Omics-based biomarkers for the identification of six Korean cultivars of sweet potato (<i>Ipomoea batatas</i>L. Lam)

Lee, S. J.; Kim, Jae-Yeon; Kim, Y. C.; Ha, Tae-Joung; Lee, B.W.; Chung, Mi Nam; Kim, S. H.; Park, Y. H.; Kim, S.T.

doi:10.1080/14620316.2013.11512999

Cited by 3 publications

(4 citation statements)

References 29 publications

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“…2DE and gel image analyses were performed as reported previously by our research group . Briefly, total proteins (500 μg) were loaded onto the 24 cm IPG strip (immobilized pH 4–7; GE HealthCare, WI, USA).…”

Section: Methodsmentioning

confidence: 99%

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Proteomics of rice and Cochliobolus miyabeanus fungal interaction: Insight into proteins at intracellular and extracellular spaces

Kim

Kwon

et al. 2014

Proteomics

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Necrotrophic fungal pathogen Cochliobolus miyabeanus causes brown spot disease in rice leaves upon infection, resulting in critical rice yield loss. To better understand the rice-C. miyabeanus interaction, we employed proteomic approaches to establish differential proteomes of total and secreted proteins from the inoculated leaves. The 2DE approach after PEG-fractionation of total proteins coupled with MS (MALDI-TOF/TOF and nESI-LC-MS/MS) analyses led to identification of 49 unique proteins out of 63 differential spots. SDS-PAGE in combination with nESI-LC-MS/MS shotgun approach was applied to identify secreted proteins in the leaf apoplast upon infection and resulted in cataloging of 501 unique proteins, of which 470 and 31 proteins were secreted from rice and C. miyabeanus, respectively. Proteins mapped onto metabolic pathways implied their reprogramming upon infection. The enzymes involved in Calvin cycle and glycolysis decreased in their protein abundance, whereas enzymes in the TCA cycle, amino acids, and ethylene biosynthesis increased. Differential proteomes also generated distribution of identified proteins in the intracellular and extracellular spaces, providing a better insight into defense responses of proteins in rice against C. miyabeanus. Established proteome of the rice-C. miyabeanus interaction serves not only as a good resource for the scientific community but also highlights its significance from biological aspects.

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Section: Methodsmentioning

confidence: 99%

“…Trypsin digestion and MALDI‐TOF/TOF‐MS (Applied Biosystems, Framingham, MA, USA) analysis of 2D protein spots were performed as described previously . Data were subjected to a Mass Standard Kit (Applied Biosystems) for the 4700 Proteomics Analyzer (calibration mixture 1).…”

Section: Methodsmentioning

confidence: 99%

Proteomics of rice and Cochliobolus miyabeanus fungal interaction: Insight into proteins at intracellular and extracellular spaces

Kim

Kwon

et al. 2014

Proteomics

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“…Prepared protein samples [T, PS‐supernatant (S), and –pellet (P)] were quantified by 2D Quant Kit (GE Healthcare, Piscatawy, NJ, USA) and resolved on 13% SDS‐PAGE and 2DE (24 cm IPG strip, pH 4–7 in first on Ettan IPGPhor II and 12% SDS‐PAGE in second dimensions on EttanDalt II system) . Western blot and MALDI‐TOF‐TOF analyses were performed as described previously. The 2DE protein spots corresponding to β‐conglycinin subunits (α, α′, and β) and glycinin‐A were eluted from the gel (Supporting Information Fig.…”

mentioning

confidence: 99%

Protamine sulfate precipitation method depletes abundant plant seed‐storage proteins: A case study on legume plants

et al. 2015

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Depletion of abundant proteins is one of the effective ways to improve detection and identification of low-abundance proteins. Our previous study showed that protamine sulfate precipitation (PSP) method can deplete abundant ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) from leaf proteins and is suitable for their in-depth proteome investigation. In this study, we provide evidence that the PSP method can also be effectively used for depletion of abundant seed-storage proteins (SSPs) from the total seed proteins of diverse legume plants including soybean, broad bean, pea, wild soybean, and peanut. The 0.05% protamine sulfate (PS) was sufficient to deplete major SSPs from all legumes tested except for peanut where 0.1% PS was required. SDS-PAGE, Western blotting and 2DE analyses of PS-treated soybean and peanut seed proteins showed enriched spots in PS-supernatant than total proteins. Coefficient of variation percentage (%CV) and principal component analysis of 2DE spots support the reproducibility, suitability, and efficacy of the PSP method for quantitative and comparative seed proteome analysis. MALDI-TOF-TOF successfully identified some protein spots from soybean and peanut. Hence, this simple, reproducible, economical PSP method has a broader application in depleting plant abundant proteins including SSPs in addition to RuBisCO, allowing discussion for comprehensive proteome establishment and parallel comparative studies in plants.

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“…The ( At -OX) Arabidopsis plants also showed an increase in carotenoid biosynthesis, thus enhancing the plant’s adaptability under environmental stress [ 126 ]. Omics-based biomarkers were developed for identifying sweet potato cultivars by applying the proteomic and metabolomic approaches [ 133 ], suggesting that the proteins and metabolites that accumulate differentially may be used as biomarkers to identify stress breeding material for developing new cultivars. The proteogenomic study was performed to functionally characterize the proteomes of sweet potatoes that contribute to map peptides on the haplotype-resolved genome and predicted transcriptome [ 134 ].…”

Section: Proteomics: a Key For Understanding Protein Structure Functi...mentioning

confidence: 99%

A comprehensive overview of omics-based approaches to enhance biotic and abiotic stress tolerance in sweet potato

Ahmed,

Khan,

Xue

et al. 2024

Horticulture Research

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Biotic and abiotic stresses negatively affect the yield and overall plant developmental process, thus causing substantial losses in global sweet potato production. To cope with stresses, sweet potato has evolved numerous strategies to tackle ever-changing surroundings and biological and environmental conditions. The invention of modern sequencing technology and the latest data processing and analysis instruments has paved the way to integrate biological information from different approaches and helps to understand plant system biology more precisely. The advancement in omics technologies has accumulated and provided a great source of information at all levels (genome, transcript, protein, and metabolite) under stressful conditions. These latest molecular tools facilitate us to understand better the plant's responses to stress signaling and help to process/integrate the biological information encoded within the biological system of plants. This review briefly addresses utilizing the latest omics strategies for deciphering the adaptive mechanisms for sweet potatoes' biotic and abiotic stress tolerance via functional genomics, transcriptomics, proteomics, and metabolomics. This information also provides a powerful reference to understand the complex, well-coordinated stress signaling genetic regulatory networks and better comprehend the plant phenotypic responses at the cellular/molecular level under various environmental stimuli, thus accelerating the design of stress-resilient sweet potato via the latest genetic engineering approaches.

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Omics-based biomarkers for the identification of six Korean cultivars of sweet potato (Ipomoea batatasL. Lam)

Cited by 3 publications

References 29 publications

Proteomics of rice and Cochliobolus miyabeanus fungal interaction: Insight into proteins at intracellular and extracellular spaces

Proteomics of rice and Cochliobolus miyabeanus fungal interaction: Insight into proteins at intracellular and extracellular spaces

Protamine sulfate precipitation method depletes abundant plant seed‐storage proteins: A case study on legume plants

A comprehensive overview of omics-based approaches to enhance biotic and abiotic stress tolerance in sweet potato

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