DOCSLIB.ORG

MIAMI UNIVERSITY the Graduate School Certificate for Approving The

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
MIAMI UNIVERSITY the Graduate School Certificate for Approving The MIAMI UNIVERSITY The Graduate School Certificate for Approving the Dissertation We hereby approve the Dissertation of Tomislav Ticak Candidate for the Degree Doctor of Philosophy _________________________________________ Director Dr. Donald J. Ferguson _________________________________________ Reader Dr. Gary R. Janssen _________________________________________ Reader Dr. Natosha L. Finley _________________________________________ Dr. Annette Bollmann _________________________________________ Graduate School Representative Dr. Carole Dabney-Smith ABSTRACT ANOXIC QUATERNARY AMINE UTILIZATION BY ARCHAEA AND BACTERIA THROUGH A NON-L-PYRROLYSINE METHYLTRANSFERASE; INSIGHTS INTO GLOBAL ECOLOGY, HUMAN HEALTH, AND EVOLUTION OF ANAEROBIC SYSTEMS by Tomislav Ticak Quaternary amines are compounds which are important for every domain of life and play roles as carbon and nitrogen sources but also are known to act as osmoregulants. One quaternary amine, glycine betaine, is considered a key osmoregulatory compound due to its chemical nature and is often the main intersection of choline and carnitine metabolism, both aerobically and anaerobically. Many organisms have the capability of degrading glycine betaine through oxygenases or dehydrogenases aerobically, but there is little literature related to the fate of glycine betaine in anaerobic systems. Many of the reported anaerobic systems for glycine betaine involve a reductase pathway that leads to the formation of trimethylamine and acetate, which are well established methanogenic precursor compounds in anaerobic environments. However, there exist a few reports of acetogens and methanogens with the capability of converting glycine betaine to dimethylglycine, which is a strict deviation from the aformentioned reductase pathway. This suggests a pathway exists for anaerobic glycine betaine metabolism that has largely gone uncharacterized. We used a series of bioinformatic, biochemical, and physiological experiments to examine carbon metabolism in Desulfitobacterium hafniense strain Y51 and demonstrated its ability to perform this novel mechanism of glycine betaine metabolism. We proposed that non-L-pyrrolysine trimethylamine methyltransferases may act as quaternary amine methyltransferases. As a result of this study; we discovered a theoretical key in explaining the evolution of the glycine betaine and trimethylamine methyltransferases regarding incorporation of L-pyrrolysine. The fact that a quaternary amine (e.g., glycine betaine) may bind into the near identical location of the proposed trimethylamine-pyrrolysine adducts may help us to better understand this widespread superfamily of methyltransferases. By using our knowledge of the glycine betaine methyltransferase, we began to investigate anaerobic communities for the presence of these methyltransferase genes by enrichments with quaternary amines resulting in the discovery of methanogens capable of glycine betaine, choline, and tetramethylammonium metabolism. Genomic analysis of these organisms revealed the presence of glycine betaine and trimethylamine methyltransferase-like genes supporting the hypothesis of quaternary amine demethylation by non-L-pyrrolysine methyltransferases. Our future work now points toward the examination of microbial distribution and physiology for anaerobic quaternary amine utilization in human systems, marine and freshwater environments to determine the evolutionary pressure(s) that may have selected for the advent of L-pyrrolysine. ANOXIC QUATERNARY AMINE UTILIZATION BY ARCHAEA AND BACTERIA THROUGH A NON-L-PYRROLYSINE METHYLTRANSFERASE; INSIGHTS INTO GLOBAL ECOLOGY, HUMAN HEALTH, AND EVOLUTION OF ANAEROBIC SYSTEMS A Dissertation Submitted to the Faculty of Miami University in partial fulfillment of the requirements for the degree of Doctor of Philosophy Department of Microbiology by Tomislav Ticak Miami University Oxford, OH 2015 Dissertation Director: Donald J. Ferguson, Ph.D. TABLE OF CONTENTS LIST OF TABLES iii LIST OF FIGURES iv LIST OF COMMON ABBREVIATIONS