Characterization of Campylobacter jejuni proteome profiles in co-incubation scenarios

Abstract

In dynamic microbial ecosystems, bacterial communication is a relevant mechanism for interactions between different microbial species. When C. jejuni resides in the intestine of either avian or human hosts, it is exposed to diverse bacteria from the microbiome. This study aimed to reveal the influence of co-incubation with Enterococcus faecalis, Enterococcus faecium, or Staphylococcus aureus on the proteome of C. jejuni 81–176 using data-independent-acquisition mass spectrometry (DIA-MS). We compared the proteome profiles during co-incubation with the proteome profile in response to the bile acid deoxycholate (DCA) and investigated the impact of DCA on proteomic changes during co-incubation, as C. jejuni is exposed to both factors during colonization. We identified 1,375 proteins by DIA-MS, which is notably high, approaching the theoretical maximum of 1,645 proteins. S. aureus had the highest impact on the proteome of C. jejuni with 215 up-regulated and 230 down-regulated proteins. However, these numbers are still markedly lower than the 526 up-regulated and 516 down-regulated proteins during DCA exposure. We identified a subset of 54 significantly differentially expressed proteins that are shared after co-incubation with all three microbial species. These proteins were indicative of a common co-incubation response of C. jejuni. This common proteomic response partly overlapped with the DCA response; however, several proteins were specific to the co-incubation response. In the co-incubation experiment, we identified three membrane-interactive proteins among the top 20 up-regulated proteins. This finding suggests that the presence of other bacteria may contribute to increased adherence, e.g., to other bacteria but eventually also epithelial cells or abiotic surfaces. Furthermore, a conjugative transfer regulon protein was typically up-expressed during co-incubation. Exposure to both, co-incubation and DCA, demonstrated that the two stressors influenced each other, resulting in a unique synergistic proteomic response that differed from the response to each stimulus alone. Data are available via ProteomeXchange with identifier PXD046477.

Proteome profiling of Campylobacter jejuni 81–176 at 37 °C and 42 °C by label-free mass spectrometry

“…While Chen et al achieved a coverage of approximately 35% in their analysis of the proteome profiles of C. jejuni under peracetic acid exposure [32], the coverage was approximately 61% in the analysis of deoxycholate-induced stress by Man et al [33]. Our analysis, with a coverage of 58.9%, shows a similarly high coverage [18], which we were able to increase to 83.6% using a modernized technique [34].…”

“…In the studies of category B, we often observe a significantly lower coverage rate of the measured or quantified proteome compared to the predicted proteome. Großeholz et al analyzed the pH adaptation of Enterococcus faecalis at approximately 53% coverage rate [25], and in a recent study of our group examining the bile acid response of E. faecalis and Enterococcus faecium the coverage rates were 43.5% and 45.8% [26], while Kang et al studied the stress response of Methicillin-resistant Staphylococcus aureus to lactobionic acid at approximately 47% coverage rate [27]. Furthermore, other studies targeting specific protein fractions, such as membrane proteins or cytosolic proteins, using different pre-separation methods, cannot be compared here as the coverage is inherently less than 10% due to the method used.…”