DOCSLIB.ORG

The Genome of Syntrophus Aciditrophicus: Life at the Thermodynamic Limit of Microbial Growth

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
The Genome of Syntrophus Aciditrophicus: Life at the Thermodynamic Limit of Microbial Growth The genome of Syntrophus aciditrophicus: Life at the thermodynamic limit of microbial growth Michael J. McInerney*, Lars Rohlin†, Housna Mouttaki*, UnMi Kim†, Rebecca S. Krupp†, Luis Rios-Hernandez*, Jessica Sieber*, Christopher G. Struchtemeyer*, Anamitra Bhattacharyya‡, John W. Campbell‡, and Robert P. Gunsalus†§ *Department of Botany and Microbiology, University of Oklahoma, Norman, OK 73019; ‡Integrated Genomics, 2201 West Campbell Park Drive, Chicago, IL 60612; and †Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA 90095 Edited by Ralph S. Wolfe, University of Illinois at Urbana–Champaign, Urbana, IL, and approved March 12, 2007 (received for review November 27, 2006) Biochemically, the syntrophic bacteria constitute the missing link in Table 1. Reactions involved in syntrophic metabolism our understanding of anaerobic flow of carbon in the biosphere. ⌬G°Ј*, ⌬GЈ†, The completed genome sequence of Syntrophus aciditrophicus SB, Reactions kJ/mol kJ/mol a model fatty acid- and aromatic acid-degrading syntrophic bac- terium, provides a glimpse of the composition and architecture of Methanogenic H2 consumption ϩ Ϫ ϩ ϩ 3 ϩ Ϫ Ϫ the electron transfer and energy-transducing systems needed to 4H2 HCO3 H CH4 3H2O 135.6 15.8 exist on marginal energy economies of a syntrophic lifestyle. The Syntrophic metabolism Ϫ ϩ 3 Ϫ ϩ Ϫ ϩ ϩ Ϫ genome contains 3,179,300 base pairs and 3,169 genes where 1,618 Propionate 3H2O Ace HCO3 76.1 16.9 ϩ ϩ genes were assigned putative functions. Metabolic reconstruction H 3H2 Ϫ ϩ 3 Ϫ ϩ ϩ ϩ ϩ Ϫ of the gene inventory revealed that most biosynthetic pathways of Butyrate 2H2O 2 Ace H 2H2 48.6 39.2 Ϫ ϩ 3 Ϫ ϩ Ϫ ϩ ϩ Ϫ a typical Gram-negative microbe were present. A distinctive fea- Benzoate 7H2O 3 Ace HCO3 70.1 68.5 ϩ ϩ ture of syntrophic metabolism is the need for reverse electron 3H 3H2 transport; the presence of a unique Rnf-type ion-translocating *Calculated from the data in Thauer et al. (46) with the free energy of electron transfer complex, menaquinone, and membrane-bound formation for benzoate given in ref. 47. Fe-S proteins with associated heterodisulfide reductase domains †Calculated on the basis of the following conditions observed in methano- suggests mechanisms to accomplish this task. Previously unde- genic ecosystems: partial pressures of H2 of 1 Pa and of CH4 of 50 kPa, 50 mM scribed approaches to degrade fatty and aromatic acids, including bicarbonate, and the concentrations of the substrates and acetate (AceϪ)at multiple AMP-forming CoA ligases and acyl-CoA synthetases seem 0.1 mM each. to be present as ways to form and dissipate ion gradients by using a sodium-based energy strategy. Thus, S. aciditrophicus, although nutritionally self-sufficient, seems to be a syntrophic specialist with interaction between microbial species is termed syntrophy. The limited fermentative and respiratory metabolism. Genomic analy- ubiquity of syntrophic metabolism in many anoxic environments sis confirms the S. aciditrophicus metabolic and regulatory com- emphasizes that metabolic cooperation among microbial species mitment to a nonconventional mode of life compared with our is required for complete destruction of organic matter where the prevailing understanding of microbiology. catalytic unit is a microbial consortium composed of two or more microbial species. Many syntrophic associations are highly or- anaerobic food chains ͉ syntrophic metabolism ͉ ganized, multicellular structures where the partners are in close fatty acid and benzoate utilization physical proximity to each other (6, 10, 11). However, little is known about the molecular mechanisms involved in the forma- tion and maintenance of these catalytic units. Even under yntrophus aciditrophicus is a rod-shaped, Gram-negative bac- optimal growth conditions, free energy changes are close to