Meta-Proteomics of Rumen Microbiota Indicates Niche
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Electromicrobial Transformations Using the Pyruvate Synthase System of Clostridium Sporogenes
I I I 1 Bioelec~rochemistryand Bioenergetics, 21 (1989) 245-259 A section of J. Electroanal. Cheni., and constituting Vol. 275 (1989) Elsevier Sequoia S.A.. Lausanne - Printed in The Netherlands b ' I L Electromicrobial transformations using the pyruvate synthase system of Clostridium sporogenes Neil M. Dixon, Eurig W. James, Robert W. Lovitt * and Douglas B. Kell Departmen1 o/ Biological Sciences, University College of IVules, Aberystwylh, Djfed SY23 3DA (Great Britain) (Received 3 December 1988; in revised form 17 January 1989) I I J A bioelectrochemical method by which the enzymology of reductive carboxylations (RCOOH +C02 +6 [H]+RCH2COOH+2 H,O) could be investigated is described. This method was used for a I detailed study of the enynnology of the overall reaction (viz. acetyl phosphate to pyruvate) catalysed by I pyruvate synthase in Clostridium sporogenes. The same method could be utilised to harness such reductive I carboxylations for commercial biotransformations of xenobiotics. By adjusting the reaction conditions it was possible to alter the proportions of the products synthesised, and to synthesise compounds more reduced and/or with a greater number of carbon atoms than pyruvate. INTRODUCTION ! The proteolytic clostridia have been the subject of renewed interest, with the attention being focussed upon biotechnologically useful enyzmes that these I organisms produce. Apart from extracellular hydrolases, most notable are enoate [I-41, nitroaryl [5],linoleate [6],2-oxoacid [7], proline [8] and glycine reductases [9]. Recent investigations in this laboratory have concentrated upon Clostridiunz sporo- 1 genes[lO-171. Dixon [I71 detailed the effects of CO, on both the inhibition/stimulation and induction/repression of some of the "capnic" enzymes of CI. -
1 Studies on 3-Hydroxypropionate Metabolism in Rhodobacter
Studies on 3-Hydroxypropionate Metabolism in Rhodobacter sphaeroides Dissertation Presented in Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy in the Graduate School of The Ohio State University By Steven Joseph Carlson Graduate Program in Microbiology The Ohio State University 2018 Dissertation Committee Dr. Birgit E. Alber, Advisor Dr. F. Robert Tabita Dr. Venkat Gopalan Dr. Joseph A. Krzycki 1 Copyrighted by Steven Joseph Carlson 2018 2 Abstract In this work, the involvement of multiple biochemical pathways used by the metabolically versatile Rhodobacter sphaeroides to assimilate 3-hydroxypropionate was investigated. In Chapter 2, evidence of a 3-hydroxypropionate oxidative path is presented. The mutant RspdhAa2SJC was isolated which lacks pyruvate dehydrogenase activity and is unable to grow with pyruvate. Robust 3-hydropropionate growth with RspdhAa2SJC indicated an alternative mechanism exists to maintain the acetyl-CoA pool. Further, RsdddCMA4, lacking the gene encoding a possible malonate semialdehyde dehydrogenase, was inhibited for growth with 3-hydroxypropionate providing support for a 3-hydroxypropionate oxidative pathway which involves conversion of malonate semialdehyde to acetyl-CoA. We propose that the 3- hydroxypropionate growth of RspdhAa2SJC is due to the oxidative conversion of 3- hydroxypropionate to acetyl-CoA. In Chapter 3, the involvement of the ethylmalonyl-CoA pathway (EMCP) during growth with 3-hydroxypropionate was studied. Phenotypic analysis of mutants of the EMCP resulted in varying degrees of 3-hydroxypropionate growth. Specifically, a mutant lacking crotonyl-CoA carboxylase/reductase grew similar to wild type with 3- hydroxypropionate. However, mutants lacking subsequent enzymes in the EMCP exhibited 3-hydroxypropionate growth defects that became progressively more severe the ii later the enzyme participated in the EMCP. -
Supplement 1 Overview of Dystonia Genes
