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alkane monooxygenase

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https://www.readbyqxmd.com/read/28821550/crystal-structure-of-the-tetr-family-repressor-alkx-from-dietzia-sp-dq12-45-1b-implicated-in-biodegradation-of-n-alkanes
#1
Jie-Liang Liang, Yuan Gao, Zheng He, Yong Nie, Meng Wang, Jing-Hong JiangYang, Xuejun C Zhang, Wen-Sheng Shu, Xiao-Lei Wu
n-Alkanes are ubiquitous in nature and are widely used by microorganisms as carbon sources. Alkane hydroxylation by alkane monooxygenases is a critical step in the aerobic biodegradation of n-alkanes, which plays important roles in natural alkane attenuation and is used in industrial and environmental applications. The alkane oxidation operon, alkW1-alkX, in an alkane-degrading strain Dietzia sp. DQ12-45-1b, is negatively auto-regulated by the TetR family repressor, AlkX, via a product positive feedback mechanism...
August 18, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28802691/the-genome-analysis-of-oleiphilus-messinensis-me102-dsm-13489-t-reveals-backgrounds-of-its-obligate-alkane-devouring-marine-lifestyle
#2
Stepan V Toshchakov, Alexei A Korzhenkov, Tatyana N Chernikova, Manuel Ferrer, Olga V Golyshina, Michail M Yakimov, Peter N Golyshin
Marine bacterium Oleiphilus messinensis ME102 (DSM 13489(T)) isolated from the sediments of the harbor of Messina (Italy) is a member of the order Oceanospirillales, class Gammaproteobacteria, representing the physiological group of marine obligate hydrocarbonoclastic bacteria (OHCB) alongside the members of the genera Alcanivorax, Oleispira, Thalassolituus, Cycloclasticus and Neptunomonas. These organisms play a crucial role in the natural environmental cleanup in marine systems. Despite having the largest genome (6...
August 9, 2017: Marine Genomics
https://www.readbyqxmd.com/read/28752038/steroids-hydroxylation-catalyzed-by-the-monooxygenase-mutant-139-3-from-bacillus-megaterium-bm3
#3
Xing Liu, Jian-Qiang Kong
The search of new substrates with pharmaceutical and industrial potential for biocatalysts including cytochrome P450 enzymes is always challenging. Cytochrome P450 BM3 mutant 139-3, a versatile biocatalyst, exhibited hydroxylation activities towards fatty acids and alkanes. However, there were limited reports about its hydroxylation activity towards steroids. Herein, an Escherichia coli-based whole-cell extract containing the recombinant 139-3 protein was used as the biocatalyst to screen 13 steroids. Results revealed that 139-3 was able to specifically hydroxylate androstenedione (1) at 1α-position, generating a hydroxylated steroid 1α-OH-androstenedione (1a)...
July 2017: Acta Pharmaceutica Sinica. B
https://www.readbyqxmd.com/read/28668640/spectroscopic-studies-of-the-cytochrome-p450-reaction-mechanisms
#4
REVIEW
Piotr J Mak, Ilia G Denisov
The cytochrome P450 monooxygenases (P450s) are thiolate heme proteins that can, often under physiological conditions, catalyze many distinct oxidative transformations on a wide variety of molecules, including relatively simple alkanes or fatty acids, as well as more complex compounds such as steroids and exogenous pollutants. They perform such impressive chemistry utilizing a sophisticated catalytic cycle that involves a series of consecutive chemical transformations of heme prosthetic group. Each of these steps provides a unique spectral signature that reflects changes in oxidation or spin states, deformation of the porphyrin ring or alteration of dioxygen moieties...
June 28, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28628786/btex-and-naphthalene-degrading-bacterium-microbacterium-esteraromaticum-strain-sbs1-7-isolated-from-estuarine-sediment
#5
Akanit Wongbunmak, Sansanee Khiawjan, Manop Suphantharika, Thunyarat Pongtharangkul
In this study, a non-pathogenic, BTEX-degrading Microbacterium esteraromaticum SBS1-7 was isolated from estuarine sediment in Thailand via an enrichment technique. M. esteraromaticum SBS1-7 was able to degrade all six BTEX components, in both liquid medium and soil slurry system, when BTEX was supplied as an individual component or a mixture. It exhibited a high level of tolerance towards a wide range of hydrocarbons and also utilized alkanes and naphthalene. Detection of metabolites produced during BTEX and naphthalene degradation revealed highly extensive biodegradation pathways used by M...
