Genome-Directed Analysis of Prophage Excision, Host Defence
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Functional Characterization of Carbohydrate-Active Enzymes from Marine Bacteria
Functional characterization of carbohydrate-active enzymes from marine bacteria I n a u g u r a l d i s s e r t a t i o n zur Erlangung des akademischen Grades eines Doktors der Naturwissenschaften (Dr. rer. nat.) der Mathematisch-Naturwissenschaftlichen Fakultät der Universität Greifswald vorgelegt von Marcus Bäumgen Greifswald, 28.02.2020 Dekan: Prof. Dr. Werner Weitschies 1. Gutachter: Prof. Dr. Uwe T. Bornscheuer 2. Gutachter: Prof. Dr. Harry Brumer Tag der Promotion: 24.06.2020 II III Wissenschaft ist das Werkzeug, welches es uns ermöglicht, das große Puzzel der Natur und des Lebens zu lösen. IV Auch wenn wir den Weg des Wissens und der Weisheit niemals bis zum Ende beschreiten können, so ist doch jeder Schritt, den wir tun, ein Schritt in eine bessere Welt. V Content Abbreviations ..................................................................................................................... IX 1. Introduction ..................................................................................................................... 1 1.1 The marine carbon cycle .............................................................................................. 1 1.1.1 Algal blooms .......................................................................................................... 1 1.1.2 The marine carbohydrates ulvan and xylan ........................................................... 2 1.1.3 Marine polysaccharide utilization ........................................................................... 4 1.2 Carbohydrate-active enzymes -
Integrated Molecular Analysis of Sugar Metabolism of Sulfolobus Solfataricus
Integrated molecular analysis of Sugar Metabolism of Sulfolobus solfataricus Stan J.J. Brouns Integrated molecular analysis of sugar metabolism of Sulfolobus solfataricus Stan J.J. Brouns Promotoren prof. dr. Willem M. de Vos hoogleraar in de Microbiologie Wageningen Universiteit prof. dr. John van der Oost persoonlijk hoogleraar Microbiologie en Biochemie Wageningen Universiteit Leden van de prof. dr. Ton J.W.G. Visser promotie bijzonder hoogleraar Microspectroscopie in de Biochemie commissie Wageningen Universiteit prof. dr. Arnold J.M. Driessen hoogleraar Moleculaire Microbiologie Rijksuniversiteit Groningen dr. Loren L. Looger Howard Hughes Medical Institute Ashburn (VA), Verenigde Staten dr. Thijs Kaper Genencor International Palo Alto (CA), Verenigde Staten Dit onderzoek is uitgevoerd binnen de onderzoekschool VLAG Integrated molecular analysis of sugar metabolism of Sulfolobus solfataricus Stan J.J. Brouns Proefschrift ter verkrijging van de graad van doctor op gezag van de rector magnificus van Wageningen Universiteit, prof. dr. M.J. Kropff, in het openbaar te verdedigen op dinsdag 2 oktober 2007 des namiddags te half twee in de Aula Cover Boiling water: the habitat of a hyperthermophile (photo: S.J.J. Brouns) Printing Gildeprint (Enschede) Sponsoring Hellma Benelux, bioMérieux Brouns, S.J.J. - Integrated molecular analysis of sugar metabolism of Sulfolobus solfataricus in Dutch Geïntegreerde moleculaire analyse van het suikermetabolisme van Sulfolobus solfataricus PhD Thesis Wageningen University, Wageningen, Netherlands (2007) 176 p. - with summary in Dutch ISBN 978-90-8504-713-1 Voor mijn ouders en Marloes DANkwooRD Met trots ligt ligt hier nu een boekje. Natuurlijk kon het niet totstandkomen zonder de hulp van anderen. In dit stukje wil ik die mensen bedanken. -
New Insights Into Clostridia Through Comparative Analyses of Their 40 Genomes
Bioenerg. Res. DOI 10.1007/s12155-014-9486-9 New Insights into Clostridia Through Comparative Analyses of Their 40 Genomes Chuan Zhou & Qin Ma & Xizeng Mao & Bingqiang Liu & Yanbin Yin & Ying Xu # Springer Science+Business Media New York 2014 Abstract The Clostridium genus of bacteria contains the gene groups are shared by all the strains, and the strain- most widely studied biofuel-producing organisms such as specific gene pool consists of 22,668 genes, which is consis- Clostridium thermocellum and also some human pathogens, tent with the fact that these bacteria live in very diverse plus a few less characterized strains. Here, we present a environments