-
ACS Synthetic Biology Feb 2012Synthetic biology enables rewiring and reconstruction of desirable biochemical routes using well-characterized BioBricks. One goal is to optimize these biological...
Synthetic biology enables rewiring and reconstruction of desirable biochemical routes using well-characterized BioBricks. One goal is to optimize these biological systems in terms of robustness, functionality, and simplicity. Thus, in addition to optimizing the molecular level of the metabolic network, choosing an optimal "chassis" can have a great significance in the constructed system. As an example, this study presents a simplified system for monitoring and studying long-chain n-alkane degradation in Acinetobacter baylyi ADP1 online, provided by a single BioBrick insertion, bacterial luciferase luxAB. The system exploits the natural alkane degradation machinery of ADP1 and a sensitive response of bacterial luciferase to a specific intermediate, providing important aspects to natural alkane degradation kinetics. The study suggests the monitoring system to be applicable in the field of environmental biotechnology and emphasizes the utility of ADP1 as a host in both model systems and applications.
Topics: Acinetobacter; Alkanes; Genetic Engineering; Kinetics; Metabolic Networks and Pathways; Models, Biological; Synthetic Biology
PubMed: 23651046
DOI: 10.1021/sb2000066 -
Chemphyschem : a European Journal of... Mar 2008
Topics: Alkanes; Carbon; Hydrogen; Spectrophotometry; Temperature
PubMed: 18275065
DOI: 10.1002/cphc.200700757 -
Journal of the American Chemical Society Aug 2010The first examples of efficient and general palladium-catalyzed intramolecular C(sp(3))-H arylation of (hetero)aryl chlorides, giving rise to a variety of valuable...
The first examples of efficient and general palladium-catalyzed intramolecular C(sp(3))-H arylation of (hetero)aryl chlorides, giving rise to a variety of valuable cyclobutarenes, indanes, indolines, dihydrobenzofurans, and indanones, are described. The use of aryl and heteroaryl chlorides significantly improves the scope of C(sp(3))-H arylation by facilitating the preparation of reaction substrates. Careful optimization studies have shown that the palladium ligand and the base/solvent combination are crucial to obtaining the desired class of product in high yields. Overall, three sets of reaction conditions employing P(t)Bu(3), PCyp(3), or PCy(3) as the palladium ligand and K(2)CO(3)/DMF or Cs(2)CO(3)/pivalic acid/mesitylene as the base/solvent combination allowed five different classes of products to be accessed using this methodology. In total, more than 40 examples of C-H arylation have been performed successfully. When several types of C(sp(3))-H bond were present in the substrate, the arylation was found to occur regioselectively at primary C-H bonds vs secondary or tertiary positions. In addition, in the presence of several primary C-H bonds, selectivity trends correlate with the size of the palladacyclic intermediate, with five-membered rings being favored over six- and seven-membered rings. Regio- and diastereoselectivity issues were studied computationally in the prototypal case of indane formation. DFT(B3PW91) calculations demonstrated that C-H activation is the rate-determining step and that the creation of a C-H agostic interaction, increasing the acidity of a geminal C-H bond, is a critical factor for the regiochemistry control.
Topics: Alkanes; Catalysis; Crystallography, X-Ray; Cyclization; Hydrocarbons, Chlorinated; Models, Molecular; Molecular Structure; Organometallic Compounds; Palladium; Stereoisomerism
PubMed: 20681703
DOI: 10.1021/ja1048847 -
International Journal of Biological... Nov 2018Microbes appear to play a key role in bioremediation of petroleum hydrocarbons pollution and little attention has been paid to the enzyme activity in the process of...
Microbes appear to play a key role in bioremediation of petroleum hydrocarbons pollution and little attention has been paid to the enzyme activity in the process of alkane bioremediation. Oil field bacterium identified as Pseudomonas synxantha LSH-7' was chosen as the tested strain. Periodically collected samples were analyzed by GC-FID (Gas Chromatography- Flame Ionization Detector) and RT-qPCR (Quantitative-Real-Time-PCR). GC-FID results showed this bacterial strain has great degradation ability on crude oil n-alkanes and RT-qPCR data indicated the differences between the three genes expression including AlkB-, Cytochromes P450-, and almA- related when grown on different-chain alkanes. Meanwhile, enzyme activity like alkane hydroxylase, alcohol dehydrogenase, dehydrogenase, protease, phosphatase, catalase and lipase were measured. Extracellular alkane hydroxylase was induced in a higher degree than intracellular in the early incubation time, alcohol dehydrogenase increased/decreased along with alkane hydroxylase, and the pH of the medium obviously decreased. Other enzymes were also described including dehydrogenase activity that reached a highest point that was slower than alcohol dehydrogenase, protease activity started multiplying after a period of culture while biomass was immediately increased, catalase activity dramatically enhanced in the presence of alkanes, phosphatase activity was closely linked to pH approximately but lipase activity was found to be moderate.
