scholarly journals Label-Free Proteomic Analysis of Flavohemoglobin Deleted Strain of Saccharomyces cerevisiae

2016 ◽  
Vol 2016 ◽  
pp. 1-12
Author(s):  
Chiranjit Panja ◽  
Rakesh K.S. Setty ◽  
Gopal Vaidyanathan ◽  
Sanjay Ghosh
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Stress Responses ◽  
Nitrosative Stress ◽  
Nitrogen Compound ◽  
Nuclear Gene ◽  
Differentially Expressed ◽  
Differentially Expressed Proteins ◽  
Label Free ◽  
Differential Proteomics ◽  
Go Terms

Yeast flavohemoglobin, YHb, encoded by the nuclear gene YHB1, has been implicated in the nitrosative stress responses in Saccharomyces cerevisiae. It is still unclear how S. cerevisiae can withstand this NO level in the absence of flavohemoglobin. To better understand the physiological function of flavohemoglobin in yeast, in the present study a label-free differential proteomics study has been carried out in wild-type and YHB1 deleted strains of S. cerevisiae grown under fermentative conditions. From the analysis, 417 proteins in Y190 and 392 proteins in ΔYHB1 were identified with high confidence. Interestingly, among the differentially expressed identified proteins, 40 proteins were found to be downregulated whereas 41 were found to be upregulated in ΔYHB1 strain of S. cerevisiae (p value < 0.05). The differentially expressed proteins were also classified according to gene ontology (GO) terms. The most enriched and significant GO terms included nitrogen compound biosynthesis, amino acid biosynthesis, translational regulation, and protein folding. Interactions of differentially expressed proteins were generated using Search Tool for the Retrieval of Interacting Genes (STRING) database. This is the first report which offers a more complete view of the proteome changes in S. cerevisiae in the absence of flavohemoglobin.

scholarly journals Comparative proteome analysis of the spinal dural arteriovenous fistula arterial draining vein with label-free quantitative proteomics

2020 ◽  
Author(s):  
Peixi Liu ◽  
Yuan Shi ◽  
Sichen Li ◽  
Yingjun Liu ◽  
Yingjie Zhou ◽  
...  
Keyword(s):  
Quantitative Proteomics ◽  
Dural Arteriovenous Fistula ◽  
Kegg Pathway ◽  
Differentially Expressed ◽  
Differentially Expressed Proteins ◽  
Label Free ◽  
Spinal Dural Arteriovenous Fistula ◽  
Differentially Expressed Protein ◽  
Kegg Pathway Analysis ◽  
Go Terms

Abstract Background: Spinal dural arteriovenous fistula (SDAVF) is the most common spinal vascular shunt lesion. Although pathological changes in the SDAVF draining vein (SDAVF-DV) have been elucidated, protein changes remain enigmatic. We investigated protein changes in the SDAVF-DV.Methods: Three SDAVF-DV samples were collected, and superficial temporal artery (STA) and superficial temporal vein (STV) samples were used as controls. After quantification and enzymolysis of the proteins, label-free quantitative proteomics was performed, and the peptide mixture was fractionated and analysed by liquid chromatography tandem mass spectrometry (LC-MS/MS) to identify the differentially expressed proteins. Bioinformatics analysis of the differentially expressed proteins was also performed using Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) and protein-protein interaction (PPI) network analyses.Results: Compared with the STA, the SDAVF-DV had 195 upregulated proteins and 303 downregulated proteins. GO analysis showed that the most differential GO terms in each category were the adenylate cyclase-modulating G protein-coupled receptor signalling pathway, U6 snRNP and SH3 domain binding. KEGG pathway analysis showed that the most differentially expressed protein pathway was focal adhesion. Compared with the STV, the SDAVF-DV had 158 upregulated proteins and 362 downregulated proteins. GO analysis showed that the most differential GO terms in each category were lamellipodium assembly, U6 snRNP, and SH3 domain binding. KEGG pathway analysis showed that the most differentially expressed protein pathway was dilated cardiomyopathy. The PPI analysis revealed PPIs among the top 300 proteins.Conclusions: We demonstrated that the SDAVF-DV showed specific protein expression changes under long-period venous hypertension. The results of the present study will provide insights into the pathogenesis of SDAVF formation at the protein level. The proteomic results provide a scientific foundation for further study to explore the pathophysiological mechanism of SDAVF.

scholarly journals Label-free quantitative proteomic analysis of the inhibition effect of Lactobacillus rhamnosus GG on Escherichia coli biofilm formation in co-culture