and have evolved a very large number of comparative genomic analysis of 40 fully sequenced clostrid- strain-specific genes to adapt to different environments. ial genomes, paying a particular attention to the biomass Across the 40 genomes, 1.4–5.8 % of genes fall into the degradation ones. Our analysis indicates that some of the carbohydrate active enzyme (CAZyme) families, and 20 out Clostridium botulinum strains may have been incorrectly clas- of the 40 genomes may encode cellulosomes with each ge- sified in the current taxonomy and hence should be renamed nome having 1 to 76 genes bearing the cellulosome-related according to the 16S ribosomal RNA (rRNA) phylogeny. A modules such as dockerins and cohesins. A phylogenetic core-genome analysis suggests that only 169 orthologous footprinting analysis identified cis-regulatory motifs that are enriched in the promoters of the CAZyme genes, giving rise to 32 statistically significant motif candidates. Keywords Clostridium . Comparative genomics . -
Gluconate Dehydratase
Europäisches Patentamt *EP001496113A1* (19) European Patent Office Office européen des brevets (11) EP 1 496 113 A1 (12) EUROPEAN PATENT APPLICATION (43) Date of publication: (51) Int Cl.7: C12N 9/88, C12N 15/55, 12.01.2005 Bulletin 2005/02 C12N 15/63, C12P 7/58 (21) Application number: 04254114.4 (22) Date of filing: 08.07.2004 (84) Designated Contracting States: • Ishibashi, Hiroki, c/o Mitsui Chemicals Inc. AT BE BG CH CY CZ DE DK EE ES FI FR GB GR Omuta-shi, Fukuoka 836-8610 (JP) HU IE IT LI LU MC NL PL PT RO SE SI SK TR • Fukuiri, Yasushi, c/o Mitsui Chemicals Inc. Designated Extension States: Omuta-shi, Fukuoka 836-8610 (JP) AL HR LT LV MK • Sakuma, Atsushi, c/o Mitsui Chemicals Inc. Omuta-shi, Fukuoka 836-8610 (JP) (30) Priority: 10.07.2003 JP 2003194680 • Komatsu, Hironori, c/o Mitsui Chemicals Inc. Sodegaura-shi, Chiba 299-0265 (JP) (71) Applicant: MITSUI CHEMICALS, INC. • Ando, Tomoyuki, c/o Mitsui Chemicals Inc. Tokyo (JP) Sodegaura-shi, Chiba 299-0265 (JP) • Togashi, Kazuhiko, c/o Mitsui Chemicals Inc. (72) Inventors: Sodegaura-shi, Chiba 299-0265 (JP) • Miyake, Hitoki, c/o Mitsui Chemicals Inc. • Umetani, Hideki, c/o Mitsui Chemicals Inc. Mobara-shi, Chiba, 297-0017 (JP) Sodegaura-shi, Chiba 299-0265 (JP) • Yamaki, Toshifumi, c/o Mitsui Chemicals Inc. Mobara-shi, Chiba, 297-0017 (JP) (74) Representative: Paget, Hugh Charles Edward et al • Oikawa, Toshihiro, c/o Mitsui Chemicals Inc. Mewburn Ellis LLP Mobara-shi, Chiba, 297-0017 (JP) York House • Nakamura, Takeshi, New Energy and Industrial 23 Kingsway Kawasaki-shi, Kanagawa 212-8554 (JP) London WC2B 6HP (GB) (54) Gluconate dehydratase (57) A novel gluconate dehydratase derived from gluconate dehydratase or a transformed cell containing Achromobacter xylosoxidans and a gene encoding the the gene with an aldonic acid, the corresponding 2-keto- gluconate dehydratase are provided. -
<I>Lactobacillus Reuteri</I>
University of Nebraska - Lincoln DigitalCommons@University of Nebraska - Lincoln Faculty Publications in Food Science and Food Science and Technology Department Technology 2014 From prediction to function using evolutionary genomics: Human-specific ecotypes of Lactobacillus reuteri have diverse probiotic functions Jennifer K. Spinler Texas Children’s Hospital, [email protected] Amrita Sontakke Baylor College of Medicine Emily B. Hollister Baylor College of Medicine Susan F. Venable Baylor College of Medicine Phaik Lyn Oh University of Nebraska, Lincoln See next page for additional authors Follow this and additional works at: http://digitalcommons.unl.edu/foodsciefacpub Spinler, Jennifer K.; Sontakke, Amrita; Hollister, Emily B.; Venable, Susan F.; Oh, Phaik Lyn; Balderas, Miriam A.; Saulnier, Delphine M.A.; Mistretta, Toni-Ann; Devaraj, Sridevi; Walter, Jens; Versalovic, James; and Highlander, Sarah K., "From prediction to function using evolutionary genomics: Human-specific ce otypes of Lactobacillus reuteri have diverse probiotic functions" (2014). Faculty Publications in Food Science and Technology. 132. http://digitalcommons.unl.edu/foodsciefacpub/132 This Article is brought to you for free and open access by the Food Science and Technology Department at DigitalCommons@University of Nebraska - Lincoln. It has been accepted for inclusion in Faculty Publications in Food Science and Technology by an authorized administrator of DigitalCommons@University of Nebraska - Lincoln. Authors Jennifer K. Spinler, Amrita Sontakke, Emily B. Hollister, -
