A Comparative Genomics Approach. the ISME
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Structural Comparison of Tonb-Dependent Receptors in Bradyrhizobium Japonicum Allie R
James Madison University JMU Scholarly Commons Senior Honors Projects, 2010-current Honors College Fall 2015 Structural comparison of TonB-dependent receptors in bradyrhizobium japonicum Allie R. Casto James Madison University Follow this and additional works at: https://commons.lib.jmu.edu/honors201019 Part of the Bioinformatics Commons, and the Biology Commons Recommended Citation Casto, Allie R., "Structural comparison of TonB-dependent receptors in bradyrhizobium japonicum" (2015). Senior Honors Projects, 2010-current. 126. https://commons.lib.jmu.edu/honors201019/126 This Thesis is brought to you for free and open access by the Honors College at JMU Scholarly Commons. It has been accepted for inclusion in Senior Honors Projects, 2010-current by an authorized administrator of JMU Scholarly Commons. For more information, please contact [email protected]. Structural Comparison of TonB-Dependent Receptors in Bradyrhizobium japonicum _______________________ An Honors Program Project Presented to the Faculty of the Undergraduate College of Sciences and Mathematics James Madison University _______________________ by Allie Renee Casto December 2015 Accepted by the faculty of the Department of Integrated Science and Technology, James Madison University, in partial fulfillment of the requirements for the Honors Program. FACULTY COMMITTEE: HONORS PROGRAM APPROVAL: Project Advisor: Stephanie Stockwell, Ph. D. Bradley R. Newcomer, Ph.D., Professor, Integrated Science and Technology Director, Honors Program Reader: Jonathan Monroe, Ph. D. Professor, -
Spatiotemporal Dynamics of Marine Bacterial and Archaeal Communities in Surface Waters Off the Northern Antarctic Peninsula
Spatiotemporal dynamics of marine bacterial and archaeal communities in surface waters off the northern Antarctic Peninsula Camila N. Signori, Vivian H. Pellizari, Alex Enrich Prast and Stefan M. Sievert The self-archived postprint version of this journal article is available at Linköping University Institutional Repository (DiVA): http://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-149885 N.B.: When citing this work, cite the original publication. Signori, C. N., Pellizari, V. H., Enrich Prast, A., Sievert, S. M., (2018), Spatiotemporal dynamics of marine bacterial and archaeal communities in surface waters off the northern Antarctic Peninsula, Deep-sea research. Part II, Topical studies in oceanography, 149, 150-160. https://doi.org/10.1016/j.dsr2.2017.12.017 Original publication available at: https://doi.org/10.1016/j.dsr2.2017.12.017 Copyright: Elsevier http://www.elsevier.com/ Spatiotemporal dynamics of marine bacterial and archaeal communities in surface waters off the northern Antarctic Peninsula Camila N. Signori1*, Vivian H. Pellizari1, Alex Enrich-Prast2,3, Stefan M. Sievert4* 1 Departamento de Oceanografia Biológica, Instituto Oceanográfico, Universidade de São Paulo (USP). Praça do Oceanográfico, 191. CEP: 05508-900 São Paulo, SP, Brazil. 2 Department of Thematic Studies - Environmental Change, Linköping University. 581 83 Linköping, Sweden 3 Departamento de Botânica, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ). Av. Carlos Chagas Filho, 373. CEP: 21941-902. Rio de Janeiro, Brazil 4 Biology Department, Woods Hole Oceanographic Institution (WHOI). 266 Woods Hole Road, Woods Hole, MA 02543, United States. *Corresponding authors: Camila Negrão Signori Address: Departamento de Oceanografia Biológica, Instituto Oceanográfico, Universidade de São Paulo, São Paulo, Brazil. -
Supporting Information