Topics: Aerobiosis; Alkanes; Biodegradation, Environmental; Enzymes; Hydrogen-Ion Concentration; Petroleum; Petroleum Pollution; Pseudomonas
PubMed: 30055278
DOI: 10.1016/j.ijbiomac.2018.07.160 -
Biotechnology Progress 2006Linear (n-hexadecane) and branched (pristane) alkanes were degraded by a mixed culture isolated from an oil-contaminated field. The degradation was accompanied by...
Linear (n-hexadecane) and branched (pristane) alkanes were degraded by a mixed culture isolated from an oil-contaminated field. The degradation was accompanied by formation of biofloccules. The culture was composed of Rhodococcus strain NTU-1, Bacillus fusiformis L-1, and Ochrobactrum sp. Rhodococcus strain NTU-1 carried out the degradation of the alkane via a hydroxylase. Bacillus fusiformis L-1 and Ochrobactrum sp. did not degrade the alkanes but aided the flocculation by forming more rigid bacterial aggregates that enhanced the trapping of alkanes. In batch cultures, transformation and removal of the linear and branched alkanes was achieved within 66 h with more than 95% efficiency.
Topics: Alkanes; Bacillus; Biodegradation, Environmental; Biotechnology; Carbon; Hydrogen-Ion Concentration; Ochrobactrum; RNA, Ribosomal, 16S; Rhodococcus; Temperature; Time Factors
PubMed: 17022676
DOI: 10.1021/bp060100u -
The Journal of Organic Chemistry Sep 2010The synthesis and properties of three related families of alkane-linked DNA hairpins are reported. The first possesses a dodecane linker (C12) and 2-8 AT base pairs. The...
The synthesis and properties of three related families of alkane-linked DNA hairpins are reported. The first possesses a dodecane linker (C12) and 2-8 AT base pairs. The second possesses six AT base pairs and straight chain alkane linkers having 8-16 methylenes. The third has three alkane linkers of different length and a constant six base-pair stem with alternating A-T bases and a single TT step. The spectroscopic properties (UV, CD, and (1)H NMR) and molecular modeling are consistent with the formation of base-paired B-DNA structures for all hairpins having four or more AT base pairs. The thermal stability of hairpins having a C12 linker is greater than that of the commonly used hexa(ethylene glycol) linker but less than that of the stilbenediether linker having the same AT base-pair domain. Hairpin stability is related to both hydrophobic interactions between the linker and the adjacent base pair (stilbene > alkane > glycol) and the overall length of the linker. The stability of the alkane-linked hairpins having six AT base pairs is greater for a tetradecane linker than for either shorter or longer linkers. The good thermal stability of alkane-linked hairpins and absence of a chromophore which absorbs in the UV region makes them well-suited for studies of the electronic spectra and photochemistry of short hairpins having variable base-pair sequences.
Topics: Alkanes; Base Pairing; Circular Dichroism; DNA; Magnetic Resonance Spectroscopy; Models, Molecular; Molecular Structure; Temperature
PubMed: 20795715
DOI: 10.1021/jo1013299 -
Free Radical Biology & Medicine 1991Interaction of active oxygen species with polyunsaturated fatty acids (PUFA) results in a series of reactions called lipid peroxidation. During the process of...
Interaction of active oxygen species with polyunsaturated fatty acids (PUFA) results in a series of reactions called lipid peroxidation. During the process of peroxidation of polyunsaturated fatty acids there is a scission of an alkane fragment extending from the methyl end of the fatty acid to the double bond. Thus, with a w-6 polyunsaturated fatty acid pentane is released, and with a w-3 polyunsaturated fatty acid ethane is released. These hydrocarbons are distributed in the body, partly metabolized, and excreted in the breath, making it possible to estimate the magnitude of in vivo lipid peroxidation by measuring pentane and ethane exhaled in breath. Advantages of this method are discussed as well as limitations and possible sources of error.
