Proteome Science[JOURNAL]
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200 papers
Proteome profiling reveals insights into cold-tolerant growth in sea buckthorn.
He C, Gao G, Zhang J … +2 more , Duan A, Luo H
Proteome Sci · 2016 · PMID 27761102 · Full text
BACKGROUND: Low temperature is one of the crucial environmental factors limiting the productivity and distribution of plants. Sea buckthorn ( L.), a well recognized multipurpose plant species, live successfully in in col...
BACKGROUND: Low temperature is one of the crucial environmental factors limiting the productivity and distribution of plants. Sea buckthorn ( L.), a well recognized multipurpose plant species, live successfully in in cold desert regions. But their molecular mechanisms underlying cold tolerance are not well understood. METHODS: Physiological and biochemical responses to low-temperature stress were studied in seedlings of sea buckthorn. Differentially expressed protein spots were analyzed using multiplexing fluorescent two-dimensional fluorescence difference gel electrophoresis (2D-DIGE) coupled with matrix-assisted laser desorption/ionization (MALDI) time-of-flight/time-of-flight (TOF/TOF) mass spectrometry (MS), the concentration of phytohormone was measured using enzyme-linked immunosorbent assay, and a spectrophotometric assay was used to measure enzymatic reactions. RESULTS: With the increase of cold stress intensity, the photosynthesis rate, transpiration rate, stomatal conductance in leaves and contents of abscisic acid (ABA) and indole acetic acid (IAA) in roots decreased significantly; however, water-use efficiency, ABA and zeatin riboside in leaves increased significantly, while cell membrane permeability, malondialdehyde and IAA in leaves increased at 7 d and then decreased at 14 d. DIGE and MS/MS analysis identified 32 of 39 differentially expressed protein spots under low-temperature stress, and their functions were mainly involved in metabolism, photosynthesis, signal transduction, antioxidative systems and post-translational modification. CONCLUSION: The changed protein abundance and corresponding physiological-biochemical response shed light on the molecular mechanisms related to cold tolerance in cold-tolerant plants and provide key candidate proteins for genetic improvement of plants.
Comparative proteomic analyses of Asian cotton ovules with attached fibers in the early stages of fiber elongation process.
Zhang B, Du SJ, Hu J … +2 more , Miao D, Liu JY
Proteome Sci · 2016 · PMID 27610046 · Full text
BACKGROUND: Plenty of proteomic studies were performed to characterize the allotetraploid upland cotton fiber elongation process, whereas little is known about the elongating diploid cotton fiber proteome. METHODS: In th...
BACKGROUND: Plenty of proteomic studies were performed to characterize the allotetraploid upland cotton fiber elongation process, whereas little is known about the elongating diploid cotton fiber proteome. METHODS: In this study, we used a two-dimensional electrophoresis-based comparative proteomic approach to profile dynamic proteomes of diploid Asian cotton ovules with attached fibers in the early stages of fiber elongation process. One-way ANOVA and Student-Newman-Keuls test were used to find the differentially displayed protein (DDP) spots. RESULTS: A total of 55 protein spots were found having different abundance ranging from 1 to 9 days post-anthesis (DPA) in a two-day interval. These 55 DDP spots were all successfully identified using high-resolution mass spectrometric analyses. Gene ontology analyses revealed that proteoforms involved in energy/carbohydrate metabolism, redox homeostasis, and protein metabolism are the most abundant. In addition, orthologues of the 13 DDP spots were also found in differential proteome of allotetraploid elongating cotton fibers, suggesting their possible essential roles in fiber elongation process. CONCLUSIONS: Our results not only revealed the dynamic proteome change of diploid Asian cotton fiber and ovule during early stages of fiber elongation process but also provided valuable resource for future studies on the molecular mechanism how the polyploidization improves the trait of fiber length.
Identifying EGFR mutation-induced drug resistance based on alpha shape model analysis of the dynamics.
Ma L, Zou B, Yan H
Proteome Sci · 2016 · PMID 27610045 · Full text
BACKGROUND: Epidermal growth factor receptor (EGFR) mutation-induced drug resistance is a difficult problem in lung cancer treatment. Studying the molecular mechanisms of drug resistance can help to develop corresponding...
BACKGROUND: Epidermal growth factor receptor (EGFR) mutation-induced drug resistance is a difficult problem in lung cancer treatment. Studying the molecular mechanisms of drug resistance can help to develop corresponding treatment strategies and benefit new drug design. METHODS: In this study, Rosetta was employed to model the EGFR mutant structures. Then Amber was carried out to conduct molecular dynamics (MD) simulation. Afterwards, we used Computational Geometry Algorithms Library (CGAL) to compute the alpha shape model of the mutants. RESULTS: We analyzed the EGFR mutation-induced drug resistance based on the motion trajectories obtained from MD simulation. We computed alpha shape model of all the trajectory frames for each mutation type. Solid angle was used to characterize the curvature of the atoms at the drug binding site. We measured the knob level of the drug binding pocket of each mutant from two ways and analyzed its relationship with the drug response level. Results show that 90 % of the mutants can be grouped correctly by setting a certain knob level threshold. CONCLUSIONS: There is a strong correlation between the geometric properties of the drug binding pocket of the EGFR mutants and the corresponding drug responses, which can be used to predict the response of a new EGFR mutant to a drug molecule.
