Determining and Comparing Protein Function in Bacterial Genome Sequences
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CUED Phd and Mphil Thesis Classes
High-throughput Experimental and Computational Studies of Bacterial Evolution Lars Barquist Queens' College University of Cambridge A thesis submitted for the degree of Doctor of Philosophy 23 August 2013 Arrakis teaches the attitude of the knife { chopping off what's incomplete and saying: \Now it's complete because it's ended here." Collected Sayings of Muad'dib Declaration High-throughput Experimental and Computational Studies of Bacterial Evolution The work presented in this dissertation was carried out at the Wellcome Trust Sanger Institute between October 2009 and August 2013. This dissertation is the result of my own work and includes nothing which is the outcome of work done in collaboration except where specifically indicated in the text. This dissertation does not exceed the limit of 60,000 words as specified by the Faculty of Biology Degree Committee. This dissertation has been typeset in 12pt Computer Modern font using LATEX according to the specifications set by the Board of Graduate Studies and the Faculty of Biology Degree Committee. No part of this dissertation or anything substantially similar has been or is being submitted for any other qualification at any other university. Acknowledgements I have been tremendously fortunate to spend the past four years on the Wellcome Trust Genome Campus at the Sanger Institute and the European Bioinformatics Institute. I would like to thank foremost my main collaborators on the studies described in this thesis: Paul Gardner and Gemma Langridge. Their contributions and support have been invaluable. I would also like to thank my supervisor, Alex Bateman, for giving me the freedom to pursue a wide range of projects during my time in his group and for advice. -
Thèse Morgane Wartel
Faculté des Sciences - Aix-Marseille Université Laboratoire de Chimie Bactérienne 163 Avenue de Luminy - Case 901 31 Chemin Joseph Aiguier 13288 Marseille 13009 Marseille Thèse En vue d’obtenir le grade de Docteur d’Aix-Marseille Université Biologie, spécialité Microbiologie Présentée et soutenue publiquement par Morgane Wartel Le Mercredi 18 Décembre 2013 A novel class of bacterial motors involved in the directional transport of a sugar at the bacterial surface: The machineries of motility and sporulation in Myxococcus xanthus. Une nouvelle classe de moteurs bactériens impliqués dans le transport de macromolécules à la surface bactérienne: Les machineries de motilité et de sporulation de Myxococcus xanthus. Membres du Jury : Dr. Christophe Grangeasse Rapporteur Dr. Patrick Viollier Rapporteur Pr. Pascale Cossart Examinateur Dr. Francis-André Wollman Examinateur Dr. Tâm Mignot Directeur de Thèse Pr. Frédéric Barras Président du Jury Faculté des Sciences - Aix-Marseille Université Laboratoire de Chimie Bactérienne 163 Avenue de Luminy - Case 901 31 Chemin Joseph Aiguier 13288 Marseille 13009 Marseille Thèse En vue d’obtenir le grade de Docteur d’Aix-Marseille Université Biologie, spécialité Microbiologie Présentée et soutenue publiquement par Morgane Wartel Le Mercredi 18 Décembre 2013 A novel class of bacterial motors involved in the directional transport of a sugar at the bacterial surface: The machineries of motility and sporulation in Myxococcus xanthus. Une nouvelle classe de moteurs bactériens impliqués dans le transport de macromolécules à la surface bactérienne: Les machineries de motilité et de sporulation de Myxococcus xanthus. Membres du Jury : Dr. Christophe Grangeasse Rapporteur Dr. Patrick Viollier Rapporteur Pr. Pascale Cossart Examinateur Dr. Francis-André Wollman Examinateur Dr. -
J. Gen. Appl. Microbiol., 48, 109–115 (2002)