June 9, 2017: Journal of Hazardous Materials
https://www.readbyqxmd.com/read/28624475/oxidoreductases-on-their-way-to-industrial-biotransformations
#6
REVIEW
Angel T Martínez, Francisco J Ruiz-Dueñas, Susana Camarero, Ana Serrano, Dolores Linde, Henrik Lund, Jesper Vind, Morten Tovborg, Owik M Herold-Majumdar, Martin Hofrichter, Christiane Liers, René Ullrich, Katrin Scheibner, Giovanni Sannia, Alessandra Piscitelli, Cinzia Pezzella, Mehmet E Sener, Sibel Kılıç, Willem J H van Berkel, Victor Guallar, Maria Fátima Lucas, Ralf Zuhse, Roland Ludwig, Frank Hollmann, Elena Fernández-Fueyo, Eric Record, Craig B Faulds, Marta Tortajada, Ib Winckelmann, Jo-Anne Rasmussen, Mirjana Gelo-Pujic, Ana Gutiérrez, José C Del Río, Jorge Rencoret, Miguel Alcalde
Fungi produce heme-containing peroxidases and peroxygenases, flavin-containing oxidases and dehydrogenases, and different copper-containing oxidoreductases involved in the biodegradation of lignin and other recalcitrant compounds. Heme peroxidases comprise the classical ligninolytic peroxidases and the new dye-decolorizing peroxidases, while heme peroxygenases belong to a still largely unexplored superfamily of heme-thiolate proteins. Nevertheless, basidiomycete unspecific peroxygenases have the highest biotechnological interest due to their ability to catalyze a variety of regio- and stereo-selective monooxygenation reactions with H2O2 as the source of oxygen and final electron acceptor...
November 1, 2017: Biotechnology Advances
https://www.readbyqxmd.com/read/28559213/phylogenomic-analysis-of-integral-diiron-membrane-histidine-motif-containing-enzymes-in-ciliates-provides-insights-into-their-function-and-evolutionary-relationships
#7
Nicolas G Cid, María L Sanchez Granel, María G Montes, María E Elguero, Clara B Nudel, Alejandro D Nusblat
The Integral Membrane Histidine Motif-containing Enzymes (IMHME) are a class of binuclear non-heme iron proteins widely distributed among prokaryotes and eukaryotes. They are characterized by a conserved tripartite motif consisting of eight to ten histidine residues. Their known function is the activation of the dioxygen moiety to serve as efficient catalysts for reactions of hydroxylation, desaturation or reduction. To date most studies on IMHME were carried out in metazoan, phototrophic or parasitic organisms, whereas genome-wide analysis in heterotrophic free living protozoa, such as the Ciliophora phylum, has not been undertaken...
May 27, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28487680/diversity-of-metabolically-active-bacteria-in-water-flooded-high-temperature-heavy-oil-reservoir
#8
Tamara N Nazina, Natalya M Shestakova, Ekaterina M Semenova, Alena V Korshunova, Nadezda K Kostrukova, Tatiana P Tourova, Liu Min, Qingxian Feng, Andrey B Poltaraus
The goal of this work was to study the overall genomic diversity of microorganisms of the Dagang high-temperature oilfield (PRC) and to characterize the metabolically active fraction of these populations. At this water-flooded oilfield, the microbial community of formation water from the near-bottom zone of an injection well where the most active microbial processes of oil degradation occur was investigated using molecular, cultural, radiotracer, and physicochemical techniques. The samples of microbial DNA and RNA from back-flushed water were used to obtain the clone libraries for the 16S rRNA gene and cDNA of 16S rRNA, respectively...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28420738/sar202-genomes-from-the-dark-ocean-predict-pathways-for-the-oxidation-of-recalcitrant-dissolved-organic-matter
#9
Zachary Landry, Brandon K Swan, Gerhard J Herndl, Ramunas Stepanauskas, Stephen J Giovannoni
Deep-ocean regions beyond the reach of sunlight contain an estimated 615 Pg of dissolved organic matter (DOM), much of which persists for thousands of years. It is thought that bacteria oxidize DOM until it is too dilute or refractory to support microbial activity. We analyzed five single-amplified genomes (SAGs) from the abundant SAR202 clade of dark-ocean bacterioplankton and found they encode multiple families of paralogous enzymes involved in carbon catabolism, including several families of oxidative enzymes that we hypothesize participate in the degradation of cyclic alkanes...