Removal of SDS from biological protein digests for proteomic analysis by mass spectrometry.
Ilavenil S, Al-Dhabi NA, Srigopalram S … +7 more , Kim YO, Agastian P, Baaru R, Choi KC, Arasu MV, Park CG, Park KH
Proteome Sci · 2016 · PMID 27601941 · Full text
BACKGROUND: Metal-organic frameworks (MOFs - MIL-101) are the most exciting, high profiled developments in nanotechnology in the last ten years, and it attracted considerable attention owing to their uniform nanoporosity...
BACKGROUND: Metal-organic frameworks (MOFs - MIL-101) are the most exciting, high profiled developments in nanotechnology in the last ten years, and it attracted considerable attention owing to their uniform nanoporosity, large surface area, outer-surface modification and in-pore functionality for tailoring the chemical properties of the material for anchoring specific guest moieties. MOF's have been particularly highlighted for their excellent gas storage and separation properties. Recently biomolecules-based MOF's were used as nanoencapsulators for antitumor and antiretroviral controlled drug delivery studies. However, usage of MOF material for removal of ionic detergent-SDS from biological samples has not been reported to date. Here, first time we demonstrate its novel applications in biological sample preparation for mass spectrometry analysis. METHODS: SDS removal using MIL-101 was assessed for proteomic analysis by mass spectrometry. We analysed removal of SDS from 0.5 % SDS solution alone, BSA mixture and HMEC cells lysate protein mixture. The removal of SDS by MIL-101 was confirmed by MALDI-TOF-MS and LC-MS techniques. RESULTS: In an initial demonstration, SDS has removed effectively from 0.5 % SDS solution by MIL-101via its binding attraction with SDS. Further, the experiment also confirmed that MIL-101 strongly removed the SDS from BSA and cell lysate mixtures. CONCLUSIONS: These results suggest that SDS removal by the MIL-101 method is a practical, simple and broad applicable in proteomic sample processing for MALDI-TOF-MS and LC-MS analysis.
Differential proteins among normal cervix cells and cervical cancer cells with HPV-16 infection, through mass spectrometry-based Proteomics (2D-DIGE) in women from Southern México.
Serafín-Higuera I, Garibay-Cerdenares OL, Illades-Aguiar B … +4 more , Flores-Alfaro E, Jiménez-López MA, Sierra-Martínez P, Alarcón-Romero Ldel C
Proteome Sci · 2016 · PMID 27601940 · Full text
BACKGROUND: Cervical cancer (CC) is the fourth most common cancer in women worldwide with an estimated 528,000 new cases in 2012. The same year México had an incidence of 13,960 and a mortality of 4769 cases. There are s...
BACKGROUND: Cervical cancer (CC) is the fourth most common cancer in women worldwide with an estimated 528,000 new cases in 2012. The same year México had an incidence of 13,960 and a mortality of 4769 cases. There are several diagnosis methods of CC; among the most frequents are the conventional Pap cytology (Pap), colposcopy, and visual inspection with acetic acid (VIA), histopathological examination, tests of imaging and detection of high-risk papilloma virus (HR-HPV) with molecular tests (PCR, hybridization, sequencing). Proteomics is a tool for the detection of new biomarkers that can be associated with clinical stage, histological type, prognosis, and/or response to treatment. In this study we performed a comparative analysis of CC cells with normal cervical cells. The proteomic analysis was carried out with the fluorescent two-dimensional electrophoresis (2D-DIGE) technique to subsequently identify differential protein profiles using Decyder Software, and the selected proteins were identified by Mass Spectrometry (MALDI-TOF). RESULTS: The proteins that showed an increased expression in cervical cancer in comparison with normal cervix cells were: Mimecan, Actin from aortic smooth muscle and Lumican. While Keratin, type II cytoskeletal 5, Peroxiredoxin-1 and 14-3-3 protein sigma showed a decrease in their protein expression level in cervical cancer in comparison with normal cervix cells. CONCLUSIONS: Thus, this study was successful in identifying biomarker signatures for cervical cancer, and might provide new insights into the mechanism of CC progression.
Comparative proteome analysis of abdominal adipose tissues between fat and lean broilers.
Wu CY, Wu YY, Liu CD … +4 more , Wang YX, Na W, Wang N, Li H
Proteome Sci · 2016 · PMID 27594807 · Full text
BACKGROUND: The molecular mechanism underlying broiler fat deposition is still poorly understood. METHOD: Currently, we used two-dimensional gel electrophoresis (2DE) to identify differentially expressed proteins in abdo...