J. Gen. Appl. Microbiol., 48, 109–115 (2002) Full Paper Haliangium ochraceum gen. nov., sp. nov. and Haliangium tepidum sp. nov.: Novel moderately halophilic myxobacteria isolated from coastal saline environments Ryosuke Fudou,* Yasuko Jojima, Takashi Iizuka, and Shigeru Yamanaka† Central Research Laboratories, Ajinomoto Co., Inc., Kawasaki 210–8681, Japan (Received November 21, 2001; Accepted January 31, 2002) Phenotypic and phylogenetic studies were performed on two myxobacterial strains, SMP-2 and SMP-10, isolated from coastal regions. The two strains are morphologically similar, in that both produce yellow fruiting bodies, comprising several sessile sporangioles in dense packs. They are differentiated from known terrestrial myxobacteria on the basis of salt requirements (2–3% NaCl) and the presence of anteiso-branched fatty acids. Comparative 16S rRNA gene sequencing studies revealed that SMP-2 and SMP-10 are genetically related, and constitute a new cluster within the myxobacteria group, together with the Polyangium vitellinum Pl vt1 strain as the clos- est neighbor. The sequence similarity between the two strains is 95.6%. Based on phenotypic and phylogenetic evidence, it is proposed that these two strains be assigned to a new genus, JCM؍) .Haliangium gen. nov., with SMP-2 designated as Haliangium ochraceum sp. nov .(DSM 14436T؍JCM 11304T؍) .DSM 14365T), and SMP-10 as Haliangium tepidum sp. nov؍11303T Key Words——Haliangium gen. nov.; Haliangium ochraceum sp. nov.; Haliangium tepidum sp. nov.; marine myxobacteria Introduction terized as Gram-negative, rod-shaped gliding bacteria with high GϩC content. Analyses of 16S rRNA gene Myxobacteria are unique in their complex life cycle. sequences reveal that they form a relatively homoge- Under starvation conditions, bacterial cells gather to- neous cluster within the d-subclass of Proteobacteria gether to form aggregates that subsequently differenti- (Shimkets and Woese, 1992). -
Electron Transfer Through the Outer Membrane of Geobacter Sulfurreducens a DISSERTATION SUBMITTED to the FACULTY of the UNIVE
Electron transfer through the outer membrane of Geobacter sulfurreducens A DISSERTATION SUBMITTED TO THE FACULTY OF THE UNIVERSITY OF MINNESOTA BY Fernanda Jiménez Otero IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR IN PHILOSOPHY Dr. Daniel R. Bond May, 2018 Fernanda Jiménez Otero, 2018, © Acknowledgements This dissertation and the degree I have gained with it, would not have been possible without the help and support from an invaluable group of people. The training I received from Chi Ho Chan and Caleb Levar continues to be essential in the way I approach scientific endeavors. The quality of genetic studies and rigor in microbiology techniques they taught me is a standard I hope to meet throughout my career. Daniel Bond has been much more than I ever expected from an advisor. I have not only gained scientific knowledge from him, but I will take with me the example of what a great mentor represents. His enthusiasm for science is only rivaled by his commitment to past and present members of his laboratory. I am extremely honored to be able to count myself in that group, and I will do my best to represent him proudly in future endeavors. Throughout these five years, Jeff Gralnick has given me numerous opportunities to explore all aspects of a scientific career. Not only is Chapter 2 a result of his vision, but I feel less intimidated by a career in science as a result of his mentoring and support. The faculty members in my committee- Carrie Wilmot, Brandy Toner, and Larry Wackett, have made sure I am well prepared for i every step through graduate school. -
Marine Myxobacteria As a Source of Antibiotics—Comparison of Physiology, Polyketide-Type Genes and Antibiotic Production of Three New Isolates of Enhygromyxa Salina
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by PubMed Central Mar. Drugs 2010, 8, 2466-2479; doi:10.3390/md8092466 OPEN ACCESS Marine Drugs ISSN 1660-3397 www.mdpi.com/journal/marinedrugs Article Marine Myxobacteria as a Source of Antibiotics—Comparison of Physiology, Polyketide-Type Genes and Antibiotic Production of Three New Isolates of Enhygromyxa salina Till F. Schäberle 1, Emilie Goralski 1, Edith Neu 1, Özlem Erol 1, Georg Hölzl 2, Peter Dörmann 2, Gabriele Bierbaum 3 and Gabriele M. König 1,* 1 Institute of Pharmaceutical Biology, University of Bonn, Nussallee 6, 53115 Bonn, Germany; E-Mails: [email protected] (T.F.S.); [email protected] (E.G.); [email protected] (E.N.); [email protected] (Ö.E.) 2 Institute of Molecular Physiology and Biotechnology of Plants (IMBIO), University of Bonn, Karlrobert-Kreiten-Str. 13, 53115 Bonn, Germany; E-Mails: [email protected] (G.H.); [email protected] (P.D.) 3 Institute of Medical Microbiology, Immunology and Parasitology (IMMIP), University of Bonn, Sigmund-Freud-Str. 25, 53127 Bonn, Germany; E-Mail: [email protected] (G.B.) * Author to whom correspondence should be addressed; E-Mail: [email protected]; Tel.: +49-228-733747; Fax: +49-228-733250. Received: 12 August 2010; in revised form: 25 August 2010 / Accepted: 1 September 2010 / Published: 3 September 2010 Abstract: Three myxobacterial strains, designated SWB004, SWB005 and SWB006, were obtained from beach sand samples from the Pacific Ocean and the North Sea. -
