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Ampc -Lactamases
CLINICAL MICROBIOLOGY REVIEWS, Jan. 2009, p. 161–182 Vol. 22, No. 1 0893-8512/09/$08.00ϩ0 doi:10.1128/CMR.00036-08 Copyright © 2009, American Society for Microbiology. All Rights Reserved. AmpC -Lactamases George A. Jacoby* Lahey Clinic, Burlington, Massachusetts INTRODUCTION .......................................................................................................................................................161 DISTRIBUTION .........................................................................................................................................................161 PHYSICAL AND ENZYMATIC PROPERTIES .....................................................................................................163 STRUCTURE AND ESSENTIAL SITES.................................................................................................................164 REGULATION ............................................................................................................................................................165 PUMPS AND PORINS ..............................................................................................................................................165 PHYLOGENY..............................................................................................................................................................166 PLASMID-MEDIATED AmpC -LACTAMASES .................................................................................................166 ONGOING EVOLUTION: EXTENDED-SPECTRUM -
Kinetic and Functional Properties of Human Mitochondrial Phosphoenolpyruvate Carboxykinase
Biochemistry and Biophysics Reports 7 (2016) 124–129 Contents lists available at ScienceDirect Biochemistry and Biophysics Reports journal homepage: www.elsevier.com/locate/bbrep Kinetic and functional properties of human mitochondrial phosphoenolpyruvate carboxykinase Miriam Escós b, Pedro Latorre a,b, Jorge Hidalgo a,b, Ramón Hurtado-Guerrero b,e, José Alberto Carrodeguas b,c,d,nn, Pascual López-Buesa a,b,n a Departamento de Producción Animal y Ciencia de los Alimentos, Facultad de Veterinaria, Universidad de Zaragoza, 50013 Zaragoza, Spain b Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), BIFI-IQFR (CSIC) Joint Unit, Universidad de Zaragoza, 50009 Zaragoza, Aragón, Spain c Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, 50009 Zaragoza, Spain d IIS Aragón, 50009 Zaragoza, Spain e Fundación ARAID, Gobierno de Aragón, Zaragoza, Spain article info abstract Article history: The cytosolic form of phosphoenolpyruvate carboxykinase (PCK1) plays a regulatory role in gluconeo- Received 21 April 2016 genesis and glyceroneogenesis. The role of the mitochondrial isoform (PCK2) remains unclear. We report Received in revised form the partial purification and kinetic and functional characterization of human PCK2. Kinetic properties of 2 June 2016 the enzyme are very similar to those of the cytosolic enzyme. PCK2 has an absolute requirement for Accepted 6 June 2016 þ þ þ Mn2 ions for activity; Mg2 ions reduce the K for Mn2 by about 60 fold. Its specificity constant is 100 Available online 8 June 2016 m fold larger for oxaloacetate than for phosphoenolpyruvate suggesting that oxaloacetate phosphorylation Keywords: À1 is the favored reaction in vivo. -
In Situ Biodegradation, Photooxidation and Dissolution of Petroleum Compounds in Arctic Seawater and Sea Ice
Water Research 148 (2019) 459e468 Contents lists available at ScienceDirect Water Research journal homepage: www.elsevier.com/locate/watres In situ biodegradation, photooxidation and dissolution of petroleum compounds in Arctic seawater and sea ice * Leendert Vergeynst a, b, , Jan H. Christensen c, Kasper Urup Kjeldsen b, Lorenz Meire d, e, Wieter Boone f, Linus M.V. Malmquist c, Søren Rysgaard a, f a Arctic Research Centre, Aarhus University, Aarhus, Denmark b Section for Microbiology and Center for Geomicrobiology, Department of Bioscience, Aarhus University, Aarhus, Denmark c Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Copenhagen, Denmark d Greenland Climate Research Centre, Greenland Institute of Natural Resources, Nuuk, Greenland e Department of Estuarine and Delta