vii DEDICATION ix INTRODUCTION 1 CHAPTER 1. A nonpyrrolysine member of the widely distributed trimethylamine 32 methyltransferase family is a glycine betaine methyltransferase CHAPTER 2. Isolation and characterization of a tetramethylammonium-degrading 78 Methanococcoides strain and a novel glycine betaine-utilizing Methanolobus strain CHAPTER 3. Analysis of the function of L-Pyrrolysine within the trimethylamine 125 methyltransferase superfamily (COG5598) by comparison to the glycine betaine methyltransferase APPENDIX A. Cloning and expression of auxiliary genes predicted to play roles 147 in quaternary amine-dependent methylotrophy in Desulfitobacterium hafniense Y51 CONCLUDING REMARKS AND FUTURE DIRECTIONS 153 REFERENCES 164 ii LIST OF TABLES Table Page 1 Gene-specific qRT-PCR and cloning primers used in this study 42 2 Comparative analysis of several Methanolobus species to B1d 95 3 Comparative analysis of several Methanococcoides species to Q3c 96 4 Primers for the generation of expression vectors in pSpeedET and pDL05c 150 iii LIST OF FIGURES Figure Page 1 Structure of base amine molecules and structures of relevant amine compounds 3 2 Overview of pathways of Car and Cho conversion to GB by microbes 5 3 Proposed mechanism of the glycine betaine/sarcosine/glycine reductase system 8 4 Schematic of methylamine dehydrogenase or oxygenases for the formation of 13 formaldehyde prior to downstream pathways 5 Overview of methanogenic pathways 17 6 Modfied vanillate:THF C1 pathway of D. hanfiense strain DCB-2 19 showing oxidation of a CH3 group from a methylated pterin molecule 7 Proposed methylotrophic models for both archaea and bacteria 21 8 Neighbor-joining 16S rRNA phylogenetic tree of the genus Desulfitobacterium 26 9 Proposed formation of the methylamine-Pyl adducts in the methylamine 30 methyltransferase during enzymatic catalysis 10 The genomic context of mttB genes suggests a role in quaternary amine metabolism 36 11 DSY3156 and DSY3157 were purified to near-homogeneity 45 12 MtgA (DSY3157) is a methylCbl:THF methyltransferase 49 13 Growth of D. hafniense Y51 in the presence of glycine betaine 52 (GB) and either fumarate (A) or nitrate (B) 14 Thin-layer chromatographic analysis of D. hafniense culture supernatants 54 15 Hypothetical pathway for the conversion of glycine betaine 56 (GB) to dimethylglycine and CO2 by D. hafniense Y51 iv 16 DSY3156 is a glycine betaine:cob(I)alamin methyltransferase 60 17 Michaelis–Menten kinetics of recombinant DSY3156 62 18 Stoichiometric demethylation of GB to produce DMG and methylCbl 65 19 Phylogenetic tree of the COG5598 Superfamily 68 20 Proposed functional relationship between MtgB and MttB 71 21 Gel electrophoresis of 16S rRNA and mcrA products 91 22 Maximum likelihood trees showing the phylogenetic position of strains B1d 93 and Q3c in relation to the most closely related organisms, based on the partial 16S rRNA gene sequence (A) or partial McrA amino acid sequence (B) 23 Microscopic examination of strains B1d and Q3c 97 24 Effect of increasing GB or QMA concentrations on the growth of 100 Methanolobus vulcani B1d and Methanococcoides methylutens Q3c 25 Growth curves are presented showing changes in OD600 as well as quaternary 103 amine and methane concentrations over time for strains B1d (A) and Q3c (B) 26 Subsystem profile of methanogen isolates generated with RAST 105 27 Proposed quaternary amine metabolic schema for methanogens 108 28 Genomic context of putative dimethylsulfide operons for B1d (A) and Q3c (B) 110 29 Maximum-likelihood tree of the COG5589 superfamily amended with non-Pyl 112 and Pyl MttBs from strains B1d and Q3 30 Gene neighborhoods of mttiB genes in strains B1d (A) and Q3c (B). 115 31 Proposed pathway of QMA breakdown in archaea and bacteria 121 32 Proposed mechanism of MMA catalysis by MtmB. 128 33 Structural superpositioning of the MtmB and MetH crystal structures. 