wrote the paper. Alvin Brian Lange. 27, 8596 (1990). 174, 17501759 (1992). Transcriptional profiling of the marine oil-degrading bacterium Alcanivorax borkumensis during growth on n-alkanes. Semi-finalist in Scientific Paper-Based Competition (National Level) "Bioremediasi Laut Menggunakan Alcanivorax borkumensis SK2 sebagai Solusi Masalah Pencemaran Limbah Industri" UNNES 2021 . Authors thank Dr, Kenneth N. Timmis at German Research Center for Biotechnology in Braunschweig, Germany for providing Alcanivorax It is known to be, Alcanivorax borkumensis is a cosmopolitan marine bacterium that uses oil hydrocarbons as its exclusive source of carbon and, International journal of systematic bacteriology, During screening for biosurfactant-producing, n-alkane-degrading marine bacteria, six heterotrophic bacterial strains were, By clicking accept or continuing to use the site, you agree to the terms outlined in our. Terwilliger, T. C. Maximum-likelihood density modification using pattern recognition of structural motifs. Biol. 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 . 189, 33293334 (2007). Langmuir : the ACS journal of surfaces and, Alcanivorax borkumensis (AB) is a marine bacterium that dominates bacterial communities around many oil spills because it, The potential of the folic acid biosynthesis pathway as a target for the development of antibiotics has been clinically validated, Alcanivorax borkumensis is a hydrocarbon degrading bacterium linked to oil degradation around oil spill sites. Biotechnol. We show experimentally that biofilm dendrites emerge from aster-like nematic defects in the thin. - 212.48.68.247, Institute of Narcology Ministry of Health (3000601956). Ethayathulla, A. S. et al. 1, 107125 (1999). We are grateful to Dr XiKui Fang (Ames Laboratory) for providing us the Na9[-SiW9O34H].23H2O complex used in this study. Part of Springer Nature. In this paper we. Search for more papers by this author. Chem. 2018 Dec 17;9:3130. doi: 10.3389/fmicb.2018.03130. Unemo, M. & Shafer, W. M. Antimicrobial resistance in Neisseria gonorrhoeae in the 21st century: past, evolution, and future. This structure was then used to refine against the 2.96--resolution data using PHENIX41 as described above. 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. When feasible to carry . The CCP4 suite: programs for protein crystallography. Scientists are . J. Biol. Purification and properties of the enzymes required for the formation of dihydropteroic acid. MeSH J. Appl. We are particularly grateful to Simon Silver (University of Illinois at Chicago) for his careful and kind proofreading of our manuscript. Papers overview. Bioassays 24, 637648 (2002). 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. 237, 536540 (1962). Anyone you share the following link with will be able to read this content: Sorry, a shareable link is not currently available for this article. Dis. Pronunciation of Alcanivorax borkumensis with 2 audio pronunciations and more for Alcanivorax borkumensis. Biochim. You searched for: Subject "Alcanivorax borkumensis" Remove constraint Subject: "Alcanivorax borkumensis" Start Over. Microbiol. When the OD600nm reached 0.5, the culture was induced with 0.2mM IPTG and the 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 then suspended in the same buffer to OD600 nm of 15. Otwinowski, Z. MLPHARE, CCP4 Proc. Envirosolutions Floor Sweep. Tseng, T. T. et al. Genome sequence of the ubiquitous hydrocarbon-degrading marine bacterium Alcanivorax borkumensis. Brown, M. H., Paulsen, I. T. & Skurray, R. A. 245, 30153025 (1970). 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. 2018; Corpus ID: 4902231. Henderson, G. B. The hunch proved correct, with the team discovering that A. borkumensis had . 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. 2008 Aug;285(1):89-96. doi: 10.1111/j.1574-6968.2008.01222.x. SK2. The knockout BL21(DE3)abgT::kan strain was selected on LB plate containing 30gml1 kanamycin, and verified by PCR. Carter, E. L. et al. Long, F. et al. 2019 Mar 30;34(1):104-107. doi: 10.1264/jsme2.ME18151. Synth. Before titration, the protein was thoroughly dialysed against buffer containing 20mM Tris-HCl pH 7.5, 50mM NaCl and 0.03% DDM. . Adams, P. D. et al. Nat. 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. Enzymatic synthesis of dihydrofolic acid from guanine and ribose compounds. 2006 Aug;24(8):997-1004. doi: 10.1038/nbt1232. The journal is dedicated to rapid publication of high quality, cutting-edge research at the interface between life sciences and their technological exploitation. 