Plasmid pAMI2 of
 Paracoccus aminophilus
 JCM 7686 Carries
 N
 ,
 N
 -Dimethylformamide Degradation-Related Genes Whose Expression Is Activated by a LuxR Family Regulator

Dziewit, Łukasz; Dmowski, Michal; Baj, Jadwiga; Bartosik, Dariusz

doi:10.1128/aem.01926-09

Cited by 40 publications

(39 citation statements)

References 42 publications

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“…strain KUFA-1 and Paracoccus aminophilus strain JCM7685 (sharing Ͼ90% amino acid identity), while having lower levels of identity with those in Paracoccus aminophilus strain JCM7686 (84% and 73%, respectively) ( Fig. 4A and B) (19,20,31). A putative LuxR family transcriptional regulator was found upstream of dmfA1A2, displaying 57% amino acid identity with its homolog in Paracoccus aminophilus strain JCM7686 (19).…”

Section: Resultsmentioning

confidence: 99%

“…In addition to a small proportion of ORFs encoding enzymes for DMF, DMA, and MA utilization, pAMV1 encodes genes facilitating the metabolism of other carbon sources, such as methanol and L-arabinose. In another isolate, P. aminophilus JCM7686, genes encoding enzymes for initial DMF degradation are separated on different replicons (pAMI2, pAMI5, and pAMI6) (19). In strain DM1, however, those genes are colocalized on the plasmid, which might increase the efficiency of genetic control in DMF degradation.…”

Section: Resultsmentioning

confidence: 99%

“…Biodegradation of DMF has been established over the past 30 years. Several DMFdegrading bacteria, such as Pseudomonas (16), Paracoccus (6,(17)(18)(19)(20), Alcaligenes (21), Ochrobactrum (22), Mycobacterium, and Methylobacterium (23,24) strains, have been isolated and identified. However, except for Paracoccus aminophilus strains JCM7685 and JCM7686, little genomic information is available for these degraders.…”

mentioning

confidence: 99%

“…strain KUFA-1, were purified and characterized in previous studies (21,31,32). The protein DmfR, which is encoded on the plasmid pAMI2 in Paracoccus aminophilus JCM7686, is the only example of a regulator of the DMFase operon (19). Although the metabolites and main degradation pathways for DMF degraders are similar, they may vary in genetic composition among different genera.…”

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confidence: 99%

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Molecular Mechanism of N , N -Dimethylformamide Degradation in Methylobacterium sp. Strain DM1

Wang

Zhang

et al. 2019

Appl Environ Microbiol

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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 Methylobacterium. IMPORTANCE 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.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

mentioning

confidence: 99%

mentioning

confidence: 99%

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Molecular Mechanism of N , N -Dimethylformamide Degradation in Methylobacterium sp. Strain DM1

Wang

Zhang

et al. 2019

Appl Environ Microbiol

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“…The treatment of DMF has gained a considerable attention; it can be recycled by distillation to mother liquors or disposed by incineration [3,8]. The chemical methods show slower rate of degradation; bioremediation might represent a viable alternative for the DMF removal from industrial effluents.…”

Section: Introductionmentioning

confidence: 99%

Development and Validation of High Performance Liquid Chromatographic Analysis of Residual N,N-Dimethylformamide in Spent Medium after Biodegradation by Paracoccus denitrificans SD1

Sanganal

Kulkarni

Karegoudar

2013

ISRN Chromatography

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N,N-Dimethylformamide (DMF) is a toxic organic solvent commonly found in the textile and pharmaceutical industrial effluents. The DMF degradation was successfully archived by bacterial strain Paracoccus denitrificans SD1. The study demonstrates the high performance liquid chromatographic (HPLC) approach for the estimation of residual DMF in liquid medium. The investigation mainly focuses on the method development for the detection and quantification of DMF. The bacterium is capable of utilizing DMF (1% v/v) as the sole source of carbon and nitrogen. Utilization of DMF by the bacterium was investigated at regular intervals of time to check the complete degradation at a particular period. The method was validated based on the precision, accuracy, limit of detection, and limit of quantification. Herein, the method was executed in liquid chromatographic condition which enables direct analysis of aqueous samples from the spent medium avoiding the extraction and prederivatization. This improved method allows estimation of residual DMF from the aqueous medium in adequate ranges of precision and accuracy with 99.17% and 99.43% recovery, respectively. The method was validated by investigating the limit of detection (LOD) and limit of quantification (LOQ) of 0.2 and 0.40 mg/l, respectively. The method was found to be precise for detection of DMF by using liquid chromatography.

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Dimethylformamidase with a Unique Iron Center

Arya¹,

Ramanathan²,

Vinothkumar³

et al. 2022

Encyclopedia of Inorganic and Bioinorganic Chemistry

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N, N ‐Dimethylformamide is an abundant and one of the most used solvents in the chemical industry. The enzyme dimethylformamidase catalyzes the hydrolytic cleavage of the highly stable formamide bond. Sequence analysis of the enzyme suggested that it does not belong to the known family of amidohydrolases. The enzyme in its smallest form, is a tetramer made of two large and two small subunits. It is a very halotolerant enzyme that oligomerizes to form a dimer of tetramers with increasing salt concentration. The domain that contains the active site is a new fold. The active site is a Fe(III) center coordinated by two tyrosines and glutamic acid. Site‐directed mutagenesis shows that glutamic acid, histidine, and asparagine around the active site are critical for the catalysis by the enzyme. The evolution of the enzyme to break down the man‐made dimethylformamide is still a mystery.

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Plasmid pAMI2 of Paracoccus aminophilus JCM 7686 Carries N , N -Dimethylformamide Degradation-Related Genes Whose Expression Is Activated by a LuxR Family Regulator

Cited by 40 publications

References 42 publications

Molecular Mechanism of N , N -Dimethylformamide Degradation in Methylobacterium sp. Strain DM1

Molecular Mechanism of N , N -Dimethylformamide Degradation in Methylobacterium sp. Strain DM1

Development and Validation of High Performance Liquid Chromatographic Analysis of Residual N,N-Dimethylformamide in Spent Medium after Biodegradation by Paracoccus denitrificans SD1

Dimethylformamidase with a Unique Iron Center

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