Supplement 1 Overview of genes that may cause dystonia in children and adolescents Gene (OMIM) Disease name/phenotype Mode of inheritance 1: (Formerly called) Primary dystonias (DYTs): TOR1A (605204) DYT1: Early-onset generalized AD primary torsion dystonia (PTD) TUBB4A (602662) DYT4: Whispering dystonia AD GCH1 (600225) DYT5: GTP-cyclohydrolase 1 AD deficiency THAP1 (609520) DYT6: Adolescent onset torsion AD dystonia, mixed type PNKD/MR1 (609023) DYT8: Paroxysmal non- AD kinesigenic dyskinesia SLC2A1 (138140) DYT9/18: Paroxysmal choreoathetosis with episodic AD ataxia and spasticity/GLUT1 deficiency syndrome-1 PRRT2 (614386) DYT10: Paroxysmal kinesigenic AD dyskinesia SGCE (604149) DYT11: Myoclonus-dystonia AD ATP1A3 (182350) DYT12: Rapid-onset dystonia AD parkinsonism PRKRA (603424) DYT16: Young-onset dystonia AR parkinsonism ANO3 (610110) DYT24: Primary focal dystonia AD GNAL (139312) DYT25: Primary torsion dystonia AD 2: Inborn errors of metabolism: GCDH (608801) Glutaric aciduria type 1 AR PCCA (232000) Propionic aciduria AR PCCB (232050) Propionic aciduria AR MUT (609058) Methylmalonic aciduria AR MMAA (607481) Cobalamin A deficiency AR MMAB (607568) Cobalamin B deficiency AR MMACHC (609831) Cobalamin C deficiency AR C2orf25 (611935) Cobalamin D deficiency AR MTRR (602568) Cobalamin E deficiency AR LMBRD1 (612625) Cobalamin F deficiency AR MTR (156570) Cobalamin G deficiency AR CBS (613381) Homocysteinuria AR PCBD (126090) Hyperphelaninemia variant D AR TH (191290) Tyrosine hydroxylase deficiency AR SPR (182125) Sepiaterine reductase -
Fifth Southeast Enzyme Conference Saturday, April 5, 2014
Saturday,April5,2014 Georgia State University Atlanta, GA Urban Life Building College of Law 140 Decatur Street Room 220 1 2 Fifth Southeast Enzyme Conference Saturday, April 5, 2014 Sponsored by generous contributions from: Department of Biochemistry, Cellular Department of Chemistry and Molecular Biology Georgia State University University of Tennessee, Knoxville Department of Biology Office of Research Engagement Georgia State University University of Tennessee, Knoxville Additional support provided by College of Arts and Sciences Anonymous donors to the SEC University of Tennessee, Knoxville Foundation Account. To become one yourself, see details on the next page. 3 Southeast Enzyme Conference Fund- 020183 The Chemistry Department at Georgia State University is the lead organizer and founder of the Southeast Enzyme Conference. This conference attracts students, research scientists and faculty members from colleges and universities throughout the southeastern region. With the assistance of the GSU Foundation, conference organizers are seeking charitable contributions to help sustain future conferences. Gifts will be used to cover conference-related expenses such as speaker fees, public relations and marketing, material and supplies, awards and administrative costs. Please consider making a charitable, tax-deductible donation to help achieve the goal. Donor(s) name(s) – First, Middle, Last Name (s) Street Address City State Zip Home Phone Cell Phone Preferred E-mail Address Outright Gift I/we would like to make a gift to the Georgia State University Foundation in the amount of $ _____ My check is enclosed. ____ Charge my credit card upon receipt (see information below). *Please make checks payable to GSU Foundation Annual Pledge I/we would like to pledge a total of $ ______________ to the Georgia State University Foundation over a period of _____ month(s). -
Structural Basis for the Sheddase Function of Human Meprin Β Metalloproteinase at the Plasma Membrane
Structural basis for the sheddase function of human meprin β metalloproteinase at the plasma membrane Joan L. Arolasa, Claudia Broderb, Tamara Jeffersonb, Tibisay Guevaraa, Erwin E. Sterchic, Wolfram Boded, Walter Stöckere, Christoph Becker-Paulyb, and F. Xavier Gomis-Rütha,1 aProteolysis Laboratory, Department of Structural Biology, Molecular Biology Institute of Barcelona, Consejo Superior de Investigaciones Cientificas, Barcelona Science Park, E-08028 Barcelona, Spain; bInstitute of Biochemistry, Unit for Degradomics of the Protease Web, University of Kiel, D-24118 Kiel, Germany; cInstitute of Biochemistry and Molecular Medicine, University of Berne, CH-3012 Berne, Switzerland; dArbeitsgruppe Proteinaseforschung, Max-Planck-Institute für Biochemie, D-82152 Planegg-Martinsried, Germany; and eInstitute of Zoology, Cell and Matrix Biology, Johannes Gutenberg-University, D-55128 Mainz, Germany