Medium and Long-Term Opportunities and Risks of the Biotechnological Production of Bulk Chemicals from Renewable Resources
Medium and Long-term Opportunities and Risks of the Biotechnological Production of Bulk Chemicals from Renewable Resources - The Potential of White Biotechnology The BREW Project Final report Prepared under the European Commission’s GROWTH Programme (DG Research) Project team: Academy Utrecht University (UU), Dept. of Science, Technology and Society (STS), Utrecht, Netherlands Fraunhofer Institute for Systems and Innovation Research (FhG-ISI), Karlsruhe, Germany Universidad Complutense de Madrid (UCM), Dept. of Chemical Engineering, Madrid, Spain Plant Research International (PRI), Wageningen, Netherlands CERISS (Centro per l'Educazione, la Ricerca, l'Informazione su Scienza e Società), Milan, Italy A&F (Agrotechnology and Food Innovations) Wageningen, Netherlands Industry partners BP Chemicals, Hull, United Kingdom Degussa AG, Hanau, Germany DSM NV, Heerlen, Netherlands DuPont, Bad Homburg, Germany NatureWorks, Naarden, Netherlands Novozymes A/S, Bagsvaerd, Denmark Roquette Frères, Lestrem, France Shell International Chemicals BV, Amsterdam, Netherlands Uniqema, Wilton/Redcar, United Kingdom Utrecht, September 2006 Authors Dr. Martin Patel (project co-ordinator) Utrecht University (UU) Manuela Crank, BE Chem Department of Science, Technology Dr. Veronika Dornburg and Society (STS) Barbara Hermann, M.Sc. Heidelberglaan 2 Lex Roes, M.Sc. NL-3584 CS Utrecht, Netherlands Tel. +31 (0) 30 253-7600 Fax +31 (0) 30 253-7601 [email protected] Dr. Bärbel Hüsing Fraunhofer Institute for Systems and Innovation Research (FhG-ISI), Karlsruhe, Germany Dr. Leo Overbeek Plant Research International (PRI) Wageningen, Netherlands Dr. Fabio Terragni CERISS (Centro per l'Educazione, la Dr. Elena Recchia Ricerca, l'Informazione su Scienza e Società), Milan, Italy Contributors Academy Dr. Ruud Weusthuis A&F (Agrotechnology and Food Innovations) Wageningen, Netherlands Prof. -
Evolution of Coenzyme BI2 Synthesis Among Enteric Bacteria
Copyright 0 1996 by the Genetics Society of America Evolution of Coenzyme BI2Synthesis Among Enteric Bacteria: Evidence for Loss and Reacquisition of a Multigene Complex Jeffrey G. Lawrence and John R. Roth Department of Biology, University of Utah, Salt Lake City, Utah 84112 Manuscript received June 16, 1995 Accepted for publication October 4, 1995 ABSTRACT We have examined the distribution of cobalamin (coenzyme BI2) synthetic ability and cobalamin- dependent metabolism among entericbacteria. Most species of enteric bacteria tested synthesize cobala- min under both aerobic and anaerobic conditions and ferment glycerol in a cobalamindependent fashion. The group of species including Escha'chia coli and Salmonella typhimurium cannot ferment glyc- erol. E. coli strains cannot synthesize cobalamin de novo, and Salmonella spp. synthesize cobalamin only under anaerobic conditions. In addition, the cobalamin synthetic genes of Salmonella spp. (cob) show a regulatory pattern different from that of other enteric taxa tested. We propose that the cobalamin synthetic genes, as well asgenes providing cobalamindependent diol dehydratase, were lostby a common ancestor of E. coli and Salmonella spp. and were reintroduced as a single fragment into the Salmonella lineage from an exogenous source. Consistent with this hypothesis, the S. typhimurium cob genes do not hybridize with the genomes of other enteric species. The Salmonella cob operon may represent a class of genes characterized by periodic loss and reacquisition by host genomes. This process may be an important aspect of bacterial population genetics and evolution. OBALAMIN (coenzyme BIZ) is a large evolution- The cobalamin biosynthetic genes have been charac- C arily ancient molecule ( GEORGOPAPADAKOUand terized in S. -
EXPERIMENTAL STUDIES on FERMENTATIVE FIRMICUTES from ANOXIC ENVIRONMENTS: ISOLATION, EVOLUTION, and THEIR GEOCHEMICAL IMPACTS By
