University, Department of Plant and Wildlife Sciences, College of Life Sciences, Provo, UT, 84602, USA
| | - Florian Maumus
- URGI, INRA, Université Paris-Saclay, 78026, Versailles, France
| | - Daniel Lewis
- Brigham Young University, Department of Plant and Wildlife Sciences, College of Life Sciences, Provo, UT, 84602, USA
| | - Leanne Wilson
- Brigham Young University, Department of Plant and Wildlife Sciences, College of Life Sciences, Provo, UT, 84602, USA
| | - Juliana Fuller
- Brigham Young University, Department of Plant and Wildlife Sciences, College of Life Sciences, Provo, UT, 84602, USA
| | - Sandra M Schmöckel
- University of Hohenheim, Institute of Crop Science, Department Physiology of Yield Stability, 70599, Stuttgart, Germany
| | - Eric N Jellen
- Brigham Young University, Department of Plant and Wildlife Sciences, College of Life Sciences, Provo, UT, 84602, USA
| | - Mark Tester
- 1King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences & Engineering Division (BESE), Thuwal, 23955-6900, Saudi Arabia
| | - David E Jarvis
- Brigham Young University, Department of Plant and Wildlife Sciences, College of Life Sciences, Provo, UT, 84602, USA.
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3
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Liu J, Wu Y, Dong G, Zhu G, Zhou G. Progress of Research on the Physiology and Molecular Regulation of Sorghum Growth under Salt Stress by Gibberellin. Int J Mol Sci 2023; 24:ijms24076777. [PMID: 37047750 PMCID: PMC10094886 DOI: 10.3390/ijms24076777] [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: 03/20/2023] [Revised: 03/30/2023] [Accepted: 04/02/2023] [Indexed: 04/14/2023] Open
Abstract
Plant growth often encounters diverse abiotic stresses. As a global resource-based ecological problem, salinity is widely distributed and one of the major abiotic stresses affecting crop yields worldwide. Sorghum, a cereal crop with medium salt tolerance and great value for the development and utilization of salted soils, is an important source of food, brewing, energy, and forage production. However, in soils with high salt concentrations, sorghum experiences low emergence and suppressed metabolism. It has been demonstrated that the effects of salt stress on germination and seedling growth can be effectively mitigated to a certain extent by the exogenous amendment of hormonal gibberellin (GA). At present, most of the studies on sorghum salt tolerance at home and abroad focus on morphological and physiological levels, including the transcriptome analysis of the exogenous hormone on sorghum salt stress tolerance, the salt tolerance metabolism pathway, and the mining of key salt tolerance regulation genes. The high-throughput sequencing technology is increasingly widely used in the study of crop resistance, which is of great significance to the study of plant resistance gene excavation and mechanism. In this study, we aimed to review the effects of the exogenous hormone GA on leaf morphological traits of sorghum seedlings and further analyze the physiological response of sorghum seedling leaves and the regulation of sorghum growth and development. This review not only focuses on the role of GA but also explores the signal transduction pathways of GA and the performance of their responsive genes under salt stress, thus helping to further clarify the mechanism of regulating growth and production under salt stress. This will serve as a reference for the molecular discovery of key genes related to salt stress and the development of new sorghum varieties.
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Affiliation(s)
- Jiao Liu
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou 225009, China
| | - Yanqing Wu
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou 225009, China
| | - Guichun Dong
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou 225009, China
| | - Guanglong Zhu
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou 225009, China
| | - Guisheng Zhou
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou 225009, China
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4
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Poza-Viejo L, Redondo-Nieto M, Matías J, Granado-Rodríguez S, Maestro-Gaitán I, Cruz V, Olmos E, Bolaños L, Reguera M. Shotgun proteomics of quinoa seeds reveals chitinases enrichment under rainfed conditions. Sci Rep 2023; 13:4951. [PMID: 36973333 PMCID: PMC10043034 DOI: 10.1038/s41598-023-32114-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 03/22/2023] [Indexed: 03/29/2023] Open
Abstract
Quinoa is an Andean crop whose cultivation has been extended to many different parts of the world in the last decade. It shows a great capacity for adaptation to diverse climate conditions, including environmental stressors, and, moreover, the seeds are very nutritious in part due to their high protein content, which is rich in essential amino acids. They are gluten-free seeds and contain good amounts of other nutrients such as unsaturated fatty acids, vitamins, or minerals. Also, the use of quinoa hydrolysates and peptides has been linked to numerous health benefits. Altogether, these aspects have situated quinoa as a crop able to contribute to food security worldwide. Aiming to deepen our understanding of the protein quality and function of quinoa seeds and how they can vary when this crop is subjected to water-limiting conditions, a shotgun proteomics analysis was performed to obtain the proteomes of quinoa seeds harvested from two different water regimes in the field: rainfed and irrigated conditions. Differentially increased levels of proteins determined in seeds from each field condition were analysed, and the enrichment of chitinase-related proteins in seeds harvested from rainfed conditions was found. These proteins are described as pathogen-related proteins and can be accumulated under abiotic stress. Thus, our findings suggest that chitinase-like proteins in quinoa seeds can be potential biomarkers of drought. Also, this study points to the need for further research to unveil their role in conferring tolerance when coping with water-deficient conditions.