130 34 Structure of the Escherichia coli ProX transporter with bound GB 133 35 Structural overlay of Pyl’s location within each MtxB MT 138 v 36 Proposed positioning of GB into MtgB apo-structure based on 141 Q-Site Finder analysis 37 SDS/PAGE of heterologously expressed D. hafniense Y51 MttB enzymes 151 vi LIST OF COMMON ABBREVIATIONS Name Abb. Quaternary amines QA Trimethylamine TMA Glycine betaine GB L-pyrrolysine Pyl Methyltransferase MT Choline Cho Carnitine Car Dimethylglycine DMG Sarcosine MMG Sulfur Reducing Bacteria SRB Monomethylamine MMA One-carbon C1 Dimethylethanolamine DMEA Dimethylamine DMA Tetramethylammonium QMA 2-mercaptoethanesulfonate CoM Knock-out KO Betaine/Choline/Carnitine Transporter BCCT Amine/Polyamine/Organocation APC vii Cluster of orthologous genes COG Corrinoid-binding protein CBP Cobalamin Cbl Tetrahydrofolate THF / FH4 Horizontal gene transfer HGT Last Universal Common Ancestor LUCA Open reading frame ORF Site-directed mutagenesis SDM Gas chromatography GC Reducing equivalents [H] Brackish media BM High-salt media HM 2QNE MtgB 1NTH MtmB Amino acid aa Base pair bp Kilodalton kDa viii DEDICATION I dedicate this work to all those who supported me through these long years of my graduate career. I thank my friends, mentors, co-workers, and family for continually believing in my capabilities as a scientist and as an educator. I finally would like to dedicate this work to all those who follow after me, as I hope this work will provide you the insights to understanding the microbial one-carbon world that captivated me. ix INTRODUCTION Quaternary amine (QA) utilization by microbes is well-understood
Load more

Recommended publications
  • Microbiology Laboratory Exercises Third Edition 2020
    MICROBIOLOGY Laboratory Exercises Third Edition Keddis & Rauschenbach 2020 Photo Credits (in order of contribution): Diane Davis, Ines Rauschenbach & Ramaydalis Keddis Acknowledgements: Many thanks to those in the Department of Biochemistry and Microbiology, Rutgers University, who have through the years inspired our enthusiasm for the science and teaching of microbiology, with special thanks to Diane Davis, Douglas Eveleigh and Max Häggblom. Safety: The experiments included in this manual have been deemed safe by the authors when all necessary safety precautions are met. The authors recommend maintaining biosafety level 2 in the laboratory setting and using risk level 1 organisms for all exercises. License: This work is licensed under a Creative Commons Attribution- NonCommercial-NoDerivatives 4.0 International License Microbiology Laboratory Exercises Third Edition 2020 Ramaydalis Keddis, Ph.D. Ines Rauschenbach, Ph.D. Department of Biochemistry and Microbiology Rutgers, The State University of New Jersey CONTENTS PAGE Introduction Schedule ii Best Laboratory Practices Iii Working in a Microbiology Laboratory iv Exercises Preparation of a Culture Medium 1 Culturing and Handling Microorganisms 3 Isolation of a Pure Culture 5 Counting Bacterial Populations 8 Controlling Microorganisms 10 Disinfectants 10 Antimicrobial Agents: Susceptibility Testing 12 Hand Washing 14 The Lethal Effects of Ultraviolet Light 15 Selection of Fungi from Air 17 Microscopy 21 Morphology and Staining of Bacteria 26 Microbial Metabolism 30 Enzyme Assay 32 Metabolic
    [Show full text]
  • Phylogenetics of Archaeal Lipids Amy Kelly 9/27/2006 Outline
    Phylogenetics of Archaeal Lipids Amy Kelly 9/27/2006 Outline • Phlogenetics of Archaea • Phlogenetics of archaeal lipids • Papers Phyla • Two? main phyla – Euryarchaeota • Methanogens • Extreme halophiles • Extreme thermophiles • Sulfate-reducing – Crenarchaeota • Extreme thermophiles – Korarchaeota? • Hyperthermophiles • indicated only by environmental DNA sequences – Nanoarchaeum? • N. equitans a fast evolving euryarchaeal lineage, not novel, early diverging archaeal phylum – Ancient archael group? • In deepest brances of Crenarchaea? Euryarchaea? Archaeal Lipids • Methanogens – Di- and tetra-ethers of glycerol and isoprenoid alcohols – Core mostly archaeol or caldarchaeol – Core sometimes sn-2- or Images removed due to sn-3-hydroxyarchaeol or copyright considerations. macrocyclic archaeol –PMI • Halophiles – Similar to methanogens – Exclusively synthesize bacterioruberin • Marine Crenarchaea Depositional Archaeal Lipids Biological Origin Environment Crocetane methanotrophs? methane seeps? methanogens, PMI (2,6,10,15,19-pentamethylicosane) methanotrophs hypersaline, anoxic Squalane hypersaline? C31-C40 head-to-head isoprenoids Smit & Mushegian • “Lost” enzymes of MVA pathway must exist – Phosphomevalonate kinase (PMK) – Diphosphomevalonate decarboxylase – Isopentenyl diphosphate isomerase (IPPI) Kaneda et al. 2001 Rohdich et al. 2001 Boucher et al. • Isoprenoid biosynthesis of archaea evolved through a combination of processes – Co-option of ancestral enzymes – Modification of enzymatic specificity – Orthologous and non-orthologous gene