Supporting Information Lozupone et al. 10.1073/pnas.0807339105 SI Methods nococcus, and Eubacterium grouped with members of other Determining the Environmental Distribution of Sequenced Genomes. named genera with high bootstrap support (Fig. 1A). One To obtain information on the lifestyle of the isolate and its reported member of the Bacteroidetes (Bacteroides capillosus) source, we looked at descriptive information from NCBI grouped firmly within the Firmicutes. This taxonomic error was (www.ncbi.nlm.nih.gov/genomes/lproks.cgi) and other related not surprising because gut isolates have often been classified as publications. We also determined which 16S rRNA-based envi- Bacteroides based on an obligate anaerobe, Gram-negative, ronmental surveys of microbial assemblages deposited near- nonsporulating phenotype alone (6, 7). A more recent 16S identical sequences in GenBank. We first downloaded the gbenv rRNA-based analysis of the genus Clostridium defined phylo- files from the NCBI ftp site on December 31, 2007, and used genetically related clusters (4, 5), and these designations were them to create a BLAST database. These files contain GenBank supported in our phylogenetic analysis of the Clostridium species in the HGMI pipeline. We thus designated these Clostridium records for the ENV database, a component of the nonredun- species, along with the species from other named genera that dant nucleotide database (nt) where 16S rRNA environmental cluster with them in bootstrap supported nodes, as being within survey data are deposited. GenBank records for hits with Ͼ98% these clusters. sequence identity over 400 bp to the 16S rRNA sequence of each of the 67 genomes were parsed to get a list of study titles Annotation of GTs and GHs. -
Sequence from B4 Sponge with (A) the First BLAST Hit Asbestopluma Lycopodium and (B) the Sequence of M
Supplementary Material Figure S1. Alignments of CO1 (PorCOI2fwd/PorCOI2rev) sequence from B4 sponge with (A) the first BLAST hit Asbestopluma lycopodium and (B) the sequence of M. acerata displaying low query cover. 1 Figure S2. Alignment of CO1 (dgLCO1490/dgHCO2198) sequence from B4 sponge with the first BLAST hit (M. acerata). 2 Figure S3. Alignment of CO1 (dgLCO1490/dgHCO2198) sequence from D4 sponge with the first BLAST hit (H. pilosus). 3 Figure S4. Taxonomy Bar Plot, reporting the relative frequencies (in percentage, %) of the bacteria taxons more representative for each of the four sponges under analysis . Sample code: B4= M. (Oxymycale) acerata; D4= H. pilosus, D6= M. sarai, C6= H. (Rhizoniera) dancoi. Each taxon is highlighted by a different color. 4 Figure S5. Krona plot at the seven increasing complexity levels: (a) Regnum, (b) Phylum, (c) Class, (d) Order, (e) Family, (f) Genus and (g) Species. a) 5 b) 6 c) 7 d) 8 e) 9 f) 10 g) 11 Figure S6. Distribution of ASV’s frequencies. 12 Figure S7. Distribution of ASV’s frequencies for each sample (reported as a blue bar). 13 Table S1. BLAST results from B4 sponge (Mycale (Oxymycale) acerata). The primer names, sequence length in base pairs (bp), first hits (highlighted in bold), hits at low significance displaying the correct species (where present), query cover and identity percentages (%) were reported. Sequence Query Identity Primers BLAST results length (bp) cover (%) (%) Mycale macilenta voucher 0CDN7203‐O small subunit 18S A/B 1700 99 98 ribosomal RNA gene, partial sequence Mycale -
Recurring Patterns in Bacterioplankton Dynamics During Coastal Spring
RESEARCH ARTICLE Recurring patterns in bacterioplankton dynamics during coastal spring algae blooms Hanno Teeling1*†, Bernhard M Fuchs1*†, Christin M Bennke1‡, Karen Kru¨ ger1, Meghan Chafee1, Lennart Kappelmann1, Greta Reintjes1, Jost Waldmann1, Christian Quast1, Frank Oliver Glo¨ ckner1, Judith Lucas2, Antje Wichels2, Gunnar Gerdts2, Karen H Wiltshire3, Rudolf I Amann1* 1Max Planck Institute for Marine Microbiology, Bremen, Germany; 2Biologische Anstalt Helgoland, Alfred Wegener Institute for Polar and Marine Research, Helgoland, Germany; 3Alfred Wegener Institute for Polar and Marine Research, List auf Sylt, Germany Abstract A process of global importance in carbon cycling is the remineralization of algae biomass by heterotrophic bacteria, most notably during massive marine algae blooms. Such blooms can trigger secondary blooms of planktonic bacteria that consist of swift successions of distinct *For correspondence: hteeling@ mpi-bremen.de (HT); bfuchs@mpi- bacterial clades, most prominently members of the Flavobacteriia, Gammaproteobacteria and the bremen.de (BMF); ramann@mpi- alphaproteobacterial Roseobacter clade. We investigated such successions during spring bremen.de (RIA) phytoplankton blooms in the southern North Sea (German Bight) for four consecutive years. Dense sampling and high-resolution taxonomic analyses allowed the detection of recurring patterns down † These authors contributed to the genus level. Metagenome analyses also revealed recurrent patterns at the functional level, in equally to this work particular with respect to algal polysaccharide degradation genes. We, therefore, hypothesize that Present address: ‡Section even though there is substantial inter-annual variation between spring phytoplankton blooms, the Biology, Leibniz Institute for accompanying succession of bacterial clades is largely governed by deterministic principles such as Baltic Sea Research, substrate-induced forcing. -
Structural Engineering of a Phage Lysin That Targets Gram-Negative Pathogens
Structural engineering of a phage lysin that targets Gram-negative pathogens Petra Lukacika, Travis J. Barnarda, Paul W. Kellerb, Kaveri S. Chaturvedic, Nadir Seddikia,JamesW.Fairmana, Nicholas Noinaja, Tara L. Kirbya, Jeffrey P. Hendersonc, Alasdair C. Stevenb, B. Joseph Hinnebuschd, and Susan K. Buchanana,1 aLaboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892; bLaboratory of Structural Biology, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda,MD 20892; cCenter for Women’s Infectious Diseases Research, Washington University School of Medicine, St. Louis, MO 63110; and dLaboratory of Zoonotic Pathogens, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840 Edited by* Brian W. Matthews, University of Oregon, Eugene, OR, and approved April 18, 2012 (received for review February 27, 2012) Bacterial pathogens are becoming increasingly resistant to antibio- ∼10 kb plasmid called pPCP1 (7). Pla facilitates invasion in bu- tics. As an alternative therapeutic strategy, phage therapy reagents bonic plague and, as such, is an important virulence factor (8, 9). containing purified viral lysins have been developed against Gram- When strains lose the pPCP1 plasmid, they are killed by pesticin positive organisms but not against Gram-negative organisms due thus ensuring maximal virulence in the bacterial population. to the inability of these types of drugs to cross the bacterial outer Bacteriocins belong to two classes. Type A bacteriocins depend membrane. We solved the crystal structures of a Yersinia pestis on the Tolsystem to traverse the outer membrane, whereas type B outer membrane transporter called FyuA and a bacterial toxin bacteriocins require the Ton system. -
Organic Matter Processing by Microbial Communities Throughout
Organic matter processing by microbial communities PNAS PLUS throughout the Atlantic water column as revealed by metaproteomics Kristin Bergauera,1, Antonio Fernandez-Guerrab,c, Juan A. L. Garciaa, Richard R. Sprengerd, Ramunas Stepanauskase, Maria G. Pachiadakie, Ole N. Jensend, and Gerhard J. Herndla,f,g aDepartment of Limnology and Bio-Oceanography, University of Vienna, A-1090 Vienna, Austria; bMicrobial Genomics and Bioinformatics Research Group, Max Planck Institute for Marine Microbiology, D-28359 Bremen, Germany; cOxford e-Research Centre, University of Oxford, Oxford OX1 3QG, United Kingdom; dDepartment of Biochemistry and Molecular Biology, VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, DK-5230 Odense M, Denmark; eBigelow Laboratory for Ocean Sciences, East Boothbay, ME 04544; fDepartment of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, Utrecht University, 1790 AB Den Burg, The Netherlands; and gVienna Metabolomics Center, University of Vienna, A-1090 Vienna, Austria Edited by David M. Karl, University of Hawaii, Honolulu, HI, and approved November 21, 2017 (received for review May 26, 2017) The phylogenetic composition of the heterotrophic microbial demand in the mesopelagic and bathypelagic waters (7, 8). Despite community is depth stratified in the oceanic water column down this apparent low contribution of DOM compared with POM in to abyssopelagic layers. In the layers below the euphotic zone, it has supporting heterotrophic microbial metabolism in the deep ocean, been suggested that heterotrophic microbes rely largely on solubi- DOM quantity and quality decreases with depth (9). The decrease in lized particulate organic matter as a carbon and energy source the overall nutritional quality of the DOM with depth might reflect rather than on dissolved organic matter. -