Edited by Brian W. Matthews, University of Oregon, Eugene, OR, and approved August 22, 2012 (received for review June 29, 2012) Ectodomain shedding at the cell surface is a major mechanism to proteolysis” step within the membrane (1). This is the case for the regulate the extracellular and circulatory concentration or the processing of Notch ligand Delta1 and of APP, both carried out by activities of signaling proteins at the plasma membrane. Human γ-secretase after action of an α/β-secretase (11), and for signal- meprin β is a 145-kDa disulfide-linked homodimeric multidomain peptide peptidase, which removes remnants of the secretory pro- type-I membrane metallopeptidase that sheds membrane-bound tein translocation from the endoplasmic membrane (13). cytokines and growth factors, thereby contributing to inflammatory Recently, human meprin β (Mβ) was found to specifically pro- diseases, angiogenesis, and tumor progression. -
1 Silencing Branched-Chain Ketoacid Dehydrogenase Or
bioRxiv preprint doi: https://doi.org/10.1101/2020.02.21.960153; this version posted February 22, 2020. 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. Silencing branched-chain ketoacid dehydrogenase or treatment with branched-chain ketoacids ex vivo inhibits muscle insulin signaling Running title: BCKAs impair insulin signaling Dipsikha Biswas1, PhD, Khoi T. Dao1, BSc, Angella Mercer1, BSc, Andrew Cowie1 , BSc, Luke Duffley1, BSc, Yassine El Hiani2, PhD, Petra C. Kienesberger1, PhD, Thomas Pulinilkunnil1†, PhD 1Department of Biochemistry and Molecular Biology, Dalhousie Medicine New Brunswick, Saint John, New Brunswick, Canada, 2Department of Physiology and Biophysics, Dalhousie University, Halifax, Nova Scotia, Canada. †Correspondence to Thomas Pulinilkunnil, PhD Department of Biochemistry and Molecular Biology, Faculty of Medicine, Dalhousie University Dalhousie Medicine New Brunswick, 100 Tucker Park Road, Saint John E2L4L5, New Brunswick, Canada. Telephone: (506) 636-6973; Fax: (506) 636-6001; email: [email protected]. 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.02.21.960153; this version posted February 22, 2020. 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 -
Protein Family Classification with Neural Networks
Protein Family Classification with Neural Networks Timothy K. Lee Tuan Nguyen Program in Biomedical Informatics Department of Statistics Stanford University Stanford University [email protected] [email protected] Abstract Understanding protein function from amino acid sequence is a fundamental prob- lem in biology. In this project, we explore how well we can represent biological function through examination of raw sequence alone. Using a large corpus of protein sequences and their annotated protein families, we learn dense vector rep- resentations for amino acid sequences using the co-occurrence statistics of short fragments. Then, using this representation, we experiment with several neural net- work architectures to train classifiers for protein family identification. We show good performance for a multi-class prediction problem with 589 protein family classes. 1 Introduction Next-generation sequencing technologies generate large amounts of biological sequence informa- tion in the form of DNA/RNA sequences. From DNA sequences we also know the amino acid sequences of proteins, which are the fundamental molecules that perform most biological functions. The functionality of a protein is thus encoded in the amino acid sequence and understanding the sequence-function relationship is a major challenge in bioinformatics. Investigating protein func- tional often involves structural studies (crystallography) or biochemical studies, which require time consuming efforts. Protein families are defined to group together proteins that share similar function, and the aim of our project is to predict protein family from raw sequence. We focus on training infor- mative vector representations for protein sequences and investigate various neural network models for the task of predicting a protein’s family. -
Pyruvate-Phosphate Dikinase of Oxymonads and Parabasalia and the Evolution of Pyrophosphate-Dependent Glycolysis in Anaerobic Eukaryotes† Claudio H