2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Huiyi Song ◽  
Ni Lou ◽  
Jianjun Liu ◽  
Hong Xiang ◽  
Dong Shang
Keyword(s):  
Escherichia Coli ◽  
Proteomic Analysis ◽  
Biofilm Formation ◽  
Lactobacillus Rhamnosus ◽  
Differentially Expressed ◽  
Differentially Expressed Proteins ◽  
Label Free ◽  
Quantitative Proteomic Analysis ◽  
E Coli ◽  
Protein Ubiquitination

Abstract Background Escherichia coli (E. coli) is the principal pathogen that causes biofilm formation. Biofilms are associated with infectious diseases and antibiotic resistance. This study employed proteomic analysis to identify differentially expressed proteins after coculture of E. coli with Lactobacillus rhamnosus GG (LGG) microcapsules. Methods To explore the relevant protein abundance changes after E. coli and LGG coculture, label-free quantitative proteomic analysis and qRT-PCR were applied to E. coli and LGG microcapsule groups before and after coculture, respectively. Results The proteomic analysis characterised a total of 1655 proteins in E. coli K12MG1655 and 1431 proteins in the LGG. After coculture treatment, there were 262 differentially expressed proteins in E. coli and 291 in LGG. Gene ontology analysis showed that the differentially expressed proteins were mainly related to cellular metabolism, the stress response, transcription and the cell membrane. A protein interaction network and Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway analysis indicated that the differentiated proteins were mainly involved in the protein ubiquitination pathway and mitochondrial dysfunction. Conclusions These findings indicated that LGG microcapsules may inhibit E. coli biofilm formation by disrupting metabolic processes, particularly in relation to energy metabolism and stimulus responses, both of which are critical for the growth of LGG. Together, these findings increase our understanding of the interactions between bacteria under coculture conditions.

scholarly journals Label-Free Comparative Proteomics of Differentially Expressed Mycobacterium tuberculosis Protein in Rifampicin-Related Drug-Resistant Strains

Pathogens ◽  
2021 ◽  
Vol 10 (5) ◽  
pp. 607
Author(s):  
Nadeem Ullah ◽  
Ling Hao ◽  
Jo-Lewis Banga Ndzouboukou ◽  
Shiyun Chen ◽  
Yaqi Wu ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Drug Targets ◽  
Control Strategies ◽  
Multidrug Resistant ◽  
Differentially Expressed ◽  
Effective Control ◽  
Drug Resistant ◽  
Differentially Expressed Proteins ◽  
Label Free ◽  
Candidate Target

Rifampicin (RIF) is one of the most important first-line anti-tuberculosis (TB) drugs, and more than 90% of RIF-resistant (RR) Mycobacterium tuberculosis clinical isolates belong to multidrug-resistant (MDR) and extensively drug-resistant (XDR) TB. In order to identify specific candidate target proteins as diagnostic markers or drug targets, differential protein expression between drug-sensitive (DS) and drug-resistant (DR) strains remains to be investigated. In the present study, a label-free, quantitative proteomics technique was performed to compare the proteome of DS, RR, MDR, and XDR clinical strains. We found iniC, Rv2141c, folB, and Rv2561 were up-regulated in both RR and MDR strains, while fadE9, espB, espL, esxK, and Rv3175 were down-regulated in the three DR strains when compared to the DS strain. In addition, lprF, mce2R, mce2B, and Rv2627c were specifically expressed in the three DR strains, and 41 proteins were not detected in the DS strain. Functional category showed that these differentially expressed proteins were mainly involved in the cell wall and cell processes. When compared to the RR strain, Rv2272, smtB, lpqB, icd1, and folK were up-regulated, while esxK, PPE19, Rv1534, rpmI, ureA, tpx, mpt64, frr, Rv3678c, esxB, esxA, and espL were down-regulated in both MDR and XDR strains. Additionally, nrp, PPE3, mntH, Rv1188, Rv1473, nadB, PPE36, and sseA were specifically expressed in both MDR and XDR strains, whereas 292 proteins were not identified when compared to the RR strain. When compared between MDR and XDR strains, 52 proteins were up-regulated, while 45 proteins were down-regulated in the XDR strain. 316 proteins were especially expressed in the XDR strain, while 92 proteins were especially detected in the MDR strain. Protein interaction networks further revealed the mechanism of their involvement in virulence and drug resistance. Therefore, these differentially expressed proteins are of great significance for exploring effective control strategies of DR-TB.