Sterium that degrades fatty acids, benzoate, cyclohexane equilibrium (12–14) and the available free energy must be shared carboxylate, cyclohex-1-ene carboxylate, and crotonate in cocul- by the different organisms (4). Truly, syntrophy represents an ture with hydrogen/formate-using methanogens or sulfate re- extreme existence, that of a marginal energy economy. ducers (1, 2). Phylogenetically, S. aciditrophicus is a member of A distinctive feature of syntrophic metabolism is the need for the delta subdivision of the Proteobacteria along with sulfate reverse electron transfer because critical oxidation-reduction reducers and Geobacter species. It is representative of a broad reactions result in a negative ⌬EЈ, i.e., a thermodynamically class of syntrophic bacteria that have an essential role in the unfavorable direction. The production of hydrogen (EЈ of Ϫ261 anaerobic recycling of organic matter to methane and carbon mV at 1 Pa H2) or formate (EЈ of Ϫ258 mV at 1 ␮M formate) dioxide, along with the fermentative and methanogenic organ- (4) from electrons generated in the oxidation of acyl-CoA isms. Whereas the carbon and energy yielding pathways of the latter two microbial groups are well understood, extremely little is known about the metabolism of syntrophs because so few Author contributions: M.J.M., A.B., J.W.C., and R.P.G. designed research; M.J.M., L.R., H.M., strains are available in pure culture. They reproduce slowly A.B., J.W.C., and R.P.G. performed research; M.J.M., L.R., L.R.-H., C.G.S., A.B., and J.W.C. (generation times of 24–50 h), with low yield, and require contributed new reagents/analytic tools; M.J.M., L.R., H.M., U.K., R.S.K., L.R.-H., J.S., C.G.S., symbiotic partners to survive and express their syntrophic life- A.B., J.W.C., and R.P.G. analyzed data; and M.J.M., L.R., J.W.C., and R.P.G. wrote the paper. style. Biochemically, they constitute the missing link in our Conflict of interest statement: J.W.C. and A.B. were employed by Integrated Genomics, Inc., which performed DNA sequencing and gene-calling analysis under contract to the Univer- understanding of anaerobic flow of carbon in the biosphere. sity of California at Los Angeles. They may be viewed as having commercial interests in the A wide range of organic compounds including alcohols, fatty product as a representation of their company’s performance. acids, aromatic acids, organic acids such as lactate and glycolate, This article is a PNAS Direct Submission. many amino acids, sugars, and hydrocarbons including methane Data deposition: The sequence reported in this paper has been deposited in the GenBank are degraded syntrophically under anaerobic conditions (3–9). database (accession no. CP000252). The degradation of these compounds is thermodynamically §To whom correspondence should be addressed. E-mail: [email protected]. unfavorable unless hydrogen and/or formate are maintained at This article contains supporting information online at www.pnas.org/cgi/content/full/ low levels by hydrogen/formate-consuming microorganisms such 0610456104/DC1. as the methanogens (Table 1). This thermodynamically based © 2007 by The National Academy of Sciences of the USA 7600–7605 ͉ PNAS ͉ May 1, 2007 ͉ vol. 104 ͉ no. 18 www.pnas.org͞cgi͞doi͞10.1073͞pnas.0610456104 Downloaded by guest on September 30, 2021 Table 2. General features of the S. aciditrophicus genome*† to individual microbial genomes, best reciprocal BLAST hits ␦ Category Amount revealed closest associations to the -proteobacteria: Geobacter metallireducens (1,118 reciprocal gene hits), Pelobacter carbin- DNA contigs 1 olicus (1,131), and Geobacter sulfurreducens (1,099) (SI Fig. 4). DNA sequenced 3,179,300 bp Approximately 1,100 genes are similar and are well conserved Coding sequence 2,812,658 bp across the 25 Gram-negative species shown. The remaining genes G ϩ C content 51.46% (Ϸ2,000) represent a recently discovered complement within the Transfer RNAs 48 S. aciditrophicus genome. Ribosomal RNA operons 1 In another comparison, the best BLAST hit to any microbial Pseudogenes 0 gene was