April 18, 2017: MBio
https://www.readbyqxmd.com/read/28206744/alkane-oxidation-methane-monooxygenases-related-enzymes-and-their-biomimetics
#10
REVIEW
Vincent C-C Wang, Suman Maji, Peter P-Y Chen, Hung Kay Lee, Steve S-F Yu, Sunney I Chan
Methane monooxygenases (MMOs) mediate the facile conversion of methane into methanol in methanotrophic bacteria with high efficiency under ambient conditions. Because the selective oxidation of methane is extremely challenging, there is considerable interest in understanding how these enzymes carry out this difficult chemistry. The impetus of these efforts is to learn from the microbes to develop a biomimetic catalyst to accomplish the same chemical transformation. Here, we review the progress made over the past two to three decades toward delineating the structures and functions of the catalytic sites in two MMOs: soluble methane monooxygenase (sMMO) and particulate methane monooxygenase (pMMO)...
July 12, 2017: Chemical Reviews
https://www.readbyqxmd.com/read/28012009/hydrolase-bioh-knockout-in-e-coli-enables-efficient-fatty-acid-methyl-ester-bioprocessing
#11
Marvin Kadisch, Andreas Schmid, Bruno Bühler
Fatty acid methyl esters (FAMEs) originating from plant oils are most interesting renewable feedstocks for biofuels and bio-based materials. FAMEs can also be produced and/or functionalized by engineered microbes to give access to, e.g., polymer building blocks. Yet, they are often subject to hydrolysis yielding free fatty acids, which typically are degraded by microbes. We identified BioH as the key enzyme responsible for the hydrolysis of medium-chain length FAME derivatives in different E. coli K-12 strains...
December 24, 2016: Journal of Industrial Microbiology & Biotechnology
https://www.readbyqxmd.com/read/27771781/a-whole-cell-biocatalyst-for-double-oxidation-of-cyclooctane
#12
C A Müller, A M Weingartner, A Dennig, A J Ruff, H Gröger, Ulrich Schwaneberg
A novel whole cell cascade for double oxidation of cyclooctane to cyclooctanone was developed. The one-pot oxidation cascade requires only a minimum of reaction components: resting E. coli cells in aqueous buffered medium (=catalyst), the target substrate and oxygen as environmental friendly oxidant. Conversion of cyclooctane was catalysed with high efficiency (50% yield) and excellent selectivity (>94%) to cyclooctanone. The reported oxidation cascade represents a novel whole cell system for double oxidation of non-activated alkanes including an integrated cofactor regeneration...
October 22, 2016: Journal of Industrial Microbiology & Biotechnology
https://www.readbyqxmd.com/read/27717568/hexadecane-degradation-of-pseudomonas-aeruginosa-ny3-promoted-by-glutaric-acid
#13
Hongyun Nie, Maiqian Nie, Ting Xiao, Yan Wang, Xiaoting Tian
For further understanding of the roles of small organic acids commonly produced during alkane degradation, glutaric acid was found to be effective for promoting hexadecane degradation by P. aeruginosa NY3. Our results demonstrated that the synchronous metabolism of glutaric acid could increase both the growth rates and hexadecane degradation ability of P. aeruginosa NY3. Glutaric acid was proved to be able to increase the ratios of the concentrations of NAD(+) and NADH inside strain NY3 cells, and subsequently accelerated cell growth rates through improving electron respiration rates...
January 1, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/27597387/salinity-and-conductivity-amendment-of-soil-enhanced-the-bioelectrochemical-degradation-of-petroleum-hydrocarbons
#14
Xiaojing Li, Xin Wang, Yueyong Zhang, Qian Zhao, Binbin Yu, Yongtao Li, Qixing Zhou
The extreme salinity and high internal resistance of saline-alkali soil contaminated by petroleum hydrocarbons were two key limitations for using the bioelectrochemical remediation. In order to solve two problems, we simply rinsed soil, added carbon fiber to polluted soil. The charge output was enhanced by 110% with increase of the maximum current densities from 81 to 304 mA·m(-2) while hydrocarbons degradation rate enhanced by 484%, especially the high molecular weight fractions (C28-C36 of n-alkanes and 4-6 rings of PAHs)...
2016: Scientific Reports
https://www.readbyqxmd.com/read/27475037/separating-and-characterizing-functional-alkane-degraders-from-crude-oil-contaminated-sites-via-magnetic-nanoparticle-mediated-isolation
#15
Xinzi Wang, Xiaohui Zhao, Hanbing Li, Jianli Jia, Yueqiao Liu, Odafe Ejenavi, Aizhong Ding, Yujiao Sun, Dayi Zhang
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...