Systems, Royal Netherlands Institute of Sea Research, Utrecht University, Yerseke, Netherlands f Centre for Earth Observation Science, University of Manitoba, Winnipeg, Canada article info abstract Article history: In pristine sea ice-covered Arctic waters the potential of natural attenuation of oil spills has yet to be Received 19 July 2018 uncovered, but increasing shipping and oil exploitation may bring along unprecedented risks of oil spills. Received in revised form We deployed adsorbents coated with thin oil films for up to 2.5 month in ice-covered seawater and sea 22 October 2018 ice in Godthaab Fjord, SW Greenland, to simulate and investigate in situ biodegradation and photooxi- Accepted 23 October 2018 dation of dispersed oil. Available online 29 October 2018 GC-MS-based chemometric methods for oil fingerprinting were used to identify characteristic signa- tures for dissolution, biodegradation and photooxidation. In sub-zero temperature seawater, fast Keywords: Oil spill degradation of n-alkanes was observed with estimated half-life times of ~7 days. -
Simulation of Deepwater Horizon Oil Plume Reveals Substrate Specialization Within a Complex Community of Hydrocarbon Degraders
Simulation of Deepwater Horizon oil plume reveals substrate specialization within a complex community of hydrocarbon degraders Ping Hua, Eric A. Dubinskya,b, Alexander J. Probstc, Jian Wangd, Christian M. K. Sieberc,e, Lauren M. Toma, Piero R. Gardinalid, Jillian F. Banfieldc, Ronald M. Atlasf, and Gary L. Andersena,b,1 aEcology Department, Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720; bDepartment of Environmental Science, Policy and Management, University of California, Berkeley, CA 94720; cDepartment of Earth and Planetary Science, University of California, Berkeley, CA 94720; dDepartment of Chemistry and Biochemistry, Florida International University, Miami, FL 33199; eDepartment of Energy, Joint Genome Institute, Walnut Creek, CA 94598; and fDepartment of Biology, University of Louisville, Louisville, KY 40292 Edited by Rita R. Colwell, University of Maryland, College Park, MD, and approved May 30, 2017 (received for review March 1, 2017) The Deepwater Horizon (DWH) accident released an estimated Many studies of the plume samples reported that the structure 4.1 million barrels of oil and 1010 mol of natural gas into the Gulf of the microbial communities shifted as time progressed (3–6, 11– of Mexico, forming deep-sea plumes of dispersed oil droplets and 16). Member(s) of the order Oceanospirillales dominated from dissolved gases that were largely degraded by bacteria. During the May to mid-June, after which their numbers rapidly declined and course of this 3-mo disaster a series of different bacterial taxa were species of Cycloclasticus and Colwellia dominated for the next enriched in succession within deep plumes, but the metabolic capa- several weeks (4, 5, 14). -
Fish Bacterial Flora Identification Via Rapid Cellular Fatty Acid Analysis
Fish bacterial flora identification via rapid cellular fatty acid analysis Item Type Thesis Authors Morey, Amit Download date 09/10/2021 08:41:29 Link to Item http://hdl.handle.net/11122/4939 FISH BACTERIAL FLORA IDENTIFICATION VIA RAPID CELLULAR FATTY ACID ANALYSIS By Amit Morey /V RECOMMENDED: $ Advisory Committe/ Chair < r Head, Interdisciplinary iProgram in Seafood Science and Nutrition /-■ x ? APPROVED: Dean, SchooLof Fisheries and Ocfcan Sciences de3n of the Graduate School Date FISH BACTERIAL FLORA IDENTIFICATION VIA RAPID CELLULAR FATTY ACID ANALYSIS A THESIS Presented to the Faculty of the University of Alaska Fairbanks in Partial Fulfillment of the Requirements for the Degree of MASTER OF SCIENCE By Amit Morey, M.F.Sc. Fairbanks, Alaska h r A Q t ■ ^% 0 /v AlA s ((0 August 2007 ^>c0^b Abstract Seafood quality can be assessed by determining the bacterial load and flora composition, although classical taxonomic methods are time-consuming and subjective to interpretation bias. A two-prong approach was used to assess a commercially available microbial identification system: confirmation of known cultures and fish spoilage experiments to isolate unknowns for identification. Bacterial isolates from the Fishery Industrial Technology Center Culture Collection (FITCCC) and the American Type Culture Collection (ATCC) were used to test the identification ability of the Sherlock Microbial Identification System (MIS). Twelve ATCC and 21 FITCCC strains were identified to species with the exception of Pseudomonas fluorescens and P. putida which could not be distinguished by cellular fatty acid analysis. The bacterial flora changes that occurred in iced Alaska pink salmon ( Oncorhynchus gorbuscha) were determined by the rapid method. -