EUKARYOTIC CELL, Jan. 2006, p. 148–154 Vol. 5, No. 1 1535-9778/06/$08.00ϩ0 doi:10.1128/EC.5.1.148–154.2006 Copyright © 2006, American Society for Microbiology. All Rights Reserved. Pyruvate-Phosphate Dikinase of Oxymonads and Parabasalia and the Evolution of Pyrophosphate-Dependent Glycolysis in Anaerobic Eukaryotes† Claudio H. Slamovits and Patrick J. Keeling* Canadian Institute for Advanced Research, Botany Department, University of British Columbia, 3529-6270 University Boulevard, Vancouver, British Columbia V6T 1Z4, Canada Received 29 September 2005/Accepted 8 November 2005 In pyrophosphate-dependent glycolysis, the ATP/ADP-dependent enzymes phosphofructokinase (PFK) and pyruvate kinase are replaced by the pyrophosphate-dependent PFK and pyruvate phosphate dikinase (PPDK), respectively. This variant of glycolysis is widespread among bacteria, but it also occurs in a few parasitic anaerobic eukaryotes such as Giardia and Entamoeba spp. We sequenced two genes for PPDK from the amitochondriate oxymonad Streblomastix strix and found evidence for PPDK in Trichomonas vaginalis and other parabasalia, where this enzyme was thought to be absent. The Streblomastix and Giardia genes may be related to one another, but those of Entamoeba and perhaps Trichomonas are distinct and more closely related to bacterial homologues. These findings suggest that pyrophosphate-dependent glycolysis is more widespread in eukaryotes than previously thought, enzymes from the pathway coexists with ATP-dependent more often than previously thought and may be spread by lateral transfer of genes for pyrophosphate-dependent enzymes from bacteria. Adaptation to anaerobic metabolism is a complex process (PPDK), respectively (for a comparison of these reactions, see involving changes to many proteins and pathways of critical reference 21). -
Gent Forms of Metalloproteinases in Hydra
Cell Research (2002); 12(3-4):163-176 http://www.cell-research.com REVIEW Structure, expression, and developmental function of early diver- gent forms of metalloproteinases in Hydra 1 2 3 4 MICHAEL P SARRAS JR , LI YAN , ALEXEY LEONTOVICH , JIN SONG ZHANG 1 Department of Anatomy and Cell Biology University of Kansas Medical Center Kansas City, Kansas 66160- 7400, USA 2 Centocor, Malvern, PA 19355, USA 3 Department of Experimental Pathology, Mayo Clinic, Rochester, MN 55904, USA 4 Pharmaceutical Chemistry, University of Kansas, Lawrence, KS 66047, USA ABSTRACT Metalloproteinases have a critical role in a broad spectrum of cellular processes ranging from the breakdown of extracellular matrix to the processing of signal transduction-related proteins. These hydro- lytic functions underlie a variety of mechanisms related to developmental processes as well as disease states. Structural analysis of metalloproteinases from both invertebrate and vertebrate species indicates that these enzymes are highly conserved and arose early during metazoan evolution. In this regard, studies from various laboratories have reported that a number of classes of metalloproteinases are found in hydra, a member of Cnidaria, the second oldest of existing animal phyla. These studies demonstrate that the hydra genome contains at least three classes of metalloproteinases to include members of the 1) astacin class, 2) matrix metalloproteinase class, and 3) neprilysin class. Functional studies indicate that these metalloproteinases play diverse and important roles in hydra morphogenesis and cell differentiation as well as specialized functions in adult polyps. This article will review the structure, expression, and function of these metalloproteinases in hydra. Key words: Hydra, metalloproteinases, development, astacin, matrix metalloproteinases, endothelin. -
Annotation of Glycolysis and Gluconeogenesis Pathways