    [Show full text]
  • Alterations of Genetic Variants and Transcriptomic Features of Response to Tamoxifen in the Breast Cancer Cell Line
    Alterations of Genetic Variants and Transcriptomic Features of Response to Tamoxifen in the Breast Cancer Cell Line Mahnaz Nezamivand-Chegini Shiraz University Hamed Kharrati-Koopaee Shiraz University https://orcid.org/0000-0003-2345-6919 seyed taghi Heydari ( [email protected] ) Shiraz University of Medical Sciences https://orcid.org/0000-0001-7711-1137 Hasan Giahi Shiraz University Ali Dehshahri Shiraz University of Medical Sciences Mehdi Dianatpour Shiraz University of Medical Sciences Kamran Bagheri Lankarani Shiraz University of Medical Sciences Research Keywords: Tamoxifen, breast cancer, genetic variants, RNA-seq. Posted Date: August 17th, 2021 DOI: https://doi.org/10.21203/rs.3.rs-783422/v1 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Page 1/33 Abstract Background Breast cancer is one of the most important causes of mortality in the world, and Tamoxifen therapy is known as a medication strategy for estrogen receptor-positive breast cancer. In current study, two hypotheses of Tamoxifen consumption in breast cancer cell line (MCF7) were investigated. First, the effect of Tamoxifen on genes expression prole at transcriptome level was evaluated between the control and treated samples. Second, due to the fact that Tamoxifen is known as a mutagenic factor, there may be an association between the alterations of genetic variants and Tamoxifen treatment, which can impact on the drug response. Methods In current study, the whole-transcriptome (RNA-seq) dataset of four investigations (19 samples) were derived from European Bioinformatics Institute (EBI). At transcriptome level, the effect of Tamoxifen was investigated on gene expression prole between control and treatment samples.
    [Show full text]
  • 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.
    [Show full text]
  • Archaeology of Eukaryotic DNA Replication
    Downloaded from http://cshperspectives.cshlp.org/ on September 25, 2021 - Published by Cold Spring Harbor Laboratory Press Archaeology of Eukaryotic DNA Replication Kira S. Makarova and Eugene V. Koonin National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894 Correspondence: [email protected] Recent advances in the characterization of the archaeal DNA replication system together with comparative genomic analysis have led to the identification of several previously un- characterized archaeal proteins involved in replication and currently reveal a nearly com- plete correspondence between the components of the archaeal and eukaryotic replication machineries. It can be inferred that the archaeal ancestor of eukaryotes and even the last common ancestor of all extant archaea possessed replication machineries that were compa- rable in complexity to the eukaryotic replication system. The eukaryotic replication system encompasses multiple paralogs of ancestral components such that heteromeric complexes in eukaryotes replace archaeal homomeric complexes, apparently along with subfunctionali- zation of the eukaryotic complex subunits. In the archaea, parallel, lineage-specific dupli- cations of many genes encoding replication machinery components are detectable as well; most of these archaeal paralogs remain to be functionally characterized. The archaeal rep- lication system shows remarkable plasticity whereby even some essential components such as DNA polymerase and single-stranded DNA-binding protein are displaced by unrelated proteins with analogous activities in some lineages. ouble-stranded DNA is the molecule that Okazaki fragments (Kornberg and Baker 2005; Dcarries genetic information in all cellular Barry and Bell 2006; Hamdan and Richardson life-forms; thus, replication of this genetic ma- 2009; Hamdan and van Oijen 2010).
