Stable isotope labelling by amino acids in cell culture (SILAC) applied to quantitative proteomics of Edwardsiella tarda ATCC 15947 under prolonged cold stress

Ma, Weixing; Jia, Jingdun; Huang, Xiaohua; Xie, Wancui; Zhang, Xiaoliang; Tang, Jing; Lin, Clement; Zhao, Lingyun; Fang, Peipei

doi:10.1016/j.micpath.2018.09.006

Cited by 6 publications

(3 citation statements)

References 46 publications

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“…These include proteomics and genomics studies as well as secretomes, transcriptomes, interactomes, and metabolomics studies. Proteomics and metabolomics studies have enabled researchers to examine protein-protein interactions between E. piscicida cells and host tissues, such as fish gills [37] and livers [106]; in antibiotics resistome variations [107] and stress adaptation [108]. RNA-seq, ChIP-seq and Tn-seq are new and powerful technologies that couple defined transposon mutant library with high-throughput sequencing of transposon insertion sites to comprehensively map genetic determinants of bacterial fitness.…”

Section: Resultsmentioning

confidence: 99%

Edwardsiella piscicida: A versatile emerging pathogen of fish

et al. 2019

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Edwardsiella piscicida is an Enterobacteriaceae that is abundant in water and causes food and waterborne infections in fish, animals, and humans. The bacterium causes Edwardsiellosis in farmed fish and can lead to severe economic losses in aquaculture worldwide. E. piscicida is an intracellular pathogen that can also cause systemic infection. Type III and type VI secretion systems are the bacterium's most lethal weapons against host defenses. It also possesses multiantibiotic resistant genes and is selected and enriched in the environment due to the overuse of antibiotics. Therefore, the bacterium has great potential to contribute to the evolution of the resistome. All these properties have made this bacterium a perfect model to study bacteria virulence mechanisms and the spread of antimicrobial genes in the environment. We summarize recent advance in E. piscicida biology and provide insights into future research in virulence mechanisms, vaccine development and novel therapeutics.

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Section: Resultsmentioning

confidence: 99%

Edwardsiella piscicida: A versatile emerging pathogen of fish

et al. 2019

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“…The similar results were also observed by Ma et al . 35 . This group have used SILAC method for analysis the proteome of Edwardsiella tarda ATCC 15947 under prolonged cold stress and reported that the enzymes of Gluconeogeneis were significantly enhanced under cold.…”

Section: Discussionmentioning

confidence: 99%

Differential protein profiling of soil diazotroph Rhodococcus qingshengii S10107 towards low-temperature and nitrogen deficiency

Suyal

Juyal

Kumar

et al. 2019

Sci Rep

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Protein-based biomarkers can be a promising approach for identification and real-time monitoring of the bio-inoculants employed under sustainable agricultural plans. In this perspective, differential proteomics of psychrophilic diazotroph Rhodococcus qingshengii S10107 (JX173283) was performed to unravel its adaptive responses towards low-temperature nitrogen deficiency and identification of a biomarker for respective physiological conditions. LC-MS/MS-based proteome analysis mapped more than 4830 proteins including 77 up-regulated and 47 down-regulated proteins (p ≤ 0.05). Differential expression of the structural genes of nif regulon viz. nifH, nifD, and nifK along with their response regulators i.e. nifA, nifL, and nifB indicated that the nitrogenase complex was activated successfully. Besides up-regulating the biosynthesis of certain amino acids viz. Leucine, Lysine, and Alanine; the expression of the peptidoglycan synthesis proteins were also increased; while, the enzymes involved in Lipid biosynthesis were found to decrease. Furthermore, two important enzymes of the pentose phosphate pathway viz. Transketolase and Transaldolase along with Ribose import ATP-binding protein RbsA were also found to induce significantly under low temperature a nitrogen deficient condition, which suggests the cellular need for ample ribose sugar instantly. Additionally, comparative protein profiling of S10107 strain with our previous studies revealed that CowN protein was significantly up-regulated in all the cases under low-temperature nitrogen deficient conditions and therefore, can be developed as a biomarker. Conclusively, present study for the first time provides an in-depth proteome profiling of R. qingshengii S10107 and proclaims CowN as a potential protein biomarker for monitoring BNF under cold niches.

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“…For example, proteomics methods were used to investigate the quantitative proteomics of Edwardsiella tarda in the midexponential growth phase at the optimal temperature of 37°C for 24 h and then through the hatch at 4°C for two weeks without vibration. Several key proteins related to DNA synthesis and transcription were significantly upregulated [18]. Similar comprehensive studies for S. putrefaciens have yet to be carried out.…”

Section: Introductionmentioning

confidence: 92%

TMT-Based Quantitative Proteomics Analysis of the Fish-Borne Spoiler Shewanella putrefaciens Subjected to Cold Stress Using LC-MS/MS

Gao

Mei

et al. 2021

Journal of Chemistry

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Shewanella putrefaciens is a specific spoilage bacterium for fish during cold storage. To better understand the molecular mechanisms of cold stress adaptation of S. putrefaciens, tandem mass tag- (TMT-) based quantitative proteomic analysis was performed to detect the effects of cold stress on protein expression profiles in S. putrefaciens which had been cultivated at 4°C and 30°C, respectively. A total of 266670 peptide spectrum matching numbers were quantified proteins after data analysis. Of the 2292 proteins quantitatively analyzed, a total of 274 were found to be differentially expressed (DE) under cold stress compared with the nonstress control. By integrating the results of Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses, 9 common KEGG terms were found notable for the cold-responsive proteins. Generally, the DE proteins involved in carbohydrate, amino acid, and fatty acid biosynthesis and metabolism were significantly upregulated, leading to a specific energy conservation survival mode. The DE proteins related to DNA repair, transcription, and translation were upregulated, implicating change of gene expression and more protein biosynthesis needed in response to cold stress.

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Stable isotope labelling by amino acids in cell culture (SILAC) applied to quantitative proteomics of Edwardsiella tarda ATCC 15947 under prolonged cold stress

Cited by 6 publications

References 46 publications

Edwardsiella piscicida: A versatile emerging pathogen of fish

Edwardsiella piscicida: A versatile emerging pathogen of fish

Differential protein profiling of soil diazotroph Rhodococcus qingshengii S10107 towards low-temperature and nitrogen deficiency

TMT-Based Quantitative Proteomics Analysis of the Fish-Borne Spoiler Shewanella putrefaciens Subjected to Cold Stress Using LC-MS/MS

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