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Journal of the American Chemical Society Jan 2023Tertiary nitroalkanes and the corresponding α-tertiary amines represent important motifs in bioactive molecules and natural products. The -alkylation of secondary...
Tertiary nitroalkanes and the corresponding α-tertiary amines represent important motifs in bioactive molecules and natural products. The -alkylation of secondary nitroalkanes with electrophiles is a straightforward strategy for constructing tertiary nitroalkanes; however, controlling the stereoselectivity of this type of reaction remains challenging. Here, we report a highly chemo- and stereoselective -alkylation of nitroalkanes with alkyl halides catalyzed by an engineered flavin-dependent "ene"-reductase (ERED). Directed evolution of the old yellow enzyme from provided a triple mutant, GkOYE-G7, capable of synthesizing tertiary nitroalkanes in high yield and enantioselectivity. Mechanistic studies indicate that the excitation of an enzyme-templated charge-transfer complex formed between the substrates and cofactor is responsible for radical initiation. Moreover, a single-enzyme two-mechanism cascade reaction was developed to prepare tertiary nitroalkanes from simple nitroalkenes, highlighting the potential to use one enzyme for two mechanistically distinct reactions.
Topics: Alkanes; Nitro Compounds; Alkylation; Catalysis
PubMed: 36608280
DOI: 10.1021/jacs.2c12197 -
Journal of Industrial Microbiology &... May 2017Advancement in metabolic engineering of microorganisms has enabled bio-based production of a range of chemicals, and such engineered microorganism can be used for... (Review)
Review
Advancement in metabolic engineering of microorganisms has enabled bio-based production of a range of chemicals, and such engineered microorganism can be used for sustainable production leading to reduced carbon dioxide emission there. One area that has attained much interest is microbial hydrocarbon biosynthesis, and in particular, alkanes and alkenes are important high-value chemicals as they can be utilized for a broad range of industrial purposes as well as 'drop-in' biofuels. Some microorganisms have the ability to biosynthesize alkanes and alkenes naturally, but their production level is extremely low. Therefore, there have been various attempts to recruit other microbial cell factories for production of alkanes and alkenes by applying metabolic engineering strategies. Here we review different pathways and involved enzymes for alkane and alkene production and discuss bottlenecks and possible solutions to accomplish industrial level production of these chemicals by microbial fermentation.
Topics: Alkanes; Alkenes; Biofuels; Fatty Acids; Fermentation; Metabolic Engineering
PubMed: 27565672
DOI: 10.1007/s10295-016-1814-y -
Natural Product Reports May 2021Covering: 2000 to 2020. trans-Bicyclo[4.4.0]decane/decene (such as trans-decalin and trans-octalin)-containing natural products display a wide range of structural... (Review)
Review
Covering: 2000 to 2020. trans-Bicyclo[4.4.0]decane/decene (such as trans-decalin and trans-octalin)-containing natural products display a wide range of structural diversity and frequently exhibit potent and selective antibacterial activities. With one of the major factors in combatting antibiotic resistance being the discovery of novel scaffolds, the efficient construction of these natural products is an attractive pursuit in the development of novel antibiotics. This highlight aims to provide a critical analysis on how the presence of dense architectural and stereochemical complexity necessitated special strategies in the synthetic pursuits of these natural trans-bicyclo[4.4.0]decane/decene antibiotics.
