Regulation Mechanism of Nicotine Catabolism in Sphingomonas melonis TY by a Dual Role Transcriptional Regulator NdpR.

A gene cluster ndp, responsible for nicotine degradation via a variant of the pyridine and pyrrolidine pathways, was previously identified in Sphingomonas melonis TY, but the regulation mechanism remains unknown. The gene ndpR within the cluster was predicted to encode a TetR family transcriptional regulator. Deletion of ndpR resulted in a notably shorter lag phase, higher maximum turbidity, and faster substrate degradation when cultivated in the presence of nicotine. Real-time quantitative PCR and promoter activity analysis in wild-type TY and TYΔndpR strains revealed that genes in the ndp cluster were negatively regulated by NdpR. However, complementation of ndpR to TYΔndpR did not restore transcription repression, but, instead, the complemented strain showed better growth than TYΔndpR. Promoter activity analysis indicates that NdpR also functions as an activator in the transcription regulation of ndpHFEGD. Further analysis through electrophoretic mobility shift assay and DNase I footprinting assay revealed that NdpR binds five DNA sequences within ndp and that NdpR has no autoregulation. These binding motifs overlap with the -35 or -10 box or are located distal upstream of the corresponding transcriptional start site. Multiple sequence alignment of these five NdpR-binding DNA sequences found a conserved motif, with two of the binding sequences being partially palindromic. 2,5-Dihydroxypyridine acted as a ligand of NdpR, preventing NdpR from binding to the promoter region of ndpASAL, ndpTB, and ndpHFEGD. This study revealed that NdpR binds to three promoters in the ndp cluster and is a dual-role transcriptional regulator in nicotine metabolism. IMPORTANCE Gene regulation is critical for microorganisms in the environment in which they may encounter various kinds of organic pollutants. Our study revealed that transcription of ndpASAL, ndpTB, and ndpHFEGD is negatively regulated by NdpR, and NdpR also exhibits a positive regulatory effect on PndpHFEGD. Furthermore, 2,5-dihydroxypyridine was identified as the effector molecular for NdpR and can both prevent the binding of free NdpR to the promoter and release NdpR from the promoters, which is different from previously reported NicR2. Additionally, NdpR was found to have both negative and positive transcription regulatory effects on the same target, PndpHFEGD, while only one binding site was identified, which is notably different from the previously reported TetR family regulators. Moreover, NdpR was revealed to be a global transcriptional regulator. This study provides new insight into the complex gene expression regulation of the TetR family.

Biotechnology progress for removal of indoor gaseous formaldehyde.

Formaldehyde is a ubiquitous carcinogenic indoor pollutant. The treatment of formaldehyde has attracted increasing social attention. Over the past few decades, an increasing number of publications have reported approaches for removing indoor formaldehyde. These potential strategies include physical adsorption, chemical catalysis, and biodegradation. Although physical adsorption is widely used, it does not really remove pollution. Chemical catalysis is very efficient but adds the risk of introducing secondary pollutants. Biological removal strategies have attracted more research attention than the first two methods, because it is more efficient, clean, and economical. Plants and bacteria are the common organisms used in formaldehyde removal. However, both have limitations and shortcomings when used alone. This review discusses the mechanisms, applications, and improvements of existing biological methods for the removal of indoor gaseous formaldehyde. A combination strategy relying on plants, bacteria, and physical adsorbents exhibits best ability to remove formaldehyde efficiently, economically, and safely. When this combination system is integrated with a heating, ventilation, air conditioning, and cooling (HVAC) system, a practical combined system can be established in formaldehyde removal. Multivariate interactions of biological and non-biological factors are needed for the future development of indoor formaldehyde removal. KEY POINTS: • Indoor gaseous formaldehyde removal is necessary especially for new residence. • Biological removal strategies have attracted increasing research attentions. • Combined system of plants, bacteria, and physical adsorbents exhibits best efficiency. • Integrated device of biological and non-biological factors will be potential practical.

Gaseous Formaldehyde Degrading by Methylobacterium sp. XJLW.