November 2016: Research in Microbiology
https://www.readbyqxmd.com/read/27340079/draft-genome-sequence-of-gordonia-sihwensis-strain-9-a-branched-alkane-degrading-bacterium
#16
Lisa M Brown, Thusitha S Gunasekera, Richard C Striebich, Oscar N Ruiz
Gordonia sihwensis strain 9 is a Gram-positive bacterium capable of efficient aerobic degradation of branched and normal alkanes. The draft genome of G. sihwensis S9 is 4.16 Mb in size, with 3,686 coding sequences and 68.1% G+C content. Alkane monooxygenase and P-450 cytochrome genes required for alkane degradation are predicted in G. sihwensis S9.
2016: Genome Announcements
https://www.readbyqxmd.com/read/27077014/metagenomic-analysis-of-nitrogen-and-methane-cycling-in-the-arabian-sea-oxygen-minimum-zone
#17
Claudia Lüke, Daan R Speth, Martine A R Kox, Laura Villanueva, Mike S M Jetten
Oxygen minimum zones (OMZ) are areas in the global ocean where oxygen concentrations drop to below one percent. Low oxygen concentrations allow alternative respiration with nitrate and nitrite as electron acceptor to become prevalent in these areas, making them main contributors to oceanic nitrogen loss. The contribution of anammox and denitrification to nitrogen loss seems to vary in different OMZs. In the Arabian Sea, both processes were reported. Here, we performed a metagenomics study of the upper and core zone of the Arabian Sea OMZ, to provide a comprehensive overview of the genetic potential for nitrogen and methane cycling...
2016: PeerJ
https://www.readbyqxmd.com/read/27053948/modulating-the-import-of-medium-chain-alkanes-in-e-coli-through-tuned-expression-of-fadl
#18
Toby P Call, M Kalim Akhtar, Frank Baganz, Chris Grant
BACKGROUND: In recent years, there have been intensive efforts to develop synthetic microbial platforms for the production, biosensing and bio-remediation of fossil fuel constituents such as alkanes. Building predictable engineered systems for these applications will require the ability to tightly control and modulate the rate of import of alkanes into the host cell. The native components responsible for the import of alkanes within these systems have yet to be elucidated. To shed further insights on this, we used the AlkBGT alkane monooxygenase complex from Pseudomonas putida GPo1 as a reporter system for assessing alkane import in Escherichia coli...
2016: Journal of Biological Engineering
https://www.readbyqxmd.com/read/27034022/complete-genome-of-zhongshania-aliphaticivorans-sm-2-t-an-aliphatic-hydrocarbon-degrading-bacterium-isolated-from-tidal-flat-sediment
#19
Baolei Jia, Hye Im Jeong, Kyung Hyun Kim, Che Ok Jeon
Zhongshania aliphaticivorans SM-2(T), a degrader of aliphatic hydrocarbons, is a Gram-negative, rod-shaped, flagellated, facultatively aerobic bacterium. Here, we report the genome sequence of strain SM-2(T), which has a size of 4,204,359bp with 44 tRNAs, 9 rRNAs, and 3664 protein-coding genes. In addition, several genes encoding aliphatic hydrocarbon degraders (alkane 1-monooxygenase, haloalkane dehalogenase, and cytochrome P450) were detected in the genome shedding light on the function of pollutants degradation...
May 20, 2016: Journal of Biotechnology
https://www.readbyqxmd.com/read/26915487/characterization-of-the-transcriptome-of-achromobacter-sp-hz01-with-the-outstanding-hydrocarbon-degrading-ability
#20
Yue-Hui Hong, Mao-Cheng Deng, Xiao-Ming Xu, Chou-Fei Wu, Xi Xiao, Qing Zhu, Xian-Xian Sun, Qian-Zhi Zhou, Juan Peng, Jian-Ping Yuan, Jiang-Hai Wang
Microbial remediation has become one of the most important strategies for eliminating petroleum pollutants. Revealing the transcript maps of microorganisms with the hydrocarbon-degrading ability contributes to enhance the degradation of hydrocarbons and further improve the effectiveness of bioremediation. In this study, we characterized the transcriptome of hydrocarbon-degrading Achromobacter sp. HZ01 after petroleum treatment for 16h. A total of 38,706,280 and 38,954,413 clean reads were obtained by RNA-seq for the petroleum-treated group and control, respectively...
June 15, 2016: Gene
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