122, 260269 (1986). need a perfect original paper? CAS 2007 Jun;18(3):257-66. doi: 10.1016/j.copbio.2007.04.006. Chem. The abgT::kan cassette, which was used to replace the chromosomal abgT gene, was produced by PCR, and then introduced into pKD46/BL21(DE3) by electroporation. The full-length YdaH protein consists of 11 methionine residues and all of these 11 selenium sites were identified in each protomer of the protein (44 total selenium sites in the asymmetric unit). Veal, W. L. & Shafer, W. M. Identification of a cell envelope protein (MtrF) involved in hydrophobic antimicrobial resistance in Neisseria gonorrhoeae. The manually built model was used as initial search model. PubMed Curr Opin Biotechnol. Int J Syst Evol Microbiol 2003; 53:331-338. By clicking accept or continuing to use the site, you agree to the terms outlined in our. 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). The multidrug efflux protein NorM is a prototype of a new family of transporters. CAS 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 PHENIX: building new software for automated crystallographic structure determination. J. Bacteriol. The concentrations of folic acid in BL21(DE3)abgTpabA expressing the mutant transporters were measured using the same procedures. It has several efficient enzymes that . Hydrocarbon-degrading bacteria feed on the hydrocarbons in the oil droplet, breaking them into inorganic compounds. Alcanivorax borkumensis (A. borkumensis) is a Gram-negative, rod-shaped hydrocarbonoclastic ("oil-degrading") bacterium. Chem. D58, 17721779 (2002). Biol. My research career began at Southern University at New Orleans when I became a work-study . Otwinowski, Z. Pape, T. & Schneider, T. R. HKL2MAP: a graphical user interface for macromolecular phasing with SHELX programs. Acta Crystallogr. USA 91, 71497153 (1994). Infect. Using a single tube of #2698 broth (5 to 6 mL), withdraw approximately 0.5 to 1.0 mL with a Pasteur or 1.0 mL pipette. 2009; Alcanivorax indicus Song et al. 236, 25342543 (1961). Phylogenetic diversity of the 16S rRNA gene asso-ciated with the domain bacteria was examined at the level of operational taxonomic units (OTUs) using the rarefaction analysis from a newly identified shallow water hydrothermal vent, Espalamaca in the Crystal structure of the Alcanivorax borkumensis YdaH transporter reveals an unusual topology. Perspective Perspective: what is known, and not known, about the connections between alkane oxidation and metal uptake in alkanotrophs in the marine environment 426, 403411 (2014). Semantic Scholar uses AI to extract papers important to this topic. designed the research. Alcanivorax strains represent one of the most studied group of n-alkane degraders able to produce biosurfactants. Kulathila, R., Kulathila, R., Indic, M. & van den Berg, B. 2010 May;86(6):1693-706. doi: 10.1007/s00253-010-2515-5. 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. D57, 17551762 (2001). Acta Crystallogr. Payler SJ, Biddle JF, Sherwood Lollar B, Fox-Powell MG, Edwards T, Ngwenya BT, Paling SM, Cockell CS. performed model building and refinement. Crystallogr. Attachment of Alcanivorax borkumensis to Hexadecane-In-Artificial Sea Water Emulsion Droplets. Google Scholar, Yakimov MM, Golyshin PN, Lang S, Moore ER, Abraham WR, Lunsdorf H, Timmis KN (1998) Alcanivorax Just back from the EMBL-IBEC Conference on Engineering Multicellular Systems which was held in Barcelona Biomedical Research Park (PRBB). PubMed Central Br. Proc. By submitting a comment you agree to abide by our Terms and Community Guidelines. Folster, J. P. & Shafer, W. M. Regulation of mtrF expression in Neisseria gonorrhoeae and its role in high-level antimicrobial resistance. Cloning and functional analysis of alkB genes in Alcanivorax borkumensis SK2. 2018. Miri, M., Bambai, B., Tabandeh, F. et al. J. Bacteriol. CAS Clin. & Brown, G. M. The biosynthesis of folic acid. The addition of dispersant to crude oil enhanced oil degradation rates and favored the abundance and expression of oil-degrading genes from a Thalassolituus sp. Bijan Bambai. 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. Biophys. Learn more about Institutional subscriptions, Azapagic A, Emsley A, Hamerton I (2003) Polymers: the environment and sustainable development. Plasmodium falciparum: a paradigm for alternative folate biosynthesis in diverse microorganisms? The specific activity of [3H]-sulfamethazine is 34.5Cimmol1. Phaser crystallographic software. Nat. Although, the sequence of alkB2 has been determined, the molecular characterization and the substrate specificity of AlkB2 require . Int J Syst Bacteriol 48:339348. J. Exp. This site needs JavaScript to work properly. Alcanivorax, first described in 1998, is a Gram-negative, halophilic, aerobic, rod-shaped, oil-degrading marine bacterium that is found in low abundances in unpolluted environments in the upper layers of the ocean, but quickly becomes the predominant microbe in oil-contaminated open oceans and coastal waters when nitrogen and phosphorus are not . Dual-view light-sheet microscopy was developed to investigate the dynamics