BACKGROUND: The molecular mechanism underlying broiler fat deposition is still poorly understood. METHOD: Currently, we used two-dimensional gel electrophoresis (2DE) to identify differentially expressed proteins in abdominal adipose tissues of birds at 4 week of age derived from Northeast Agricultural University broiler lines divergently selected for abdominal fat content (NEAUHLF). RESULTS: Thirteen differentially expressed protein spots were screened out and identified by matrix-assisted laser desorption-ionization time-of-flight mass spectrometry (MALDI-TOF-MS). The protein spots were matched to thirteen proteins by searching against the NCBInr database. These identified proteins were apolipoprotein A-I (Apo A-I), cytokeratin otokeratin, ATP synthase subunit alpha, peptidyl-prolyl cis-trans isomerase FKBP4 (PPIase FKBP4), aspartate aminotransferase, carbonic anhydrase II (CA-II), prostaglandin-H2 D-isomerase precursor, fibrinogen alpha chain, lamin-A (LMNA), superoxide dismutase [Mn] (MnSOD), heat shock protein beta-1 (HSPβ1) and two predicted proteins. These differentially expressed proteins are involved mainly in lipid metabolism, amino acid metabolism, signal transduction, energy conversion, antioxidant, and cytoskeleton. Differential expression of Apo A-I, PPIase FKBP4, and cytokeratin otokeratin proteins were further confirmed by Western blot analysis. Quantitative real-time RT-PCR analyses showed that, of these 13 differentially expressed proteins, only PPIase FKBP4 and cytokeratin otokeratin were differentially expressed at mRNA level between the two lines. CONCLUSIONS: Our results have provided further information for understanding the basic genetics control of growth and development of broiler adipose tissue.
Investigation of proteome changes in osteoclastogenesis in low serum culture system using quantitative proteomics.
Xiong Q, Zhang L, Zhan S … +2 more , Ge W, Tang P
Proteome Sci · 2016 · PMID 27034619 · Full text
BACKGROUND: RAW 264.7 cells can differentiate into osteoclasts when cultured in medium supplemented with 1 % FBS. However, the proteomic changes in the development of RAW 264.7 cells into osteoclasts in low serum culture...
BACKGROUND: RAW 264.7 cells can differentiate into osteoclasts when cultured in medium supplemented with 1 % FBS. However, the proteomic changes in the development of RAW 264.7 cells into osteoclasts in low serum culture system have not been elucidated. Therefore, we conducted quantitative proteomics analysis to investigate proteomic changes during osteoclastogenesis in low serum culture system. RESULTS: Our study confirmed that mature multinucleated osteoclasts were generated in a low serum culture system, validated by upregulated expression of 15 characteristic marker proteins, including TRAP, CTSK, MMP9, V-ATPase and ITGAV. Proteomics results demonstrated that 549 proteins expressed differentially in osteoclastogenesis in low serum culture system. In-depth bioinformatics analysis suggested that the differentially expressed proteins were mainly involved in mitochondrial activities and energy metabolism, including the electron transport chain pathway, TCA cycle pathway, mitochondrial LC-fatty acid beta-oxidation pathway and fatty acid biosynthesis pathway. The data have been deposited to the ProteomeXchange with identifier PXD001935. CONCLUSION: Osteoclast formation is an ATP consuming procedure, whether occurring in a low serum culture system or a conventional culture system. In contrast to osteoclasts formed in conventional culture system, the fatty acid biosynthesis pathway was upregulated in osteoclasts cultured in low serum condition.
The association of plasma cystatin C proteoforms with diabetic chronic kidney disease.
Yassine HN, Trenchevska O, Dong Z … +5 more , Bashawri Y, Koska J, Reaven PD, Nelson RW, Nedelkov D
Proteome Sci · 2016 · PMID 27019641 · Full text
BACKGROUND: Cystatin C (CysC) is an endogenous cysteine protease inhibitor that can be used to assess the progression of kidney function. Recent studies demonstrate that CysC is a more specific indicator of glomerular fi...
BACKGROUND: Cystatin C (CysC) is an endogenous cysteine protease inhibitor that can be used to assess the progression of kidney function. Recent studies demonstrate that CysC is a more specific indicator of glomerular filtration rate (GFR) than creatinine. CysC in plasma exists in multiple proteoforms. The goal of this study was to clarify the association of native CysC, CysC missing N-terminal Serine (CysC des-S), and CysC without three N-terminal residues (CysC des-SSP) with diabetic chronic kidney disease (CKD). RESULTS: Using mass spectrometric immunoassay, the plasma concentrations of native CysC and the two CysC truncation proteoforms were examined in 111 individuals from three groups: 33 non-diabetic controls, 34 participants with type 2 diabetes (DM) and without CKD and 44 participants with diabetic CKD. Native CysC concentrations were 1.4 fold greater in CKD compared to DM group (p = 0.02) and 1.5 fold greater in CKD compared to the control group (p = 0.001). CysC des-S concentrations were 1.55 fold greater in CKD compared to the DM group (p = 0.002) and 1.9 fold greater in CKD compared to the control group (p = 0.0002). CysC des-SSP concentrations were 1.8 fold greater in CKD compared to the DM group (p = 0.008) and 1.52 fold greater in CKD compared to the control group (p = 0.002). In addition, the concentrations of CysC proteoforms were greater in the setting of albuminuria. The truncated CysC proteoform concentrations were associated with estimated GFR independent of native CysC concentrations. CONCLUSION: Our findings demonstrate a greater amount of CysC proteoforms in diabetic CKD. We therefore suggest assessing the role of cystatin C proteoforms in the progression of CKD.
Stathmin involvement in the maternal embryonic leucine zipper kinase pathway in glioblastoma.