A metabolic insight into the Asian citrus psyllid: Annotation of glycolysis and gluconeogenesis pathways Blessy Tamayo, Kyle Kercher, Tom D’Elia, Helen Wiersma-Koch, Surya Saha, Teresa Shippy, Susan J. Brown, and Prashant Hosmani Introduction Glycolysis, as in other animals, is the major metabolic pathway that insects use to extract energy from carbohydrates [1]. This process consists of ten reactions that convert one molecule of glucose into two molecules of pyruvate within the cytosol, generating a net gain of two molecules of ATP. Simple carbohydrates are acquired through the insect diet and processed through glycolysis and the central carbohydrate metabolic steps. Comparative genomic analysis of Apis mellifera, Drosophila melanogaster, and Anopheles gambiae has revealed the presence of genes for metabolic pathways that support dietary habits dependent on sugar-rich substrates ([2]; [3]; [4]; [5]). In addition to processing sugars for energy, glycolysis also serves as a central pathway that serves as both a source of important precursors and destination for key intermediates from many metabolic pathways. Gluconeogenesis is the process through which glucose is synthesized from non- carbohydrate substrates, and is closely associated with glycolysis. Eleven enzymatic reactions occur during gluconeogenesis. Eight of the enzymes involved in the steps also catalyze the reverse reactions in glycolysis and the three remaining enzymes are specific to gluconeogenesis. 1 Gluconeogenesis generated carbohydrates are required as substrate for anaerobic glycolysis, synthesis of chitin, glycoproteins, polyols and glycoside detoxication products [1]. Gluconeogenesis is essential in insects to maintain sugar homeostasis and serves as the initial process towards the generation of glucose disaccharide trehalose, which is the main circulating sugar in the insect hemolymph ([6]; [7]). -
SUPPY Liglucosexlmtdh
US 20100314248A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2010/0314248 A1 Worden et al. (43) Pub. Date: Dec. 16, 2010 (54) RENEWABLE BOELECTRONIC INTERFACE Publication Classification FOR ELECTROBOCATALYTC REACTOR (51) Int. Cl. (76) Inventors: Robert M. Worden, Holt, MI (US); C25B II/06 (2006.01) Brian L. Hassler, Lake Orion, MI C25B II/2 (2006.01) (US); Lawrence T. Drzal, Okemos, GOIN 27/327 (2006.01) MI (US); Ilsoon Lee, Okemo s, MI BSD L/04 (2006.01) (US) C25B 9/00 (2006.01) (52) U.S. Cl. ............... 204/403.14; 204/290.11; 204/400; Correspondence Address: 204/290.07; 427/458; 204/252: 977/734; PRICE HENEVELD COOPER DEWITT & LIT 977/742 TON, LLP 695 KENMOOR, S.E., PO BOX 2567 (57) ABSTRACT GRAND RAPIDS, MI 495.01 (US) An inexpensive, easily renewable bioelectronic device useful for bioreactors, biosensors, and biofuel cells includes an elec (21) Appl. No.: 12/766,169 trically conductive carbon electrode and a bioelectronic inter face bonded to a surface of the electrically conductive carbon (22) Filed: Apr. 23, 2010 electrode, wherein the bioelectronic interface includes cata lytically active material that is electrostatically bound directly Related U.S. Application Data or indirectly to the electrically conductive carbon electrode to (60) Provisional application No. 61/172,337, filed on Apr. facilitate easy removal upon a change in pH, thereby allowing 24, 2009. easy regeneration of the bioelectronic interface. 7\ POWER 1 - SUPPY|- LIGLUCOSEXLMtDH?till pi 6.0 - esses&aaaas-exx-xx-xx-xx-xxxxixax-e- Patent Application Publication Dec. 16, 2010 Sheet 1 of 18 US 2010/0314248 A1 Potential (nV) Patent Application Publication Dec. -
Rubisco Biogenesis and Assembly in Chlamydomonas Reinhardtii Wojciech Wietrzynski
Rubisco biogenesis and assembly in Chlamydomonas reinhardtii Wojciech Wietrzynski To cite this version: Wojciech Wietrzynski. Rubisco biogenesis and assembly in Chlamydomonas reinhardtii. Molecular biology. Université Pierre et Marie Curie - Paris VI, 2017. English. NNT : 2017PA066336. tel- 01770412 HAL Id: tel-01770412 https://tel.archives-ouvertes.fr/tel-01770412 Submitted on 19 Apr 2018 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. PhD Thesis of the Pierre and Marie Curie University (UPMC) Prepared in the Laboratory of Molecular and Membrane Physiology of the Chloroplast, UMR7141, CNRS/UPMC Doctoral school: Life Science Complexity, ED515 Presented by Wojciech Wietrzynski for the grade of Doctor of the Pierre and Marie Curie University Rubisco biogenesis and assembly in Chlamydomonas reinhardtii Defended on the 17th of October 2017 at the Institut of Physico-Chemical Biology in Paris, France Phd Jury: Angela Falciatore, CNRS/UPMC, president Michel Goldschmidt-Clermont, Univeristy of Geneva, reviewer Michael Schroda, University of Kaiserslautern,