    [Show full text]
  • Amino Acid Catabolism in Staphylococcus Aureus
    University of Nebraska Medical Center DigitalCommons@UNMC Theses & Dissertations Graduate Studies Fall 12-16-2016 Amino Acid Catabolism in Staphylococcus aureus Cortney Halsey University of Nebraska Medical Center Follow this and additional works at: https://digitalcommons.unmc.edu/etd Part of the Bacteriology Commons Recommended Citation Halsey, Cortney, "Amino Acid Catabolism in Staphylococcus aureus" (2016). Theses & Dissertations. 160. https://digitalcommons.unmc.edu/etd/160 This Dissertation is brought to you for free and open access by the Graduate Studies at DigitalCommons@UNMC. It has been accepted for inclusion in Theses & Dissertations by an authorized administrator of DigitalCommons@UNMC. For more information, please contact [email protected]. Amino Acid Catabolism in Staphylococcus aureus By Cortney R. Halsey A DISSERTATION Presented to the Faculty of The Graduate College in the University of Nebraska In Partial Fulfillment of the Requirements For the Degree of Doctor of Philosophy Pathology and Microbiology Under the Supervision of Dr. Paul D. Fey University of Nebraska Medical Center Omaha, Nebraska October 2016 Supervisory Committee: Kenneth Bayles, Ph.D. Steven Carson, Ph.D. Paul Dunman, Ph.D. Rakesh Singh, Ph.D. ii Acknowledgements First and foremost, I would like to thank my mentor, Dr. Paul Fey, whose patience and support over the past six years has been critical to my success as a graduate student. Paul has given me opportunities to grow as a scientist and person, for which I will be forever thankful. I would also like to thank Dr. Ken Bayles, Dr. Steven Carson, Dr. Paul Dunman, and Dr. Rakesh Singh for serving on my supervisory committee.
    [Show full text]
  • Rapid Identification Ofbacteroides Fragilis with Bile and Antibiotic Disks D
    JOURNAL OF CuNICAL MICROBIOLOGY, Apr. 1977, p. 439-443 Vol. 5, No. 4 Copyright C 1977 American Society for Microbiology Printed in U.S.A. Rapid Identification ofBacteroides fragilis with Bile and Antibiotic Disks D. L. DRAPER1 AND A. L. BARRY* Section ofInfectious and Immunologic Diseases, School of Medicine, University of California, Davis, California 95616, and Clinical Microbiology Laboratories, Medical Center, Sacramento, California 95817* Received for publication 21 December 1976 A simple screening test is described for separating Bacteroides fragilis from other anaerobic gram-negative bacilli. The test utilizes filter paper disks im- pregnated with 25 mg of oxgall (Difco), tested in conjunction with antibiotic identification disks. The bile disks and antibiotic disks are placed on a supple- mented brucella blood agar plate which has been inoculated by swabbing with a standardized cell suspension. After 24 h at 350C in a GasPak jar, resistance to kanamycin and bile is taken as a presumptive identification of B. fragilis. Susceptibility to one or both disks indicates the need for further identification and additional biochemical tests are required. Those strains that produce insuf- ficient growth within 24 h are not likely to be B. fragilis. The reliability of the bile disk method was tested by comparing results with 100 clinical isolates versus results with bile in thioglycolate broth, peptone-yeast extract-glucose broth, and tryptic soy agar. All four bile test methods gave equilvalent results, but the broth media required much longer periods of incubation. Bacteroides fragilis is the anaerobic gram- would quickly identify most B. fragilis strains negative bacillus most frequently recovered could significantly reduce the number of iso- from human infections.
