Insights from label free-based proteomic analysis into inhibitory effects ε-Poly-lysine against Vibrio parahaemolyticus

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.

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Label-free proteomic analysis revealed the mechanisms of protein oxidation induced by hydroxyl radicals in whiteleg shrimp (Litopenaeus vannamei) muscle

Food & Function ◽

10.1039/d1fo00380a ◽

2021 ◽

Author(s):

Hui-min Lin ◽

Xue-er Qi ◽

Shan-shan Shui ◽

Soottawat Benjakul ◽

Santiago P. Aubourg ◽

...

Keyword(s):

Ascorbic Acid ◽

Hydroxyl Radicals ◽

Litopenaeus Vannamei ◽

Protein Oxidation ◽

Proteomic Analysis ◽

Muscle Proteins ◽

Label Free ◽

Whiteleg Shrimp ◽

The Stability ◽

Oxidative Effects

The oxidative effects of hydroxyl radicals derived from a FeCl3/ascorbic acid/H2O2 system on the stability of muscle proteins in peeled shrimp (Litopenaeus vannamei) were investigated.

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Label-free proteomic analysis of serum exosomes from paroxysmal atrial fibrillation patients

Clinical Proteomics ◽

10.1186/s12014-020-09304-8 ◽

2021 ◽

Vol 18 (1) ◽

Author(s):

Hanwen Ni ◽

Wenqi Pan ◽

Qi Jin ◽

Yucai Xie ◽

Ning Zhang ◽

...

Keyword(s):

Atrial Fibrillation ◽

Protein Folding ◽

Protein Content ◽

Complement System ◽

Proteomic Analysis ◽

Surface Composition ◽

Label Free ◽

Healthy Donors ◽

Variable Surface ◽

Serum Exosomes

Abstract Background Atrial fibrillation (AF) is the most common cardiac heterogeneous rhythm disorder. It represents a major cause of mortality and morbidity, mainly related to embolic events and heart failure. Mechanisms of AF are complex and remain incompletely understood. Recent evidence suggests exosomes are membrane-coated objects released by many cell-types. Their presence in body fluids and the variable surface composition and content render them attractive as a mechanism for potential biomarkers. However, the content of serum exosomes of AF patients has not been fully delineated. Methods In this work, the serum exosomes from AF patients and healthy donors were used to compare changes in the exosome protein content. Exosomes were isolated from serum of AF patients and healthy donors and their purity was confirmed by Western blotting assays and transmission electron microscopy (TEM). Label-free LC–MS/MS quantitative proteomic analysis was applied to analyze protein content of serum exosomes. Results A total of 440 exosomal protein groups were identified, differentially expressed proteins were filtrated with fold change ≥ 2.0 (AF/controls protein abundance ratio ≥ 2 or ≤ 0.5) and p value less than 0.05 (p < 0.05), significantly changed in abundance group contains 39 elevated proteins and 18 reduced proteins, while consistent presence/absence expression profile group contains 40 elevated proteins and 75 reduced proteins. Bioinformatic analysis of differential exosomal proteins confirmed the significant enrichment of components involved in the anticoagulation, complement system and protein folding. Parallel-Reaction Monitoring Relative Quantitative Analysis (PRM) further suggested that AF related to complement system and protein folding. Conclusions These results revealed the composition and potential function of AF serum exosomes, thus providing a new perspective on the complement system and protein folding to AF.

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Chromatin-Associated Proteins Revealed by SILAC-Proteomic Analysis Exhibit a High Likelihood of Requirement for Growth Fitness under DNA Damage Stress

International Journal of Proteomics ◽

10.1155/2012/630409 ◽

2012 ◽

Vol 2012 ◽

pp. 1-12

Author(s):

Han Wang ◽

Pornpimol Tipthara ◽

Lei Zhu ◽

Suk Yean Poon ◽

Kai Tang ◽

...

Keyword(s):

Dna Damage ◽

Proteomic Analysis ◽

Ribosomal Proteins ◽

Cell Extract ◽

Label Free ◽

High Likelihood ◽

Nonhistone Proteins ◽

Quantitative Proteomic Analysis ◽

Proteomic Approach ◽

Associated Functions

Chromatin-associated nonhistone proteins (CHRAPs) are readily collected from the DNaseI digested crude chromatin preparation. In this study, we show that the absolute abundance-based label-free quantitative proteomic analysis fail to identify potential CHRAPs from the CHRAP-prep. This is because that the most-highly abundant cytoplasmic proteins such as ribosomal proteins are not effectively depleted in the CHRAP-prep. Ribosomal proteins remain the top-ranked abundant proteins in the CHRAP-prep. On the other hand, we show that relative abundance-based SILAC-mediated quantitative proteomic analysis is capable of discovering the potential CHRAPs in the CHRAP-prep when compared to the whole-cell-extract. Ribosomal proteins are depleted from the top SILAC ratio-ranked proteins. In contrast, nucleus-localized proteins or potential CHRAPs are enriched in the top SILAC-ranked proteins. Consistent with this, gene-ontology analysis indicates that CHRAP-associated functions such as transcription, regulation of chromatin structures, and DNA replication and repair are significantly overrepresented in the top SILAC-ranked proteins. Some of the novel CHRAPs are confirmed using the traditional method. Notably, phenotypic assessment reveals that the top SILAC-ranked proteins exhibit the high likelihood of requirement for growth fitness under DNA damage stress. Taken together, our results indicate that the SILAC-mediated proteomic approach is capable of determining CHRAPs without prior knowledge.

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