Marie SK, Oba-Shinjo SM, da Silva R … +5 more , Gimenez M, Nunes Reis G, Tassan JP, Rosa JC, Uno M
Proteome Sci · 2016 · PMID 26973435 · Full text
BACKGROUND: Maternal Embryonic Leucine Zipper Kinase (MELK) is a serine/threonine kinase involved in cell cycle, differentiation, proliferation, and apoptosis. These multiple features are consistent with it being a poten...
BACKGROUND: Maternal Embryonic Leucine Zipper Kinase (MELK) is a serine/threonine kinase involved in cell cycle, differentiation, proliferation, and apoptosis. These multiple features are consistent with it being a potential anticancer target. Nevertheless, the MELK pathway in tumorigenesis is not yet completely understood. This study aims to identify proteins associated with MELK pathway in astrocytomas. To this end, proteomic data of the human glioma cell line U87MG transfected with siRNA for MELK were compared with non-target transfected control cells and compared with oligonucleotide microarray data. RESULTS: In both assays, we identified stathmin/oncoprotein 18 (STMN1), involved in cell cycle. STMN1 gene expression was further assessed in a series of 154 astrocytomas and 22 non-neoplastic brain samples by qRT-PCR. STMN1 expression was significantly increased in malignant diffusely infiltrative astrocytomas compared with pilocytic astrocytoma (p < 0.0001). A strong correlation between MELK and STMN1 expressions was observed (r = 0.741, p < 0.0001) in glioblastoma (GBM) samples. However, no difference on survival times was found when compared GBM cases with upregulated and downregulated STMN1 (Breslow = 0.092, median survival time: 11 and 13 months, respectively). Functional assays knocking down MELK by siRNA in GBM cell line showed that gene and protein expression of both MELK and stathmin were diminished. On the other hand, when the same analysis was performed for STMN1, only stathmin gene and protein was silenced. CONCLUSIONS: The results presented herein point stahtmin as a downstream target in the MELK pathway that plays a role in malignant progression of astrocytomas.
Analysis of the immune response of human dendritic cells to Mycobacterium tuberculosis by quantitative proteomics.
Kuo CP, Chang KS, Hsu JL … +5 more , Tsai IF, Lin AB, Wei TY, Wu CL, Lu YT
Proteome Sci · 2016 · PMID 26957948 · Full text
BACKGROUND: The cellular immune response for Mycobacterium tuberculosis (M. tuberculosis) infection remained incompletely understood. To uncover membrane proteins involved in this infection mechanism, an integrated appro...
BACKGROUND: The cellular immune response for Mycobacterium tuberculosis (M. tuberculosis) infection remained incompletely understood. To uncover membrane proteins involved in this infection mechanism, an integrated approach consisting of an organic solvent-assisted membrane protein digestion, stable-isotope dimethyl labeling and liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis was used to comparatively profile the membrane protein expression of human dendritic cells upon heat-killed M. tuberculosis (HKTB) treatment. RESULTS: Organic solvent-assisted trypsin digestion coupled with stable-isotope labeling and LC-MS/MS analysis was applied to quantitatively analyze the membrane protein expression of THP-1 derived dendritic cells. We evaluated proteins that were upregulated in response to HKTB treatment, and applied STRING website database to analyze the correlations between these proteins. Of the investigated proteins, aminopeptidase N (CD13) was found to be largely expressed after HKTB treatment. By using confocal microscopy and flow cytometry, we found that membranous CD13 expression was upregulated and was capable of binding to live mycobacteria. Treatment dendritic cell with anti-CD13 antibody during M. tuberculosis infection enhanced the ability of T cell activation. CONCLUSIONS: Via proteomics data and STRING analysis, we demonstrated that the highly-expressed CD13 is also associated with proteins involved in the antigen presenting process, especially with CD1 proteins. Increasing expression of CD13 on dendritic cells while M. tuberculosis infection and enhancement of T cell activation after CD13 treated with anti-CD13 antibody indicates CD13 positively involved in the pathogenesis of M. tuberculosis.
Label-free proteomic methodology for the analysis of human kidney stone matrix composition.
Witzmann FA, Evan AP, Coe FL … +3 more , Worcester EM, Lingeman JE, Williams JC
Proteome Sci · 2016 · PMID 26924944 · Full text
BACKGROUND: Kidney stone matrix protein composition is an important yet poorly understood aspect of nephrolithiasis. We hypothesized that this proteome is considerably more complex than previous reports have indicated an...
BACKGROUND: Kidney stone matrix protein composition is an important yet poorly understood aspect of nephrolithiasis. We hypothesized that this proteome is considerably more complex than previous reports have indicated and that comprehensive proteomic profiling of the kidney stone matrix may demonstrate relevant constitutive differences between stones. We have analyzed the matrices of two unique human calcium oxalate stones (CaOx-Ia and CaOx-Id) using a simple but effective chaotropic reducing solution for extraction/solubilization combined with label-free quantitative mass spectrometry to generate a comprehensive profile of their proteomes, including physicochemical and bioinformatic analysis.`. RESULTS: We identified and quantified 1,059 unique protein database entries in the two human kidney stone samples, revealing a more complex proteome than previously reported. Protein composition reflects a common range of proteins related to immune response, inflammation, injury, and tissue repair, along with a more diverse set of proteins unique to each stone. CONCLUSION: The use of a simple chaotropic reducing solution and moderate sonication for extraction and solubilization of kidney stone powders combined with label-free quantitative mass spectrometry has yielded the most comprehensive list to date of the proteins that constitute the human kidney stone proteome.
