A global Staphylococcus aureus proteome resource applied to the in vivo characterization of host-pathogen interactions

Abstract

Data-independent acquisition mass spectrometry promises higher performance in terms of quantification and reproducibility compared to data-dependent acquisition mass spectrometry methods. To enable high-accuracy quantification of Staphylococcus aureus proteins, we have developed a global ion library for data-independent acquisition approaches employing high-resolution time of flight or Orbitrap instruments for this human pathogen. We applied this ion library resource to investigate the time-resolved adaptation of S. aureus to the intracellular niche in human bronchial epithelial cells and in a murine pneumonia model. In epithelial cells, abundance changes for more than 400 S. aureus proteins were quantified, revealing, e.g., the precise temporal regulation of the SigB-dependent stress response and differential regulation of translation, fermentation, and amino acid biosynthesis. Using an in vivo murine pneumonia model, our data-independent acquisition quantification analysis revealed for the first time the in vivo proteome adaptation of S. aureus. From approximately 2.15 × 105 S. aureus cells, 578 proteins were identified. Increased abundance of proteins required for oxidative stress response, amino acid biosynthesis, and fermentation together with decreased abundance of ribosomal proteins and nucleotide reductase NrdEF was observed in post-infection samples compared to the pre-infection state.

Importance of superoxide dismutases A and M for protection ofStaphylococcus aureusin the oxidative stressful environment of cystic fibrosis airways

“…Congruent with our data, a supportive activity of SodM was also described by Valderas et al, who showed that a S. aureus sodA deletion mutant was unaffected by the addition of paraquat during the late exponential growth phase, when sodM expression was maximal (Valderas & Hart, 2001). Our results extend these findings and give evidence that this unique compensatory rela- (Michalik et al, 2017), our study revealed an upregulation of sodA and sodM in intracellular compared with extracellular bacteria and, with regard to our aforementioned results, we assume that intraepithelial bacteria are exposed to ROS, which was also demonstrated for Chlamydia trachomatis infecting HeLa cells (Boncompain et al, 2010).…”

“…In contrast to the results of Battistoni et al, who observed a slightly reduced survival of an Escherichia coli sodC deletion mutant and an enhanced viability of sodC overexpressing E. coli strains compared with the respective wild type upon infection of HeLa cells (Battistoni et al, ), we detected neither clear advantages nor disadvantages during the invasion and intracellular survival of the staphylococcal SOD deletion mutants in CF and non‐CF airway epithelial cells, indicating that in S. aureus , (a) the loss of one SOD can be counterbalanced by the other SOD, or (b) both SODs do not play essential roles in these processes. Nevertheless, additional to the findings of Michalik et al, who detected a higher abundance of SodA and SodM in S. aureus that resided in human bronchial epithelial cells compared with nonadherent bacteria (Michalik et al, ), our study revealed an upregulation of sodA and sodM in intracellular compared with extracellular bacteria and, with regard to our aforementioned results, we assume that intraepithelial bacteria are exposed to ROS, which was also demonstrated for Chlamydia trachomatis infecting HeLa cells (Boncompain et al, ).…”

Survival of the drowsiest: the hibernating 100S ribosome in bacterial stress management

“…Consistent with this observation, the levels of HPF long or RMF are substantially elevated in a murine pneumonia model (Michalik et al 2017), in starved cells (Aiso et al 2005; Sanchuki et al 2017), in biofilms (Williamson et al 2012), and in non-replicating persisters (Tkachenko et al 2017). Moreover, HPF long reduces translational efficiency of a subset of genes in vivo (Basu and Yap 2016; Hood et al 2016) and in cell-free translation assays (Basu and Yap 2016; Ueta et al 2008, 2013), presumably because 70S dimerization titrates functional ribosomes away from translational initiation.…”

Identification of Genes Regulating Cell Death inStaphylococcus aureus

“…Interestingly, our screen revealed that mutants of hslO and mfd were more death-resistant which may appear contradictory given that expression of HslO and Mfd are protective for the cell during stress [47, 48]. HslO (or Hsp33) has been shown to be upregulated especially during oxidative stress and that HslO levels were decreased when S. aureus cells were transitioning to slow/non-growing status [49]. It is well known that Mfd is involved in prevent DNA damage from oxidative stress, immune response, and drugs [47, 50].…”