What I would like you to try is to use your literature search and find several labs who have published papers using A. borkumensis. In brief, E. coli BL21(DE3)abgTpabA carrying pET15bydaH or pET15b were grown in LB broth with 100gml1 ampicillin at 37C. 28, 11981200 (1982). Chem. PubMedGoogle Scholar. D Biol. 1998 [1] Type strain. Perspective Perspective: what is known, and not known, about the connections between alkane oxidation and metal uptake in alkanotrophs in the marine environment 5, 3009 (2014). The .gov means its official. borkumensis, a hydrocarbon-degrading bacterium that plays a global role in oil removal from marine systems. Species. Natl Acad. Researchers have genecally engineered other bacteria to consume petroleum . Ofer Prinz Setter and Ester Segal * Department of Biotechnology and Food Engineering, Technion - Israel Institute of Technology, Technion City, 3200003 Haifa, Israel. Crystal structure of the Alcanivorax borkumensis YdaH transporter reveals an unusual topology. It is likely that there is some limit to this model, but the limit was not determined in this paper. Six heavy-atom sites for the tungsten derivative were identified using SHELXC and SHELXD34 as implemented in the HKL2MAP package35. The specific activity of [3H]-sulfamethazine is 34.5Cimmol1. borkumensis gen., nov., sp., nov., a new hydrocarbon-degrading and surfactant-producing marine bacterium. Part of Springer Nature. 276, 307326 (1997). Bacteria that changed the world: Alcanivorax - More Than A Dodo Alcanivorax borkumensis is a marine bacterium that uses exclusively petroleum oil hydrocarbons as sources of carbon and energy (and is therefore designated "hydrocarbonoclastic"). Chemical Papers 2017 Ostatn autoi. CAS J. Bacteriol. borkumensis SK2. The protein sample was then adjusted to a final concentration of 20M. 236, 25342543 (1961). Because of its abundance in oil spill regions, it has great potential to be used actively in oil spill remediation. Schneiker S, Martins dos Santos VA, Bartels D, Bekel T, Brecht M, Buhrmester J, Chernikova TN, Denaro R, Ferrer M, Gertler C, Goesmann A, Golyshina OV, Kaminski F, Khachane AN, Lang S, Linke B, McHardy AC, Meyer F, Nechitaylo T, Phler A, Regenhardt D, Rupp O, Sabirova JS, Selbitschka W, Yakimov MM, Timmis KN, Vorhlter FJ, Weidner S, Kaiser O, Golyshin PN. D Biol. This site needs JavaScript to work properly. Acta Crystallogr. The deletion of pabA from BL21(DE3)abgT was done using similar procedures as described above to generate the final BL21(DE3)abgTpabA double-knockout strain. Mix well. Google Scholar. Google Scholar, van Beilen JB, Marin MM, Smits THM, Rthlisberger M, Franchini AG, Witholt B, Rojo F (2004) Characterization of two alkane hydroxylase genes from the marine hydrocarbonoclastic bacterium Alcanivorax borkumensis. Lecture Chapter 3 and E.W.Y. Shaping the lipid composition of bacterial membranes for membrane protein production, Structural models of the NaPi-II sodium-phosphate cotransporters, Transporters Through the Looking Glass: An Insight into the Mechanisms of Ion-Coupled Transport and Methods That Help Reveal Them, Energetic evolution of cellular Transportomes, Structure and function of the divalent anion/Na+ symporter from Vibrio cholerae and a humanized variant, The bacterial dicarboxylate transporter VcINDY uses a two-domain elevator-type mechanism, Crystal structures reveal the molecular basis of ion translocation in sodium/proton antiporters. The overall focus of the research is to mutate mNeonGreen through random mutagenesis, a tool for modifying proteins, in order to improve its emission properties and/or discover novel properties of the fluorescent protein. Otwinowski, Z. MLPHARE, CCP4 Proc. 40, 658674 (2007). View 10 excerpts, references methods and background. Recombinant AlkB2 is produced in an active form and rubredoxin is the intermediate electron donor to AlkB2 and can replace AlkG function, when NADH is the prime electron donor. 