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Affiliation(s)
- Laura Poza-Viejo
- Department of Biology, Universidad Autónoma de Madrid, Madrid, Spain
| | | | - Javier Matías
- Centro de Investigaciones Científicas y Tecnológicas de Extremadura (CICYTEX), Guadajira, Spain
| | | | | | - Verónica Cruz
- Centro de Investigaciones Científicas y Tecnológicas de Extremadura (CICYTEX), Guadajira, Spain
| | - Enrique Olmos
- Department of Abiotic Stress and Plant Pathology, Centro de Edafología y Biología Aplicada del Segura (CEBAS-CSIC), Murcia, Spain
| | - Luis Bolaños
- Department of Biology, Universidad Autónoma de Madrid, Madrid, Spain
| | - Maria Reguera
- Department of Biology, Universidad Autónoma de Madrid, Madrid, Spain.
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5
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Rasouli F, Kiani-Pouya A, Movahedi A, Wang Y, Li L, Yu M, Pourkheirandish M, Zhou M, Chen Z, Zhang H, Shabala S. Guard Cell Transcriptome Reveals Membrane Transport, Stomatal Development and Cell Wall Modifications as Key Traits Involved in Salinity Tolerance in Halophytic Chenopodium quinoa. PLANT & CELL PHYSIOLOGY 2023; 64:204-220. [PMID: 36355785 DOI: 10.1093/pcp/pcac158] [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: 07/16/2022] [Revised: 11/06/2022] [Accepted: 11/09/2022] [Indexed: 06/16/2023]
Abstract
A comparative investigation was conducted to evaluate transcriptional changes in guard cells (GCs) of closely related halophytic (Chenopodium quinoa) and glycophytic (Spinacia oleracea) species. Plants were exposed to 3 weeks of 250 mM sodium chloride treatment, and GC-enriched epidermal fragments were mechanically prepared. In both species, salt-responsive genes were mainly related to categories of protein metabolism, secondary metabolites, signal transduction and transport systems. Genes related to abscisic acid (ABA) signaling and ABA biosynthesis were strongly induced in quinoa but not in spinach GCs. Also, expression of the genes encoding transporters of amino acids, proline, sugars, sucrose and potassium increased in quinoa GCs under salinity stress. Analysis of cell-wall-related genes suggests that genes involved in lignin synthesis (e.g. lignin biosynthesis LACCASE 4) were highly upregulated by salt in spinach GCs. In contrast, transcripts related to cell wall plasticity Pectin methylesterase3 (PME3) were highly induced in quinoa. Faster stomatal response to light and dark measured by observing kinetics of changes in stomatal conductance in quinoa might be associated with higher plasticity of the cell wall regulated by PME3 Furthermore, genes involved in the inhibition of stomatal development and differentiation were highly expressed by salt in quinoa, but not in spinach. These changes correlated with reduced stomatal density and index in quinoa, thus improving its water use efficiency. The fine modulation of transporters, cell wall modification and controlling stomatal development in GCs of quinoa may have resulted in high K+/Na+ ratio, lower stomatal conductance and higher stomatal speed for better adaptation to salinity stress in quinoa.