Quantitative succinylome analysis in the liver of non-alcoholic fatty liver disease rat model.
Cheng Y, Hou T, Ping J … +2 more , Chen G, Chen J
Proteome Sci · 2016 · PMID 26843850 · Full text
BACKGROUND: Non-alcoholic fatty liver disease (NAFLD) is a clinical frequent disease. However, its pathogenesis still needs further study, especially the mechanism at the molecular level. The recent identified novel prot...
BACKGROUND: Non-alcoholic fatty liver disease (NAFLD) is a clinical frequent disease. However, its pathogenesis still needs further study, especially the mechanism at the molecular level. The recent identified novel protein post-translational modification, lysine succinylation was reported involved in diverse metabolism and cellular processes. In this study, we performed the quantitative succinylome analysis in the liver of NAFLD model to elucidate the regulatory role of lysine succinylation in NAFLD progression. METHODS: Firstly, experimental model of NAFLD was induced by carbon tetrachloride injection and supplementary high-lipid and low-protein diet. Then series histochemical and biochemical variables were determined. For the quantitative succinylome analysis, tandem mass tags (TMT)-labeling, highly sensitive immune-affinity purification, liquid chromatography-tandem mass spectrometry techniques were applied. Bioinformatics analysis including gene ontology annotation based classification; Wolfpsort based subcellular prediction; function enrichment; protein-protein interaction network construction and conserved succinylation site motifs extraction were performed to decipher the differentially changed succinylated proteins and sites and p-value < 0.05 was selected as threshold. RESULTS: Totally, 815 succinylation sites on 407 proteins were identified, of which 243 succinylation acetylation sites on 178 proteins showed changed succinylation level with the threshold fold change > 1.5. Theses differentially changed succinylated proteins were involved in diverse metabolism pathways and cellular processes including carbon metabolism, amino acid metabolism, fat acid metabolism, binding and catalyzing, anti-oxidation and xenobiotics metabolism. Besides, these differentially changed succinylated proteins were prominently localized to cytoplasm and mitochondria. Moreover, 8 conserved succinylation site motifs were extracted around the succinylation sites. CONCLUSIONS: Protein succinylation was an extensive post-translation modification in rat. The changed succinylation level in diverse proteins may disturb multiple metabolism pathways and promote non-alcoholic fatty liver disease development. This study provided a basis for further characterization of the pathophysiological role of lysine succinylation in NAFLD progression, which laid a foundation for the innovation of novel NAFLD drugs and therapies.
Secretome analysis of rice suspension-cultured cells infected by Xanthomonas oryzae pv.oryza (Xoo).
Chen X, Deng Z, Yu C … +2 more , Yan C, Chen J
Proteome Sci · 2016 · PMID 26839515 · Full text
BACKGROUND: Rice bacterial blight (BB) caused by Xanthomonas oryzae pv.oryzae (Xoo) is one of the most devastating bacterial diseases in rice-growing regions worldwide. The rice-Xoo interaction is a classical model for s...
BACKGROUND: Rice bacterial blight (BB) caused by Xanthomonas oryzae pv.oryzae (Xoo) is one of the most devastating bacterial diseases in rice-growing regions worldwide. The rice-Xoo interaction is a classical model for studying the interaction between plants and pathogens. Secreted proteins play important roles in plant-bacterial interactions, but are poorly studied in the rice-Xoo system. Rice cv. Nipponbare is highly susceptible to Xoo. Here, we used two-dimensional difference gel electrophoresis (2D-DIGE) coupled with MALDI-TOF/TOF mass spectrometry (MS), to investigate secreted proteins in Nipponbare embryo cell suspension culture infected by Xoo. RESULTS: A total of 32 protein spots changed significantly (p < 0.05) by more than 1.5 fold in gel intensity after Xoo inoculation, and were identified by MS. They represent protein products of 11 unique genes, seven from rice and four from Xoo. Of the rice proteins, six up-regulated proteins are involved in cell wall modification, the TCA cycle, glycolysis and redox, while a down-regulated protein, CHIT16, is involved in plant defense. Quantitative Real-Time PCR showed that transcript levels were not correlated with secreted protein levels. Of the Xoo proteins, three of them were possibly located in the extracellular space as shown by transient expression assays in rice protoplasts. Two of the Xoo proteins were previously reported to be likely involved in pathogenicity, and the third gene, Xoo3654, is likely a negative regulator of Xoo virulence as its overexpression reduced Xoo pathogenicity in our study. CONCLUSION: Among the secreted proteins that responded to Xoo inoculation, we identified rice proteins involved in cell defense and Xoo proteins involved in pathogenicity. Our study also showed that Xoo3654 (X2) protein is likely a novel negative regulator of Xoo virulence. These results not only help us better understand the interaction between susceptible rice and Xoo, but also serve as a reference for studying the interaction between other plants and their pathogens.
Isolation and characterization of Bradykinin potentiating peptides from Agkistrodon bilineatus venom.
