Mass spectrometry-based profiling of the carbon starved Escherichia coli proteome reveals upregulation of stress-inducible pathways implicated in biofilm formation and antibiotic resistance

Abstract

Starvation is a complex adaptive response to insufficiency of nutrients that has been known to implicate a number of stress networks, and modulate pathogenicity and antibiotic resistance in bacteria. However, naturally occurring abrupt elimination of nutrients and prolonged periods of their complete absence, e.g. when bacteria are placed in natural or artificial water reservoirs, are qualitatively different from in-culture late stationary phase energy source diminution. Despite the obvious importance of proteomic investigation of bacteria exposed to nutrient deficiency, no comprehensive study on the subject has been published. In order to address the said shortage of knowledge, we decided to quantitatively look into the proteome-level alterations elicited by the complete lack of nutrients that constitute a viable source of carbon, i.e. carbon starvation, in the Escherichia coli HT115-derived SLE1 strain cells using the combination of label-free and SILAC-based proteomics. As a result, we obtained protein ratios for 1,757 and 1,241 protein groups for each technique respectively, 2D-annotated the quantifiable proteins present in both datasets, identified over-and underrepresented Gene Ontology terms, and isolated protein groups ≥2-fold up-and downregulated in response to carbon starvation (44 and 36 protein groups respectively). We observed upregulation of proteins implicated in various stress-related networks, most notably those that constitute the Gene Ontology term 'Biological adhesion', as well as various terms related to stress. Additionally, we identified several uncharacterized proteins, and our report is the first to ascribe them to a stress-induced proteome. Our data are available via ProteomeXchange with identifier ABSTRACT Starvation is a complex adaptive response to insufficiency of nutrients that has been known to implicate a number of stress networks, and modulate pathogenicity and antibiotic resistance in bacteria. However, naturally occurring abrupt elimination of nutrients and prolonged periods of their complete absence, e.g. when bacteria are placed in natural or artificial water reservoirs, are qualitatively different from in-culture late stationary phase energy source diminution. Despite the obvious importance of proteomic investigation of bacteria exposed to nutrient deficiency, no comprehensive study on the subject has been published. In order to address the said shortage of knowledge, we decided to quantitatively look into the proteome-level alterations elicited by the complete lack of nutrients that constitute a viable source of carbon, i.e. carbon starvation, in the Escherichia coli HT115-derived SLE1 strain cells using the combination of label-free and SILAC-based proteomics. As a result, we obtained protein ratios for 1,757 and 1,241 protein groups for each technique respectively, 2D-annotated the quantifiable proteins present in both datasets, identified over-and underrepresented Gene Ontology terms, and isolated protein groups ≥2-fold up-and downregulated in response to carbon starvati...

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“…Bacterial starvation is a complex phenotype of growth retardation, reduced viability, and overall switching of cellular metabolic machinery to a more robust energy-saving mode in response to the stress of nutritional scarcity. Given the implication of stress-induced pathways in modulation of pathogenicity (Fang et al, 1992;Suh et al, 1999;Thompson et al, 2003) and antibiotic resistance (Nachin, Nannmark & Nyström, 2005;Petrosino et al, 2009;Nguyen et al, 2011;Poole, 2012;Bernier et al, 2013;Bokinsky et al, 2013;Prax & Bertram, 2014), the study of proteome-level alterations evoked by starvation possesses a significant theoretical and practical interest. However, upon having closely examined the available literature, we have to admit that the research which truly looks into the proteome of a nutrient-deprived bacterial cell is lacking.…”