    [Show full text]
  • Supplementary Table S4. FGA Co-Expressed Gene List in LUAD
    Supplementary Table S4. FGA co-expressed gene list in LUAD tumors Symbol R Locus Description FGG 0.919 4q28 fibrinogen gamma chain FGL1 0.635 8p22 fibrinogen-like 1 SLC7A2 0.536 8p22 solute carrier family 7 (cationic amino acid transporter, y+ system), member 2 DUSP4 0.521 8p12-p11 dual specificity phosphatase 4 HAL 0.51 12q22-q24.1histidine ammonia-lyase PDE4D 0.499 5q12 phosphodiesterase 4D, cAMP-specific FURIN 0.497 15q26.1 furin (paired basic amino acid cleaving enzyme) CPS1 0.49 2q35 carbamoyl-phosphate synthase 1, mitochondrial TESC 0.478 12q24.22 tescalcin INHA 0.465 2q35 inhibin, alpha S100P 0.461 4p16 S100 calcium binding protein P VPS37A 0.447 8p22 vacuolar protein sorting 37 homolog A (S. cerevisiae) SLC16A14 0.447 2q36.3 solute carrier family 16, member 14 PPARGC1A 0.443 4p15.1 peroxisome proliferator-activated receptor gamma, coactivator 1 alpha SIK1 0.435 21q22.3 salt-inducible kinase 1 IRS2 0.434 13q34 insulin receptor substrate 2 RND1 0.433 12q12 Rho family GTPase 1 HGD 0.433 3q13.33 homogentisate 1,2-dioxygenase PTP4A1 0.432 6q12 protein tyrosine phosphatase type IVA, member 1 C8orf4 0.428 8p11.2 chromosome 8 open reading frame 4 DDC 0.427 7p12.2 dopa decarboxylase (aromatic L-amino acid decarboxylase) TACC2 0.427 10q26 transforming, acidic coiled-coil containing protein 2 MUC13 0.422 3q21.2 mucin 13, cell surface associated C5 0.412 9q33-q34 complement component 5 NR4A2 0.412 2q22-q23 nuclear receptor subfamily 4, group A, member 2 EYS 0.411 6q12 eyes shut homolog (Drosophila) GPX2 0.406 14q24.1 glutathione peroxidase
    [Show full text]
  • Chemistry of Proteins and Amino Acids • Proteins Are the Most Abundant Organic Molecules of the Living System
    Chemistry of Proteins and Amino Acids • Proteins are the most abundant organic molecules of the living system. • They occur in the every part of the cell and constitute about 50% of the cellular dry weight. • Proteins form the fundamental basis of structure and function of life. • In 1839 Dutch chemist G.J.Mulder while investing the substances such as those found in milk, egg, found that they could be coagulated on heating and were nitrogenous compounds. • The term protein is derived from a Greek word proteios, meaning first place. • Berzelius ( Swedish chemist ) suggested the name proteins to the group of organic compounds that are utmost important to life. • The proteins are nitrogenous macromolecules composed of many amino acids. Biomedical importance of proteins: • Proteins are the main structural components of the cytoskeleton. They are the sole source to replace nitrogen of the body. • Bio chemical catalysts known as enzymes are proteins. • Proteins known as immunoglobulins serve as the first line of defense against bacterial and viral infections. • Several hormones are protein in nature. • Structural proteins like actin and myosin are contractile proteins and help in the movement of muscle fibre. Some proteins present in cell membrane, cytoplasm and nucleus of the cell act as receptors. • The transport proteins carry out the function of transporting specific substances either across the membrane or in the body fluids. • Storage proteins bind with specific substances and store them, e.g. iron is stored as ferritin. • Few proteins are constituents of respiratory pigments and occur in electron transport chain, e.g. Cytochromes, hemoglobin, myoglobin • Under certain conditions proteins can be catabolized to supply energy.
    [Show full text]
  • Supplementary Information
    Retroconversion of estrogens into androgens by bacteria via a cobalamin-mediated methylation Po-Hsiang Wang, Yi-Lung Chen, Sean Ting-Shyang Wei, Kan Wu, Tzong-Huei Lee, Tien-Yu Wu, and Yin-Ru Chiang Supplementary Information Table of Contents Dataset Dataset S1. Genome annotation of strain DHT3 and transcriptomic analysis (RNA-Seq) of bacterial cells grown anaerobically with testosterone or estradiol. SI Tables Table S1. Oligonucleotides used in this study. Table S2. Selection of housekeeping genes of strain DHT3 used for constructing the linear regression line in the global gene expression profiles (RNA-Seq). Table S3. Selection of the cobalamin-dependent methyltransferases used for the un-rooted maximum likelihood tree construction. Table S4. UPLC–APCI–HRMS data of the intermediates involved in anaerobic estrone catabolism by strain DHT3. Table S5. 1H- (600 MHz) and 13C-NMR (150 MHz) spectral data of the HPLC-purified metabolite (AND2) and the authentic standard 5-androstan-3,17-diol Table S6. Selection of the bacteria used for comparative analysis of the gene organization for HIP degradation. SI Figures Fig. S1 Scanning electron micrographs of strain DHT3 cells. Fig. S2 Cobalamin as an essential vitamin during the anaerobic growth of strain DHT3 on estradiol. Fig. S3 Arrangement and expression analysis of the emt genes in strain DHT3. Fig. S4 The anaerobic growth of the wild type (A) and the emtA-disrupted mutant (B) of strain DHT3 with testosterone and estradiol. Fig. S5 APCI–HRMS spectrum of the HIP produced by estrone-fed strain DHT3. 1 Fig. S6 UPLC–APCI–HRMS spectra of two TLC-purified androgen metabolites, 17β-hydroxyandrostan-3-one (A) and 3β,17β-dihydroxyandrostane (B).