Topics: Alkanes; Antioxidants; Breath Tests; Diet; Fatty Acids, Unsaturated; Free Radicals; Humans; Lipid Peroxidation; Pentanes; Respiration; Vitamin E
PubMed: 1864524
DOI: 10.1016/0891-5849(91)90075-e -
Applied Microbiology and Biotechnology Oct 2007Degradation of alkanes is a widespread phenomenon in nature, and numerous microorganisms, both prokaryotic and eukaryotic, capable of utilizing these substrates as a... (Review)
Review
Degradation of alkanes is a widespread phenomenon in nature, and numerous microorganisms, both prokaryotic and eukaryotic, capable of utilizing these substrates as a carbon and energy source have been isolated and characterized. In this review, we summarize recent advances in the understanding of bacterial metabolism of long-chain n-alkanes. Bacterial strategies for accessing these highly hydrophobic substrates are presented, along with systems for their enzymatic degradation and conversion into products of potential industrial value. We further summarize the current knowledge on the regulation of bacterial long-chain n-alkane metabolism and survey progress in understanding bacterial pathways for utilization of n-alkanes under anaerobic conditions.
Topics: Alkanes; Anaerobiosis; Bacteria; Biodegradation, Environmental
PubMed: 17673997
DOI: 10.1007/s00253-007-1119-1 -
Journal of Hazardous Materials Oct 2021Oil spillages lead to the formation of hydrocarbon and metal mixtures possessing effects on alkane-degrading bacteria that are responsible for the bioremediation of...
Oil spillages lead to the formation of hydrocarbon and metal mixtures possessing effects on alkane-degrading bacteria that are responsible for the bioremediation of oil-contaminated soils and waters. Studies of bacterial responses to the mixture of petroleum and metal can inform appropriate strategies for bioremediation. We employed a luminescent bioreporter Acinetobacter baylyi ADPWH_recA with alkane degradation capability to evaluate the combined effects from heavy metals (Cd, Pb and Cu) and alkanes (dodecane, tetradecane, hexadecane and octadecane). Bioluminescent ratios of ADPWH_recA in single Cd or Pb treatments ranged from 0.25 to 1.98, indicating both genotoxicity and cytotoxicity of these two metals, while ratios < 1.0 postexposure to Cu showed its cytotoxic impacts on ADPWH_recA bioreporter. Metal mixtures exhibited enhanced antagonistic effects (Ti>4.0) determined by the Toxic Unit model. With 100 mg/L alkane, the morbidity of ADPWH-recA reduced to < 20%, showing the inhibition of alkanes on Cd toxicity. Exposed to the metal mixture containing 10 mg/L Cu, the weak binding affinity of Cu with alkanes contributed to a high morbidity of > 85% in ADPWH_recA cells. This study provides a new way to understand the toxicity of mixture contaminants, which can help to optimize treatment efficiencies of bacterial remediation for oil contamination.
Topics: Acinetobacter; Alkanes; Hydrocarbons; Metals, Heavy
PubMed: 34216972
DOI: 10.1016/j.jhazmat.2021.126471 -
Journal of Toxicology and Environmental... Jan 1978Linear alkanes of specific chain length between 6 and 16 carbon atoms, an aryl derivative of dodecane, and a phorbol diester were tested in a cell culture system for...
Linear alkanes of specific chain length between 6 and 16 carbon atoms, an aryl derivative of dodecane, and a phorbol diester were tested in a cell culture system for relative ability to enhance mutagenesis induced by a chemical carcinogen, methylazoxymethanol acetate (MAM). Mutation frequencies at the ouabain-resistance locus were measured. Results indicated an excellent correlation between the relative activities of the above compounds in enhancing mutagenesis in the in vitro culture system and their tumor-promoting activities in mouse skin. None of the compounds tested showed mutagenic activity per se, further lending support to the theory that promoters act via derepression of latent carcinogen-induced damage to the genome.
Topics: Alkanes; Carcinogens; Cells, Cultured; Mutagens
PubMed: 633409
DOI: 10.1080/15287397809529642