determined (SI Fig. 5) and showed only 374, 250, and ORFs‡, total 3,169 (100%) 224 closest hits to the genomes of G. metallireducens, G. sul- ORFs with assigned function 1,618 (51%) furreducens, and Pelobacter carbinolicus, respectively. Notably ORFs without assigned function 1,551 (49%) three archaeal genomes, Methanosarcina mazei, Methanospiril- ORFs without function, no database match 421 (13.3%) lum hungatei, and Methanosarcina acetivorans gave 14–31 best ORFs in chromosomal clusters 1,493 (47.1) BLAST hits each, suggesting the possibility of lateral gene ORFs in paralog clusters 786 (24.8%) transfer events from these potential syntrophic partners. A ORFs with Pfam matches 1,852 (58.4%) significant fraction of these genes have energy/Co-A related ORFs with COG matches 1,986 (62.8%) functions or are transposases. *According to ERGO database (www.integratedgenomics.com). †The protein similarity cutoff score used was 1.0eϪ05. Central Metabolism. The 1,618 functionally assigned S. aciditro- ‡ORFs, open-reading frames, coding regions phicus genes were organized into pathways, revealing that most biosynthetic pathways considered essential for viability of a typical Gram-negative organism seem to be present (e.g., bio- intermediates to their respective enoyl-CoA intermediates [EЈ synthesis of amino acids, purines, pyrimidines, and many cofac- of Ϫ10 mV; (15)] represents a considerable energy barrier (i.e., tors). The undetected steps in amino acid formation include ⌬EЈϳϪ250 mV). Thus, the membrane components involved in genes encoding homoserine kinase (threonine biosynthesis), the generation and use of ion gradients are predicted to be key threonine deaminase (conversion of threonine to isoleucine), features of syntrophic metabolism. 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltrans- The genome sequence of S. aciditrophicus provides the first ferase or acetyldiaminopimelate aminotransferase (lysine bio- glimpse of the genetic program directing energy conservation synthesis), phosphoribosyl-ATP diphosphatase, and histidinol and reverse electron transport, which are essential features of the phosphatase (histidine biosynthesis).
Load more

Recommended publications
  • METACYC ID Description A0AR23 GO:0004842 (Ubiquitin-Protein Ligase
    Electronic Supplementary Material (ESI) for Integrative Biology This journal is © The Royal Society of Chemistry 2012 Heat Stress Responsive Zostera marina Genes, Southern Population (α=0.
    [Show full text]
  • Supplementary Materials
    Supplementary Materials Figure S1. Differentially abundant spots between the mid-log phase cells grown on xylan or xylose. Red and blue circles denote spots with increased and decreased abundance respectively in the xylan growth condition. The identities of the circled spots are summarized in Table 3. Figure S2. Differentially abundant spots between the stationary phase cells grown on xylan or xylose. Red and blue circles denote spots with increased and decreased abundance respectively in the xylan growth condition. The identities of the circled spots are summarized in Table 4. S2 Table S1. Summary of the non-polysaccharide degrading proteins identified in the B. proteoclasticus cytosol by 2DE/MALDI-TOF. Protein Locus Location Score pI kDa Pep. Cov. Amino Acid Biosynthesis Acetylornithine aminotransferase, ArgD Bpr_I1809 C 1.7 × 10−4 5.1 43.9 11 34% Aspartate/tyrosine/aromatic aminotransferase Bpr_I2631 C 3.0 × 10−14 4.7 43.8 15 46% Aspartate-semialdehyde dehydrogenase, Asd Bpr_I1664 C 7.6 × 10−18 5.5 40.1 17 50% Branched-chain amino acid aminotransferase, IlvE Bpr_I1650 C 2.4 × 10−12 5.2 39.2 13 32% Cysteine synthase, CysK Bpr_I1089 C 1.9 × 10−13 5.0 32.3 18 72% Diaminopimelate dehydrogenase Bpr_I0298 C 9.6 × 10−16 5.6 35.8 16 49% Dihydrodipicolinate reductase, DapB Bpr_I2453 C 2.7 × 10−6 4.9 27.0 9 46% Glu/Leu/Phe/Val dehydrogenase Bpr_I2129 C 1.2 × 10−30 5.4 48.6 31 64% Imidazole glycerol phosphate synthase Bpr_I1240 C 8.0 × 10−3 4.7 22.5 8 44% glutamine amidotransferase subunit Ketol-acid reductoisomerase, IlvC Bpr_I1657 C 3.8 × 10−16
