N-terminome and proteogenomic analysis of the Methylobacterium extorquens DM4 reference strain for dichloromethane utilization

摘要

Methylobacterium strains can use one-carbon compounds, such as methanol, for methylotrophic growth. In addition to methanol, a few strains also utilize dichloromethane, a major industrial chlorinated solvent pollutant. With a fully assembled and annotated genome, M. extorquens DM4 is the reference bacterium for aerobic dichloromethane degradation. The doublet N-terminal oriented proteomics (dN-TOP) strategy was applied to further improve its genome annotation and a differential proteomics approach was performed to compare M. extorquens DM4 grown either with methanol or dichloromethane as the sole source of carbon and energy. These approaches led to experimental confirmation of 259 hypothetical proteins, correction of 78 erroneous predicted start codons, discovery of 39 new proteins and annotation of 66 signal peptides, including essential enzymes involved in methylotrophic growth.