N,N-Dimethylformamide (DMF) is one of the most common xenobiotic chemicals, and it can be easily emitted into the environment, where it causes harm to human beings. Herein, an efficient DMF-degrading strain, DM1, was isolated and identified as Methylobacterium sp. This strain can use DMF as the sole source of carbon and nitrogen. Whole-genome sequencing of strain DM1 revealed that it has a 5.66-Mbp chromosome and a 200-kbp megaplasmid. The plasmid pLVM1 specifically harbors the genes essential for the initial steps of DMF degradation, and the chromosome carries the genes facilitating subsequent methylotrophic metabolism. Through analysis of the transcriptome sequencing data, the complete mineralization pathway and redundant gene clusters of DMF degradation were elucidated. The dimethylformamidase (DMFase) gene was heterologously expressed, and DMFase was purified and characterized. Plasmid pLVM1 is catabolically crucial for DMF utilization, as evidenced by the phenotype identification of the plasmid-free strain. This study systematically elucidates the molecular mechanisms of DMF degradation by MethylobacteriumIMPORTANCE DMF is a hazardous pollutant that has been used in the chemical industry, pharmaceutical manufacturing, and agriculture. Biodegradation as a method for removing DMF has received increasing attention. Here, we identified an efficient DMF degrader, Methylobacterium sp. strain DM1, and characterized the complete DMF mineralization pathway and enzymatic properties of DMFase in this strain. This study provides insights into the molecular mechanisms and evolutionary advantage of DMF degradation facilitated by plasmid pLVM1 and redundant genes in strain DM1, suggesting the emergence of new ecotypes of Methylobacterium.

Background Benzofuran and its derivatives contain central pharmacophores and are important structures in medicinal chemistry. Chemical synthesis of benzofuran rings often requires expensive catalysts and stringent operational conditions. Biosynthesis is recognized as a promising way to save energy and produce valuable compounds. Dioxin biodegradation pathways can form several benzofuran derivatives, and these pathways may be a better choice for further synthesis of important biological compounds. 2-Hydroxy-4-(3′-oxo-3′ H -benzofuran-2′-yliden)but-2-enoic acid (HOBB), a benzofuran derivative, can be biosynthesized from dibenzofuran (DBF) through co-metabolic degradation in a lateral dioxygenation pathway. Results Efficient biosynthesis of HOBB was observed using whole cells of Pseudomonas putida strain B6-2. After cultivation in LB medium containing biphenyl, the cells were suspended to an OD 600 of 5 to conduct biosynthesis in the presence of 0.5-mM DBF at pH 7 for 8 h. The bacterial cells were used twice to degrade approximately 0.70-mM DBF, and in batch process, accumulated about 0.29-mM HOBB. HOBB could be easily purified from the reaction with ethyl acetate using the neutral-acid extraction method, and 13.58 ± 0.31 mg of HOBB was obtained from 22.49 ± 0.74-mg DBF with an overall production yield of 60.4% (w/w). The product HOBB, which is a yellow powder, could be detected and identified by LC–MS, GC–MS, and NMR. Conclusions In this study, a new biological route was developed to produce HOBB from DBF using whole cells of P. putida B6-2 (DSM 28064). The biosynthesis of HOBB may contribute to studies of the DBF lateral pathway and provide a new green route for synthesizing benzofuran derivatives with pharmacological activities.

Environmental problems are the most serious challenges in the 21st century. With the rapid development of modern industry and agriculture, ecological and environmental deterioration have become the most important factors to restrict the sustainable development of social economy. Microbial cells have strong ability for environmental remediation, but their evolution speed is slower than the speed of emerging pollutants. Therefore, the treatment using the synthetic biology is in urgent need. Full understanding of the microbial degradation characteristics (pathways) of refractory organic pollutants with the help of abundant microbial and gene resources in China is important. Using synthetic biology to redesign and transform the existing degrading strain will be used to degrade particular organic pollutants or multiple organic pollutants. For the complex pollutants, such as wastewater, based on the establishment of metabolic or regulation or resistance related gene modules of typical organic pollutants, artificial flora could be designed to solve the complex pollutants. The rational design and construction of engineering bacteria for typical environmental organic pollutants can effectively promote microbial catabolism of emerging contaminants, providing technical support for environmental remediation in China.