2019 Mar 12;10:426. doi: 10.3389/fmicb.2019.00426. USA 97, 66406645 (2000). & Brown, G. M. The biosynthesis of folic acid. Discover the world's research 20 . Cells were grown in LB medium with 100gml1 ampicillin at 37C. need a perfect paper? But while decades of research has shown that in-place, or in-situ, burning (ISB) can remove up to 90 percent of spilled oil, the clean-up method has seen only limited use. The hunch proved correct, with the team discovering that A. borkumensis had . Science and Research Branch of Tehran, Islamic Azad University, Tehran, 1477893855, Iran, Faculty of Biological Sciences, Shahid Beheshti University, GC, Tehran, 19839, Iran, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, 14178, Iran, Genetics Department, Tarbiat Modares University, Tehran, 14115, Iran, Malek-Ashtar University of Technology, Tehran, 83145, Iran, You can also search for this author in Iterations of refinement using PHENIX41 and CNS42 and model building in Coot39 lead to the 4.10--resolution structural model of the YdaH transporter. PubMed These heavy-atom sites were refined using the programme MLPHARE36,37. Functional genome analysis of Alcanivorax borkumensis, an ubiquitous . Microbes Environ. Samples of 100l were taken at intervals, applied directly to prewetted glass-fibre filters, and washed twice with 5-ml aliquots of the same buffer; 0.5-m glass-fiber filters (MFS, Dubbin, CA) were used with a filter apparatus. The resulting phases were of excellent quality, which enabled us to trace of most of the molecule. government site. Plasmodium falciparum: a paradigm for alternative folate biosynthesis in diverse microorganisms? Google Scholar. Biochim. & Minor, M. Processing of X-ray diffraction data collected in oscillation mode. Differential expression of the three Alcanivorax borkumensis SK2 genes Production of a recombinant alkane hydroxylase (AlkB2) from Alcanivorax eCollection 2019. In this sense, the aim of this study was to establish a scale-up process using the constant oxygen mass transfer . Alcanivorax - Wikipedia Alcanivorax borkumensis is a marine bacterium that uses exclusively petroleum oil hydrocarbons as sources of carbon and energy (and is therefore designated "hydrocarbonoclastic"). 58, 19481954 (2002). Synth. Chem. When needed, a final concentration of 5mM NaCl or KCl was also added at the same time. Search for more papers by this author. 24, 502508 (2008). A status is an integer in the range 0 to 999, inclusive. D Biol. Feasibility of treating emulsified oily and salty wastewaters through coagulation and bio-regenerated GAC filtration. 244, 15821592 (1969). Efran Manilla-Prez, Efran Manilla-Prez. The site is secure. Cells were then incubated for 10min, pelleted, washed twice and resuspended in the same buffer to OD600nm of 10. Sci. nov. and reclassification of Fundibacter jadensis DSM 1 21 78T (Bruns and Berthe-Corti 1999) as Alcanivorax jadensis comb. Various edge cases in . 47, S216S224 (2008). Polyribosyl-ribitol-phosphate (PRP) from Haemophilus influenzae type b (Hib) is an active immunizing molecule used in the production of the vaccine against H. influenzae, and industrial production could contribute to satisfying a world demand especially in developing countries. Microbiol. Because of its abundance in oil spill regions, it has great potential to be used actively in oil spill remediation. Cass Avenue, Argonne, 60439, Illinois, USA, You can also search for this author in Cells were incubated for 15min, and a final concentration of 0.2% glucose was then added to the cell suspension. Longitudinal tracking of bacteria-covered oil droplets using microfluidics, reveals distinct biofilm phenotypes: thick and spherical versus thin and dendritic, with the latter having a faster consumption rate. J. Mol. Acta 1618, 7992 (2003). 