Reclassification of Eubacterium Hallii As Anaerobutyricum Hallii Gen. Nov., Comb
TAXONOMIC DESCRIPTION Shetty et al., Int J Syst Evol Microbiol 2018;68:3741–3746 DOI 10.1099/ijsem.0.003041 Reclassification of Eubacterium hallii as Anaerobutyricum hallii gen. nov., comb. nov., and description of Anaerobutyricum soehngenii sp. nov., a butyrate and propionate-producing bacterium from infant faeces Sudarshan A. Shetty,1,* Simone Zuffa,1 Thi Phuong Nam Bui,1 Steven Aalvink,1 Hauke Smidt1 and Willem M. De Vos1,2,3 Abstract A bacterial strain designated L2-7T, phylogenetically related to Eubacterium hallii DSM 3353T, was previously isolated from infant faeces. The complete genome of strain L2-7T contains eight copies of the 16S rRNA gene with only 98.0– 98.5 % similarity to the 16S rRNA gene of the previously described type strain E. hallii. The next closest validly described species is Anaerostipes hadrus DSM 3319T (90.7 % 16S rRNA gene similarity). A polyphasic taxonomic approach showed strain L2-7T to be a novel species, related to type strain E. hallii DSM 3353T. The experimentally observed DNA–DNA hybridization value between strain L2-7T and E. hallii DSM 3353T was 26.25 %, close to that calculated from the genomes T (34.3 %). The G+C content of the chromosomal DNA of strain L2-7 was 38.6 mol%. The major fatty acids were C16 : 0,C16 : 1 T cis9 and a component with summed feature 10 (C18 : 1c11/t9/t6c). Strain L2-7 had higher amounts of C16 : 0 (30.6 %) compared to E. hallii DSM 3353T (19.5 %) and its membrane contained phosphatidylglycerol and phosphatidylethanolamine, which were not detected in E. -
Mining the Yucatan Coastal Microbiome for the Identification of Non
toxins Article Mining the Yucatan Coastal Microbiome for the Identification of Non-Ribosomal Peptides Synthetase (NRPS) Genes Mario Alberto Martínez-Núñez * and Zuemy Rodríguez-Escamilla * UMDI-Sisal, Facultad de Ciencias, Universidad Nacional Autónoma de México, Puerto de Abrigo s/n, Sisal, Yucatán CP 97355, Mexico * Correspondence: [email protected] (M.A.M.-N.); [email protected] (Z.R.-E.); Tel.: +52-999-341-0860 (ext. 7631) (M.A.M.-N.) Received: 21 February 2020; Accepted: 16 April 2020; Published: 26 May 2020 Abstract: Prokaryotes represent a source of both biotechnological and pharmaceutical molecules of importance, such as nonribosomal peptides (NRPs). NRPs are secondary metabolites which their synthesis is independent of ribosomes. Traditionally, obtaining NRPs had focused on organisms from terrestrial environments, but in recent years marine and coastal environments have emerged as an important source for the search and obtaining of nonribosomal compounds. In this study, we carried out a metataxonomic analysis of sediment of the coast of Yucatan in order to evaluate the potential of the microbial communities to contain bacteria involved in the synthesis of NRPs in two sites: one contaminated and the other conserved. As well as a metatranscriptomic analysis to discover nonribosomal peptide synthetases (NRPSs) genes. We found that the phyla with the highest representation of NRPs producing organisms were the Proteobacteria and Firmicutes present in the sediments of the conserved site. Similarly, the metatranscriptomic analysis showed that 52% of the sequences identified as catalytic domains of NRPSs were found in the conserved site sample, mostly (82%) belonging to Proteobacteria and Firmicutes; while the representation of Actinobacteria traditionally described as the major producers of secondary metabolites was low. -
Marine-Derived Myxobacteria of the Suborder Nannocystineae: an Underexplored Source of Structurally Intriguing and Biologically Active Metabolites
