Proteomic analysis of mouse liver plasma membrane: Use of differential extraction to enrich hydrophobic membrane proteins

Zhang, Lijun; Xie, Jimin; Xie, Wang; Liu, Xiaohui; Tang, Xinke; Cao, Rui; Hu, Weijun; Nie, Song; Fan, Chen; Liang, Songping

doi:10.1002/pmic.200401318

Cited by 73 publications

(94 citation statements)

References 35 publications

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“…3B). Similar results have been reported in 2-DGE-based studies of other organisms, even though those studies contained technical differences like extraction of membrane proteins with Triton X-114 to enrich membrane proteins (Klein et al, 2005;Zhang et al, 2005;Mattow et al, 2007). For example, the very recent 2-DGE analysis of the plasma membrane proteome of mycobacteria identified a maximal number of three TMDs in a protein (Mattow et al, 2007).…”

Section: Sec-mudpit Approach Identifies a 3-fold Higher Number Of Memsupporting

confidence: 67%

In-Depth Investigation of the Soybean Seed-Filling Proteome and Comparison with a Parallel Study of Rapeseed

Agrawal

Hajdúch²,

Graham³

et al. 2008

Plant Physiology

111

123

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To better understand the metabolic processes of seed filling in soybean (Glycine max), two complementary proteomic approaches, two-dimensional gel electrophoresis (2-DGE) and semicontinuous multidimensional protein identification technology (Sec-MudPIT) coupled with liquid chromatography-mass spectrometry, were employed to analyze whole seed proteins at five developmental stages. 2-DGE and Sec-MudPIT analyses collectively identified 478 nonredundant proteins with only 70 proteins common to both datasets. 2-DGE data revealed that 38% of identified proteins were represented by multiple 2-DGE species. Identified proteins belonged to 13 (2-DGE) and 15 (Sec-MudPIT) functional classes. Proteins involved in metabolism, protein destination and storage, and energy were highly represented, collectively accounting for 61.1% (2-DGE) and 42.2% (Sec-MudPIT) of total identified proteins. Membrane proteins, based upon transmembrane predictions, were 3-fold more prominent in Sec-MudPIT than 2-DGE. Data were integrated into an existing soybean proteome database (www.oilseedproteomics.missouri.edu). The integrated quantitative soybean database was compared to a parallel study of rapeseed (Brassica napus) to further understand the regulation of intermediary metabolism in protein-rich versus oil-rich seeds. Comparative analyses revealed (1) up to 3-fold higher expression of fatty acid biosynthetic proteins during seed filling in rapeseed compared to soybean; and (2) approximately a 48% higher number of protein species and a net 80% higher protein abundance for carbon assimilatory and glycolytic pathways leading to fatty acid synthesis in rapeseed versus soybean. Increased expression of glycolytic and fatty acid biosynthetic proteins in rapeseed compared to soybean suggests that a possible mechanistic basis for higher oil in rapeseed involves the concerted commitment of hexoses to glycolysis and eventual de novo fatty acid synthesis pathways.Plant seeds accumulate proteins, oils, and carbohydrates because these nitrogen and carbon reserves are necessary for early seed germination and seedling growth (for review, see Weber et al., 2005). These reserve components are synthesized during an extended phase of seed development, loosely termed seed filling. Seed filling is the period when rapid metabolic and morphological (size, weight, and color) changes occur, encompassing cellular processes that include cell expansion and the early stage of desiccation (Rubel et al., 1972;Mienke et al., 1981;Agrawal and Thelen, 2006). Seed filling is also the period that largely determines the relative levels of storage reserves in seeds. The relative proportion of storage components in seeds varies dramatically among different plant species. For example, soybean (Glycine max) seed contains approximately 40% protein and 20% oil (Hill and Breidenbach, 1974;Ohlrogge and Kuo, 1984). In contrast, seed of oilseed rape (Brassica napus; also called rapeseed or canola) contains approximately 15% protein and 40% oil (Norton and Harris, 1975). To gain insight into...

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Section: Sec-mudpit Approach Identifies a 3-fold Higher Number Of Memsupporting

confidence: 67%

In-Depth Investigation of the Soybean Seed-Filling Proteome and Comparison with a Parallel Study of Rapeseed

Agrawal

Hajdúch²,

Graham³

et al. 2008

Plant Physiology

111

123

View full text Add to dashboard Cite

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“…yeast membrane proteins with a grand average of hydropathy (GRAVY) value ,0.4 [9], which falls into the solubility range commonly detected on 2D gels. Our previous study [30] also showed that PM proteins can be better separated by 2-DE through an optimized extraction method. So in this work, 2-DE methodology was used to analyze the liver PM proteome, and 13 protein spots with a greater than 2-fold difference were identified.…”

Section: Discussionmentioning

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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“…Membrane proteins were extracted with 2% Triton X-114 detergent for temperature-dependent phase separation and precipitated by ice-cold acetone (37). Samples from different culture conditions were analyzed by SDS-polyacrylamide gel electrophoresis.…”

Section: Methodsmentioning

confidence: 99%

Characterization and Molecular Mechanism of AroP as an Aromatic Amino Acid and Histidine Transporter in Corynebacterium glutamicum

Shang

Zhang

et al. 2013

Journal of Bacteriology

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bCorynebacterium glutamicum is equipped with abundant membrane transporters to adapt to a changing environment. Many amino acid transporters have been identified in C. glutamicum, but histidine uptake has not been investigated in detail. Here, we identified the aromatic amino acid transporter encoded by aroP as a histidine transporter in C. glutamicum by a combination of the growth and histidine uptake features. Characterization of histidine uptake showed that AroP has a moderate affinity for histidine, with a K m value of 11.40 ؎ 2.03 M, and histidine uptake by AroP is competitively inhibited by the aromatic amino acids. Among the four substrates, AroP exhibits a stronger preference for tryptophan than for tyrosine, phenylalanine, and histidine. Homology structure modeling and molecular docking were performed to predict the substrate binding modes and conformational changes during substrate transport. These results suggested that tryptophan is best accommodated in the binding pocket due to shape compatibility, strong hydrophobic interactions, and the lowest binding energy, which is consistent with the observed substrate preference of AroP. Furthermore, the missense mutations of the putative substrate binding sites verified that Ser24, Ala28, and Gly29 play crucial roles in substrate binding and are highly conserved in the Gram-positive bacteria. Finally, the expression of aroP is not significantly affected by extracellular histidine or aromatic amino acids, indicating that the physiological role of AroP may be correlated with the increased fitness of C. glutamicum to assimilate extracellular amino acid for avoiding the high energy cost of amino acid biosynthesis.

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Proteomic analysis of mouse liver plasma membrane: Use of differential extraction to enrich hydrophobic membrane proteins

Cited by 73 publications

References 35 publications

In-Depth Investigation of the Soybean Seed-Filling Proteome and Comparison with a Parallel Study of Rapeseed

In-Depth Investigation of the Soybean Seed-Filling Proteome and Comparison with a Parallel Study of Rapeseed

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

Characterization and Molecular Mechanism of AroP as an Aromatic Amino Acid and Histidine Transporter in Corynebacterium glutamicum

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