Bacterial Diversity Obtained by Culturable Approaches in the Gut Of
Bacterial diversity obtained by culturable approaches in the gut of Glossina pallidipes population from a non sleeping sickness focus in Tanzania: preliminary results Imna Malele, Hamis Nyingilili, Eugen Lyaruu, Marc Tauzin, Bernard Ollivier, Jean-Luc Cayol, Marie-Laure Fardeau, Anne Geiger To cite this version: Imna Malele, Hamis Nyingilili, Eugen Lyaruu, Marc Tauzin, Bernard Ollivier, et al.. Bacterial diversity obtained by culturable approaches in the gut of Glossina pallidipes population from a non sleeping sickness focus in Tanzania: preliminary results. BMC Microbiology, BioMed Central, 2018, 18 (S1), pp.811-823. 10.1186/s12866-018-1288-3. hal-02053582 HAL Id: hal-02053582 https://hal.archives-ouvertes.fr/hal-02053582 Submitted on 9 Jul 2019 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Distributed under a Creative Commons Attribution - NonCommercial - NoDerivatives| 4.0 International License Malele et al. BMC Microbiology _#####################_ https://doi.org/10.1186/s12866-018-1288-3 RESEARCH Open Access Bacterial diversity obtained by culturable approaches in the gut of Glossina pallidipes population from a non sleeping sickness focus in Tanzania: preliminary results Imna Malele1*, Hamis Nyingilili1, Eugen Lyaruu1, Marc Tauzin2, B. -
Effects of Dispersants and Biosurfactants on Crude-Oil Biodegradation and Bacterial Community Succession
microorganisms Article Effects of Dispersants and Biosurfactants on Crude-Oil Biodegradation and Bacterial Community Succession Gareth E. Thomas 1,* , Jan L. Brant 2 , Pablo Campo 3 , Dave R. Clark 1,4, Frederic Coulon 3 , Benjamin H. Gregson 1, Terry J. McGenity 1 and Boyd A. McKew 1 1 School of Life Sciences, University of Essex, Wivenhoe Park, Essex CO4 3SQ, UK; [email protected] (D.R.C.); [email protected] (B.H.G.); [email protected] (T.J.M.); [email protected] (B.A.M.) 2 Centre for Environment, Fisheries and Aquaculture Science, Pakefield Road, Lowestoft, Suffolk NR33 0HT, UK; [email protected] 3 School of Water, Energy and Environment, Cranfield University, Cranfield MK43 0AL, UK; p.campo-moreno@cranfield.ac.uk (P.C.); f.coulon@cranfield.ac.uk (F.C.) 4 Institute for Analytics and Data Science, University of Essex, Wivenhoe Park, Essex CO4 3SQ, UK * Correspondence: [email protected]; Tel.: +44-1206-873333 (ext. 2918) Abstract: This study evaluated the effects of three commercial dispersants (Finasol OSR 52, Slickgone NS, Superdispersant 25) and three biosurfactants (rhamnolipid, trehalolipid, sophorolipid) in crude- oil seawater microcosms. We analysed the crucial early bacterial response (1 and 3 days). In contrast, most analyses miss this key period and instead focus on later time points after oil and dispersant addition. By focusing on the early stage, we show that dispersants and biosurfactants, which reduce Citation: Thomas, G.E.; Brant, J.L.; the interfacial surface tension of oil and water, significantly increase the abundance of hydrocarbon- Campo, P.; Clark, D.R.; Coulon, F.; degrading bacteria, and the rate of hydrocarbon biodegradation, within 24 h. -
Natural Gas and Temperature Structured a Microbial Community Response to the Deepwater Horizon Oil Spill