of biofilm development from a founder cell to a mature three-dimensional community and revealed how multicellular structures form from a single founder cell. Alcanivorax borkumensis, a marine bacterium highly specialized in degrading linear and branched alkanes, plays a key ecological role in the removal of marine oil spills.It contains several alternative enzyme systems for terminal hydroxylation of alkanes, including three P450 cytochromes (P450-1, P450-2 and P450-3). J Biol Chem 279:40844092, Article 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. Semantic Scholar is a free, AI-powered research tool for scientific literature, based at the Allen Institute for AI. Article How effective is in-situ burning? The authors declare no competing financial interests. Gel filtration suggested an average molecular weight of 107.08.8kDa for the YdaH transporter (Supplementary Fig. Researchers have genecally engineered other bacteria to consume petroleum . It is likely that there is some limit to this model, but the limit was not determined in this paper. [3H]-sulfamethazine was then added to a final concentration of 37nM. 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. Energy recovery Research Agency for funding under the scope of from secondary pulp/paper-mill sludge and sewage Cavitation as a Potential Technology for Wastewater Management - An Example of Enhanced Nutrient Release from Secondary Pulp and Paper Mill Sludge 647 Strojniki vestnik - Journal of Mechanical Engineering 65(2019)11-12, 641-649 . Rev. Sign up for the Nature Briefing newsletter what matters in science, free to your inbox daily. How they are named. Blue dextran (Sigma-Aldrich, St Louis, MO) was used to determine the column void volume. official website and that any information you provide is encrypted D60, 2126 (2004). Inhibition by sulfonamides. Hussein, M. J., Green, J. M. & Nichols, B. P. Characterization of mutations that allow p-aminobenzoyl-glutamate utilization by Escherichia coli. As there are no commercially available membrane protein markers, we used the well-characterized N. gonorrhoeae NorM multidrug efflux pump43,44 (which exists as a monomer in solution with the monomeric molecular weight equals 50.6kDa) and E. coli CusC outer membrane channel45,46 (which exists as a trimer in solution with the trimeric molecular weight equals 147.7kDa) as standards. Its ubiquity, unusual physiology and demonstrated role in . & Huennekens, F. M. Membrane-associated folate transport proteins. & Wanner, B. L. One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. J Mol Microbiol Biotechnol 1:6370, CAS The amphiphilic amphibactin siderophores produced by the oil-associated bacteria, Vibrio sp. A. borkumensis is a biosurfactant producing bacteria as mentioned above. 37, 843844 (2004). Mnster, Germany. Genome sequence completed of Alcanivorax borkumensis, a hydrocarbon-degrading . Alcanivorax borkumensis gen. nov., sp. Biophys. 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. Bacterial strains, media, and cultivation conditions. Alcanivorax borkumensis is a hydrocarbon degrading bacterium linked to oil degradation around oil spill sites. Alcanivorax borkumensis are prominent actors in oil spill bioremediation; however, the interfacial dynamics of their biofilms and its role in oil degradation remain unclear. 2019 Mar 12;10:426. doi: 10.3389/fmicb.2019.00426. 2018. . 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. No change in heat was observed in the injections throughout the experiment. Google Scholar. A protein liquid chromatography Superdex 200 16/60 column (GE Healthcare, Pittsburgh, PA) with a mobile phase containing 20mM Na-HEPES (pH 7.5) and 0.05% (w/v) DDM was used in the gel filtration experiments. Alcanivorax borkumensis is a cosmopolitan marine bacterium that uses oil hydrocarbons as its exclusive source of carbon and energy. However, after the disruption of both the AtfA1 and AtfA2 genes, reduced but substantial accumulation of TAGs was still observed . I do not know if it is only found in salt water, some references I have found place it in inland bodies of water, which typically have a lower salt concentration, and the ever useful microbe wiki places it in fresh water as well. Ability of the So-Called Obligate Hydrocarbonoclastic Bacteria to Utilize Nonhydrocarbon Substrates Thus Enhancing Their Activities Despite their Misleading Name. Bacterial strains and plasmids used in this study are listed in Table Table1. Commun. This is a preview of subscription content, access via your institution. The specific activity of [3H]-PABA is 30.4Cimmol1. J. Biol. Niche-specificity factors of a marine oil-degrading bacterium Alcanivorax borkumensis SK2. Alcanivorax borkumensis is a hydrocarbon degrading bacterium linked to oil degradation around oil spill sites. We used ITC to examine the binding