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Affiliation(s)
- Fatemeh Rasouli
- Tasmanian Institute of Agriculture, College of Science and Engineering, University of Tasmania, Hobart, TAS 7001, Australia
- International Research Centre for Environmental Membrane Biology, Foshan University, Foshan 528000, China
- State Key Laboratory of Molecular Plant Genetics, Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 201602, China
| | - Ali Kiani-Pouya
- School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC 3010, Australia
- State Key Laboratory of Molecular Plant Genetics, Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 201602, China
| | - Ali Movahedi
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Yuan Wang
- State Key Laboratory of Molecular Plant Genetics, Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 201602, China
| | - Leiting Li
- State Key Laboratory of Molecular Plant Genetics, Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 201602, China
| | - Min Yu
- International Research Centre for Environmental Membrane Biology, Foshan University, Foshan 528000, China
| | - Mohammad Pourkheirandish
- School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Meixue Zhou
- Tasmanian Institute of Agriculture, College of Science and Engineering, University of Tasmania, Hobart, TAS 7001, Australia
| | - Zhonghua Chen
- School of Science and Health, Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW 2747, Australia
| | - Heng Zhang
- State Key Laboratory of Molecular Plant Genetics, Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 201602, China
| | - Sergey Shabala
- Tasmanian Institute of Agriculture, College of Science and Engineering, University of Tasmania, Hobart, TAS 7001, Australia
- International Research Centre for Environmental Membrane Biology, Foshan University, Foshan 528000, China
- School of Biological Sciences, University of Western Australia, Perth, WA 6009, Australia
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6
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A Proteomics Data Mining Strategy for the Identification of Quinoa Grain Proteins with Potential Immunonutritional Bioactivities. Foods 2023; 12:foods12020390. [PMID: 36673481 PMCID: PMC9858122 DOI: 10.3390/foods12020390] [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: 12/21/2022] [Revised: 01/10/2023] [Accepted: 01/11/2023] [Indexed: 01/18/2023] Open
Abstract
Quinoa proteins are attracting global interest for their wide amino acid profile and as a promising source for the development of biomedical treatments, including those against immune-mediated diseases. However, information about the bioactivity of quinoa proteins is scarce. In this study, a quinoa grain proteome map obtained by label-free mass spectrometry-based shotgun proteomics was investigated for the identification of quinoa grain proteins with potential immunonutritional bioactivities, including those related to cancer. After carefully examining the sequence similarities of the 1211 identified quinoa grain proteins against already described bioactive proteins from other plant organisms, 71, 48, and 3 of them were classified as antimicrobial peptides (AMPs), oxidative stress induced peptides (OSIPs), and serine-type protease inhibitors (STPIs), respectively, suggesting their potential as immunomodulatory, anti-inflammatory, and anticancer agents. In addition, data interpretation using Venn diagrams, heat maps, and scatterplots revealed proteome similarities and differences with respect to the AMPs, OSIPs, and STPIs, and the most relevant bioactive proteins in the predominant commercial quinoa grains (i.e., black, red, white (from Peru), and royal (white from Bolivia)). The presented proteomics data mining strategy allows easy screening for potentially relevant quinoa grain proteins and commercial classes for immunonutrition, as a basis for future bioactivity testing.
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7
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Li C, Li Y, Chu P, Hao-hao Z, Wei Z, Cheng Y, Liu X, Zhao F, Li YJ, Zhang Z, Zheng Y, Mu Z. Effects of salt stress on sucrose metabolism and growth in Chinese rose ( Rosa chinensis). BIOTECHNOL BIOTEC EQ 2022. [DOI: 10.1080/13102818.2022.2116356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Affiliation(s)
- Caihua Li
- Economic Crop Research Laboratory, Economic Crops Institute, Jilin Academy of Agricultural Sciences, Changchun, PR China
| | - Yuhuan Li
- Economic Crop Research Laboratory, Economic Crops Institute, Jilin Academy of Agricultural Sciences, Changchun, PR China
| | - Peiyu Chu
- Laboratory of Economic Crops, Agricultural College, Heilongjiang Bayi Agriculture University, Daqing, PR China
| | - Zhao Hao-hao
- Laboratory of Economic Crops, Agricultural College, Heilongjiang Bayi Agriculture University, Daqing, PR China
| | - Zunmiao Wei
- Economic Crop Research Laboratory, Economic Crops Institute, Jilin Academy of Agricultural Sciences, Changchun, PR China
| | - Yan Cheng
- Economic Crop Research Laboratory, Economic Crops Institute, Jilin Academy of Agricultural Sciences, Changchun, PR China
| | - Xianxian Liu
- Economic Crop Research Laboratory, Economic Crops Institute, Jilin Academy of Agricultural Sciences, Changchun, PR China
| | - Fengzhou Zhao
- Laboratory of Economic Crops, Agricultural College, Heilongjiang Bayi Agriculture University, Daqing, PR China
| | - Yan-jun Li
- Economic Crop Research Laboratory, Economic Crops Institute, Jilin Academy of Agricultural Sciences, Changchun, PR China
| | - Zhiwen Zhang
- Laboratory of Economic Crops, Agricultural College, Heilongjiang Bayi Agriculture University, Daqing, PR China
| | - Yi Zheng
- Economic Crop Research Laboratory, Economic Crops Institute, Jilin Academy of Agricultural Sciences, Changchun, PR China
| | - Zhongsheng Mu
- Economic Crop Research Laboratory, Economic Crops Institute, Jilin Academy of Agricultural Sciences, Changchun, PR China
- Laboratory of Economic Crops, Agricultural College, Heilongjiang Bayi Agriculture University, Daqing, PR China
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8
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Cárdenas-Pérez S, Niedojadło K, Mierek-Adamska A, Dąbrowska GB, Piernik A. Maternal salinity influences anatomical parameters, pectin content, biochemical and genetic modifications of two Salicornia europaea populations under salt stress. Sci Rep 2022; 12:2968. [PMID: 35194050 PMCID: PMC8863803 DOI: 10.1038/s41598-022-06385-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 01/17/2022] [Indexed: 11/09/2022] Open
Abstract
Salicornia europaea is among the most salt-tolerant of plants, and is widely distributed in non-tropical regions. Here, we investigated whether maternal habitats can influence different responses in physiology and anatomy depending on environmental conditions. We studied the influence of maternal habitat on S. europaea cell anatomy, pectin content, biochemical and enzymatic modifications under six different salinity treatments of a natural-high-saline habitat (~ 1000 mM) (Ciechocinek [Cie]) and an anthropogenic-lower-saline habitat (~ 550 mM) (Inowrocław [Inw]). The Inw population showed the highest cell area and roundness of stem water storing cells at high salinity and had the maximum proline, carotenoid, protein, catalase activity within salt treatments, and a maximum high and low methyl esterified homogalacturonan content. The Cie population had the highest hydrogen peroxide and peroxidase activity along with the salinity gradient. Gene expression analysis of SeSOS1 and SeNHX1 evidenced the differences between the studied populations and suggested the important role of Na+ sequestration into the vacuoles. Our results suggest that the higher salt tolerance of Inw may be derived from a less stressed maternal salinity that provides a better adaptive plasticity of S. europaea. Thus, the influence of the maternal environment may provide physiological and anatomical modifications of local populations.
