Elucidating Syntrophic Metabolism through Noncanonical Protein Modifications and Protein Sequences

Carbon is recycled in the anaerobic environment by fatty acid and aromatic compound-degrading syntrophic bacteria. These linchpins to sustaining life on earth survive at the limits of thermodynamic feasibility. They use two-thirds of the generated ATP in substrate degradation, leaving one-third (1/3 mole ATP per mole substrate, or a minimum energy quantum) to sustain microbial life. Despite their importance to biogeochemical cycles and alternative energy, syntrophic bacteria remain poorly understood.With energy so limited, how do they adjust their metabolism to environmental changes or altered nutrient availability? Complex “proteoforms” generated by integrating protein sequence variants and/or protein modifications could hold the key to their metabolic regulation. Studying the proteomes of Syntrophus aciditrophicus and Syntrophomonas wolfei, two model syntrophic bacteria, we discovered many protein sequence variants, including fusion forms of adjacent proteins on the same operons. Many protein modifications were also observed. Many are known, many are first recorded, and many belong to the rising family of lysine acylations, which has emerged as an important regulatory mechanism coordinating metabolism in response to changes in nutrient availability and metabolic fluxes