The Evolution of Enzyme Function in the Isomerases
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Functional Assignments in the Enolase Superfamily: Investigations of Two Divergent Groups of D-Galacturonate Dehydratases and Galactarate Dehydratase-Iii
FUNCTIONAL ASSIGNMENTS IN THE ENOLASE SUPERFAMILY: INVESTIGATIONS OF TWO DIVERGENT GROUPS OF D-GALACTURONATE DEHYDRATASES AND GALACTARATE DEHYDRATASE-III BY FIONA PATRICIA GRONINGER-POE i DISSERTATION Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Biochemistry in the Graduate College of the University of Illinois at Urbana-Champaign, 2014 Urbana, Illinois Doctoral Committee: Professor John A. Gerlt, Chair Professor John E. Cronan, Jr. Associate Professor Rutilo Fratti Associate Professor Raven H. Huang ABSTRACT More than a decade after the genomic age, full genome sequencing is cost-effective and fast, allowing for the deposit of an ever increasing number of DNA sequences. New fields have arisen from this availability of genomic information, and the way we think about biochemistry and enzymology has been transformed. Unfortunately, there is no robust method for accurately determining the functions of enzymes encoded by these sequences that matches the speed in which genomes are deposited into public databases. Functional assignment of enzymes remains of utmost importance in understanding microbial metabolism and has applications in agriculture by examining bacterial plant pathogen metabolism and additionally in human health by providing metabolic context to the human gut microbiome. To aid in the functional identification of proteins, enzymes can be grouped into superfamilies which share common structural motifs as well as mechanistic features. To this end, the enolase superfamily is an excellent model system for functional assignment because more than half of the members still lack functional identification. Structurally, these enzymes contain substrate specificity residues in the N-terminal capping domain and catalytic residues in the C-terminal barrel domain. -
Reprogramming of Metabolism by the Arabidopsis Thaliana Bzip11 Tran- Scription Factor
Reprogramming of metabolism by the Arabidopsis thaliana bZIP11 tran- scription factor Jingkun Ma Layout, cover & invitation design: Jingkun Ma Printing: Offpage ISBN: 978-94-6182-112-6 The study presented in this thesis was performed in the group of Molecular Plant Physiology, Utrecht University, Padualaan 8, 3584CH, Utrecht, The Netherlands. The presented work was supported by Centre for BioSystems Genomics (CBSG). Reprogramming of metabolism by the Arabidopsis thaliana bZIP11 tran- scription factor Herprogrammering van het metabolisme door de Arabidopsis thaliana bZIP11 transcriptie factor (met een samenvatting in het Nederlands) Proefschrift ter verkrijging van de graad van doctor aan de Universiteit Utrecht op gezag van de rector magnificus, prof. dr. G. J. van der Zwaan, ingevolge het besluit van het college voor promoties in het openbaar te verdedigen op vrijdag 11 mei 2012 des mid- dags te 12.45 uur door Jingkun Ma geboren op 24 januari 1982 te Xiangfan, P.R.China Promoter: Prof.dr. J.C.M.Smeekens Co-promoter: Dr. S.J.Hanson CONTENTS Chapter 1 Introduction Sugar sensingChapter and signaling 3 networks 1 Chapter 2 Metabolic reprogramming mediated by bZIP11 37 ChapterProtoplast 3 The functiontranscriptomics of S1/C bZIPs in analysis gene regulation reveals the overlapping 77 and distinct functions of S1/C bZIP transcription factors in Chapter 4 The overlapping functiongene of T6Pregulation signal, SnRK1 and S1/C bZIPs 99 Chapter 5 Summarizing discussion 123 Summary in Dutch 131 AcknowledgementsJingkun Ma, Micha Hanssen, Johannes -
Letters to Nature
