Proteomic analysis of a multi-resistant clinical Escherichia coli isolate of unknown genomic background

Tomazella, Gisele G.; Risberg, Kine; Mylvaganam, Haima; Lindemann, Paul Christoffer; Thiede, Bernd; Souza, Gustavo; Wiker, Harald G.

doi:10.1016/j.jprot.2011.12.024

Cited by 16 publications

(10 citation statements)

References 43 publications

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“…Toxin/antitoxin systems such as hok/sok are present on the majority of large plasmids isolated from clinical strains of enteric pathogens [16][17][18][19][20]. The plasmid stabilization function of the hok/sok locus was found to be affected by factors such as temperature, growth rate and dilution rates in a study in which a temperature sensitive plasmid was used without antibiotic selection [21].…”

Section: Discussionmentioning

confidence: 99%

The role of the hok/sok locus in bacterial response to stressful growth conditions

Chukwudi

Good

2015

Microbial Pathogenesis

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Section: Discussionmentioning

confidence: 99%

The role of the hok/sok locus in bacterial response to stressful growth conditions

Chukwudi

Good

2015

Microbial Pathogenesis

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“…While several works evaluated individually the application of the above mentioned detergent-based procedures for the LC-MS/MS characterization of microbial samples [37][38][39][40][41][42][43][44][45], to the best of our knowledge no reports specifically aimed at comparing different cutting-edge sample preparation workflows for the MS analysis of a whole bacterial proteome were available in the scientific literature at the time of this writing. Moreover, a special attention should be paid to the specific structural features of bacterial cell envelopes, where a great deal of molecules with pivotal functions for hostpathogen interactions, quorum sensing, drug resistance, and antigenicity, are located.…”

Section: Introductionmentioning

confidence: 99%

Comparison of detergent-based sample preparation workflows for LTQ-Orbitrap analysis of the Escherichia coli proteome

et al. 2013

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This work presents a comparative evaluation of several detergent-based sample preparation workflows for the MS-based analysis of bacterial proteomes, performed using the model organism Escherichia coli. Initially, RapiGest- and SDS-based buffers were compared for their protein extraction efficiency and quality of the MS data generated. As a result, SDS performed best in terms of total protein yields and overall number of MS identifications, mainly due to a higher efficiency in extracting high molecular weight (MW) and membrane proteins, while RapiGest led to an enrichment in periplasmic and fimbrial proteins. Then, SDS extracts underwent five different MS sample preparation workflows, including: detergent removal by spin columns followed by in-solution digestion (SC), protein precipitation followed by in-solution digestion in ammonium bicarbonate or urea buffer, filter-aided sample preparation (FASP), and 1DE separation followed by in-gel digestion. On the whole, about 1000 proteins were identified upon LC-MS/MS analysis of all preparations (>1100 with the SC workflow), with FASP producing more identified peptides and a higher mean sequence coverage. Each protocol exhibited specific behaviors in terms of MW, hydrophobicity, and subcellular localization distribution of the identified proteins; a comparative assessment of the different outputs is presented.

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“…Few proteomic studies (e.g. Tomazella et al (2012), dos Santos et al (2010), or Sirichoat et al (2016) explicitly investigate potential HGT organisms. Since they often have very specific objectives and since the data is either not suitable for our generic HGT question or is simply not available, verification is hard to obtain.…”

Section: Discussionmentioning

confidence: 99%

“…Tomazella et al (2012), and dos Santos et al (2010), e.g., studied relevant mechanisms of multi-resistant Escherichia coli, the most common bacterial pathogen. Multi-resistant Staphylococcus aureus strains The resulting PSMs are classified to be either uniquely matching to the acceptor or donor, or shared between both.…”

Section: Introductionmentioning

confidence: 99%

Hortense: Horizontal gene transfer detection directly from proteomic MS/MS data

Trappe

Wulf

Doellinger

et al. 2017

Preprint

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Horizontal gene transfer (HGT) is a powerful mechanism that allows bacteria to directly transfer long stretches of genomic sequence from one individual to another. The transfer of antimicrobial resistance genes is a prominent example of HGT events in the context of multi-resistant bacteria which pose a high risk to human health. While several approaches for HGT detection exist on the genomic level, to the best of our knowledge, HGT events have not been investigated in a detailed mass spectrometry (MS)-based proteomic study. However, the mere presence of a gene does not necessarily correlate with its expression at the protein level. Consequently, to draw conclusions with respect to the expression of HGT-mediated genes, MS-based proteomics can be employed. We developed a first computational approach -called Hortense -for automated HGT detection directly from shotgun proteomics experiments. We extend the standard database search by a critical cross-validation to unravel potential HGT proteins. A proteogenomic extension gives information about the genomic origin and enables an integration with existing genome-based methods. We successfully validated our approach on simulated data, and further evaluated it on real data from a transgenic organism and a negative control from an organism not harboring a transferred gene. Our results indicate that our method facilitates MS-based analysis for proteomic evidence of HGT events. Especially as an orthogonal approach to genome-based HGT detection methods, our proposed workflow is a first step toward a systematic and large scale analysis of HGT events in, e.g., antimicrobial resistance context. Hortense is publicly available at https://gitlab.com/rki bioinformatics/.

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Proteomic analysis of a multi-resistant clinical Escherichia coli isolate of unknown genomic background

Cited by 16 publications

References 43 publications

The role of the hok/sok locus in bacterial response to stressful growth conditions

The role of the hok/sok locus in bacterial response to stressful growth conditions

Comparison of detergent-based sample preparation workflows for LTQ-Orbitrap analysis of the Escherichia coli proteome

Hortense: Horizontal gene transfer detection directly from proteomic MS/MS data

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