Gel-Based and Gel-Free Proteomic Technologies

Scherp, Peter; Ku, Ginger; Coleman, Liana; Kheterpal, Indu

doi:10.1007/978-1-61737-960-4_13

Cited by 48 publications

(27 citation statements)

References 32 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The difference in pretreatment, depth of proteome coverage, analyses of isoforms and quantification statistical power often result in poor correspondence between the proteins identified by different proteomic techniques (Scherp et al, 2011). For example, Yin et al (2014) found only 9 of 115 in soybean root tips were commonly detected by gel-based and gel-free proteomics under flooding stress.…”

Section: Discussionmentioning

confidence: 99%

Proteomics and SSH Analyses of ALA-Promoted Fruit Coloration and Evidence for the Involvement of a MADS-Box Gene, MdMADS1

Feng

Zheng

et al. 2016

Front. Plant Sci.

View full text Add to dashboard Cite

Skin color is a key quality attribute of fruits and how to improve fruit coloration has long been a major concern. 5-Aminolevulinic acid (ALA), a natural plant growth regulator, can significantly increase anthocyanin accumulation in fruit skin and therefore effectively improve coloration of many fruits, including apple. However, the molecular mechanism how ALA stimulates anthocyanin accumulation in fruit skin remains unknown. Here, we investigated the impact of ALA on apple skin at the protein and mRNA levels. A total of 85 differentially expressed proteins in apple skins between ALA and water treatment (control) were identified by complementary gel-based and gel-free separation techniques. Most of these differentially expressed proteins were up-regulated by ALA. Function analysis suggested that 87.06% of the ALA-responsive proteins were associated with fruit ripening. To further screen ALA-responsive regulators, we constructed a subtracted cDNA library (tester: ALA treatment; driver: control) and obtained 104 differentially expressed unigenes, of which 38 unigenes were indicators for the fruit ripening-related genes. The differentially changed proteins and transcripts did not correspond well at an individual level, but showed similar regulated direction in function at the pathway level. Among the identified fruit ripening-related genes, the expression of MdMADS1, a developmental transcription regulator of fruit ripening, was positively correlated with expression of anthocyanin biosynthetic genes (MdCHS, MdDFR, MdLDOX, and MdUFGT) in apple skin under ALA treatment. Moreover, overexpression of MdMADS1 enhanced anthocyanin content in transformed apple calli, which was further enhanced by ALA. The anthocyanin content in MdMADS1-silenced calli was less than that in the control with ALA treatment, but higher than that without ALA treatment. These results indicated that MdMADS1 is involved in ALA-induced anthocyanin accumulation. In addition, anthocyanin-related verification in apple calli suggested that the regulation of MdMADS1 on anthocyanin biosynthesis was partially independent of fruit ripening process. Taken together, our findings provide insight into the mechanism how ALA regulates anthocyanin accumulation and add new information on transcriptase regulators of fruit coloration.

show abstract

Section: Discussionmentioning

confidence: 99%

Proteomics and SSH Analyses of ALA-Promoted Fruit Coloration and Evidence for the Involvement of a MADS-Box Gene, MdMADS1

Feng

Zheng

et al. 2016

Front. Plant Sci.

View full text Add to dashboard Cite

show abstract

“…Proteins from all samples were extracted by adding 1 mL of lysis buffer (5M Urea, 2M Thiourea, 2% CHAPS, 2% SB3-10, 0.2% Bio-Lyte (pH 3-10), 2% n-dodecyl-b-d-maltoside, 40 mM Tris, 5 mM PMSF, 2 mM TBP and 150U Benzonase) followed by sonication and addition of 50 mM dithiothreitol (DTT) as described previously [11, 30, 31]. The resulting sample mixture was centrifuged for 30 min at 20,800 x g, and the supernatant was acetone precipitated and resolubilized in 0.5 M triethylammonium bicarbonate buffer (TEAB; pH 8.5) and 0.8 M urea.…”

Section: Methodsmentioning

confidence: 99%

Proteomic analysis reveals cellular pathways regulating carbohydrate metabolism that are modulated in primary human skeletal muscle culture due to treatment with bioactives from Artemisia dracunculus L.