Marine-derived myxobacteria of the suborder Nannocystineae: An underexplored source of structurally intriguing and biologically active metabolites Antonio Dávila-Céspedes‡, Peter Hufendiek‡, Max Crüsemann‡, Till F. Schäberle and Gabriele M. König* Review Open Access Address: Beilstein J. Org. Chem. 2016, 12, 969–984. Institute for Pharmaceutical Biology, University of Bonn, Nussallee 6, doi:10.3762/bjoc.12.96 53115 Bonn, Germany Received: 22 February 2016 Email: Accepted: 25 April 2016 Gabriele M. König* - [email protected] Published: 13 May 2016 * Corresponding author ‡ Equal contributors This article is part of the Thematic Series "Natural products in synthesis and biosynthesis II". Keywords: Enhygromyxa; genome mining; myxobacteria; Nannocystineae; Guest Editor: J. S. Dickschat natural products © 2016 Dávila-Céspedes et al; licensee Beilstein-Institut. License and terms: see end of document. Abstract Myxobacteria are famous for their ability to produce most intriguing secondary metabolites. Till recently, only terrestrial myxobac- teria were in the focus of research. In this review, however, we discuss marine-derived myxobacteria, which are particularly inter- esting due to their relatively recent discovery and due to the fact that their very existence was called into question. The to-date- explored members of these halophilic or halotolerant myxobacteria are all grouped into the suborder Nannocystineae. Few of them were chemically investigated revealing around 11 structural types belonging to the polyketide, non-ribosomal peptide, hybrids thereof or terpenoid class of secondary metabolites. A most unusual structural type is represented by salimabromide from Enhygromyxa salina. In silico analyses were carried out on the available genome sequences of four bacterial members of the Nannocystineae, revealing the biosynthetic potential of these bacteria. -
The Soil Microbial Food Web Revisited: Predatory Myxobacteria As Keystone Taxa?
The ISME Journal https://doi.org/10.1038/s41396-021-00958-2 ARTICLE The soil microbial food web revisited: Predatory myxobacteria as keystone taxa? 1 1 1,2 1 1 Sebastian Petters ● Verena Groß ● Andrea Söllinger ● Michelle Pichler ● Anne Reinhard ● 1 1 Mia Maria Bengtsson ● Tim Urich Received: 4 October 2018 / Revised: 24 February 2021 / Accepted: 4 March 2021 © The Author(s) 2021. This article is published with open access Abstract Trophic interactions are crucial for carbon cycling in food webs. Traditionally, eukaryotic micropredators are considered the major micropredators of bacteria in soils, although bacteria like myxobacteria and Bdellovibrio are also known bacterivores. Until recently, it was impossible to assess the abundance of prokaryotes and eukaryotes in soil food webs simultaneously. Using metatranscriptomic three-domain community profiling we identified pro- and eukaryotic micropredators in 11 European mineral and organic soils from different climes. Myxobacteria comprised 1.5–9.7% of all obtained SSU rRNA transcripts and more than 60% of all identified potential bacterivores in most soils. The name-giving and well-characterized fi 1234567890();,: 1234567890();,: predatory bacteria af liated with the Myxococcaceae were barely present, while Haliangiaceae and Polyangiaceae dominated. In predation assays, representatives of the latter showed prey spectra as broad as the Myxococcaceae. 18S rRNA transcripts from eukaryotic micropredators, like amoeba and nematodes, were generally less abundant than myxobacterial 16S rRNA transcripts, especially in mineral soils. Although SSU rRNA does not directly reflect organismic abundance, our findings indicate that myxobacteria could be keystone taxa in the soil microbial food web, with potential impact on prokaryotic community composition. -
Mechanisms of Novel Anaerobic Aromatic Degradation Pathways in Geobacter Daltonii