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Affiliation(s)
- S Cárdenas-Pérez
- Chair of Geobotany and Landscape Planning, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University, Lwowska 1, 87-100, Toruń, Poland.
| | - K Niedojadło
- Department of Cellular and Molecular Biology, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University, Lwowska 1, 87-100, Toruń, Poland
| | - A Mierek-Adamska
- Department of Genetics, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University, Lwowska 1, 87-100, Toruń, Poland
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Wileńska 4, 87-100, Toruń, Poland
| | - G B Dąbrowska
- Department of Genetics, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University, Lwowska 1, 87-100, Toruń, Poland
| | - A Piernik
- Chair of Geobotany and Landscape Planning, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University, Lwowska 1, 87-100, Toruń, Poland
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9
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Amnan MAM, Aizat WM, Khaidizar FD, Tan BC. Drought Stress Induces Morpho-Physiological and Proteome Changes of Pandanus amaryllifolius. PLANTS (BASEL, SWITZERLAND) 2022; 11:221. [PMID: 35050109 PMCID: PMC8778612 DOI: 10.3390/plants11020221] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Revised: 01/12/2022] [Accepted: 01/13/2022] [Indexed: 05/20/2023]
Abstract
Drought is one of the significant threats to the agricultural sector. However, there is limited knowledge on plant response to drought stress and post-drought recovery. Pandanus amaryllifolius, a moderate drought-tolerant plant, is well-known for its ability to survive in low-level soil moisture conditions. Understanding the molecular regulation of drought stress signaling in this plant could help guide the rational design of crop plants to counter this environmental challenge. This study aimed to determine the morpho-physiological, biochemical, and protein changes of P. amaryllifolius in response to drought stress and during recovery. Drought significantly reduced the leaf relative water content and chlorophyll content of P. amaryllifolius. In contrast, relative electrolyte leakage, proline and malondialdehyde contents, and the activities of antioxidant enzymes in the drought-treated and recovered samples were relatively higher than the well-watered sample. The protein changes between drought-stressed, well-watered, and recovered plants were evaluated using tandem mass tags (TMT)-based quantitative proteomics. Of the 1415 differentially abundant proteins, 74 were significantly altered. The majority of proteins differing between them were related to carbon metabolism, photosynthesis, stress response, and antioxidant activity. This is the first study that reports the protein changes in response to drought stress in Pandanus. The data generated provide an insight into the drought-responsive mechanisms in P. amaryllifolius.
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Affiliation(s)
- Muhammad Asyraf Mohd Amnan
- Centre for Research in Biotechnology for Agriculture (CEBAR), Universiti Malaya, Kuala Lumpur 50603, Malaysia; (M.A.M.A.); (F.D.K.)
| | - Wan Mohd Aizat
- Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, Bangi 43600, Malaysia;
| | - Fiqri Dizar Khaidizar
- Centre for Research in Biotechnology for Agriculture (CEBAR), Universiti Malaya, Kuala Lumpur 50603, Malaysia; (M.A.M.A.); (F.D.K.)
| | - Boon Chin Tan
- Centre for Research in Biotechnology for Agriculture (CEBAR), Universiti Malaya, Kuala Lumpur 50603, Malaysia; (M.A.M.A.); (F.D.K.)