Natural gas and temperature structured a microbial community response to the Deepwater Horizon oil spill Molly C. Redmond and David L. Valentine1 Department of Earth Science and Marine Science Institute, University of California, Santa Barbara, CA 93106 Edited by Paul G. Falkowski, Rutgers, The State University of New Jersey, New Brunswick, Brunswick, NJ, and approved September 7, 2011 (received for review June 1, 2011) Microbial communities present in the Gulf of Mexico rapidly Although the ability to degrade hydrocarbons is found in many responded to the Deepwater Horizon oil spill. In deep water types of bacteria, the most abundant oil-degraders in marine plumes, these communities were initially dominated by members environments are typically Gammaproteobacteria, particularly of Oceanospirillales, Colwellia, and Cycloclasticus. None of these organisms such as Alcanivorax, which primarily degrades alkanes, groups were abundant in surface oil slick samples, and Colwellia or Cycloclasticus, which specializes in the degradation of aro- was much more abundant in oil-degrading enrichment cultures in- matic compounds (16). However, most studies of microbial cubated at 4 °C than at room temperature, suggesting that the community response to hydrocarbons have been conducted in colder temperatures at plume depth favored the development of oil-amended mesocosm experiments with sediment, beach sand, these communities. These groups decreased in abundance after the or surface water (16), and little is known about the response to well was capped in July, but the addition of hydrocarbons in labo- oil inputs in the deep ocean or the impact of natural gas on these ratory incubations of deep waters from the Gulf of Mexico stimu- communities. -
Analysis of the Impact of Organic Pollutants on Marine Microbial Communities
Analysis of the impact of organic pollutants on marine microbial communities Elena Cerro Gálvez ADVERTIMENT La consulta d’aquesta tesi queda condicionada a l’acceptació de les següents condicions d'ús: La difusió d’aquesta tesi per mitjà del r e p o s i t o r i i n s t i t u c i o n a l UPCommons (http://upcommons.upc.edu/tesis) i el repositori cooperatiu TDX ( h t t p : / / w w w . t d x . c a t / ) ha estat autoritzada pels titulars dels drets de propietat intel·lectual únicament per a usos privats emmarcats en activitats d’investigació i docència. No s’autoritza la seva reproducció amb finalitats de lucre ni la seva difusió i posada a disposició des d’un lloc aliè al servei UPCommons o TDX. No s’autoritza la presentació del seu contingut en una finestra o marc aliè a UPCommons (framing). Aquesta reserva de drets afecta tant al resum de presentació de la tesi com als seus continguts. En la utilització o cita de parts de la tesi és obligat indicar el nom de la persona autora. ADVERTENCIA La consulta de esta tesis queda condicionada a la aceptación de las siguientes condiciones de uso: La difusión de esta tesis por medio del repositorio institucional UPCommons (http://upcommons.upc.edu/tesis) y el repositorio cooperativo TDR (http://www.tdx.cat/?locale- attribute=es) ha sido autorizada por los titulares de los derechos de propiedad intelectual únicamente para usos privados enmarcados en actividades de investigación y docencia. No se autoriza su reproducción con finalidades de lucro ni su difusión y puesta a disposición desde un sitio ajeno al servicio UPCommons No se autoriza la presentación de su contenido en una ventana o marco ajeno a UPCommons (framing). -
First Insights Into the Microbiology of Three Antarctic Briny Systems of the Northern Victoria Land
diversity Review First Insights into the Microbiology of Three Antarctic Briny Systems of the Northern Victoria Land Maria Papale 1,† , Carmen Rizzo 1,2,† , Gabriella Caruso 1 , Rosabruna La Ferla 1, Giovanna Maimone 1, Angelina Lo Giudice 1,* , Maurizio Azzaro 1,‡ and Mauro Guglielmin 3,‡ 1 Institute of Polar Sciences, National Research Council (CNR-ISP), Spianata San Raineri 86, 98122 Messina, Italy; [email protected] (M.P.); [email protected] (C.R.); [email protected] (G.C.); [email protected] (R.L.F.); [email protected] (G.M.); [email protected] (M.A.) 2 Stazione Zoologica Anton Dohrn, Department BIOTECH, National Institute of Biology, Villa Pace, Contrada Porticatello 29, 98167 Messina, Italy 3 Dipartimento di Scienze Teoriche e Applicate, University of Insubria, Via J.H. Dunant 3, 21100 Varese, Italy; [email protected] * Correspondence: [email protected]; Tel.: +39-090-6015-414 † Equal contribution as first author. ‡ Equal contribution as last author. Abstract: Different polar environments (lakes and glaciers), also in Antarctica, encapsulate brine pools characterized by a unique combination of extreme conditions, mainly in terms of high salinity and low temperature. Since 2014, we have been focusing our attention on the microbiology of brine pockets from three lakes in the Northern Victoria Land (NVL), lying in the Tarn Flat (TF) and Boulder Clay (BC) areas. The microbial communities have been analyzed for community structure by next generation sequencing, extracellular enzyme activities, metabolic potentials, and microbial abundances. In this Citation: Papale, M.; Rizzo, C.; study, we aim at reconsidering all available data to analyze the influence exerted by environmental Caruso, G.; La Ferla, R.; Maimone, G.; parameters on the community composition and activities. -