    [Show full text]
  • Abstracts from the 10Th World Congress for Microcirculation
    DOI:10.1111/micc.12246 Abstracts Abstracts from the 10th World Congress for Microcirculation September 25th – 27th, 2015 Kyoto, Japan PLENARY LECTURES vascular neutrophils that constantly patrol the lung and can detect and phagocytose bacteria attached to endothelium suggesting some communication inter-cellular communica- PL1 tion. Clearly much anti-microbial activity occurs in the Imaging the microcirculation in infections vasculature prior to dissemination of bacteria into tissues. P Kubes University of Calgary, Calgary, Canada PL2 Using spinning disk microscopy has allowed us to track pathogens and immune cells in the microcirculation. Mapping oxygen in the brain of awake resting Observing the liver microvasculature revealed numerous mice immune speed bumps that slowed, delayed and even S Charpak prevented bacteria from disseminating to other organs. For Laboratory of Neurophysiology and New Microscopies, Inserm U1128, example, when Borrelia burgdorferi enters the vasculature Paris Descartes University, Paris, France they are immediately caught by the liver vascular macro- The brain is extremely sensitive to hypoxia. Yet, the phage, the Kupffer cells and are engulfed and antigens are physiological values of oxygen concentration in the brain presented on CD1d to resident vascular immune cells remain elusive because high resolution measurements have including invariant Natural Killer T cells (iNKT cells). These only been performed during anesthesia, which affects two iNKT cells receive messages and rapidly make gamma main parameters modulating tissue oxygenation, i.e. interferon to help with immunity. Absence of these events neuronal activity and cerebral blood flow. Using the recent leads to massive dissemination of borrelia especially to joints. finding that measurements of capillary erythrocyte-associ- In the joints the iNKT cells live closely apposed but outside ated transients i.e.
    [Show full text]
  • Detoxification of Lignocellulose-Derived Microbial Inhibitory Compounds by Clostridium Beijerinckii NCIMB 8052 During Acetone-Butanol-Ethanol Fermentation
    Detoxification of Lignocellulose-derived Microbial Inhibitory Compounds by Clostridium beijerinckii NCIMB 8052 during Acetone-Butanol-Ethanol Fermentation DISSERTATION Presented in Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy in the Graduate School of The Ohio State University By Yan Zhang Graduate Program in Animal Sciences The Ohio State University 2013 Dissertation Committee: Thaddeus C. Ezeji, Advisor Steven C. Loerch Sandra G. Velleman Zhongtang Yu Venkat Gopalan Copyrighted by Yan Zhang 2013 Abstract Pretreatment and hydrolysis of lignocellulosic biomass to fermentable sugars generate a complex mixture of microbial inhibitors such as furan aldehydes (e.g., furfural), which at sublethal concentration in the fermentation medium can be tolerated or detoxified by acetone butanol ethanol (ABE)-producing Clostridium beijerinckii NCIMB 8052. The response of C. beijerinckii to furfural at the molecular level, however, has not been directly studied. Therefore, this study was to elucidate mechanism employed by C. beijerinckii to detoxify lignocellulose-derived microbial inhibitors and use this information to develop inhibitor-tolerant C. beijerinckii. Towards the long-term goal of developing inhibitor-tolerant Clostridium strains, the first objective was to evaluate ABE fermentation by C. beijerinckii using different proportions of Miscanthus giganteus hydrolysates as carbon source. Compared to the growth of C. beijerinckii in control medium, C. beijerinckii experienced different degrees of inhibition. The degree of inhibition was dose-dependent, and C. beijerinckii did not grow in P2 medium with greater than 25% (v/v) Miscanthus giganteus hydrolysates. To improve tolerance of C. beijerinckii to inhibitors, supplementation of P2 medium with undiluted (100%) Miscanthus giganteus hydrolysates with 4 g/L CaCO3 resulted in successful growth of and ABE production by C.