Topics: Alkanes; Anti-Bacterial Agents; Biological Products; Bridged Bicyclo Compounds; Molecular Structure
PubMed: 33206093
DOI: 10.1039/d0np00052c -
MBio May 2021The recent leveraging of genome-resolved metagenomics has generated an enormous number of genomes from novel uncultured microbial lineages yet left many clades... (Comparative Study)
Comparative Study
The recent leveraging of genome-resolved metagenomics has generated an enormous number of genomes from novel uncultured microbial lineages yet left many clades undescribed. Here, we present a global analysis of genomes belonging to Binatota (UBP10), a globally distributed, yet-uncharacterized bacterial phylum. All orders in Binatota encoded the capacity for aerobic methylotrophy using methanol, methylamine, sulfomethanes, and chloromethanes as the substrates. Methylotrophy in Binatota was characterized by order-specific substrate degradation preferences, as well as extensive metabolic versatility, i.e., the utilization of diverse sets of genes, pathways, and combinations to achieve a specific metabolic goal. The genomes also encoded multiple alkane hydroxylases and monooxygenases, potentially enabling growth on a wide range of alkanes and fatty acids. Pigmentation is inferred from a complete pathway for carotenoids (lycopene, β- and γ-carotenes, xanthins, chlorobactenes, and spheroidenes) production. Further, the majority of genes involved in bacteriochlorophyll , , and biosynthesis were identified, although absence of key genes and failure to identify a photosynthetic reaction center preclude proposing phototrophic capacities. Analysis of 16S rRNA databases showed the preferences of Binatota to terrestrial and freshwater ecosystems, hydrocarbon-rich habitats, and sponges, supporting their potential role in mitigating methanol and methane emissions, breakdown of alkanes, and their association with sponges. Our results expand the lists of methylotrophic, aerobic alkane-degrading, and pigment-producing lineages. We also highlight the consistent encountering of incomplete biosynthetic pathways in microbial genomes, a phenomenon necessitating careful assessment when assigning putative functions based on a set-threshold of pathway completion. A wide range of microbial lineages remain uncultured, yet little is known regarding their metabolic capacities, physiological preferences, and ecological roles in various ecosystems. We conducted a thorough comparative genomic analysis of 108 genomes belonging to the Binatota (UBP10), a globally distributed, yet-uncharacterized bacterial phylum. We present evidence that members of the order Binatota specialize in methylotrophy and identify an extensive repertoire of genes and pathways mediating the oxidation of multiple one-carbon (C) compounds in Binatota genomes. The occurrence of multiple alkane hydroxylases and monooxygenases in these genomes was also identified, potentially enabling growth on a wide range of alkanes and fatty acids. Pigmentation is inferred from a complete pathway for carotenoids production. We also report on the presence of incomplete chlorophyll biosynthetic pathways in all genomes and propose several evolutionary-grounded scenarios that could explain such a pattern. Assessment of the ecological distribution patterns of the Binatota indicates preference of its members to terrestrial and freshwater ecosystems characterized by high methane and methanol emissions, as well as multiple hydrocarbon-rich habitats and marine sponges.
Topics: Alkanes; Bacteria; Ecosystem; Genome, Bacterial; Genomics; Phylogeny; Pigments, Biological; RNA, Ribosomal, 16S
PubMed: 34006650
DOI: 10.1128/mBio.00985-21 -
Research in Microbiology 2016Uncultivable microorganisms account for over 99% of all species on the planet, but their functions are yet not well characterized. Though many cultivable degraders for...
Uncultivable microorganisms account for over 99% of all species on the planet, but their functions are yet not well characterized. Though many cultivable degraders for n-alkanes have been intensively investigated, the roles of functional n-alkane degraders remain hidden in the natural environment. This study introduces the novel magnetic nanoparticle-mediated isolation (MMI) technology in Nigerian soils and successfully separates functional microbes belonging to the families Oxalobacteraceae and Moraxellaceae, which are dominant and responsible for alkane metabolism in situ. The alkR-type n-alkane monooxygenase genes, instead of alkA- or alkP-type, were the key functional genes involved in the n-alkane degradation process. Further physiological investigation via a BIOLOG PM plate revealed some carbon (Tween 20, Tween 40 and Tween 80) and nitrogen (tyramine, l-glutamine and d-aspartic acid) sources promoting microbial respiration and n-alkane degradation. With further addition of promoter carbon or nitrogen sources, the separated functional alkane degraders significantly improved n-alkane biodegradation rates. This suggests that MMI is a promising technology for separating functional microbes from complex microbiota, with deeper insight into their ecological functions and influencing factors. The technique also broadens the application of the BIOLOG PM plate for physiological research on functional yet uncultivable microorganisms.
Topics: Alkanes; Bacteriological Techniques; Biotransformation; Carbon; Magnetics; Metabolome; Microarray Analysis; Moraxellaceae; Nanoparticles; Nitrogen; Oxalobacteraceae; Petroleum; Phenotype; Soil Microbiology; Soil Pollutants
PubMed: 27475037
DOI: 10.1016/j.resmic.2016.07.004 -
International Journal of Environmental... Jan 2023The volatile organic compounds (VOCs) released from a plastic track can cause stimulation and damage to the human body; the temperature, relative humidity (RH) and air...