The Long-Chain Alkane Metabolism Network of Alcanivorax Dieselolei
ARTICLE Received 30 Jan 2014 | Accepted 5 Nov 2014 | Published 12 Dec 2014 DOI: 10.1038/ncomms6755 The long-chain alkane metabolism network of Alcanivorax dieselolei Wanpeng Wang1,2,3,4 & Zongze Shao1,2,3,4 Alkane-degrading bacteria are ubiquitous in marine environments, but little is known about how alkane degradation is regulated. Here we investigate alkane sensing, chemotaxis, signal transduction, uptake and pathway regulation in Alcanivorax dieselolei. The outer membrane protein OmpS detects the presence of alkanes and triggers the expression of an alkane chemotaxis complex. The coupling protein CheW2 of the chemotaxis complex, which is induced only by long-chain (LC) alkanes, sends signals to trigger the expression of Cyo, which participates in modulating the expression of the negative regulator protein AlmR. This change in turn leads to the expression of ompT1 and almA, which drive the selective uptake and hydroxylation of LC alkanes, respectively. AlmA is confirmed as a hydroxylase of LC alkanes. Additional factors responsible for the metabolism of medium-chain-length alkanes are also identified, including CheW1, OmpT1 and OmpT2. These results provide new insights into alkane metabolism pathways from alkane sensing to degradation. 1 State Key Laboratory Breeding Base of Marine Genetic Resources, Third Institute of Oceanography, SOA, Xiamen 361005, China. 2 Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, SOA, Xiamen 361005, China. 3 Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen 361005, China. 4 Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Xiamen 361005, China. Correspondence and requests for materials should be addressed to Z.S. -
Genome Sequence and Functional Genomic Analysis of the Oil-Degrading Bacterium Oleispira Antarctica
ARTICLE Received 30 Oct 2012 | Accepted 18 Jun 2013 | Published 23 Jul 2013 DOI: 10.1038/ncomms3156 OPEN Genome sequence and functional genomic analysis of the oil-degrading bacterium Oleispira antarctica Michael Kube1,2, Tatyana N. Chernikova3,4, Yamal Al-Ramahi5, Ana Beloqui5, Nieves Lopez-Cortez5, Marı´a-Eugenia Guazzaroni5,6, Hermann J. Heipieper7, Sven Klages1, Oleg R. Kotsyurbenko3, Ines Langer1, Taras Y. Nechitaylo3, Heinrich Lu¨nsdorf3, Marisol Ferna´ndez8, Silvia Jua´rez8, Sergio Ciordia8, Alexander Singer9,10, Olga Kagan9,10, Olga Egorova10,11, Pierre Alain Petit11, Peter Stogios11, Youngchang Kim10,12, Anatoli Tchigvintsev9, Robert Flick9, Renata Denaro13, Maria Genovese13, Juan P. Albar8, Oleg N. Reva14, Montserrat Martı´nez-Gomariz15, Hai Tran4, Manuel Ferrer5, Alexei Savchenko9,10,11, Alexander F. Yakunin11, Michail M. Yakimov13, Olga V. Golyshina3,4, Richard Reinhardt1,w & Peter N. Golyshin3,4 Ubiquitous bacteria from the genus Oleispira drive oil degradation in the largest environment on Earth, the cold and deep sea. Here we report the genome sequence of Oleispira antarctica and show that compared with Alcanivorax borkumensis—the paradigm of mesophilic hydrocarbonoclastic bacteria—O. antarctica has a larger genome that has witnessed massive gene-transfer events. We identify an array of alkane monooxygenases, osmoprotectants, siderophores and micronutrient-scavenging pathways. We also show that at low tempera- tures, the main protein-folding machine Cpn60 functions as a single heptameric barrel that uses larger proteins as substrates compared with the classical double-barrel structure observed at higher temperatures. With 11 protein crystal structures, we further report the largest set of structures from one psychrotolerant organism. The most common structural feature is an increased content of surface-exposed negatively charged residues compared to their mesophilic counterparts.