Formaldehyde is harmful to human beings. It is widely used in chemical industry, medicine, and agriculture and is frequently discharged into the sewage. Microbial metabolism of formaldehyde has attracted increasing attention for its potential application in formaldehyde removal, especially for indoor gaseous formaldehyde degradation. Methylobacterium sp. XJLW capable of degrading formaldehyde was isolated and exhibited a strong activity for liquid formaldehyde degradation. In the present study, the survival rate of XJLW was evaluated under drought, 30 °C, 4 °C, 15 °C, 35 °C, and 40 °C. After 4 days, the average survival rate under 30°C is the greatest (83.97%) among the five temperatures. Whether the temperature was above or below 30°C, the average survival rate decreased significantly. However, the resistance of XJLW to reduced temperatures seemed better than that to increased temperatures. The average survival rate under 15°C and 4°C was 71.1% and 58.67%, while that under 35 °C and 40 °C was 49.47% and 0.1%. Two batches of gaseous formaldehyde treatments were carried out in an analog device with super absorbent polymer (SAP) as the carrier materials of XJLW. The results showed that XJLW could effectively degrade gaseous formaldehyde in the analog device for a long period.

Comparative genomics and transcriptomics insights into the C1 metabolic model of a formaldehyde-degrading strain Methylobacterium sp. XJLW.

A formaldehyde-degrading strain Methylobacterium sp. XJLW was isolated and exhibited a special phenotype for formaldehyde utilization. The accumulation of formic acid in large quantities and lower cell growth was detected when XJLW utilized formaldehyde as the sole carbon source, suggesting XJLW has a potentially novel pathway to transfer formaldehyde to methanol and then enter the serine cycle for C1 metabolism. This mechanism requires exploration via molecular omics. Thus, the complete genome of XJLW was sequenced, and the transcriptome difference was also analyzed based on the RNA-seq data of strain XJLW cultivated with methanol and glucose, respectively. XJLW has a chromosome DNA and a mega-plasmid DNA. Ten percent of genes on chromosome DNA are strain-specific in genus Methylobacterium. Transcriptome analysis results showed that 623 genes were significantly up-regulated and that 207 genes were significantly down-regulated for growth in methanol. Among the up-regulated genes, 90 genes belong to strain-specific regions and are densely distributed in three areas. A specific gene (A3862_27225) annotated as methyltransferase was found ranking in the top 4 of up-regulated genes. This methyltransferase may play a role in the specific C1 metabolism of XJLW. Methylobacterium sp. XJLW should contain a potential methyl transport pathway via the novel methyltransferase, which is different from known pathways. These findings provide the basis for additional possibilities, which improve the formaldehyde-degrading ability of Methylobacterium sp. XJLW.

Selective and faster nicotine biodegradation by genetically modified Pseudomonas sp. JY-Q in the presence of glucose.

Pseudomonas sp. JY-Q is a nicotine-degrading strain isolated from tobacco waste extract (TWE). In TWE, the nicotine is a toxic chemical and requires removal. However, it was found that glucose in TWE inhibited the degradation of nicotine. Bioinformatics analysis of JY-Q complete genome found five genes encoding the first-step enzymes of glucose metabolism, one glucokinase (gck, AA098_22370) and four glucose dehydrogenases (gdh, AA098_12490, 22860, 11910, and 05800). Homogonous recombinant strategy was utilized to delete all the five genes from JY-Q genome one by one. The resultant quinary mutant strain JY-Q/5∆ exhibited no growth on glucose as the sole carbon source and selective degradation of nicotine in medium coexisting with glucose. The result of single complementation in the quinary mutant showed that only gck and gdh-05800 genes exhibited significant effect on the initial steps of glucose metabolism. Although the growth of JY-Q/5∆ seemed worse in basic inorganic medium (BSM) with coexisting glucose and nicotine, the nicotine degradation rate per cell weight of JY-Q/5∆ reached 12.68 mg/mg/h, about four times higher than that of the wild-type strain. The resting cells of JY-Q/5∆ also showed better ability of nicotine degradation than the wild type in BSM coexisting with glucose. In 5% diluted TWE containing 0.8 g/L nicotine, the resting cells of JY-Q/5∆ degraded all nicotine within 24 h, 20% faster than the wild-type strain. JY-Q/5∆ is potential to selectively degrade nicotine in glucose-nicotine coexisting environment.