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10
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Di Silvestre D, Passignani G, Rossi R, Ciuffo M, Turina M, Vigani G, Mauri PL. Presence of a Mitovirus Is Associated with Alteration of the Mitochondrial Proteome, as Revealed by Protein–Protein Interaction (PPI) and Co-Expression Network Models in Chenopodium quinoa Plants. BIOLOGY 2022; 11:biology11010095. [PMID: 35053093 PMCID: PMC8773257 DOI: 10.3390/biology11010095] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Revised: 01/03/2022] [Accepted: 01/05/2022] [Indexed: 11/16/2022]
Abstract
Simple Summary Plants often harbor persistent plant virus infection transmitted only vertically through seeds, resulting in no obvious symptoms (cryptic infections). Several studies have shown that such cryptic infections provide resilience against abiotic (and biotic) stress. We have recently discovered a new group of cryptic plant viruses infecting mitochondria (plant mitovirus). Mitochondria are cellular organelles displaying a pivotal role in protecting cells from the stress of nature . Here, we look at the proteomic alterations caused by the mitovirus cryptic infection of Chenopodium quinoa by Systems Biology approaches allowing one to evaluate data at holistic level. Quinoa is a domesticated plant species with many exciting features of abiotic stress resistance, and it is distinguished by its exceptional nutritional characteristics, such as the content and quality of proteins, minerals, lipids, and tocopherols. These features determined the growing interest for the quinoa crop by the scientific community and international organizations since they provide opportunities to produce high-value grains in arid, high-salt and high-UV agroecological environments. We discovered that quinoa lines hosting mitovirus activate some metabolic processes that might help them face drought. These findings present a new perspective for breeding crop plants through the augmented genome provided by accessory cryptic viruses to be investigated in the future. Abstract Plant mitoviruses belong to Mitoviridae family and consist of positive single-stranded RNA genomes replicating exclusively in host mitochondria. We previously reported the biological characterization of a replicating plant mitovirus, designated Chenopodium quinoa mitovirus 1 (CqMV1), in some Chenopodium quinoa accessions. In this study, we analyzed the mitochondrial proteome from leaves of quinoa, infected and not infected by CqMV1. Furthermore, by protein–protein interaction and co-expression network models, we provided a system perspective of how CqMV1 affects mitochondrial functionality. We found that CqMV1 is associated with changes in mitochondrial protein expression in a mild but well-defined way. In quinoa-infected plants, we observed up-regulation of functional modules involved in amino acid catabolism, mitochondrial respiratory chain, proteolysis, folding/stress response and redox homeostasis. In this context, some proteins, including BCE2 (lipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase complex), DELTA-OAT (ornithine aminotransferase) and GR-RBP2 (glycine-rich RNA-binding protein 2) were interesting because all up-regulated and network hubs in infected plants; together with other hubs, including CAT (catalase) and APX3 (L-ascorbate peroxidase 3), they play a role in stress response and redox homeostasis. These proteins could be related to the higher tolerance degree to drought we observed in CqMV1-infected plants. Although a specific causative link could not be established by our experimental approach at this stage, the results suggest a new mechanistic hypothesis that demands further in-depth functional studies.
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Affiliation(s)
- Dario Di Silvestre
- Laboratory of Proteomics and Metabolomics, Institute for Biomedical Technologies (ITB), Department of Biomedical Sciences, National Research Council (CNR), 20054 Milan, Italy; (G.P.); (R.R.); (P.L.M.)
- Correspondence: (D.D.S.); (G.V.)
| | - Giulia Passignani
- Laboratory of Proteomics and Metabolomics, Institute for Biomedical Technologies (ITB), Department of Biomedical Sciences, National Research Council (CNR), 20054 Milan, Italy; (G.P.); (R.R.); (P.L.M.)
| | - Rossana Rossi
- Laboratory of Proteomics and Metabolomics, Institute for Biomedical Technologies (ITB), Department of Biomedical Sciences, National Research Council (CNR), 20054 Milan, Italy; (G.P.); (R.R.); (P.L.M.)
| | - Marina Ciuffo
- Institute for Sustainable Plant Protection, Department of Bio-Food Sciences, National Research Council (CNR), 10135 Turin, Italy; (M.C.); (M.T.)
| | - Massimo Turina
- Institute for Sustainable Plant Protection, Department of Bio-Food Sciences, National Research Council (CNR), 10135 Turin, Italy; (M.C.); (M.T.)
| | - Gianpiero Vigani
- Plant Physiology Unit, Department of Life Sciences and Systems Biology, University of Turin, 10135 Turin, Italy
- Correspondence: (D.D.S.); (G.V.)
| | - Pier Luigi Mauri
- Laboratory of Proteomics and Metabolomics, Institute for Biomedical Technologies (ITB), Department of Biomedical Sciences, National Research Council (CNR), 20054 Milan, Italy; (G.P.); (R.R.); (P.L.M.)