Munawar A, Zahid A, Negm A … +3 more , Akrem A, Spencer P, Betzel C
Proteome Sci · 2016 · PMID 26770072 · Full text
BACKGROUND: Snake venom is a source of many pharmacologically important molecules. Agkistrodon bilineatus commonly known as Cantil, is spread over Central America particularly in Mexico and Costa Rica. From the venom of...
BACKGROUND: Snake venom is a source of many pharmacologically important molecules. Agkistrodon bilineatus commonly known as Cantil, is spread over Central America particularly in Mexico and Costa Rica. From the venom of Agkistrodon bilineatus we have isolated and characterised six hypotensive peptides, and two bradykinin inhibitor peptides. The IC-50 value of four synthesized peptides was studied, towards angiotensin converting enzyme, in order to study the structure-function relationship of these peptides. RESULTS: The purification of the peptides was carried out by size exclusion chromatography, followed by reverse phase chromatography. Sequences of all peptides were determined applying MALDI-TOF/TOF mass spectrometry. These hypotensive peptides bear homology to bradykinin potentiating peptides and venom vasodilator peptide. The peptide with m/z 1355.53 (M + H)(+1), and the corresponding sequence ZQWAQGRAPHPP, we identified for the first time. A precursor protein containing a fragment of this peptide was reported at genome level, (Uniprot ID P68515), in Bothrops insularis venom gland. These proline rich hypotensive peptides or bradykinin potentiating peptides are usually present in the venom of Crotalinae, and exhibit specificity in binding to the C domain of somatic angiotensin converting enzyme. Four of these hypotensive peptides, were selected and synthesized to obtain the required quantity to study their IC50 values in complex with the angiotensin converting enzyme. The peptide with the sequence ZLWPRPQIPP displayed the lowest IC50 value of 0.64 μM. The IC50 value of the peptide ZQWAQGRAPHPP was 3.63 μM. CONCLUSION: The canonical snake venom BPPs classically display the IPP motif at the C-terminus. Our data suggest that the replacement of the highly conserved hydrophobic isoleucine by histidine does not affect the inhibitory activity, indicating that isoleucine is not mandatory to inhibit the angiotensin converting enzyme. The evaluation of IC 50 values show that the peptide with basic pI value exhibits a lower IC 50 value.
Analysis of protein expression in periodontal pocket tissue: a preliminary study.
Monari E, Cuoghi A, Bellei E … +6 more , Bergamini S, Lucchi A, Tomasi A, Cortellini P, Zaffe D, Bertoldi C
Proteome Sci · 2015 · PMID 26719749 · Full text
BACKGROUND: The periodontal disease is caused by a set of inflammatory disorders characterized by periodontal pocket formation that lead to tooth loss if untreated. The proteomic profile and related molecular conditions...
BACKGROUND: The periodontal disease is caused by a set of inflammatory disorders characterized by periodontal pocket formation that lead to tooth loss if untreated. The proteomic profile and related molecular conditions of pocket tissue in periodontally-affected patients are not reported in literature. To characterize the proteomic profile of periodontally-affected patients, their interproximal periodontal pocket tissue was compared with that of periodontally-healthy patients. Pocket-associated and healthy tissue samples, harvested during surgical therapy, were treated to extract the protein content. Tissues were always collected at sites where no periodontal-pathogenic bacteria were detectable. Proteins were separated using two-dimensional gel electrophoresis and identified by liquid chromatography/mass spectrometry. After identification, four proteins were selected for subsequent Western Blot quantitation both in pathological and healty tissues. RESULTS: A significant unbalance in protein expression between healthy and pathological sites was recorded. Thirty-two protein spots were overall identified, and four proteins (S100A9, HSPB1, LEG7 and 14-3-3) were selected for Western blot analysis of both periodontally-affected and healthy patients. The four selected proteins resulted over-expressed in periodontal pocket tissue when compared with the corresponding tissue of periodontally-healthy patients. The results of Western blot analysis are congruent with the defensive and the regenerative reaction of injured periodontal tissues. CONCLUSIONS: The proteomic analysis was performed for the first time directly on periodontal pocket tissue. The proteomic network highlighted in this study enhances the understanding of periodontal disease pathogenesis necessary for specific therapeutic strategies setting.
Gender-specific effects of intrauterine growth restriction on the adipose tissue of adult rats: a proteomic approach.
de Souza AP, Pedroso AP, Watanabe RL … +7 more , Dornellas AP, Boldarine VT, Laure HJ, do Nascimento CM, Oyama LM, Rosa JC, Ribeiro EB
Proteome Sci · 2015 · PMID 26633942 · Full text
BACKGROUND: Intrauterine growth restriction (IUGR) may program metabolic alterations affecting physiological functions and lead to diseases in later life. The adipose tissue is an important organ influencing energy homeo...
