Proteomic analysis of low-abundant integral plasma membrane proteins based on gels

Zhang, L. J.; Wang, X. e.; Xu, Peng; Wei, Yehua; Cao, Rui; Liu, Z.; Xiong, Jixian; Yin, Xiaomao; Ping, Cai; Liang, Songping

doi:10.1007/s00018-006-6126-3

Cited by 40 publications

(47 citation statements)

References 38 publications

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“…However, MALDI-MS/MS is known to identify the most prevalent protein present in a gel spot sample (Jun et al, 2012), and the top-ranked hit resulting from LC-MS/MS analysis has also been shown typically to correspond to the most abundant protein among multiple proteins present in a spot (Yang et al, 2007). The spot intensities of different protein constituents were determined using the protein abundance index and the exponentially modified protein abundance index (emPAI; Supplemental Table S3), which have been routinely applied in proteomics workflows (Perkins et al, 1999;Ishihama et al, 2005;Zhang et al, 2006;Yang et al, 2007;Cilia et al, 2011;Taylor et al, 2011). In this study, if more than one protein was identified in a spot, the relative abundance of each protein was determined by calculating the emPAI from the MS/MS data, and the assumption was made that the most abundant protein would account for the observed regulation (Ishihama et al, 2005).…”

Section: Proteomic Changes In Low-oxalate Transgenic Fruitmentioning

confidence: 99%

Reduction of Oxalate Levels in Tomato Fruit and Consequent Metabolic Remodeling Following Overexpression of a Fungal Oxalate Decarboxylase

Chakraborty

Ghosh

et al. 2013

Plant Physiology

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The plant metabolite oxalic acid is increasingly recognized as a food toxin with negative effects on human nutrition. Decarboxylative degradation of oxalic acid is catalyzed, in a substrate-specific reaction, by oxalate decarboxylase (OXDC), forming formic acid and carbon dioxide. Attempts to date to reduce oxalic acid levels and to understand the biological significance of OXDC in crop plants have met with little success. To investigate the role of OXDC and the metabolic consequences of oxalate down-regulation in a heterotrophic, oxalic acid-accumulating fruit, we generated transgenic tomato (Solanum lycopersicum) plants expressing an OXDC (FvOXDC) from the fungus Flammulina velutipes specifically in the fruit. These E8.2-OXDC fruit showed up to a 90% reduction in oxalate content, which correlated with concomitant increases in calcium, iron, and citrate. Expression of OXDC affected neither carbon dioxide assimilation rates nor resulted in any detectable morphological differences in the transgenic plants. Comparative proteomic analysis suggested that metabolic remodeling was associated with the decrease in oxalate content in transgenic fruit. Examination of the E8.2-OXDC fruit proteome revealed that OXDC-responsive proteins involved in metabolism and stress responses represented the most substantially up-and down-regulated categories, respectively, in the transgenic fruit, compared with those of wild-type plants. Collectively, our study provides insights into OXDC-regulated metabolic networks and may provide a widely applicable strategy for enhancing crop nutritional value.

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Section: Proteomic Changes In Low-oxalate Transgenic Fruitmentioning

confidence: 99%

Reduction of Oxalate Levels in Tomato Fruit and Consequent Metabolic Remodeling Following Overexpression of a Fungal Oxalate Decarboxylase

Chakraborty

Ghosh

et al. 2013

Plant Physiology

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“…The differential proteins were then analyzed by Ultimate 3000 instruments (Dionex, Germering, Germany) tandem nanoESI-MS-MS (mass spectrometry, Bruker Daltonics, Bremen, Germany) as previously described [19,21]. Briefly, the peptide mixture (5 ml) was directly subjected to a nanoLC-ESI-tandem MS system, including a PepMap TM C18 m-pre-column (300 mm i.d.…”

Section: -De/ms Technologymentioning

confidence: 99%

Plasma membrane proteome analysis of the early effect of alcohol on liver: implications for alcoholic liver disease