    [Show full text]
  • (10) Patent No.: US 8119385 B2
    US008119385B2 (12) United States Patent (10) Patent No.: US 8,119,385 B2 Mathur et al. (45) Date of Patent: Feb. 21, 2012 (54) NUCLEICACIDS AND PROTEINS AND (52) U.S. Cl. ........................................ 435/212:530/350 METHODS FOR MAKING AND USING THEMI (58) Field of Classification Search ........................ None (75) Inventors: Eric J. Mathur, San Diego, CA (US); See application file for complete search history. Cathy Chang, San Diego, CA (US) (56) References Cited (73) Assignee: BP Corporation North America Inc., Houston, TX (US) OTHER PUBLICATIONS c Mount, Bioinformatics, Cold Spring Harbor Press, Cold Spring Har (*) Notice: Subject to any disclaimer, the term of this bor New York, 2001, pp. 382-393.* patent is extended or adjusted under 35 Spencer et al., “Whole-Genome Sequence Variation among Multiple U.S.C. 154(b) by 689 days. Isolates of Pseudomonas aeruginosa” J. Bacteriol. (2003) 185: 1316 1325. (21) Appl. No.: 11/817,403 Database Sequence GenBank Accession No. BZ569932 Dec. 17. 1-1. 2002. (22) PCT Fled: Mar. 3, 2006 Omiecinski et al., “Epoxide Hydrolase-Polymorphism and role in (86). PCT No.: PCT/US2OO6/OOT642 toxicology” Toxicol. Lett. (2000) 1.12: 365-370. S371 (c)(1), * cited by examiner (2), (4) Date: May 7, 2008 Primary Examiner — James Martinell (87) PCT Pub. No.: WO2006/096527 (74) Attorney, Agent, or Firm — Kalim S. Fuzail PCT Pub. Date: Sep. 14, 2006 (57) ABSTRACT (65) Prior Publication Data The invention provides polypeptides, including enzymes, structural proteins and binding proteins, polynucleotides US 201O/OO11456A1 Jan. 14, 2010 encoding these polypeptides, and methods of making and using these polynucleotides and polypeptides.
    [Show full text]
  • The Microbiota-Produced N-Formyl Peptide Fmlf Promotes Obesity-Induced Glucose
    Page 1 of 230 Diabetes Title: The microbiota-produced N-formyl peptide fMLF promotes obesity-induced glucose intolerance Joshua Wollam1, Matthew Riopel1, Yong-Jiang Xu1,2, Andrew M. F. Johnson1, Jachelle M. Ofrecio1, Wei Ying1, Dalila El Ouarrat1, Luisa S. Chan3, Andrew W. Han3, Nadir A. Mahmood3, Caitlin N. Ryan3, Yun Sok Lee1, Jeramie D. Watrous1,2, Mahendra D. Chordia4, Dongfeng Pan4, Mohit Jain1,2, Jerrold M. Olefsky1 * Affiliations: 1 Division of Endocrinology & Metabolism, Department of Medicine, University of California, San Diego, La Jolla, California, USA. 2 Department of Pharmacology, University of California, San Diego, La Jolla, California, USA. 3 Second Genome, Inc., South San Francisco, California, USA. 4 Department of Radiology and Medical Imaging, University of Virginia, Charlottesville, VA, USA. * Correspondence to: 858-534-2230, [email protected] Word Count: 4749 Figures: 6 Supplemental Figures: 11 Supplemental Tables: 5 1 Diabetes Publish Ahead of Print, published online April 22, 2019 Diabetes Page 2 of 230 ABSTRACT The composition of the gastrointestinal (GI) microbiota and associated metabolites changes dramatically with diet and the development of obesity. Although many correlations have been described, specific mechanistic links between these changes and glucose homeostasis remain to be defined. Here we show that blood and intestinal levels of the microbiota-produced N-formyl peptide, formyl-methionyl-leucyl-phenylalanine (fMLF), are elevated in high fat diet (HFD)- induced obese mice. Genetic or pharmacological inhibition of the N-formyl peptide receptor Fpr1 leads to increased insulin levels and improved glucose tolerance, dependent upon glucagon- like peptide-1 (GLP-1). Obese Fpr1-knockout (Fpr1-KO) mice also display an altered microbiome, exemplifying the dynamic relationship between host metabolism and microbiota.