BACKGROUND: Intrauterine growth restriction (IUGR) may program metabolic alterations affecting physiological functions and lead to diseases in later life. The adipose tissue is an important organ influencing energy homeostasis. The present study was aimed at exploring the consequences of IUGR on the retroperitoneal adipose tissue of adult male and female rats, using a proteomic approach. METHODS AND RESULTS: Pregnant Wistar rats were fed with balanced chow, either ad libitum (control group) or restricted to 50 % of control intake (restricted group) during the whole gestation. The offspring were weaned to ad libitum chow and studied at 4 months of age. Retroperitoneal fat was analyzed by two-dimensional gel electrophoresis followed by mass spectrometry. Both male and female restricted groups had low body weight at birth and at weaning but normal body weight at adulthood. The restricted males had normal fat pads weight and serum glucose levels, with a trend to hyperinsulinemia. The restricted females had increased fat pads weight with normal glucose and insulin levels. The restricted males showed up-regulated levels of proteasome subunit α type 3, branched-chain-amino-acid aminotransferase, elongation 1- alpha 1, fatty acid synthase levels, cytosolic malate dehydrogenase and ATP synthase subunit alpha. These alterations point to increased proteolysis and lipogenesis rates and favoring of ATP generation. The restricted females showed down-regulated levels of L-lactate dehydrogenase perilipin-1, mitochondrial branched-chain alpha-keto acid dehydrogenase E1, and transketolase. These findings suggest impairment of glycemic control, stimulation of lipolysis and inhibition of proteolysis, pentose phosphate pathway and lipogenesis rates. In both genders, several proteins involved in oxidative stress and inflammation were affected, in a pattern compatible with impairment of these responses. CONCLUSIONS: The proteomic analysis of adipose tissue showed that, although IUGR affected pathways of substrate and energy metabolism in both males and females, important gender differences were evident. While IUGR males displayed alterations pointing to a predisposition to later development of obesity, the alterations observed in IUGR females pointed to a metabolic status of established obesity, in agreement with their increased fat pads mass.
Hepatocytes respond differently to major dietary trans fatty acid isomers, elaidic acid and trans-vaccenic acid.
Krogager TP, Nielsen LV, Kahveci D … +4 more , Dyrlund TF, Scavenius C, Sanggaard KW, Enghild JJ
Proteome Sci · 2015 · PMID 26628894 · Full text
BACKGROUND: It has been discussed if the adverse health effect associated with the ingestion of trans fatty acids correlates with the food source, as the composition of the isomers varies in different foods. We have inve...
BACKGROUND: It has been discussed if the adverse health effect associated with the ingestion of trans fatty acids correlates with the food source, as the composition of the isomers varies in different foods. We have investigated the hepatocellular responses to the predominant trans fatty acid isomers in industrially produced partially hydrogenated vegetable oils (elaidic acid) and products of ruminant origin (trans-vaccenic acid). RESULTS: The responses of HepG2-SF cells exposed to 100 μM fatty acids during 7 days were examined. Elaidic acid decreased the cellular proliferation rate while trans-vaccenic acid had no effect. Analysis of cellular triacylglycerol fractions showed, that both trans fatty acids were metabolized by HepG2-SF cells, although elaidic acid, to a higher degree than trans-vaccenic, accumulated in the triacylglycerol fraction. Proteome analysis revealed that the overlap of differentially regulated proteins only contained four proteins, suggesting that the two trans fatty acid isomers affect the cells in different ways. The data are available via ProteomeXchange with identifier PXD000760. CONCLUSIONS: Our investigations revealed that the hepatocellular response to the two most abundant dietary positional C18:1 trans fatty acid isomers differ substantially. In addition, the results suggest that trans-vaccenic acid does not affect cholesterol metabolism adversely compared to elaidic acid.
Alteration of actin dependent signaling pathways associated with membrane microdomains in hyperlipidemia.
Suica VI, Uyy E, Boteanu RM … +2 more , Ivan L, Antohe F
Proteome Sci · 2015 · PMID 26628893 · Full text
BACKGROUND: Membrane microdomains represent dynamic membrane nano-assemblies enriched in signaling molecules suggesting their active involvement in not only physiological but also pathological molecular processes. The hy...
BACKGROUND: Membrane microdomains represent dynamic membrane nano-assemblies enriched in signaling molecules suggesting their active involvement in not only physiological but also pathological molecular processes. The hyperlipidemic stress is a major risk factor of atherosclerosis, but its exact mechanisms of action at the membrane microdomains level remain elusive. The aim of the present study was to determine whether membrane-cytoskeleton proteome in the pulmonary tissue could be modulated by the hyperlipidemic stress, a major risk factor of atherosclerosis. RESULTS: High resolution mass spectrometry based proteomics analysis was performed for detergent resistant membrane microdomains isolated from lung homogenates of control, ApoE deficient and statin treated ApoE deficient mice. The findings of the study allowed the identification with high confidence of 1925 proteins, 291 of which were found significantly altered by the modified genetic background, by the statin treatment or both conditions. Principal component analysis revealed a proximal partitioning of the biological replicates, but also a distinct spatial scattering of the sample groups, highlighting different quantitative profiles. The statistical significant over-representation of Regulation of actin cytoskeleton, Focal adhesion and Adherens junction Kyoto Encyclopedia of Genes and Genomes signaling pathways was demonstrated through bioinformatics analysis. The three inter-relation maps comprised 29 of regulated proteins, proving membrane-cytoskeleton coupling targeting and alteration by hyperlipidemia and/or statin treatment. CONCLUSIONS: The findings of the study allowed the identification with high confidence of the main proteins modulated by the hyperlipidemic stress involved in the actin-dependent pathways. Our study provides the basis for future work probing how the protein activities at the membrane-cytoskeleton interface are dependent upon genetic induced hyperlipidemia.