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Athar HUR, Zulfiqar F, Moosa A, Ashraf M, Zafar ZU, Zhang L, Ahmed N, Kalaji HM, Nafees M, Hossain MA, Islam MS, El Sabagh A, Siddique KHM. Salt stress proteins in plants: An overview. FRONTIERS IN PLANT SCIENCE 2022; 13:999058. [PMID: 36589054 PMCID: PMC9800898 DOI: 10.3389/fpls.2022.999058] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 11/23/2022] [Indexed: 05/04/2023]
Abstract
Salinity stress is considered the most devastating abiotic stress for crop productivity. Accumulating different types of soluble proteins has evolved as a vital strategy that plays a central regulatory role in the growth and development of plants subjected to salt stress. In the last two decades, efforts have been undertaken to critically examine the genome structure and functions of the transcriptome in plants subjected to salinity stress. Although genomics and transcriptomics studies indicate physiological and biochemical alterations in plants, it do not reflect changes in the amount and type of proteins corresponding to gene expression at the transcriptome level. In addition, proteins are a more reliable determinant of salt tolerance than simple gene expression as they play major roles in shaping physiological traits in salt-tolerant phenotypes. However, little information is available on salt stress-responsive proteins and their possible modes of action in conferring salinity stress tolerance. In addition, a complete proteome profile under normal or stress conditions has not been established yet for any model plant species. Similarly, a complete set of low abundant and key stress regulatory proteins in plants has not been identified. Furthermore, insufficient information on post-translational modifications in salt stress regulatory proteins is available. Therefore, in recent past, studies focused on exploring changes in protein expression under salt stress, which will complement genomic, transcriptomic, and physiological studies in understanding mechanism of salt tolerance in plants. This review focused on recent studies on proteome profiling in plants subjected to salinity stress, and provide synthesis of updated literature about how salinity regulates various salt stress proteins involved in the plant salt tolerance mechanism. This review also highlights the recent reports on regulation of salt stress proteins using transgenic approaches with enhanced salt stress tolerance in crops.
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Affiliation(s)
- Habib-ur-Rehman Athar
- Institute of Pure and Applied Biology, Bahauddin Zakariya University, Multan, Pakistan
- College of Life Sciences, Northwest A&F University, Yangling, China
| | - Faisal Zulfiqar
- Department of Horticultural Sciences, Faculty of Agriculture and Environment, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
- *Correspondence: Faisal Zulfiqar, ; Kadambot H. M. Siddique,
| | - Anam Moosa
- Department of Plant Pathology, Faculty of Agriculture and Environment, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Muhammad Ashraf
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Lahore, Pakistan
| | - Zafar Ullah Zafar
- Institute of Pure and Applied Biology, Bahauddin Zakariya University, Multan, Pakistan
| | - Lixin Zhang
- College of Life Sciences, Northwest A&F University, Yangling, China
| | - Nadeem Ahmed
- College of Life Sciences, Northwest A&F University, Yangling, China
- Department of Botany, Mohy-ud-Din Islamic University, Nerian Sharif, Pakistan
| | - Hazem M. Kalaji
- Department of Plant Physiology, Institute of Biology, Warsaw University of Life Sciences SGGW, Warsaw, Poland
| | - Muhammad Nafees
- Department of Horticultural Sciences, Faculty of Agriculture and Environment, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Mohammad Anwar Hossain
- Department of Genetics and Plant Breeding, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Mohammad Sohidul Islam
- Department of Agronomy, Hajee Mohammad Danesh Science and Technology University, Dinajpur, Bangladesh
| | - Ayman El Sabagh
- Faculty of Agriculture, Department of Field Crops, Siirt University, Siirt, Türkiye
- Agronomy Department, Faculty of Agriculture, Kafrelsheikh University, Kafrelsheikh, Egypt
| | - Kadambot H. M. Siddique
- The UWA Institute of Agriculture, The University of Western Australia, Petrth WA, Australia
- *Correspondence: Faisal Zulfiqar, ; Kadambot H. M. Siddique,
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Jain N, Farhat S, Kumar R, Singh N, Singh S, Sreevathsa R, Kalia S, Singh NK, Teruhiro T, Rai V. Alteration of proteome in germinating seedlings of piegonpea ( Cajanus cajan) after salt stress. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2021; 27:2833-2848. [PMID: 35035139 PMCID: PMC8720132 DOI: 10.1007/s12298-021-01116-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 10/07/2021] [Accepted: 12/07/2021] [Indexed: 06/14/2023]
Abstract