    [Show full text]
  • Production of Butyric Acid and Hydrogen by Metabolically Engineered Mutants of Clostridium Tyrobutyricum
    PRODUCTION OF BUTYRIC ACID AND HYDROGEN BY METABOLICALLY ENGINEERED MUTANTS OF CLOSTRIDIUM TYROBUTYRICUM DISSERTATION Presented in Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy in the Graduate School of The Ohio State University By Xiaoguang Liu, M.S. ***** The Ohio State University 2005 Dissertation committee: Approved by Professor Shang-Tian Yang, Adviser Professor Barbara E Wyslouzil Adviser Professor Hua Wang Department of Chemical Engineering ABSTRACT Butyric acid has many applications in chemical, food and pharmaceutical industries. The production of butyric acid by fermentation has become an increasingly attractive alternative to current petroleum-based chemical synthesis. Clostridium tyrobutyricum is an anaerobic bacterium producing butyric acid, acetic acid, hydrogen and carbon dioxide as its main products. Hydrogen, as an energy byproduct, can add value to the fermentation process. The goal of this project was to develop novel bioprocess to produce butyric acid and hydrogen economically by Clostridial mutants. Conventional fermentation technologies for butyric acid and hydrogen production are limited by low reactor productivity, product concentration and yield. In this project, novel engineered mutants of C. tyrobutyricum were created by gene manipulation and cell adaptation. Fermentation process was also optimized using immobilizing cells in the fibrous-bed bioreactor (FBB) to enhance butyric acid and hydrogen production. First, metabolic engineered mutants with knocked-out acetate formation pathway were created and characterized. Gene inactivation technology was used to delete the genes of phosphotransacetylase (PTA) and acetate kinase (AK), two key enzymes in the acetate-producing pathway of C. tyrobutyricum, through homologous recombination. The metabolic engineered mutants were characterized by Southern hybridization, enzyme assay, protein expression and metabolites production.
    [Show full text]
  • 1.4. Shear-Stress Sensing of Vascular Endothelial Cells
    Mechanisms of Ca2+ entry and mechanical sensation in the vasculature Bing Hou Submitted in accordance with the requirements for the Degree of Doctor of Philosophy The University of Leeds School of Biomedical Sciences September 2014 Funded by CSC and the University of Leeds The candidate confirms that the work submitted is his own and that appropriate credit has been given where reference has been made to the work of others. This copy has been submitted on the understanding that it is copyright material and that no quotation from the thesis may be published without proper acknowledgement. 2 Acknowledgements I would like to express my sincerest gratitude to my supervisor Professor David Beech for all his support and guidance throughout my PhD. I came as a foreigner with English as my second language. However with his patience and help, I quickly found my feet and have learnt a great amount over the last 4 years. I am really grateful for his understanding and backing up during my PhD. I have really enjoyed my life at Leeds, and have been feeling proud to be a member in the Beech lab. I would also like to thank my co-supervisor Dr. Lin- Hua Jiang and my assessor Prof. Asipu Sivaprasadarao for all their assistance throughout my PhD. I have learnt a lot from all of the Beech lab members who helped and supported during my PhD, for which I am really grateful. I would like to express my special thanks to Jing, who not only taught me many experimental techniques but also helped me a lot in my life.