EXPERIMENTAL STUDIES ON FERMENTATIVE FIRMICUTES FROM ANOXIC ENVIRONMENTS: ISOLATION, EVOLUTION, AND THEIR GEOCHEMICAL IMPACTS By JESSICA KEE EUN CHOI A dissertation submitted to the School of Graduate Studies Rutgers, The State University of New Jersey In partial fulfillment of the requirements For the degree of Doctor of Philosophy Graduate Program in Microbial Biology Written under the direction of Nathan Yee And approved by _______________________________________________________ _______________________________________________________ _______________________________________________________ _______________________________________________________ New Brunswick, New Jersey October 2017 ABSTRACT OF THE DISSERTATION Experimental studies on fermentative Firmicutes from anoxic environments: isolation, evolution and their geochemical impacts by JESSICA KEE EUN CHOI Dissertation director: Nathan Yee Fermentative microorganisms from the bacterial phylum Firmicutes are quite ubiquitous in subsurface environments and play an important biogeochemical role. For instance, fermenters have the ability to take complex molecules and break them into simpler compounds that serve as growth substrates for other organisms. The research presented here focuses on two groups of fermentative Firmicutes, one from the genus Clostridium and the other from the class Negativicutes. Clostridium species are well-known fermenters. Laboratory studies done so far have also displayed the capability to reduce Fe(III), yet the mechanism of this activity has not been investigated -
Ultrastructure of the Obligately Anaerobic Bacteria Clostridium Kluyveri and Cl
ULTRASTRUCTURE OF THE OBLIGATELY ANAEROBIC BACTERIA CLOSTRIDIUM KLUYVERI AND CL. ACETOBUTYLICUM By K. Y. CHO*t and C. H. DoY* [Manuscript received 22 August 1972J Abstract The morphology of Cl. kluyveri is compared with that of CI. acetobutylicum. The multilayered cell wall of both organisms differ in the number of layers and total thickness. The plasma membrane of Cl. acetobutylicum is asymmetric in electron density and can be separated from the rest of the cell by plasmolysis. Tubular or vesicular structures are observed between the wall and the plasma membrane. In contrast, the plasma membrane of Cl. kluyveri is more symmetrical, with no structures between the cell wall and the plasma membrane. Intracytoplasmic membrane systems present in Cl. acetobutylicum are morpholo gically similar to the mesosomes of Gram-positive aerobes. The intracytoplasmic mem brane systems' of ct. kluyveri are characteristically rough in appearance, and differ in general morphology from systems usually described as mesosomes. Roughness is attributed to membrane-bound ribosomes, these being smaller than those of Escheri chia coli. Polygonal structures containing moderately electron-dense material (possibly DNA) were observed in C/. kluyveri. Cl. acetobutylicum possesses membrane-bounded inclusions containing electron-dense particles similar in dimensions to E. coli ribo somes. Rows of electron-dense bands were also observed. It is suggested that the polygonal structures and rough membranes of Cl. kluyveri are components of a system for the functional expression of genetic informa tion. I. INTRODUCTION Investigations of the ultrastructure of bacteria have been mainly with aerobic species (Salton 1967). In comparative studies of the ultrastructure of bacteria differing in oxygen requirements (Cho 1968) the obligate anaerobes Clostridium kluyveri and CI. -
Clostridial Iron-Sulphur Proteins
J. Mol. Microbiol. Biotechnol. (2000) 2(1): 9-14. FermentationClostridial Symposium Fe-S Proteins 9 JMMB Minireview Clostridial Iron-Sulphur Proteins Jacques Meyer* The aim of this review is twofold: first, to point out the importance of Fe-S proteins in clostridial metabolism, and Département de Biologie Moléculaire et Structurale, second, to show that clostridia, as efficient and versatile CEA-Grenoble, 38054 Grenoble, France synthesizers of Fe-S proteins, provide a cornucopia of information on the structure and function of these proteins in all kinds of organisms. Abstract Rubredoxins Iron-sulfur proteins are ubiquitous catalysts of a wide range of biological reactions, and are particularly As the simplest of all Fe-S proteins, rubredoxins from abundant in clostridia which lack the ability to anaerobic bacteria comprise 45 to 54 residues, and their synthesize hemes. The development of research on active site consists of a single iron coordinated to four these metalloproteins has therefore been strongly cysteinyl sulfurs. Rubredoxin-encoding genes have been associated with biochemical investigations