FIG 1.

Molecular mechanisms of DMF degradation in strain DM1. (A) Genomic analysis revealing the circular replicons in the genome of strain DM1. The genome contains a plasmid, named pLVM1. From the inside to the outside of the plasmid (left) and chromosome (right), the circles are as follows: circle 1, scale; circle 2, G+C skew; circle 3, G+C content; circles 4 and 7, clusters of orthologous groups; circles 5 and 6, locations of coding sequence, tRNA, and rRNA genes. (B) Clusters of putative DMF degradation genes in strain DM1. Genes are colored based on their different functions (pink, DMF hydrolysis; yellow, DMA oxidation; blue, MA utilization; green, NMGP; light gray, formaldehyde oxidation; dark gray, formate oxidation; light blue, serine cycle). The arrows indicate the sizes of the genes and the direction of transcription. The full names of the enzymes and corresponding genes are summarized in Table S1 in the supplemental material. (C) Putative DMF mineralization pathway and enzymes involved. The pathway is based on analogy with previously established pathways and bioinformatics identification of putative genes. The solid and dashed lines indicate pathways catabolizing via one step and multiple steps, respectively. The colors of the arrows correspond to the functional genes in panel B. (D) Transcriptional analysis by RT-qPCR of genes related to DMF degradation in strain DM1; 16S rRNA was used as the reference gene. The fold change in mauD (in the absence of DMF) was set to 1 as a reference, and the relative fold changes in the expression of other genes in the presence of DMF (colored bars) and in the absence of DMF (gray bars) were calculated according to this reference. The colors of the bars correspond to the functional genes in panel B. DMF, treatment group with 2,000 mg liter⁻¹ DMF induction; glycerol, control group. (E, F, and G) Identification of intermediates of DMF degradation. GC-MS mass spectra of benzene sulfonyl chloride derivatives of DMA (E), MA (F), and ammonium (G) generated in a resting cell reaction are shown.