Zhang¹,

Jia²,

Feng³

et al. 2011

ABBS

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In humans, the over-consumption of alcohol can lead to serious liver disease. To examine the early effects of alcohol on liver disease, rats were given sufficient ethanol to develop liver cirrhosis. Rats before the onset of fibrosis were studied in this work. Plasma membranes (PM) of liver were extracted by twice sucrose density gradient centrifugation. The proteome profiles of PM from ethanol-treated rats and the controls were analyzed using two-dimensional gel electrophoresis (2-DE) and isobaric tag for relative and absolute quantitation (iTRAQ) technology. Ethanol treatment altered the amount of 15 different liver proteins: 10 of them were detected by 2-DE and 5 by iTRAQ. Keratin 8 was detected by both methods. Gene ontology analysis of these differentially detected proteins indicated that most of them were involved in important cell functions such as binding activity (including ion, DNA, ATP binding, etc.), cell structure, or enzyme activity. Among these, annexin A2, keratin 8, and keratin 18 were further verified using western blot analysis and annexin A2 was verified by immunohistochemistry. Our results suggested that alcohol has the potential to affect cell structure, adhesion and enzyme activity by altering expression levels of several relevant proteins in the PM. To the best of our knowledge, this is the first time to study the effect of alcohol on the liver PM proteome and it might be helpful for understanding the possible mechanisms of alcohol-induced liver disease.

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“…Pooled NPCs from 4-and 8-week time points were analyzed by 2DE using an IPGphor isoelectronic focusing system (GE Healthcare, USA) and Protein II electrophoresis apparatus (Bio-Rad, USA) as described previously [21,25]. A total of 1 mg of protein from each sample was applied to IPG dry strips (pH 3-10 NL, 180 mm×30 mm×0.5 mm).…”

Section: De and Gel Stainingmentioning

confidence: 99%

“…The Protein II electrophoresis apparatus was used to run the 11.5% separation gels. The gels were then stained with Coomassie Blue G-250 as described previously [25].…”

Section: De and Gel Stainingmentioning

confidence: 99%

Proteome analysis of hepatic non-parenchymal cells of immune liver fibrosis rats

Zhao

Feng

Jia

et al. 2014

Sci. China Life Sci.

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Elucidation of the mechanisms of liver fibrogenesis is important to treat liver fibrosis. In this study, we established rat models of liver fibrosis with stages from 0-1, 2, and 3-4 to 4 at 2, 4, 6, and 8 weeks, respectively, by injection of pig serum. Liver fibrogenesis was detected by Masson's trichrome staining. Rat non-parenchymal cells (NPCs) were enriched 4-fold by Percoll density gradient centrifugation. Protein extracts from NPCs were prepared at 4 and 8 weeks, separated by two-dimensional electrophoresis, and then stained with Coomassie Blue G-250. At 4 weeks, we identified 18 non-redundant differentially expressed proteins of which protein disulfide-isomerase associated protein 3 (PDIA3) and NDUV showed consistent expression at protein and mRNA levels from 4 to 8 weeks. PDIA3 was found to be down-regulated by Western blotting in the rat model and immunohistochemically in human liver. Our results revealed important aspects of the pathogenesis/progression of liver fibrosis and demonstrated important changes in protein expression levels of NPCs at various stages of liver fibrosis. liver fibrosis, proteomics, non-parenchymal cells, protein disulfide-isomerase associated protein 3 Citation:Zhao QQ, Feng YL, Jia XF, Yin L, Zheng Y, Ouyang DS, Zhou HH, Zhang LJ. Proteome analysis of hepatic non-parenchymal cells of immune liver fibrosis rats.

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Proteomic analysis of low-abundant integral plasma membrane proteins based on gels

Cited by 40 publications

References 38 publications

Reduction of Oxalate Levels in Tomato Fruit and Consequent Metabolic Remodeling Following Overexpression of a Fungal Oxalate Decarboxylase

Reduction of Oxalate Levels in Tomato Fruit and Consequent Metabolic Remodeling Following Overexpression of a Fungal Oxalate Decarboxylase

Plasma membrane proteome analysis of the early effect of alcohol on liver: implications for alcoholic liver disease

Proteome analysis of hepatic non-parenchymal cells of immune liver fibrosis rats

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