Quantitative proteomics analysis of FFPE tumor samples reveals the influences of novel targeting nanobubbles conjugated with NET-1 siRNA on tetraspanin protein involved in HCC

2020 ◽  
Author(s):  
Bolin Wu ◽  
Haitao Shang ◽  
Xitian Liang ◽  
Huajing Yang Huajing Yang ◽  
Hui Jing ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Interaction Analysis ◽  
Enrichment Analysis ◽  
Differentially Expressed ◽  
Pathway Enrichment Analysis ◽  
Differentially Expressed Proteins ◽  
Label Free ◽  
Protein Protein Interaction ◽  
Study Results ◽  
Ffpe Tumor

Abstract Background: Hepatocellular carcinoma (HCC) poses a severe threat to human health. The NET-1 protein has been proved to be strongly associated with HCC proliferation and metastasis in our previous study. Methods: Here, we developed a label-free proteome mass spectrometry workflow to analyze formalin-fixed and paraffin-embedded HCC xenograft samples collected in our previous study. Results: The result showed that 78 proteins were differentially expressed after NET-1 protein inhibited. Among them, the expression of 61 proteins up-regulated and the expression of 17 proteins were significantly down-regulated. Of the differentially expressed proteins, the vast majority of Gene Ontology enrichment terms belong to the biological process. The KEGG pathway enrichment analysis showed that the 78 differentially expressed proteins significantly enriched in 45 pathways. We concluded that the function of the NET-1 gene is not only to regulate HCC but also to participate in a variety of biochemical metabolic pathways in the human body. Furthermore, the protein-protein interaction analysis indicated that the interactions of differentially expressed proteins are incredibly sophisticated. All the protein-protein interactions happened after the NET-1 gene has been silenced. Conclusions: Finally, our study also provides a useful proposal for targeted therapy based on tetraspanin proteins to treat HCC, and further mechanism investigations are needed to reveal a more detailed mechanism of action for NET-1 protein regulation of HCC.

scholarly journals Proteomic Analysis of Radiation-Induced Acute Liver Damage in a Rabbit Model

Dose-Response ◽  
2019 ◽  
Vol 17 (4) ◽  
pp. 155932581988950 ◽  
Author(s):  
Lingong Jiang ◽  
Huimin Jia ◽  
Zhicheng Tang ◽  
Xiaofei Zhu ◽  
Yangsen Cao ◽  
...  
Keyword(s):  
Signaling Pathway ◽  
Liver Damage ◽  
Rabbit Model ◽  
Mapk Signaling ◽  
Differentially Expressed ◽  
Mitogen Activated Protein Kinase ◽  
Differentially Expressed Proteins ◽  
Label Free ◽  
Radiation Induced ◽  
Liver Tissues

Radiation-induced liver damage (RILD) has become a limitation in radiotherapy for hepatocellular carcinoma. We established a rabbit model of RILD by CyberKnife. Electron microscopy analysis revealed obvious nuclear atrophy and disposition of fat in the nucleus after irradiation. We then utilized a mass spectrometry-based label-free relative quantitative proteomics approach to compare global proteomic changes of rabbit liver in response to radiation. In total, 2365 proteins were identified, including 338 proteins that were significantly dysregulated between irradiated and nonirradiated liver tissues. These differentially expressed proteins included USP47, POLR2A, CSTB, MCFD2, and CSNK2A1. Real-time polymerase chain reaction confirmed that USP47 and CABLES1 transcripts were significantly higher in irradiated liver tissues, whereas MCFD2 and CSNK2A1 expressions were significantly reduced. In Clusters of Orthologous Groups of proteins analysis, differentially expressed proteins were annotated and divided into 24 categories, including posttranslational modification, protein turnover, and chaperones. Kyoto Encyclopedia of Genes and Genomes analysis revealed that the enriched pathways in dysregulated proteins included the vascular endothelial growth factors (VEGF) signaling pathway, the mitogen-activated protein kinase (MAPK) signaling pathway, and the adipocytokine signaling pathway. The identification of proteins and pathways is crucial toward elucidating the radiation response process of the liver, which may facilitate the discovery of novel therapeutic targets.