6:6874 doi: 10.1038/ncomms7874 (2015). . Article Clin. Hydrocarbon-degrading bacteria feed on the hydrocarbons in the oil droplet, breaking them into inorganic compounds. Would you like email updates of new search results? enie des Proc ed es et Mat eriaux, Ecole Centrale Paris, Grande voie des vignes, 92295 Chatenay-Malabry Cedex, France Abstract: Limiting factors induced by the formation of a biofilm on the. PLoS ONE 6, 15610 (2011). Inorg. Burg, A. W. & Brown, G. M. The biosynthesis of folic acid VI. Accession code: Atomic coordinates and structure factors for the structure of YdaH have been deposited at the RCSB Protein Data Bank with an accession code 4R0C. 31, 394395 (1999). Research paper by Julia S JS Sabirova, Anke A Becker, Heinrich H Lnsdorf, Jean-Marc JM Nicaud, Kenneth N KN Timmis, Peter N PN Golyshin by Julia S JS Sabirova, Anke A Becker, Heinrich H Lnsdorf, Jean-Marc JM Nicaud, Kenneth N KN Bioassays 24, 637648 (2002). The influence of calcium ions on properties of lipid bodies isolated from Alcanivorax borkumensis 10/2010 - 6/2011. Yakimov et al. . D54, 905921 (1998). The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. The strain uses aliphatic hydrocarbons as its main carbon source . High-resolution optical microscopy is used to image all individual cells in Vibrio cholerae biofilms at different stages of development and extracted the precise 3D cellular arrangements, cell shapes, sizes, and global morphological features during biofilm growth on submerged glass substrates under flow. A. Proc. 51, 2737 (2003). Insights into the Potential of the Atlantic Cod Gut Microbiome as Biomarker of Oil Contamination in the Marine Environment. Contain the spill to prevent it spreading. Brown, G. M., Weisman, R. A. Zobrazit publikaci. Longitudinal tracking of bacteria-covered oil droplets using microfluidics, reveals distinct biofilm phenotypes: thick and spherical versus thin and dendritic, with the latter having a faster consumption rate. sharing sensitive information, make sure youre on a federal J. Bacteriol. Its ubiquity, unusual physiology and demonstrated role in . An official website of the United States government. Bacterial strains and plasmids used in this study are listed in Table Table1. Biotechnol. Biochemical Engineering Journal , 2018; 132: 279 DOI: 10.1016/j.bej.2018.01.014 Cite This Page : Cloning and functional analysis of alkB genes in Alcanivorax borkumensis SK2. Datsenko, K. A. Nayal, M. & Di Cera, E. Valence screening of water in protein crystals reveals potential Na+ binding sites. Interaction of Alcanivorax borkumensis with a Surfactant - PubMed The marine hydrocarbonoclastic bacterium Alcanivorax borkumensis is well known for its ability to successfully degrade various mixtures of n-alkanes occurring in marine oil spills. Filters were then incubated for 30min in scintillation fluid (ScintiVerse BD) and counted with a Packard Tri-Carb 1600TR liquid scintillation counter (Perkin Elmer, Waltham, MA). In this paper, we provide background to the genome sequencing project of Alcanivorax borkumensis, which is a marine bacterium that uses exclusively petroleum oil hydrocarbons as sources of carbon and energy (therefore designated "hydrocarbonoclastic"). Sabirova JS, Chernikova TN, Timmis KN, Golyshin PN. Sci. Bermingham, A. 245, 30153025 (1970). D Biol. Alcanivorax borkumensis are prominent actors in oil spill bioremediation; however, the interfacial dynamics of their biofilms and its role in oil degradation remain unclear. Nat Commun 6, 6874 (2015). [3H]-sulfamethazine was then added to a final concentration of 37nM. 2019 Mar 30;34(1):104-107. doi: 