of sulfamethazine, sulfadiazine, sulfathiazole or sulfanilamide to the purified YdaH transporter. Alcanivorax borkumensis. Google Scholar. Alcanivorax balearicus Rivas et al. PubMed Central Hyde, J. E. et al. Proc. Sci. Biotechnology Letters Cartwright K. A. V. The strain uses aliphatic hydrocarbons as its main carbon source . E. coli BL21(DE3)abgTpabA carrying pET15bydaH or pET15b were grown in LB broth with 100gml1 ampicillin at 37C. Acta 1618, 7992 (2003). Alcanivorax borkumensis (AB) is a marine bacterium that dominates bacterial communities . Alcanivorax borkumensis is whats called a halophilic organism, meaning it can survive in salt rich environments. Semantic Scholar is a free, AI-powered research tool for scientific literature, based at the Allen Institute for AI. Agents Chemother. 2003 Fernandez-Martinez J, Pujalte MJ, Garcia-Martinez J, Mata M, Garay E, Rodriguez-Valeral F. Description of Alcanivorax venustensis sp. Various edge cases in . PubMed Sci. 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. Aseptically transfer this aliquot back into the broth tube. Alcanivorax borkumensis skyrocketed, helping to get rid of the oil. The primers used for these mutations are listed in Supplementary Table 2. Disclaimer, National Library of Medicine & Herv, G. -, -, and -dodecatungstosilicic acids: isomers and related lacunary compounds. 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. nov., a new, hydrocarbon-degrading and surfactant-producing marine bacterium. 239, 317325 (1964). borkumensis, a hydrocarbon-degrading bacterium that plays a global role in oil removal from marine systems. How to cite this article: Bolla, J.R. et al. DE-AC02-06CH11357. All diffraction data were collected at 100K at beamline 24ID-C located at the Advanced Photon Source, using a Platus 6M detector. Titration curves were fitted by a non-linear least-squares method to a function for the binding of a ligand to a macromolecule. 27, 587613 (2014). & Nichols, B. P. Nucleotide sequence of Escherichia coli pabA and its evolutionary relationship to trp(G)D. J. Mol. Ex-situ biodegradation of petroleum hydrocarbons using Alcanivorax borkumensis enzymes. Biotechnol Lett 32, 497502 (2010). Google Scholar, Feng L, Wang W, Cheng J, Ren Y, Zhao G, Gao C et al (2007) Genome and proteome of long-chain alkane degrading Geobacillus thermodenitrificans NG80-2 isolated from a deep-subsurface oil reservoir. Microbes Environ. PubMedGoogle Scholar. Furthermore, the activity of the enzyme in the presence of the accessory proteins, rubredoxin (RubA) and rubredoxin reductase (RubB), produced in E. coli BL21(DE3)plysS cells, was determined. Alcanivorax borkumensis are prominent actors in oil spill bioremediation; however, the interfacial dynamics of their biofilms and its role in oil degradation remain unclear. Halloysite nanotubes - the nano-bio interface. Unable to load your collection due to an error, Unable to load your delegates due to an error. Although, the sequence of alkB2 has been determined, the molecular characterization and the substrate specificity of AlkB2 require . 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"). Species. Alcanivorax borkumensis is a marine bacterium that uses exclusively petroleum oil hydrocarbons as sources of carbon and energy (and is therefore designated "hydrocarbonoclastic"). Biochemical Engineering Journal , 2018; 132: 279 DOI: 10.1016/j.bej.2018.01.014 Cite This Page : 2004 Mar;6(3):191-7. doi: 10.1046/j.1462-2920.2003.00550.x. Google Scholar. HHS Vulnerability Disclosure, Help https://doi.org/10.1007/s10529-009-0177-0, DOI: https://doi.org/10.1007/s10529-009-0177-0. Bookshelf Epub 2008 Jun 28. When the OD600nm reached 0.5, the cultures were induced with 0.2mM IPTG and harvested for 2h after induction. and E.W.Y. Microbiol. eCollection 2018. 21, 7490 (1940). In this study, AlkB2 from A. borkumensis SK2 was expressed in Escherichia coli to examine the functionality of AlkB2 as a hydroxylating enzyme. Density-modified phases allowed us to visualize the helical structural features of the molecule. Biotechnol. PMC On the basis of the values of KA, the change in free energy (G) and entropy (S) were calculated with the equation: G=RT lnKa=HTS, where T is 273K and R is 1.9872, calK1 per mol. Diffraction data were processed using DENZO and scaled using SCALEPACK32. Mathis, J. The ion transporter superfamily. 31, 394395 (1999). Use of the Advanced Photon Source is supported by the U.S. Department of Energy, Office of Basic Energy Sciences, under Contract No. Alcanivorax borkumensis is an oil-degrading marine bacterium. Hara A, Baik SH, Syutsubo K, Misawa N, Smits TH, van Beilen JB, Harayama S. Environ Microbiol. Sci. . D Biol. It is found in low numbers in all oceans of the world and becomes abundant in oil-contaminated waters.
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