Bacterial Community Structure in a Sympagic Habitat Expanding with Global Warming: Brackish Ice Brine at 85€“90 °N
The ISME Journal (2019) 13:316–333 https://doi.org/10.1038/s41396-018-0268-9 ARTICLE Bacterial community structure in a sympagic habitat expanding with global warming: brackish ice brine at 85–90 °N 1,11 1,2 3 4 5,8 Beatriz Fernández-Gómez ● Beatriz Díez ● Martin F. Polz ● José Ignacio Arroyo ● Fernando D. Alfaro ● 1 1 2,6 5 4,7 Germán Marchandon ● Cynthia Sanhueza ● Laura Farías ● Nicole Trefault ● Pablo A. Marquet ● 8,9 10 10 Marco A. Molina-Montenegro ● Peter Sylvander ● Pauline Snoeijs-Leijonmalm Received: 12 February 2018 / Revised: 11 June 2018 / Accepted: 24 July 2018 / Published online: 18 September 2018 © International Society for Microbial Ecology 2018 Abstract Larger volumes of sea ice have been thawing in the Central Arctic Ocean (CAO) during the last decades than during the past 800,000 years. Brackish brine (fed by meltwater inside the ice) is an expanding sympagic habitat in summer all over the CAO. We report for the first time the structure of bacterial communities in this brine. They are composed of psychrophilic extremophiles, many of them related to phylotypes known from Arctic and Antarctic regions. Community structure displayed strong habitat segregation between brackish ice brine (IB; salinity 2.4–9.6) and immediate sub-ice seawater (SW; – 1234567890();,: 1234567890();,: salinity 33.3 34.9), expressed at all taxonomic levels (class to genus), by dominant phylotypes as well as by the rare biosphere, and with specialists dominating IB and generalists SW. The dominant phylotypes in IB were related to Candidatus Aquiluna and Flavobacterium, those in SW to Balneatrix and ZD0405, and those shared between the habitats to Halomonas, Polaribacter and Shewanella. -
Owenweeksia Hongkongensis UST20020801T
Lawrence Berkeley National Laboratory Recent Work Title Genome sequence of the orange-pigmented seawater bacterium Owenweeksia hongkongensis type strain (UST20020801(T)). Permalink https://escholarship.org/uc/item/8734g6jx Journal Standards in genomic sciences, 7(1) ISSN 1944-3277 Authors Riedel, Thomas Held, Brittany Nolan, Matt et al. Publication Date 2012-10-01 DOI 10.4056/sigs.3296896 Peer reviewed eScholarship.org Powered by the California Digital Library University of California Standards in Genomic Sciences (2012) 7:120-130 DOI:10.4056/sigs.3296896 Genome sequence of the orange-pigmented seawater bacterium Owenweeksia hongkongensis type strain (UST20020801T) Thomas Riedel1, Brittany Held2,3, Matt Nolan2, Susan Lucas2, Alla Lapidus2, Hope Tice2, Tijana Glavina Del Rio2, Jan-Fang Cheng2, Cliff Han2,3, Roxanne Tapia2,3, Lynne A. Goodwin2,3, Sam Pitluck2, Konstantinos Liolios2, Konstantinos Mavromatis2, Ioanna Pagani2, Natalia Ivanova2, Natalia Mikhailova2, Amrita Pati2, Amy Chen4, Krishna Palaniappan4, Manfred Rohde1, Brian J. Tindall6, John C. Detter2,3, Markus Göker6, Tanja Woyke2, James Bristow2, Jonathan A. Eisen2,7, Victor Markowitz4, Philip Hugenholtz2,8, Hans-Peter Klenk6*, and Nikos C. Kyrpides2 1 HZI – Helmholtz Centre for Infection Research, Braunschweig, Germany 2 DOE Joint Genome Institute, Walnut Creek, California, USA 3 Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA 4 Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA 5 Oak -
Metagenomics Unveils the Attributes of the Alginolytic Guilds of Sediments from Four Distant Cold Coastal Environments Marina N