10.1264/jsme2.ME18151. Analysis of Lipid Export in Hydrocarbonoclastic Bacteria of the Genus Google Scholar, Yakimov MM, Golyshin PN, Lang S, Moore ER, Abraham WR, Lunsdorf H, Timmis KN (1998) Alcanivorax Institut fr Molekulare Mikrobiologie und Biotechnologie, Westflische Wilhelms-Universitt Mnster. They hope that their new understanding of the biochemistry of the micro-organism will lead to the development of new, effective, environmentally friendly methods to clean up oil-contaminated waters. Nature Communications (Nat Commun) Biotechnol Lett 32, 497502 (2010). Many organisms including Alcanivorax borkumensis (A. borkumensis) are capable of degrading petroleum oil as they rely on . D60, 2126 (2004). In-situ burning for oil spill countermeasures? How To Clean An Oil Spill On Land - Realonomics Mnster, Germany. Global topology analysis of the Escherichia coli inner membrane proteome. Provided by the Springer Nature SharedIt content-sharing initiative, Over 10 million scientific documents at your fingertips, Not logged in Brown, M. H., Paulsen, I. T. & Skurray, R. A. The inoculum and hydrocarbons concentration have a remarkable effect on the biodegradation with the crude enzymes. [PDF] Alcanivorax borkumensis Biofilms Enhance Oil Degradation By Google Scholar, Rozhkova-Novosad EA, Chae JC, Zylstra GJ, Bertrand EM, Alexander-Ozinskas M, Deng D, Moe LA, van Beilen JB, Danahy M, Groves JT, Austin RN (2007) Profiling mechanisms of alkane hydroxylase activity in vivo using the diagnostic substrate norcarane. Semantic Scholar uses AI to extract papers important to this topic. kveech2 - Environmental Microbiology Ask an Expert: Where to buy Alcanivorax borkumensis? - Science Buddies Neutral lipid production in Alcanivorax borkumensis SK2 and other Chem Biol 14:165172, Sabirova JS, Ferrer M, Regenhardt D, Timmis KN, Golyshin PN (2006) Proteomic insights into metabolic adaptations in Alcanivorax borkumensis induced by alkane utilization. Here, we constructed three artificial self-sufficient P450s (ArtssP450s) using CYP153A13 from Alcanivorax borkumensis and cytochrome P450 reductase (CPR) domains of natural self-sufficient P450s (CYP102A1, CYP102A5, and 102D1). It is known to be a surface bacterium leading to substantial interaction with the oil-water interface. Unemo, M. & Shafer, W. M. Antimicrobial resistance in Neisseria gonorrhoeae in the 21st century: past, evolution, and future. Purification and properties of the enzymes required for the formation of dihydropteroic acid. Purification and properties of dihydroneopterin aldolase. The resulting phases were subjected to density modification and fourfold NCS averaging by RESOLVE38 using the native structure factor amplitudes. Alcanivorax borkumensis is a hydrocarbon degrading bacterium linked to oil degradation around oil spill sites. Bachelor's thesis Cells were incubated with 0.3M [3H]-PABA for 15min, applied directly to prewetted glass-fibre filters and washed immediately twice with 5-ml aliquots of the same buffer. CIP 105606. Dos Santos, V. A., Kaiser, O., Ferrer, M., Sabirova, Y. S., Lnsdorf, H., et al. Transposon mutagenesis was used for functional genome analysis of Alcanivorax SK2 to reveal the genetic basis of other environmentally relevant phenotypes, pointing at complex and tightly controlled cellular interactions involving oxygen as a primary messenger and cyclic-di-GMP as a secondary messenger required for Alcanvorax responses to environmental stresses. The protein and ligand samples were degassed before they were loaded into the cell and syringe. Front Microbiol. 180, 62606268 (1998). (PDF) Culturable bacterial phylogeny from a shallow water hydrothermal The CCP4 suite: programs for protein crystallography. In this paper we. The genome sequence provides the basis for the future design of strategies to mitigate the ecological damage caused by oil spills and provides A. borkumensis SK2 with a competitive edge in oil-polluted environments. Enzymatic synthesis of dihydrofolic acid from guanine and ribose compounds. 