The volatile organic compounds (VOCs) released from a plastic track can cause stimulation and damage to the human body; the temperature, relative humidity (RH) and air exchange rate (AER) have a significant impact on the release of VOCs from materials. In this study, we used a 0.1 m environmental chamber; a qualitative and quantitative analysis of VOCs released from a plastic track was conducted by gas chromatography-mass spectrometry with a temperature range of 23-60 °C, RH of 5-65% and AER of 0.5-1.5 h. The formation rate, the speciation, the nature of the main compounds and the mass concentration of VOCs under different environmental conditions were determined. It is shown that with the increase of temperature, the concentration of some main VOCs gradually increased and the and were larger by 736.13 μg·m and 984.22 μg·m at 60 °C, respectively. Additionally, with the increase of RH, the concentration of different VOCs gradually increased. Nonetheless, the change in RH had no effect on the concentration percentage of different VOCs in the total VOC. With the increase in AER, the concentration of different main VOCs significantly declined, as did the VOC detection rate. When the AER was increased from 0.5 h to 1.5 h, the decreased by 206.74-254.21 μg·m and decreased by 73.06-241.82 μg·m, and the number of non-detected VOC monomers increased from 1 to 7-12 species. The conclusion is that the increase in temperature and RH can promote the emission of VOCs from a plastic track, while increasing AER significantly reduces the concentrations of VOCs. Environmental temperature mainly causes the changes in the concentrations of different VOCs, and RH is a main factor leading to the variation in the detection rate of main VOCs. Overall, the release of VOCs from a plastic track is affected by environmental temperature, AER and RH in sequence. Through this paper, we clarify the effects of ambient temperature, RH and AER on the emission of VOCs from a plastic track, and furthermore, we determine the release characteristics of plastic track VOCs.
Topics: Humans; Volatile Organic Compounds; Environmental Monitoring; Air Pollutants; Plastics; Alkanes
PubMed: 36767201
DOI: 10.3390/ijerph20031828 -
Chemical Society Reviews Jul 2022Transition metal-catalysed carbene- and nitrene transfer to the C1-building blocks carbon monoxide and isocyanides provides heteroallenes ( ketenes, isocyanates,... (Review)
Review
Transition metal-catalysed carbene- and nitrene transfer to the C1-building blocks carbon monoxide and isocyanides provides heteroallenes ( ketenes, isocyanates, ketenimines and carbodiimides). These are versatile and reactive compounds allowing transformation towards numerous functional groups and organic compounds, including heterocycles. Both one-pot and tandem processes have been developed providing valuable synthetic methods for the organic chemistry toolbox. This review discusses all known transition metal-catalysed carbene- and nitrene transfer reactions towards carbon monoxide and isocyanides and transformation of the heteroallenes hereby obtained, with a special focus on the general mechanistic considerations.
Topics: Carbon Monoxide; Cyanides; Imines; Methane; Transition Elements
PubMed: 35748338
DOI: 10.1039/d1cs00305d -
Applied and Environmental Microbiology Jul 2020Bacterial alkane metabolism is associated with a number of cellular stresses, including membrane stress and oxidative stress, and the limited uptake of charged ions such...
Bacterial alkane metabolism is associated with a number of cellular stresses, including membrane stress and oxidative stress, and the limited uptake of charged ions such as sulfate. In the present study, the genes and in DR1 cells, which encode an alkanesulfonate monooxygenase and a taurine dioxygenase, respectively, were found to be responsible for hexadecanesulfonate (CSOH) and taurine metabolism, and Cbl was experimentally identified as a potential regulator of and expression. The expression of and occurred under sulfate-limited conditions generated during -hexadecane degradation. Interestingly, expression analysis and knockout experiments suggested that both genes are required to protect cells against oxidative stress, including that generated by -hexadecane degradation and HO exposure. Measurable levels of intracellular hexadecanesulfonate were also produced during -hexadecane degradation. Phylogenetic analysis suggested that and are mainly present in soil-dwelling aerobes within the and classes, which suggests that they function as controllers of the sulfur cycle and play a protective role against oxidative stress in sulfur-limited conditions. and , which play a role in the degradation of organosulfonate, were expressed during -hexadecane metabolism and oxidative stress conditions in DR1. Our study confirmed that hexadecanesulfonate was accidentally generated during bacterial -hexadecane degradation in sulfate-limited conditions. Removal of this by-product by SsuD and TauD must be necessary for bacterial survival under oxidative stress generated during -hexadecane degradation.