    [Show full text]
  • Molekularbiologie Und Pharmakologie Neuer G-Protein-Gekoppelter Purin-Rezeptoren
    Molekularbiologie und Pharmakologie neuer G-Protein-gekoppelter Purin-Rezeptoren Dissertation zur Erlangung des Doktorgrades (Dr. rer. nat.) der Mathematisch-Naturwissenschaftlichen Fakultät der Rheinischen Friedrich-Wilhelms-Universität Bonn vorgelegt von Melanie Knospe (geb. Hulbert) aus Bonn Bonn 2012 Angefertigt mit Genehmigung der Mathematisch-Naturwissenschaftlichen Fakultät der Rheinischen Friedrich-Wilhelms-Universität Bonn. 1. Gutachter: Prof. Dr. Christa E. Müller 2. Gutachter: Prof. Dr. Ivar von Kügelgen Tag der Promotion: 28.03.2012 Erscheinungsjahr: 2012 Diese Dissertation ist auf dem Hochschulserver der ULB Bonn (http://hss.ulb. uni-bonn.de/diss_online) elektronisch publiziert. Die vorliegende Arbeit wurde in der Zeit von Juni 2008 bis Dezember 2011 am Pharmazeutischen Institut der Rheinischen Friedrich-Wilhelms-Universität Bonn unter der Leitung von Frau Prof. Dr. Christa E. Müller durchgeführt. Mein besonderer Dank gebührt Frau Prof. Dr. Christa E. Müller für die Über- lassung des interessanten Themas, die fachliche Unterstützung, für die vielen wertvollen Anregungen und Diskussionen sowie die konstruktive Kritik beim Erstellen dieser Arbeit. Herrn Prof. Dr. Ivar von Kügelgen danke ich für die freundliche Übernahme des Koreferats. Für die Mitwirkung in meiner Prüfungskommission bedanke ich mich bei Herrn Prof. Dr. med. Klaus Mohr und Herrn Prof. Dr. Günther Mayer. Ich danke der NRW International Graduate Research School LIMES Chemical Biology für die finanzielle Unterstützung in Form eines Doktorandenstipendiums sowie
    [Show full text]
  • Supplementary Informations SI2. Supplementary Table 1
    Supplementary Informations SI2. Supplementary Table 1. M9, soil, and rhizosphere media composition. LB in Compound Name Exchange Reaction LB in soil LBin M9 rhizosphere H2O EX_cpd00001_e0 -15 -15 -10 O2 EX_cpd00007_e0 -15 -15 -10 Phosphate EX_cpd00009_e0 -15 -15 -10 CO2 EX_cpd00011_e0 -15 -15 0 Ammonia EX_cpd00013_e0 -7.5 -7.5 -10 L-glutamate EX_cpd00023_e0 0 -0.0283302 0 D-glucose EX_cpd00027_e0 -0.61972444 -0.04098397 0 Mn2 EX_cpd00030_e0 -15 -15 -10 Glycine EX_cpd00033_e0 -0.0068175 -0.00693094 0 Zn2 EX_cpd00034_e0 -15 -15 -10 L-alanine EX_cpd00035_e0 -0.02780553 -0.00823049 0 Succinate EX_cpd00036_e0 -0.0056245 -0.12240603 0 L-lysine EX_cpd00039_e0 0 -10 0 L-aspartate EX_cpd00041_e0 0 -0.03205557 0 Sulfate EX_cpd00048_e0 -15 -15 -10 L-arginine EX_cpd00051_e0 -0.0068175 -0.00948672 0 L-serine EX_cpd00054_e0 0 -0.01004986 0 Cu2+ EX_cpd00058_e0 -15 -15 -10 Ca2+ EX_cpd00063_e0 -15 -100 -10 L-ornithine EX_cpd00064_e0 -0.0068175 -0.00831712 0 H+ EX_cpd00067_e0 -15 -15 -10 L-tyrosine EX_cpd00069_e0 -0.0068175 -0.00233919 0 Sucrose EX_cpd00076_e0 0 -0.02049199 0 L-cysteine EX_cpd00084_e0 -0.0068175 0 0 Cl- EX_cpd00099_e0 -15 -15 -10 Glycerol EX_cpd00100_e0 0 0 -10 Biotin EX_cpd00104_e0 -15 -15 0 D-ribose EX_cpd00105_e0 -0.01862144 0 0 L-leucine EX_cpd00107_e0 -0.03596182 -0.00303228 0 D-galactose EX_cpd00108_e0 -0.25290619 -0.18317325 0 L-histidine EX_cpd00119_e0 -0.0068175 -0.00506825 0 L-proline EX_cpd00129_e0 -0.01102953 0 0 L-malate EX_cpd00130_e0 -0.03649016 -0.79413596 0 D-mannose EX_cpd00138_e0 -0.2540567 -0.05436649 0 Co2 EX_cpd00149_e0
    [Show full text]
  • Effects of High Forage/Concentrate Diet on Volatile Fatty Acid