426, 403411 (2014). Some species, such as Alcanivorax borkumensis, produce surfactants that solubilize the oil, while other bacteria degrade the oil into carbon dioxide. event horizon calamity DSM 11573. J. Mol. J Bacteriol 184:17331742, van Beilen JB, Li Z, Duetz WA, Smits THM, Witholt B (2003) Diversity of alkane hydroxylase systems in the environment. 2019 Jul 22;7(7):209. doi: 10.3390/microorganisms7070209. Binding experiments were carried out with the protein solution (1.5ml) in the cell and the ligand as the injectant. nov., a new, hydrocarbon-degrading and surfactant-producing marine bacterium. Alcanivorax borkumensis. Int J Syst Bacteriol 48:339348. Jani Reddy Bolla and Chih-Chia Su: These authors contributed equally to this work, Department of Chemistry, Iowa State University, Ames, 50011, Iowa, USA, Jani Reddy Bolla,Abhijith Radhakrishnan,Nitin Kumar&Edward W. Yu, Department of Physics and Astronomy, Iowa State University, Ames, 50011, Iowa, USA, Chih-Chia Su,Jared A. Delmar,Tsung-Han Chou,Feng Long&Edward W. Yu, NE-CAT and Department of Chemistry and Chemical Biology, Cornell University, Building 436E, Argonne National Laboratory, 9700S. Iterations of refinement using PHENIX41 and CNS42 and model building in Coot39 lead to the current 2.96--resolution model with excellent geometrical characteristics (Table 1). This work is based on research conducted at the Northeastern Collaborative Access Team beamlines of the Advanced Photon Source, supported by an award GM103403 from the National Institutes of General Medical Sciences. Alcanivorax borkumensis is whats called a halophilic organism, meaning it can survive in salt rich environments. This bacterium is significant . & Molnar, D. A. Efran ManillaPrez and Alvin Brian Lange contributed equally to this work. Bijan Bambai. For effective growth on these compounds, the bacteria possess the unique capability not only to incorporate but also to modify fatty intermediates derived from the alkane degradation pathway. Alcanivorax borkumensis is an oil-degrading marine bacterium. The Editors will consider papers for publication based on their novelty, their immediate or future impact as well as their contribution to the advancement of medical biotechnology . Manilla-Prez E, Lange AB, Hetzler S, Steinbchel A. Appl Microbiol Biotechnol. XI. Emendations: Fernndez-Martnez et al. Crystallography & NMR system: a new software suite for macromolecular structure determination. Proc. Alcanivorax borkumensis - Wikipedia 2022 Springer Nature Switzerland AG. Epub 2019 Feb 16. J. Biol. Alcanivorax borkumensis (A. borkumensis) is a Gram-negative, rod-shaped hydrocarbonoclastic ("oil-degrading") bacterium. Site-directed point mutations on residues D180, N390, W400, P418, R426, D429 and N433, which are expected to be critical for the function of the YdaH transporter, were performed to generate the single point mutants D180A, N390A, W400A, P418A, R426A, D429A and N433A. Long, F., Rouquette-Loughlin, C., Shafer, W. M. & Yu, E. W. Functional cloning and characterization of the multidrug efflux pumps NorM from Neisseria gonorrhoeae and YdhE from Escherichia coli. It is found in low numbers in all oceans of the world and in high numbers in oil-contaminated waters. Just back from the EMBL-IBEC Conference on Engineering Multicellular Systems which was held in Barcelona Biomedical Research Park (PRBB). 