Gel-free quantitative proteomic approach to identify cotyledon proteins in soybean under flooding stress

Kamal, Abu Hena Mostafa; Hamid, Rizwan; Sakata, Katsumi; Komatsu, Setsuko

doi:10.1016/j.jprot.2014.08.014

Cited by 37 publications

(19 citation statements)

References 70 publications

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“…Ferrous iron and H 2 O 2 produce the hydroxyl radicals through Fenton reactions that are most hazardous type of ROS in plant cells that are potentially neutralized by the ferritin. Triosephosphate isomerase generates the reversible alteration of dihydroxyacetone phosphate to glyceraldehyde-3-phosphate and is involved in many metabolic pathways, including glycolysis, the Calvin cycle, and glycerol metabolism (Kamal et al, 2015 ). Glucose catabolism might be amplified under salt stress in wheat for supplementary energy for the detoxification and repair of damage caused by oxidative molecules (Gao et al, 2011 ).…”

Section: Changes In Wheat Proteome Composition Under Drought and Salimentioning

confidence: 99%

Wheat proteomics: proteome modulation and abiotic stress acclimation

2014

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Cellular mechanisms of stress sensing and signaling represent the initial plant responses to adverse conditions. The development of high-throughput “Omics” techniques has initiated a new era of the study of plant molecular strategies for adapting to environmental changes. However, the elucidation of stress adaptation mechanisms in plants requires the accurate isolation and characterization of stress-responsive proteins. Because the functional part of the genome, namely the proteins and their post-translational modifications, are critical for plant stress responses, proteomic studies provide comprehensive information about the fine-tuning of cellular pathways that primarily involved in stress mitigation. This review summarizes the major proteomic findings related to alterations in the wheat proteomic profile in response to abiotic stresses. Moreover, the strengths and weaknesses of different sample preparation techniques, including subcellular protein extraction protocols, are discussed in detail. The continued development of proteomic approaches in combination with rapidly evolving bioinformatics tools and interactive databases will facilitate understanding of the plant mechanisms underlying stress tolerance.

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Section: Changes In Wheat Proteome Composition Under Drought and Salimentioning

confidence: 99%

Wheat proteomics: proteome modulation and abiotic stress acclimation

2014

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“…The downside of flood disasters is that it resulted in serious negative effects on the psychology of local residents, food security, the environment, and the regional economy [2][3][4][5][6][7][8]. Flood events, on the contrary, play a vital role in agriculture by transporting and providing a huge amount of silt and fertilized sediment to feed the agricultural land in inundated areas [9][10][11][12]. The aquatic fauna is diversified and becomes a valuable source of protein for local people.…”

Section: Introductionmentioning

confidence: 99%

Object-Based Flood Mapping and Affected Rice Field Estimation with Landsat 8 OLI and MODIS Data

Dao

Liou

2015

Remote Sensing

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Cambodia is one of the most flood-prone countries in Southeast Asia. It is geographically situated in the downstream region of the Mekong River with a lowland floodplain in the middle, surrounded by plateaus and high mountains. It usually experiences devastating floods induced by an overwhelming concentration of rainfall water over the Tonle Sap Lake's and Mekong River's banks during monsoon seasons. Flood damage assessment in the rice ecosystem plays an important role in this region as local residents rely heavily on agricultural production. This study introduced an object-based approach to flood mapping and affected rice field estimation in central Cambodia. In this approach, image segmentation processing was conducted with optimal scale parameter estimation based on the variation of objects' local variances. The inundated area was identified by using Landsat 8 images with an overall accuracy of higher than 95% compared to those derived from finer spatial resolution images. Moderate Resolution Imaging Spectroradiometer (MODIS) vegetation index products were utilized to identify the paddy rice field based on seasonal inter-variation between vegetation and water index during the transplanting stage. The rice classification result was well correlated with the statistical data at a commune level (R 2 = 0.675). The flood mapping and affected rice estimation results are useful to provide local governments with valuable information for flooding mitigation and post-flooding compensation and restoration.

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“…In the present study, we investigated the seed proteome of G. max and G. soja by a label‐free quantitative technique combined with PSP to elucidate the differences in low‐abundant proteins. Gel‐free label‐free quantitative proteomics (Neilson et al., 2011) has been conducted in crops including soybean (Kamal, Rashid, Sakata, & Komatsu, 2015; Nouri & Komatsu, 2010), tomato ( Solanum lycopersicum L.; Kilambi et al., 2016), barley ( Hordeum vulgare L.; Mahalingam, 2017), rice ( Oryza sativa L.; Neilson et al., 2011), and corn ( Zea mays L.; Marcon et al., 2013). The difficulty in seed proteomics is that the abundant seed storage proteins have often hampered deep coverage of the seed proteome.…”

Section: Discussionmentioning

confidence: 99%

“…Unlike genomic information, the proteome, which is located at downstream, is diverse and modified according to environmental conditions even in the same accession. There are reports of proteomic analyses of soybean at different developmental stages or under several environmental stresses, including flooding, hormone treatment, and salt stress (Kamal et al., 2015; Komatsu et al., 2013). A soybean proteome database (http://proteome.dc.affrc.go.jp/Soybean/) has also been constructed and has provided us with valuable information, including both proteomic and other omic data.…”

Section: Discussionmentioning

confidence: 99%

Comparative analysis of seed proteome of Glycine max and Glycine soja

Hashiguchi

Tanaka

et al. 2020

Crop Science

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Soybean, a globally important grain legume, contains large amounts of proteins, lipids, and secondary metabolites and, when ingested, has a wide array of physiological functions that may improve human health. In the development of cultivated soybean [Glycine max (L.) Merr.] with improved abiotic and biotic stress resistance, high yield, and seed quality, wild soybean (Glycine soja Siebold & Zucc.) has been an excellent source of germplasm, owing to its genetic diversity. Although genomic differences between the two species have been intensively studied, the differences in seed protein expression remain poorly understood. In the present study, we used a shotgun proteomic comparative analysis approach to further characterize the seed proteome in cultivated and wild soybean. Protamine sulfate-mediated precipitation successfully decreased the levels of two major proteins that had previously masked the detection of low-abundant proteins. We identified 65 differentially expressed proteins between the two species, with 39 proteins expressed more highly in G. soja and 26 proteins expressed more highly in G. max. Among these proteins, various stress tolerance-related proteins were found in wild soybean, perhaps reflecting its adaptation to diverse ecological conditions. Cultivated soybean expressed high levels of sucrose and lipid biosynthesis proteins, and this was also confirmed at the transcriptional level. Bioinformatic analyses revealed that cellular and metabolic process was the functional category most frequently linked to the differentially expressed proteins. These data provide valuable information that will contribute to a better understanding of soybean seed biology and help to promote G. max breeding for improved agronomic traits using wild relatives.

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Gel-free quantitative proteomic approach to identify cotyledon proteins in soybean under flooding stress

Cited by 37 publications

References 70 publications

Wheat proteomics: proteome modulation and abiotic stress acclimation

Wheat proteomics: proteome modulation and abiotic stress acclimation

Object-Based Flood Mapping and Affected Rice Field Estimation with Landsat 8 OLI and MODIS Data

Comparative analysis of seed proteome of Glycine max and Glycine soja

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