Identification and characterisation of cold stress-related proteins in Oryza rufipogon at the seedling stage using label-free quantitative proteomic analysis

2021 ◽  
Author(s):  
Li-Wei-Dan Bai ◽  
Jian Liu ◽  
Liang-Fang Dai ◽  
Qian-Wen Deng ◽  
Ya-Ling Chen ◽  
...  
Keyword(s):  
Cold Stress ◽  
Proteomic Analysis ◽  
Oryza Rufipogon ◽  
Seedling Stage ◽  
Label Free ◽  
Quantitative Proteomic Analysis ◽  
Related Proteins

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

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.

scholarly journals Highly Reproducible Label Free Quantitative Proteomic Analysis of RNA Polymerase Complexes

2010 ◽  
Vol 10 (2) ◽  
pp. M110.000687 ◽  
Author(s):  
Amber L. Mosley ◽  
Mihaela E. Sardiu ◽  
Samantha G. Pattenden ◽  
Jerry L. Workman ◽  
Laurence Florens ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Proteomic Analysis ◽  
Label Free ◽  
Quantitative Proteomic Analysis

Label-free Quantitative Proteomic Analysis of Drought-Responsive Proteins in Panax ginseng Meyer

2021 ◽  
Vol 29 (6) ◽  
pp. 369-379
Author(s):  
Ju Young Jung ◽  
Cheol Woo Min ◽  
Hye Won Shin ◽  
Truong Van Nguyen ◽  
Ji hyun Kim ◽  
...  
Keyword(s):  
Panax Ginseng ◽  
Proteomic Analysis ◽  
Label Free ◽  
Quantitative Proteomic Analysis

Label-free quantitative proteomic analysis of Lactobacillus fermentum NCDC 400 during bile salt exposure

2017 ◽  
Vol 167 ◽  
pp. 36-45 ◽  
Author(s):  
Gurjeet Kaur ◽  
Syed Azmal Ali ◽  
Sudarshan Kumar ◽  
Ashok Kumar Mohanty ◽  
Pradip Behare
Keyword(s):  
Bile Salt ◽  
Proteomic Analysis ◽  
Lactobacillus Fermentum ◽  
Label Free ◽  
Quantitative Proteomic Analysis
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