1, 107125 (1999). place your first order and save 15% using coupon: When the OD600nm reached 0.5, the culture was treated with 0.2mM IPTG to induce ydaH expression, and cells were harvested within 2h. Cells were washed twice with buffer containing 50mM potassium phosphate (pH 7.5), twice with buffer containing 100mM Tris-HCl (pH 7.5) and 5mM NaCl, and then suspended in the same buffer to OD600nm of 15. Titration curves were fitted by a non-linear least-squares method to a function for the binding of a ligand to a macromolecule. 4. Antimicrob. By submitting a comment you agree to abide by our Terms and Community Guidelines. It is found in low numbers in all oceans of the world and becomes abundant in oil-contaminated waters. Triglia, T., Menting, J. G., Wilson, C. & Cowman, A. F. Mutations in dihydropteroate synthase are responsible for sulfon and sulfonamide resistance in Plasmodium falciparum. Dispersants are thought to be important in the creation of oil . The SeMet data were then used to help determine the 4.10--resolution structure of YdaH by molecular replacement with single-wavelength anomalous diffraction using the programme Phaser40. Bioremediation (bioaugmentation/biostimulation) trials of oil polluted seawater: a mesocosm simulation study. Mathis, J. Semantic Scholar uses AI to extract papers important to this topic. Proc. A. Abbasi, G. Bothun, A. Bose; . Semi-finalist in Scientific Paper-Based Competition (National Level) "Bioremediasi Laut Menggunakan Alcanivorax borkumensis SK2 sebagai Solusi Masalah Pencemaran Limbah Industri" UNNES 2021 . 24, 9971004 (2006). J. Bacteriol. . Hussein, M. J., Green, J. M. & Nichols, B. P. Characterization of mutations that allow p-aminobenzoyl-glutamate utilization by Escherichia coli. Veal, W. L. & Shafer, W. M. Identification of a cell envelope protein (MtrF) involved in hydrophobic antimicrobial resistance in Neisseria gonorrhoeae. Gregson BH, Metodieva G, Metodiev MV, Golyshin PN, McKew BA. Emsley, P. & Cowtan, K. Coot: model-building tools for molecular graphics. 2010 May;86(6):1693-706. doi: 10.1007/s00253-010-2515-5. & Wanner, B. L. One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. official website and that any information you provide is encrypted Biophys. PubMed Long, F. et al. need a perfect original paper? Non-linear regression fitting to the binding isotherm provided us with the equilibrium binding constant (Ka=1/Kd) and enthalpy of binding (H). 4). (ed.) McCoy, A. J. et al. Chem. Brnger, A. T. et al. Disclaimer, National Library of Medicine Filters were then incubated for 30min in scintillation fluid (ScintiVerse BD) and counted with a Packard Tri-Carb 1600TR liquid scintillation counter (Perkin Elmer, Waltham, MA). 23, 979986 (1997). . The current study aimed to use Alcanivorax borkumensis crude enzymes preparation as an agent for enhanced microbial hydrocarbons biodegradation in contaminated water and soil. The minimum growth inhibitory concentrations (MICs) of sulfamethazine and sulfanilamide for E. coli BL21(DE3)abgTpabA (incoculum, 500 cellsml1) harbouring these vectors were then determined using LB agar containing 50gml1 ampicillin, 0.1mM IPTG and different concentrations of sulfamethazine and sulfanilamide, respectively. 27, 587613 (2014). J.R.B., C.-C.S. Although, the sequence of alkB2 has been determined, the molecular characterization and the substrate specificity of AlkB2 require . Wilson, S. D. & Horne, W. D. Use of glycerol-crypotected Lactobacillus casei for microbiological assay of folic acid. Statuses. ', Paper presented at European School of Genetic Medicine, 1st Course in Microbial Bioremediation and Environmental Genomics, March 11-16, 2006, Bertinoro, Italy., 3/01/01. Gel filtration suggested an average molecular weight of 107.08.8kDa for the YdaH transporter (Supplementary Fig. Although, the sequence of alkB2 has been determined, the molecular characterization and the substrate specificity of AlkB2 require .
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