Proteins with potential role in analgesic effect of spinal cord stimulation on neuropathic pain

2014 ◽  
Vol 5 (3) ◽  
pp. 209-210
Author(s):  
A. Lind ◽  
P. Emami ◽  
M. Sjödin ◽  
L. Katila ◽  
M. Wetterhall ◽  
...  
Keyword(s):  
Spinal Cord ◽  
Neuropathic Pain ◽  
Network Analysis ◽  
Spinal Cord Stimulation ◽  
Analgesic Effect ◽  
Functional Enrichment ◽  
Differentially Expressed ◽  
Differentially Expressed Proteins ◽  
Label Free ◽  
Ionization Source

AbstractAimsWe aimed to find proteins of relevance to the prolonged analgesic effect of spinal cord stimulation (SCS) for patients with neuropathic pain.MethodsThe proteomes of cerebrospinal fluid (CSF) from 14 neuropathic pain patients using spinal cord stimulation (SCS) was compared to the CSF proteomes of the same patients when not using the stimulator. Samples were analyzed by dimethyl label and label free shotgun proteomics approach. Samples were prepared by immunoaffinity fractionation and then separated by reversed phase nanoliquid chromatography coupled to an electrospray ionization source and analyzed by high resolution tandem mass spectrometry. The proteins were comparatively quantified on the peptide level and ranked based on numbers of regulated peptides. Then the dimethyl and label free analysis results were combined. In order to group proteins by function and interactions, a functional enrichment network analysis was performed using the String (Search Tool for the Retrieval of Interacting Genes/Proteins) database on all significantly differentially expressed proteins.ResultsWe found 87 differentially expressed proteins. Network analysis showed a high level of enrichment in interactions between the proteins involved in platelet degranulation and wound healing with p-values 2.48E−11 and 4.58E−08. We also recognized two additional clusters related to complement and coagulation cascades and neuropeptides. None of these proteins have been implicated in SCS mechanism previously.ConclusionsUp- and down-regulations of immunological proteins and neuropeptides may explain the prolonged relief of neuropathic pain obtained after SCS. These findings contribute a new basis for understanding of SCS analgesic mechanism in human neuropathic pain. Further verification studies of these initial findings are needed.

Proteomic analysis of differentially expressed proteins in the roots of Columbia-0 and Landsberg erecta ecotypes of Arabidopsis thaliana in response to aluminum toxicity

2012 ◽  
Vol 92 (7) ◽  
pp. 1267-1282 ◽  
Author(s):  
T. Karuppanapandian ◽  
S-J. Rhee ◽  
E-J. Kim ◽  
B. K. Han ◽  
O. A. Hoekenga ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Stress Responses ◽  
Proteomic Analysis ◽  
Crop Production ◽  
Aluminum Toxicity ◽  
Expression Patterns ◽  
Differentially Expressed ◽  
Monodehydroascorbate Reductase ◽  
Differentially Expressed Proteins ◽  
Al Stress

Karuppanapandian, T., Rhee, S.-J., Kim, E.-J., Han, B. K., Hoekenga, O. A. and Lee, G. P. 2012. Proteomic analysis of differentially expressed proteins in the roots of Columbia-0 and Landsberg erecta ecotypes of Arabidopsis thaliana in response to aluminum-toxicity. Can. J. Plant Sci. 92: 1267–1282. Aluminum (Al) is phytotoxic when solubilized into Al3+ in acidic soils and represents a major constraint for crop production. The present study describes Al-stress responses in roots of Al-tolerant and Al-sensitive Arabidopsis ecotypes, Columbia-0 (Col-0) and Landsberg erecta (Ler), respectively. Comparative proteomic analysis was applied to plants grown in hydroponic solution culture under acidic pH (4.2) conditions. To investigate time-dependent responses, 6-d-old seedlings were treated with 30 µM AlCl3 for 24, 48, or 72 h; total proteins were prepared from roots and separated by two-dimensional gel electrophoresis (2-DE). From 2-DE analysis, were 600 proteins were inspected, 29 proteins were differentially responsive to Al-treatment. The 2-DE patterns were compared and differentially expressed proteins identified by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS). Analysis of protein expression patterns revealed that a set of proteins is functionally associated with tricarboxylic acid (TCA) cycle and glycolysis, reactive oxygen quenching and detoxification mechanism, and signal transduction pathways, etc., could play important roles in mediating plant response to Al in Arabidopsis ecotypes. Comparison of the changes in the protein profiles revealed that Al-stress increased Al-tolerance related proteins in Al-tolerant Col-0, but only generic stress responses occurred in Al-sensitive Ler. Specifically, Al up-regulated proteins such as alcohol dehydrogenase, monodehydroascorbate reductase, GTP-binding nuclear protein Ran-2, and leucine aminopeptidase in Col-0 but not in Ler.

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