Probing post-translational modifications in environmentally impactful bacteria using mass spectrometry

Microbes are found in all corners of the globe, and demonstrate extreme diversity in the roles they play within their niches. Syntrophic bacteria are a group of anaerobic microbes that break down fatty and aromatic acids, a process that forces them to survive at the edges of thermodynamic feasibility. Both the energetically limited state they exist, in combination with the large abundance of reactive acyl-CoA species present as metabolic intermediates, suggest a possibility of widespread lysine acylation, a common class of post-translational modification. We hypothesized that reactive acyl-CoA species would modify lysine residue with the corresponding acyl-lysine modification. Mass spectrometry was used to identify a wide array of lysine acylations in two species of bacteria, Syntrophus aciditrophicus and Syntrophomonas wolfei. As overly broad analysis could result in misidentifications, we identified diagnostic ion markers and developed methods utilizing these markers for detecting acyl-lysine modifications that could confidently identify even previously unknown modifications. Shotgun proteomics iii identified seven acylations in S. aciditrophicus, including those previously unidentified in the bacterial domain. Modifications identified were correlated with acyl-CoA intermediates in the cells. Acylations were enriched in pathways associated with aromatic acid degradation pathways. Mass spectrometry data acquired for the S. wolfei system revealed the same trends and suggested that lysine acylations changed quantitatively under different growth conditions. Together, the data support the “carbon stress” model of lysine acylation, whereby a buildup of reactive acyl-CoA species will non-enzymatically modify lysine residue in response to cellular conditions. The data also lays out a roadmap for future studies to determine the role these acylations play in regulating syntrophic cell metabolism