Topics: Acinetobacter; Alkanes; Alkanesulfonates; Bacterial Proteins; Hydrogen Peroxide; Mixed Function Oxygenases; Oxidative Stress
PubMed: 32503904
DOI: 10.1128/AEM.00692-20 -
The Plant Journal : For Cell and... Oct 2022The cuticular wax layer on leaf surfaces limits non-stomatal water loss to the atmosphere and protects against pathogen invasion. Although many genes associated with wax...
The cuticular wax layer on leaf surfaces limits non-stomatal water loss to the atmosphere and protects against pathogen invasion. Although many genes associated with wax biosynthesis and wax transport in plants have been identified, their regulatory mechanisms remain largely unknown. Here, we show that the MYB transcription factor OsMYB60 positively regulates cuticular wax biosynthesis and this helps rice (Oryza sativa) plants tolerate drought stress. Compared with the wild type (japonica cultivar 'Dongjin'), osmyb60 null mutants (osmyb60-1 and osmyb60-2) exhibited increased drought sensitivity, with more chlorophyll leaching and higher rates of water loss. Quantitative reverse-transcription PCR showed that the loss of function of OsMYB60 led to downregulation of wax biosynthesis genes, leading to reduced amounts of total wax components on leaf surfaces under normal conditions. Yeast one-hybrid, luciferase transient transcriptional activity, and chromatin immunoprecipitation assays revealed that OsMYB60 directly binds to the promoter of OsCER1 (a key gene involved in very-long-chain alkane biosynthesis) and upregulates its expression. Taken together, these results demonstrate that OsMYB60 enhances rice resilience to drought stress by promoting cuticular wax biosynthesis on leaf surfaces.
Topics: Oryza; Droughts; Gene Expression Regulation, Plant; Plant Proteins; Waxes; Plants, Genetically Modified; Plant Leaves; Transcription Factors; Mutation; Chlorophyll; Water; Alkanes; Luciferases
PubMed: 35984735
DOI: 10.1111/tpj.15947 -
MBio Aug 2019Crude oil and gases in the seabed provide an important energy source for subsurface microorganisms. We investigated the role of archaea in the anaerobic degradation of...
Crude oil and gases in the seabed provide an important energy source for subsurface microorganisms. We investigated the role of archaea in the anaerobic degradation of non-methane alkanes in deep-sea oil seeps from the Gulf of Mexico. We identified microscopically the ethane and short-chain alkane oxidizers " Argoarchaeum" and " Syntrophoarchaeum" forming consortia with bacteria. Moreover, we found that the sediments contain large numbers of cells from the archaeal clade " Methanoliparia," which was previously proposed to perform methanogenic alkane degradation. " Methanoliparia" occurred abundantly as single cells attached to oil droplets in sediments without apparent bacterial or archaeal partners. Metagenome-assembled genomes of " Methanoliparia" encode a complete methanogenesis pathway including a canonical methyl-coenzyme M reductase (MCR) but also a highly divergent MCR related to those of alkane-degrading archaea and pathways for the oxidation of long-chain alkyl units. Its metabolic genomic potential and its global detection in hydrocarbon reservoirs suggest that " Methanoliparia" is an important methanogenic alkane degrader in subsurface environments, producing methane by alkane disproportionation as a single organism. Oil-rich sediments from the Gulf of Mexico were found to contain diverse alkane-degrading groups of archaea. The symbiotic, consortium-forming " Argoarchaeum" and " Syntrophoarchaeum" are likely responsible for the degradation of ethane and short-chain alkanes, with the help of sulfate-reducing bacteria. " Methanoliparia" occurs as single cells associated with oil droplets. These archaea encode two phylogenetically different methyl-coenzyme M reductases that may allow this organism to thrive as a methanogen on a substrate of long-chain alkanes. Based on a library survey, we show that "" is frequently detected in oil reservoirs and may be a key agent in the transformation of long-chain alkanes to methane. Our findings provide evidence for the important and diverse roles of archaea in alkane-rich marine habitats and support the notion of a significant functional versatility of the methyl coenzyme M reductase.
Topics: Alkanes; Anaerobiosis; Bacteria; Biodegradation, Environmental; Euryarchaeota; Fatty Acids; Geologic Sediments; Gulf of Mexico; Hydrocarbons; Metagenomics; Methane; Oil and Gas Fields; Oxidation-Reduction; Oxidoreductases; Phylogeny; RNA, Ribosomal, 16S
PubMed: 31431553
DOI: 10.1128/mBio.01814-19