of found in C. pasteurianum (Mathieu et al., 1992), clostridial metabolism. Major breakthroughs in the C. beijerinckii (Wilkinson and Young, 1995), C. perfringens field, from the first isolation of an iron-sulfur protein (Katayama et al., 1995), C. acetobutylicum (Cornillot et al., in 1962, to the recent determination of an Fe- 1997), and C. butyricum (Gérard et al., 1999). At least four hydrogenase structure, have been made with primary structures (C. pasteurianum, C.perfringens, clostridia. These data, as well as others obtained C. sticklandii, and C. thermosaccharolyticum) of clostridial through studies on clostridia, are transferable to many rubredoxins have been determined either by protein or by other bioenergetic machineries, due to the strong DNA sequencing (reviewed in Mathieu et al., 1992). -
A Phylogenetic Analysis of the Mycoplasmas: Basis for Their Lc Assification W
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by DigitalCommons@University of Nebraska University of Nebraska - Lincoln DigitalCommons@University of Nebraska - Lincoln Public Health Resources Public Health Resources 9-1989 A Phylogenetic Analysis of the Mycoplasmas: Basis for Their lC assification W. G. Weisburg University of Illinois J. G. Tully National Institute of Allergy and Infectious Diseases D. L. Rose National Institute of Allergy and Infectious Diseases J. P. Petzel Iowa State University H. Oyaizu University of Illinois See next page for additional authors Follow this and additional works at: https://digitalcommons.unl.edu/publichealthresources Weisburg, W. G.; Tully, J. G.; Rose, D. L.; Petzel, J. P.; Oyaizu, H.; Yang, D.; Mandelco, L.; Sechrest, J.; Lawrence, T. G.; Van Etten, James L.; Maniloff, J.; and Woese, C. R., "A Phylogenetic Analysis of the Mycoplasmas: Basis for Their lC assification" (1989). Public Health Resources. 310. https://digitalcommons.unl.edu/publichealthresources/310 This Article is brought to you for free and open access by the Public Health Resources at DigitalCommons@University of Nebraska - Lincoln. It has been accepted for inclusion in Public Health Resources by an authorized administrator of DigitalCommons@University of Nebraska - Lincoln. Authors W. G. Weisburg, J. G. Tully, D. L. Rose, J. P. Petzel, H. Oyaizu, D. Yang, L. Mandelco, J. Sechrest, T. G. Lawrence, James L. Van Etten, J. Maniloff, and C. R. Woese This article is available at DigitalCommons@University of Nebraska - Lincoln: https://digitalcommons.unl.edu/ publichealthresources/310 JOURNAL OF BACTERIOLOGY, Dec. 1989, p. 6455-6467 Vol. 171, No. -
Clostridium</I> <I>Pasteurianum</I> Spoilage of Shelf
1886 Journal of Food Protection, Vol. 73, No. 10, 2010, Pages 1886–1890 Copyright G, International Association for Food Protection Thermoaciduric Clostridium pasteurianum Spoilage of Shelf-Stable Apple Juice GUOPING FENG, JOHN J. CHUREY, AND RANDY W. WOROBO* Department of Food Science, Cornell University, Geneva, New York 14456, USA Downloaded from http://meridian.allenpress.com/jfp/article-pdf/73/10/1886/1679035/0362-028x-73_10_1886.pdf by guest on 02 October 2021 MS 10-181: Received 28 April 2010/Accepted 4 June 2010 ABSTRACT Clostridium pasteurianum BB, a saccharolytic and spore-forming obligate anaerobe, was isolated and identified from shelf- stable apple juice that was responsible for multiple large spoilage outbreaks. The growth and sporulation conditions of C. pasteurianum were atypical compared with those previously published. C. pasteurianum spores were heat resistant in apple juice at pH 3.80, with D-values at 80, 85, and 90uC being 34.4, 15.9, and 4.4 min, respectively, and a z-value of 11uC. The survival curves for thermal inactivation obeyed linear first-order kinetics. Apple juice with varying pH values was used to determine the effect of pH on germination capability of C. pasteurianum spores. The spores were found to be able to germinate at pH as low as 4.3 in pH-adjusted apple juice at low contamination levels. It was confirmed by PCR that C. pasteurianum isolated from spoiled apple juice did not contain the genes for botulinum toxins B and E, which were more commonly found in neurotoxigenic butyric clostridia. Control of finished-juice pH to below 4.0 in combination with mild heating was proposed to prevent potential spoilage of shelf-stable apple juice made with spore-contaminated apple juice concentrate.