Georgia State University ScholarWorks @ Georgia State University Biology Dissertations Department of Biology Summer 8-12-2014 Benzene and Beyond: Mechanisms of Novel Anaerobic Aromatic Degradation Pathways in Geobacter daltonii Alison Kanak Follow this and additional works at: https://scholarworks.gsu.edu/biology_diss Recommended Citation Kanak, Alison, "Benzene and Beyond: Mechanisms of Novel Anaerobic Aromatic Degradation Pathways in Geobacter daltonii." Dissertation, Georgia State University, 2014. https://scholarworks.gsu.edu/biology_diss/143 This Dissertation is brought to you for free and open access by the Department of Biology at ScholarWorks @ Georgia State University. It has been accepted for inclusion in Biology Dissertations by an authorized administrator of ScholarWorks @ Georgia State University. For more information, please contact [email protected]. BENZENE AND BEYOND: MECHANISMS OF NOVEL ANAEROBIC AROMATIC DEGRADATION PATHWAYS IN GEOBACTER DALTONII by ALISON KANAK Under the Direction of Kuk-Jeong Chin ABSTRACT Petroleum spills causes contamination of drinking water with carcinogenic aromatic compounds including benzene and cresol. Current knowledge of anaerobic benzene and cresol degradation is extremely limited and it makes bioremediation challenging. Geobacter daltonii strain FRC-32 is a metal-reducing bacterium isolated from radionuclides and hydrocarbon- contaminated subsurface sediments. It is notable for its anaerobic oxidation of benzene and its unique ability to metabolize p-, m-, or o-cresol as a sole carbon source. Location of genes involved in aromatic compound degradation and genes unique to G. daltonii were elucidated by genomic analysis using BLAST. Genes predicted to play a role in aromatic degradation cluster into an aromatic island near the start of the genome. Of particular note, G. -
Comparative Analysis of Type IV Pilin in Desulfuromonadales
ORIGINAL RESEARCH published: 21 December 2016 doi: 10.3389/fmicb.2016.02080 Comparative Analysis of Type IV Pilin in Desulfuromonadales Chuanjun Shu, Ke Xiao, Qin Yan and Xiao Sun * State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China During anaerobic respiration, the bacteria Geobacter sulfurreducens can transfer electrons to extracellular electron accepters through its pilus. G. sulfurreducens pili have been reported to have metallic-like conductivity that is similar to doped organic semiconductors. To study the characteristics and origin of conductive pilin proteins found in the pilus structure, their genetic, structural, and phylogenetic properties were analyzed. The genetic relationships, and conserved structures and sequences that were obtained were used to predict the evolution of the pilins. Homologous genes that encode conductive pilin were found using PilFind and Cluster. Sequence characteristics and protein tertiary structures were analyzed with MAFFT and QUARK, respectively. The origin of conductive pilins was explored by building a phylogenetic tree. Truncation is a characteristic of conductive pilin. The structures of truncated pilins and their accompanying proteins were found to be similar to the N-terminal and C-terminal ends Edited by: of full-length pilins respectively. The emergence of the truncated pilins can probably be Marina G. Kalyuzhanaya, ascribed to the evolutionary pressure of their extracellular electron transporting function. San Diego State University, USA Genes encoding truncated pilins and proteins similar to the C-terminal of full-length pilins, Reviewed by: Fengfeng Zhou, which contain a group of consecutive anti-parallel beta-sheets, are adjacent in bacterial Shenzhen Institutes of Advanced genomes. -
Downloaded from IMG-JGI and NCBI (See Table 1 for Taxon Object Ids)
bioRxiv preprint doi: https://doi.org/10.1101/668343; this version posted October 15, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 Phylogenetic and structural diversity of aromatically dense pili from environmental 2 metagenomes 3 M. S. Bray1,2@, J. Wu1, C.C. Padilla1#, F. J. Stewart1, D. A. Fowle3, C. Henny4, R. L. Simister5, 4 K. J. Thompson5, S. A. Crowe2,5, J. B. Glass1, 2* 5 6 1School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA; 7 2School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA, USA; 8 3Department of Geology, University of Kansas, Lawrence, KS, USA; 9 4Research Center for Limnology, Indonesian Institute of Sciences, Cibinong, Indonesia; 10 5Department of Earth, Ocean, & Atmospheric Sciences; Department of Microbiology & 11 Immunology, University of British Columbia, Vancouver, BC, Canada 12 13 *Correspondence to: [email protected] 14 15 Running Title: Predicting e-pili 16 @Now at: Department of Biological Sciences, San Diego State University, San Diego, CA, USA 17 18 #Now at: Dovetail Genomics, LLC, Santa Cruz, CA, USA 19 1 bioRxiv preprint doi: https://doi.org/10.1101/668343; this version posted October 15, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license.