    [Show full text]
  • Methanogens Diversity During Anaerobic Sewage Sludge Stabilization and the Effect of Temperature
    processes Article Methanogens Diversity during Anaerobic Sewage Sludge Stabilization and the Effect of Temperature Tomáš Vítˇez 1,2, David Novák 3, Jan Lochman 3,* and Monika Vítˇezová 1,* 1 Department of Experimental Biology, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic; [email protected] 2 Department of Agricultural, Food and Environmental Engineering, Faculty of AgriSciences, Mendel University, 61300 Brno, Czech Republic 3 Department of Biochemistry, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic; [email protected] * Correspondence: [email protected] (J.L.); [email protected] (M.V.); Tel.: +420-549-495-602 (J.L.); Tel.: +420-549-497-177 (M.V.) Received: 29 June 2020; Accepted: 10 July 2020; Published: 12 July 2020 Abstract: Anaerobic sludge stabilization is a commonly used technology. Most fermenters are operated at a mesophilic temperature regime. Modern trends in waste management aim to minimize waste generation. One of the strategies can be achieved by anaerobically stabilizing the sludge by raising the temperature. Higher temperatures will allow faster decomposition of organic matter, shortening the retention time, and increasing biogas production. This work is focused on the description of changes in the community of methanogenic microorganisms at different temperatures during the sludge stabilization. At higher temperatures, biogas contained a higher percentage of methane, however, there was an undesirable accumulation of ammonia in the fermenter. Representatives of the hydrogenotrophic genus Methanoliea were described at all temperatures tested. At temperatures up to 50 ◦C, a significant proportion of methanogens were also formed by acetoclastic representatives of Methanosaeta sp. and acetoclastic representatives of the order Methanosarcinales.
    [Show full text]
  • An Evolutionary Approach to Bibliographic Classification
    University of Tennessee, Knoxville TRACE: Tennessee Research and Creative Exchange Doctoral Dissertations Graduate School 8-2018 AN EVOLUTIONARY APPROACH TO BIBLIOGRAPHIC CLASSIFICATION David Linn Sims University of Tennessee Follow this and additional works at: https://trace.tennessee.edu/utk_graddiss Recommended Citation Sims, David Linn, "AN EVOLUTIONARY APPROACH TO BIBLIOGRAPHIC CLASSIFICATION. " PhD diss., University of Tennessee, 2018. https://trace.tennessee.edu/utk_graddiss/5006 This Dissertation is brought to you for free and open access by the Graduate School at TRACE: Tennessee Research and Creative Exchange. It has been accepted for inclusion in Doctoral Dissertations by an authorized administrator of TRACE: Tennessee Research and Creative Exchange. For more information, please contact [email protected]. To the Graduate Council: I am submitting herewith a dissertation written by David Linn Sims entitled "AN EVOLUTIONARY APPROACH TO BIBLIOGRAPHIC CLASSIFICATION." I have examined the final electronic copy of this dissertation for form and content and recommend that it be accepted in partial fulfillment of the requirements for the degree of Doctor of Philosophy, with a major in Communication and Information. Suzanne L. Allard, Major Professor We have read this dissertation and recommend its acceptance: David G. Anderson, Bradley Wade Bishop, Stuart N. Brotman Accepted for the Council: Dixie L. Thompson Vice Provost and Dean of the Graduate School (Original signatures are on file with official studentecor r ds.) AN EVOLUTIONARY APPROACH TO BIBLIOGRAPHIC CLASSIFICATION A Dissertation Presented for the Doctor of Philosophy Degree The University of Tennessee, Knoxville David Linn Sims August 2018 Copyright © 2018 by David L. Sims All rights reserved. ii ACKNOWLEDGEMENTS If it had not been for my dissertation chair, Suzie Allard, I may not have completed this degree.
    [Show full text]