The calcified eggshell matrix proteome of a songbird, the zebra finch (Taeniopygia guttata).
Mann K
Proteome Sci · 2015 · PMID 26628892 · Full text
BACKGROUND: The proteins of avian eggshell organic matrices are thought to control the mineralization of the eggshell in the shell gland (uterus). Proteomic analysis of such matrices identified many candidates for such a...
BACKGROUND: The proteins of avian eggshell organic matrices are thought to control the mineralization of the eggshell in the shell gland (uterus). Proteomic analysis of such matrices identified many candidates for such a role. However, all matrices analyzed to date come from species of one avian family, the Phasianidae. To analyze the conservation of such proteins throughout the entire class Aves and to possibly identify a common protein toolkit enabling eggshell mineralization, it is important to analyze eggshell matrices from other avian families. Because mass spectrometry-based in-depth proteomic analysis still depends on sequence databases as comprehensive and accurate as possible, the obvious choice for a first such comparative study was the eggshell matrix of zebra finch, the genome sequence of which is the only songbird genome published to date. RESULTS: The zebra finch eggshell matrix comprised 475 accepted protein identifications. Most of these proteins (84 %) were previously identified in species of the Phasianidae family (chicken, turkey, quail). This also included most of the so-called eggshell-specific proteins, the ovocleidins and ovocalyxins. Ovocleidin-116 was the second most abundant protein in the zebra finch eggshell matrix. Major proteins also included ovocalyxin-32 and -36. The sequence of ovocleidin-17 was not contained in the sequence database, but a presumptive homolog was tentatively identified by N-terminal sequence analysis of a prominent 17 kDa band. The major proteins also included three proteins similar to ovalbumin, the most abundant of which was identified as ovalbumin with the aid of two characteristic phosphorylation sites. Several other proteins identified in Phasianidae eggshell matrices were not identified. When the zebra finch sequence database contained a sequence similar to a missing phasianid protein it may be assumed that the protein is missing from the matrix. This applied to ovocalyxin-21/gastrokine-1, a major protein of the chicken eggshell matrix, to EDIL3 and to lactadherin. In other cases failure to identify a particular protein may be due to the absence of this protein from the sequence database, highlighting the importance of better, more comprehensive sequence databases. CONCLUSIONS: The results indicate that ovocleidin-116, ovocleidin-17, ovocalyxin-36 and ovocalyxin-32 may be universal avian eggshell-mineralizing proteins. All the more important it is to elucidate the role of these proteins at the molecular level. This cannot be achieved by proteomic studies but will need application of other methods, such as atomic force microscopy or gene knockouts. However, it will also be important to analyze more eggshell matrices of different avian families to unequivocally identify other mineralization toolkit proteins apart from ovocleidins and ovocalyxins. Progress in this respect will depend critically on the availability of more, and more comprehensive, sequence databases. The development of faster and cheaper nucleotide sequencing methods has considerably accelerated genome and transcriptome sequencing, but this seems to concur with frequent publication of incomplete and fragmented sequence databases.
Differential abundance analysis of mesocarp protein from high- and low-yielding oil palms associates non-oil biosynthetic enzymes to lipid biosynthesis.
Ooi TE, Yeap WC, Daim LD … +6 more , Ng BZ, Lee FC, Othman AM, Appleton DR, Chew FT, Kulaveerasingam H
Proteome Sci · 2015 · PMID 26617468 · Full text
BACKGROUND: The oil palm Elaeis guineensis Jacq. which produces the highest yield per unit land area of the oil crops is the most important commercial oil crop in South East Asia. The fleshy mesocarp of oil palm fruit, w...
BACKGROUND: The oil palm Elaeis guineensis Jacq. which produces the highest yield per unit land area of the oil crops is the most important commercial oil crop in South East Asia. The fleshy mesocarp of oil palm fruit, where oil is mostly derived from, contains up to 90 % dry weight of oil (one of the most concentrated in plant tissues). Hence, there is attention given to gain insights into the processes of oil deposition in this oil rich tissue. For that purpose, two-dimensional differential gel electrophoresis (DIGE) coupled with western assays, were used here to analyze differential protein levels in genetically-related high-and low-yielding oil palm mesocarps. RESULTS: From the DIGE comparative analysis in combination with western analysis, 41 unique differentially accumulated proteins were discovered. Functional categorization of these proteins placed them in the metabolisms of lipid, carbohydrate, amino acids, energy, structural proteins, as well as in other functions. In particular, higher abundance of fructose-1,6-biphosphate aldolase combined with reduced level of triosephosphate isomerase and glyceraldehyde-3-phosphate dehydrogenase may be indicative of important flux balance changes in glycolysis, while amino acid metabolism also appeared to be closely linked with oil yield. CONCLUSIONS: Forty-one proteins in several important biological pathways were identified as exhibiting differential in abundance at critical oil production stages. These confirm that oil yield is a complex trait involving the regulation of genes in multiple biological pathways. The results also provide insights into key control points of lipid biosynthesis in oil palm and can assist in the development of genetic markers for use in oil palm breeding programmes.
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