Scherp

Putluri

LeBlanc

et al. 2012

Journal of Proteomics

Self Cite

View full text Add to dashboard Cite

Insulin resistance is a major pathophysiologic abnormality that characterizes metabolic syndrome and type 2 diabetes. A well characterized ethanolic extract of Artemisia dracunculus L., termed PMI 5011, has been shown to improve insulin action in vitro and in vivo, but the cellular mechanisms remain elusive. Using differential proteomics, we have studied mechanisms by which PMI 5011 enhances insulin action in primary human skeletal muscle culture obtained by biopsy from obese, insulin-resistant individuals. Using iTRAQ™ labeling and LC-MS/MS, we have identified over 200 differentially regulated proteins due to treatment with PMI 5011 and insulin stimulation. Bioinformatics analyses determined that several metabolic pathways related to glycolysis, glucose transport and cell signaling were highly represented and differentially regulated in the presence of PMI 5011 indicating that this extract affects several pathways modulating carbohydrate metabolism, including translocation of GLUT4 to the plasma membrane. These findings provide a molecular mechanism by which a botanical extract improves insulin stimulated glucose uptake, transport and metabolism at the cellular level resulting in enhanced whole body insulin sensitivity.

show abstract

“…Methods for protein labeling, electrophoresis, imaging and analysis have been described in detail previously 24, 25, 41, 42. Briefly, protein samples were covalently labeled at lysines with spectrally resolvable CyDye fluorophores (Cy2, Cy3 and Cy5).…”

Section: Methodsmentioning

confidence: 99%

Proteome of Human Subcutaneous Adipose Tissue Stromal Vascular Fraction Cells versus Mature Adipocytes Based on DIGE

Kheterpal

Ku²,

Coleman³

et al. 2011

J. Proteome Res.

Self Cite

View full text Add to dashboard Cite

Adipose tissue contains a heterogeneous population of mature adipocytes, endothelial cells, immune cells, pericytes, and pre-adipocytic stromal/stem cells. To date, the majority of proteomic analyses have focused on intact adipose tissue or isolated adipose stromal/stem cells in vitro. In this study, human subcutaneous adipose tissue from multiple depots (arm and abdomen) obtained from female donors was separated into populations of stromal vascular fraction cells and mature adipocytes. Out of 960 features detected by 2-D gel electrophoresis, a total of 200 features displayed a 2-fold up-or down-regulation relative to each cell population. The protein identity of 136 features was determined. Immunoblot analyses comparing SVF relative to adipocytes confirmed that carbonic anhydrase II was up-regulated in both adipose depots while catalase was up-regulated in the arm only. Bioinformatic analyses of the dataset determined that cytoskeletal, glycogenic, glycolytic, lipid metabolic, and oxidative stress related pathways were highly represented as differentially regulated between the mature adipocytes and stromal vascular fraction cells. These findings extend previous reports in the literature with respect to the adipose tissue proteome and the consequences of adipogenesis. The proteins identified may have value as biomarkers for monitoring the physiology and pathology of cell populations within subcutaneous adipose depots.

show abstract

Gel-Based and Gel-Free Proteomic Technologies

Cited by 48 publications

References 32 publications

Proteomics and SSH Analyses of ALA-Promoted Fruit Coloration and Evidence for the Involvement of a MADS-Box Gene, MdMADS1

Proteomics and SSH Analyses of ALA-Promoted Fruit Coloration and Evidence for the Involvement of a MADS-Box Gene, MdMADS1

Proteomic analysis reveals cellular pathways regulating carbohydrate metabolism that are modulated in primary human skeletal muscle culture due to treatment with bioactives from Artemisia dracunculus L.

Proteome of Human Subcutaneous Adipose Tissue Stromal Vascular Fraction Cells versus Mature Adipocytes Based on DIGE

Contact Info

Product

Resources

About