Pigeonpea (Cajanus cajan) is an important crop in semi-arid regions and a significant source of dietary proteins in India. The plant is sensitive to salinity stress, which adversely affects its productivity. Based on the dosage-dependent influence of salinity stress on the growth and ion contents in the young seedlings of pigeonpea, a comparative proteome analysis of control and salt stressed (150 mM NaCl) plants was conducted using 7 days-old seedlings. Among various amino acids, serine, aspartate and asparagine were the amino acids that showed increment in the root, whereas serine, aspartate and phenylalanine showed an upward trend in shoots under salt stress. Furthermore, a label-free and gel-free comparative Q-Tof, Liquid Chromatography-Mass spectrometry (LC-MS) revealed total of 118 differentially abundant proteins in roots and shoots with and without salt stress conditions. Proteins related to DNA-binding with one finger (Dof) transcription factor family and glycine betaine (GB) biosynthesis were differentially expressed in the shoot and root of the salinity-stressed seedlings. Exogenous application of choline on GB accumulation under salt stress showed the increase of GB pathway in C. cajan. Gene expression analysis for differentially abundant proteins revealed the higher induction of ethanolamine kinase (CcEthKin), choline-phosphate cytidylyltransferase 1-like (CcChoPh), serine hydroxymethyltransferase (CcSHMT) and Dof protein (CcDof29). The results indicate the importance of, choline precursor, serine biosynthetic pathways and glycine betaine synthesis in salinity stress tolerance. The glycine betaine protects plant from cellular damages and acts as osmoticum under stress condition. Protein interaction network (PIN) analysis demonstrated that 61% of the differentially expressed proteins exhibited positive interactions and 10% of them formed the center of the PIN. Further, The PIN analysis also highlighted the potential roles of the cytochrome c oxidases in sensing and signaling cascades governing salinity stress responses in pigeonpea. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s12298-021-01116-w.
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Affiliation(s)
- Neha Jain
- ICAR-National Institute for Plant Biotechnology, Lal Bahadur Shastri Building, Pusa Road, New Delhi, 110012 India
| | - Sufia Farhat
- ICAR-National Institute for Plant Biotechnology, Lal Bahadur Shastri Building, Pusa Road, New Delhi, 110012 India
- IK Gujral Punjab Technical University, Jalandhar, Punjab India
| | - Ram Kumar
- ICAR-National Institute for Plant Biotechnology, Lal Bahadur Shastri Building, Pusa Road, New Delhi, 110012 India
| | - Nisha Singh
- ICAR-National Institute for Plant Biotechnology, Lal Bahadur Shastri Building, Pusa Road, New Delhi, 110012 India
| | - Sangeeta Singh
- ICAR-National Institute for Plant Biotechnology, Lal Bahadur Shastri Building, Pusa Road, New Delhi, 110012 India
| | - Rohini Sreevathsa
- ICAR-National Institute for Plant Biotechnology, Lal Bahadur Shastri Building, Pusa Road, New Delhi, 110012 India
| | | | - Nagendra Kumar Singh
- ICAR-National Institute for Plant Biotechnology, Lal Bahadur Shastri Building, Pusa Road, New Delhi, 110012 India
| | - Takabe Teruhiro
- Research Institute, Meijo University, Nagoya, 468-8502 Japan
| | - Vandna Rai
- ICAR-National Institute for Plant Biotechnology, Lal Bahadur Shastri Building, Pusa Road, New Delhi, 110012 India
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Rao YR, Ansari MW, Sahoo RK, Wattal RK, Tuteja N, Kumar VR. Salicylic acid modulates ACS, NHX1, sos1 and HKT1;2 expression to regulate ethylene overproduction and Na + ions toxicity that leads to improved physiological status and enhanced salinity stress tolerance in tomato plants cv. Pusa Ruby. PLANT SIGNALING & BEHAVIOR 2021; 16:1950888. [PMID: 34252347 PMCID: PMC8526040 DOI: 10.1080/15592324.2021.1950888] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 06/06/2021] [Accepted: 06/26/2021] [Indexed: 05/30/2023]
Abstract
Tomato is an important crop for its high nutritional and medicinal properties. The role of salicylic acid (SA) in 1-aminocyclopropane-1-carboxylate synthase (ACS), sodium-hydrogen exchanger (NHX1), salt overly sensitive 1 (sos1) and high-affinity K+ transporter (HKT1;2) transcripts, and ACS enzyme activity and ethylene (ET) production, and growth and physiological attributes was evaluated in tomato cv. Pusa Ruby under salinity stress. Thirty days-old seedlings treated with 0 mM NaCl, 250 mM NaCl, 250 mM NaCl plus 100 µM SA were assessed for different growth and physiological parameters at 45 DAS. Results showed ACS, NHX1, sos1 and HKT1;2 transcripts were significantly changed in SA treated plants. The ACS enzyme activity and ET content were considerably decreased in SA treated plants. Shoot length (SL), root length (RL), number of leaves (NL), leaf area per plant (LA), shoot fresh weight (SFW) and root fresh weight (RFW) were also improved under SA treatment. Conversely, the electrolyte leakage and sodium ion (Na+) content were significantly reduced in SA treated plants. In addition, the endogenous proline and potassium ion (K+) content, and K+/Na+ ratio were considerably increased under SA treatment. Likewise, antioxidant enzymes (SOD, CAT, APX and GR) profile were better in SA treated plant. The present findings suggest that SA reverse the negative effects of salinity stress and stress induced ET production by modulating ACS, NHX, sos1 and HKT1;2 transcript level, and improving various growth and physiological parameters, and antioxidants enzymes profile. This will contribute to a better understanding of salinity stress tolerance mechanisms of tomato plants involving SA and ET cross talk and ions homeostasis to develop more tolerant plant.