Metagenomics unveils the attributes of the alginolytic guilds of sediments from four distant cold coastal environments Marina N. Matos, Mariana Lozada, Luciano E. Anselmino, Matias A. Musumeci, Bernard Henrissat, Janet K. Jansson, Walter P. Mac Cormack, Jolynn Carroll, Sara Sjoling, Leif Lundgren, et al. To cite this version: Marina N. Matos, Mariana Lozada, Luciano E. Anselmino, Matias A. Musumeci, Bernard Henrissat, et al.. Metagenomics unveils the attributes of the alginolytic guilds of sediments from four distant cold coastal environments. Environmental Microbiology, Society for Applied Microbiology and Wiley- Blackwell, 2016, 18 (12), pp.4471-4484. 10.1111/1462-2920.13433. hal-01601908 HAL Id: hal-01601908 https://hal.archives-ouvertes.fr/hal-01601908 Submitted on 27 May 2020 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 - ShareAlike| 4.0 International License Environmental Microbiology (2016) 18(12), 4471–4484 doi:10.1111/1462-2920.13433 Metagenomics unveils the attributes of the alginolytic guilds of sediments from four distant cold coastal environments Marina N. Matos,1 Mariana Lozada,1 Summary Luciano E. Anselmino,1 Matıas A. Musumeci,1 Alginates are abundant polysaccharides in brown Bernard Henrissat,2,3,4 Janet K. -
Escherichia Coli and Other Gram-Negative Bacteria
Biochimica et Biophysica A cta, 737 (1983) 51 - 115 51 Elsevier Biomedical Press BBA 85241 MOLECULAR ARCHITECTURE AND FUNCTIONING OF THE OUTER MEMBRANE OF ESCHERICHIA COLI AND OTHER GRAM-NEGATIVE BACTERIA BEN LUGTENBERG a,, and LOEK VAN ALPHEN h " Department of Molecular Cell Biology' and Institute for Molecular Biology', State University, Transitorium 3, Padualaan 8, 3584 CH Utrecht and h Laboratorium voor de Gezondheidsleer, University of Amsterdam, Mauritskade 57, 1092 AD Amsterdam (The Netherlands) (Received July 26th, 1982) Contents Introduction ............................................................................. 52 A. Scope of this review ...................................................................... 52 B. Ecological considerations relevant to structure and functioning of the outer membrane of Enterobacteriaceae ........ 53 C. General description of the cell envelope of Gram-negative bacteria ..................................... 53 II. Methods for the isolation of outer membranes ...................................................... 58 A. E. coli and S. typhimurium ................................................................. 58 1. Isolation of peptidoglycan-less outer membranes after spheroplast formation ............................ 58 2. Isolation of outer membrane-peptidoglycan complexes ........................................... 58 3. Differential membrane solubilization using detergents ............................................ 59 4. Membrane separation based on charge differences of vesicles ...................................... -
Structural Insights Into Decreased Enzymatic Activity Induced by an Insert Sequence in Mannonate Dehydratase from Gram Negative Bacterium
Journal of Structural Biology 180 (2012) 327–334 Contents lists available at SciVerse ScienceDirect Journal of Structural Biology journal homepage: www.elsevier.com/locate/yjsbi Structural insights into decreased enzymatic activity induced by an insert sequence in mannonate dehydratase from Gram negative bacterium Xiaoting Qiu, Yuyong Tao, Yuwei Zhu, Ye Yuan, Yujie Zhang, Hejun Liu, Yongxiang Gao, ⇑ ⇑ Maikun Teng , Liwen Niu Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Key Laboratory of Structural Biology, Chinese Academy of Sciences, Hefei, Anhui 230026, PR China article info abstract Article history: Mannonate dehydratase (ManD; EC4.2.1.8) catalyzes the dehydration of D-mannonate to 2-keto-3-deoxyg- Received 30 April 2012 luconate. It is the third enzyme in the pathway for dissimilation of D-glucuronate to 2-keto-3-deoxygluc- Received in revised form 21 June 2012 onate involving in the Entner–Doudoroff pathway in certain bacterial and archaeal species. ManD from Accepted 26 June 2012 Gram negative bacteria has an insert sequence as compared to those from Gram positives revealed by Available online 14 July 2012 sequence analysis. To evaluate the impact of this insert sequence on the catalytic efficiency, we solved the crystal structures of ManD from Escherichia coli strain K12 and its complex with D-mannonate, which Keywords: reveal that this insert sequence forms two a helices locating above the active site. The two insert a helices Mannonate dehydratase introduce a loop that forms a cap covering the substrate binding pocket, which restricts the tunnels of sub- Gram negative bacteria Insert sequence strate entering and product releasing from the active site.