    animals Article Effects of High Forage/Concentrate Diet on Volatile Fatty Acid Production and the Microorganisms Involved in VFA Production in Cow Rumen Lijun Wang 1,2, Guangning Zhang 2, Yang Li 2 and Yonggen Zhang 2,* 1 College of Animal Science and Technology, Qingdao Agricultural university, No. 700 of Changcheng Road, Qingdao 266000, China; [email protected] 2 College of Animal Science and Technology, Northeast Agricultural University, No. 600 of Changjiang Road, Harbin 150030, China; [email protected] (G.Z.); [email protected] (Y.L.) * Correspondence: [email protected]; Tel./Fax: +86-451-5519-0840 Received: 15 January 2020; Accepted: 28 January 2020; Published: 30 January 2020 Simple Summary: The rumen is well known as a natural bioreactor for highly efficient degradation of fibers, and rumen microbes play an important role on fiber degradation. Carbohydrates are fermented by a variety of bacteria in the rumen and transformed into volatile fatty acids (VFAs) by the corresponding enzymes. However, the content of forage in the diet affects the metabolism of cellulose degradation and VFA production. Therefore, we combine metabolism and metagenomics to explore the effects of High forage/concentrate diets and sampling time on enzymes and microorganisms involved in the metabolism of fiber and VFA in cow rumen. This study showed that propionate formation via the succinic pathway, in which succinate CoA synthetase (EC 6.2.1.5) and propionyl CoA carboxylase (EC 2.8.3.1) were key enzymes. Butyrate formation via the succinic pathway, in which phosphate butyryltransferase (EC 2.3.1.19), butyrate kinase (EC 2.7.2.7) and pyruvate ferredoxin oxidoreductase (EC 1.2.7.1) are the important enzymes.
    [Show full text]
  • Native Potatoes Apyrase Cat
    Native Potatoes Apyrase Cat. No. NATE-0085 Lot. No. (See product label) Introduction Description Apyrase is found in all eukaryotes and some prokaryotes. Apyrase, from potato, has a crucial role in regulating growth and development. Apyrase is involved in the inactivation of synaptic ATP as a neurotransmitter following nerve stimulation and in the inhibition of ADP induced platelet aggregation to prevent thrombosis. Divalent metal ions are required for activity and best activity is observed with calcium ion at 5 mM. Applications At least two isoenzymes are found in different varieties of S. tuberosum:4,5 one with a high ATPase/ADPase ratio (∼10) and another with a low ratio (∼1). Reaction: ATP → ADP+Pi → AMP+2Pi.Apyrase is used to hydrolyze nucleoside triphosphates and diphosphates. For hydrolysis of organic di and triphosphates, the optimal pH is 6, and for inorganic substrates, the optimal pH is 5.1. Apyrase, from Creative Enzymes, has been used in inhibition studies of platelet-aggregation. Synonyms ATP-diphosphatase; adenosine diphosphatase; ADPase; ATP diphosphohydrolase; apyrase; EC 3.6.1.5; 9000-95-7 Product Information Source Potatoes Form lyophilized powder. Partially purified, lyophilized powder containing potassium succinate buffer salts. EC Number EC 3.6.1.5 CAS No. 9000-95-7 Activity > 200 units/mg protein; > 600 units/mg protein Buffer H2O: soluble 1.0 mg/mL Pathway Purine metabolism, organism-specific biosystem; Pyrimidine metabolism, organism-specific biosystem; Pyrimidine metabolism, conserved biosystem Unit Definition One unit will liberate 1.0 μmole of inorganic phosphate from ATP or ADP per min at pH 6.5 at 30°C.
    [Show full text]