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Affiliation(s)
- Yalaga Rama Rao
- Department of Biotechnology, Vignan University, Vadlamudi, India
| | - Mohammad Wahid Ansari
- Department of Botany, Zakir Husain Delhi College, University of Delhi, New Delhi, India
| | - Ranjan Kumar Sahoo
- Department of Biotechnology, Centurion University of Technology and Management, Bhubaneswar, India
| | - Ratnum Kaul Wattal
- Department of Botany, Zakir Husain Delhi College, University of Delhi, New Delhi, India
| | - Narendra Tuteja
- Plant Molecular Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
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14
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Hussain T, Asrar H, Zhang W, Gul B, Liu X. Combined Transcriptome and Proteome Analysis to Elucidate Salt Tolerance Strategies of the Halophyte Panicum antidotale Retz. FRONTIERS IN PLANT SCIENCE 2021; 12:760589. [PMID: 34804096 PMCID: PMC8598733 DOI: 10.3389/fpls.2021.760589] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 10/05/2021] [Indexed: 05/24/2023]
Abstract
Panicum antidotale, a C4 monocot, has the potential to reclaim saline and drylands and to be utilized as fodder and forage. Its adaptability to survive saline stress has been proven with eco-physiological and biochemical studies. However, little is known about its molecular mechanisms of salt tolerance. In this study, an integrated transcriptome and proteome analysis approach, based on RNA sequencing and liquid chromatography tandem mass spectrometry (LC-MS/MS), was used to identify the said mechanisms. Plants were treated with control (0 mM), low (100 mM), and high (300 mM) sodium chloride (NaCl) treatments to distinguish beneficial and toxic pathways influencing plant biomass. The results indicated differential expression of 3,179 (1,126 upregulated/2,053 downregulated) and 2,172 (898 upregulated/1,274 downregulated) genes (DEGs), and 514 (269 upregulated/245 downregulated) and 836 (494 upregulated/392 downregulated) proteins (DEPs) at 100 and 300 mM NaCl, respectively. Among these, most upregulated genes and proteins were involved in salt resistance strategies such as proline biosynthesis, the antioxidant defense system, ion homeostasis, and sugar accumulation at low salinity levels. On the other hand, the expression of several genes and proteins involved in the respiratory process were downregulated, indicating the inability of plants to meet their energy demands at high salinity levels. Moreover, the impairments in photosynthesis were also evident with the reduced expression of genes regulating the structure of photosystems and increased expression of abscisic acid (ABA) mediated pathways which limits stomatal gas exchange. Similarly, the disturbance in fatty acid metabolism and activation of essential ion transport blockers damaged the integrity of the cell membrane, which was also evident with enhanced malondialdehyde (MDA). Overall, the analysis of pathways revealed that the plant optimal performance at low salinity was related to enhanced metabolism, antioxidative defense, cell growth, and signaling pathways, whereas high salinity inhibited biomass accumulation by altered expression of numerous genes involved in carbon metabolism, signaling, transcription, and translation. The data provided the first global analysis of the mechanisms imparting salt stress tolerance of any halophyte at transcriptome and proteome levels.
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Affiliation(s)
- Tabassum Hussain
- Chinese Academy of Sciences Engineering Laboratory for Efficient Utilization of Saline Resources, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, China
- Dr. M. Ajmal Khan Institute of Sustainable Halophyte Utilization, University of Karachi, Karachi, Pakistan
| | - Hina Asrar
- Dr. M. Ajmal Khan Institute of Sustainable Halophyte Utilization, University of Karachi, Karachi, Pakistan
| | - Wensheng Zhang
- Chinese Academy of Sciences Engineering Laboratory for Efficient Utilization of Saline Resources, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, China
| | - Bilquees Gul
- Dr. M. Ajmal Khan Institute of Sustainable Halophyte Utilization, University of Karachi, Karachi, Pakistan
| | - Xiaojing Liu
- Chinese Academy of Sciences Engineering Laboratory for Efficient Utilization of Saline Resources, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, China
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