letters to nature Received 7 July; accepted 21 September 1998. 26. Tronrud, D. E. Conjugate-direction minimization: an improved method for the re®nement of macromolecules. Acta Crystallogr. A 48, 912±916 (1992). 1. Dalbey, R. E., Lively, M. O., Bron, S. & van Dijl, J. M. The chemistry and enzymology of the type 1 27. Wolfe, P. B., Wickner, W. & Goodman, J. M. Sequence of the leader peptidase gene of Escherichia coli signal peptidases. Protein Sci. 6, 1129±1138 (1997). and the orientation of leader peptidase in the bacterial envelope. J. Biol. Chem. 258, 12073±12080 2. Kuo, D. W. et al. Escherichia coli leader peptidase: production of an active form lacking a requirement (1983). for detergent and development of peptide substrates. Arch. Biochem. Biophys. 303, 274±280 (1993). 28. Kraulis, P.G. Molscript: a program to produce both detailed and schematic plots of protein structures. 3. Tschantz, W. R. et al. Characterization of a soluble, catalytically active form of Escherichia coli leader J. Appl. Crystallogr. 24, 946±950 (1991). peptidase: requirement of detergent or phospholipid for optimal activity. Biochemistry 34, 3935±3941 29. Nicholls, A., Sharp, K. A. & Honig, B. Protein folding and association: insights from the interfacial and (1995). the thermodynamic properties of hydrocarbons. Proteins Struct. Funct. Genet. 11, 281±296 (1991). 4. Allsop, A. E. et al.inAnti-Infectives, Recent Advances in Chemistry and Structure-Activity Relationships 30. Meritt, E. A. & Bacon, D. J. Raster3D: photorealistic molecular graphics. Methods Enzymol. 277, 505± (eds Bently, P. H. & O'Hanlon, P. J.) 61±72 (R. Soc. Chem., Cambridge, 1997). -
Exploring the Chemistry and Evolution of the Isomerases
Exploring the chemistry and evolution of the isomerases Sergio Martínez Cuestaa, Syed Asad Rahmana, and Janet M. Thorntona,1 aEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom Edited by Gregory A. Petsko, Weill Cornell Medical College, New York, NY, and approved January 12, 2016 (received for review May 14, 2015) Isomerization reactions are fundamental in biology, and isomers identifier serves as a bridge between biochemical data and ge- usually differ in their biological role and pharmacological effects. nomic sequences allowing the assignment of enzymatic activity to In this study, we have cataloged the isomerization reactions known genes and proteins in the functional annotation of genomes. to occur in biology using a combination of manual and computa- Isomerases represent one of the six EC classes and are subdivided tional approaches. This method provides a robust basis for compar- into six subclasses, 17 sub-subclasses, and 245 EC numbers cor- A ison and clustering of the reactions into classes. Comparing our responding to around 300 biochemical reactions (Fig. 1 ). results with the Enzyme Commission (EC) classification, the standard Although the catalytic mechanisms of isomerases have already approach to represent enzyme function on the basis of the overall been partially investigated (3, 12, 13), with the flood of new data, an integrated overview of the chemistry of isomerization in bi- chemistry of the catalyzed reaction, expands our understanding of ology is timely. This study combines manual examination of the the biochemistry of isomerization. The grouping of reactions in- chemistry and structures of isomerases with recent developments volving stereoisomerism is straightforward with two distinct types cis-trans in the automatic search and comparison of reactions. -
Putative Genes Involved in Saikosaponin Biosynthesis in Bupleurum Species
Int. J. Mol. Sci. 2013, 14, 12806-12826; doi:10.3390/ijms140612806 OPEN ACCESS International Journal of Molecular Sciences ISSN 1422-0067 www.mdpi.com/journal/ijms Review Putative Genes Involved in Saikosaponin Biosynthesis in Bupleurum Species Tsai-Yun Lin 1,*, Chung-Yi Chiou 1 and Shu-Jiau Chiou 2 1 Institute of Bioinformatics and Structural Biology & Department of Life Science, National Tsing Hua University, No. 101, Sec. 2, Kuang Fu Rd., Hsinchu 30013, Taiwan; E-Mail: [email protected] 2 Biomedical Technology and Device Research Laboratories, Industrial Technology Research Institute, No. 321, Sec. 2, Kuang Fu Rd., Hsinchu 30011, Taiwan; E-Mail: [email protected] * Author to whom correspondence should be addressed; E-Mail: [email protected]; Tel.: +886-3-574-2758; Fax: +886-3-571-5934. Received: 22 April 2013; in revised form: 13 June 2013 / Accepted: 14 June 2013 / Published: 19 June 2013 Abstract: Alternative medicinal agents, such as the herb Bupleurum, are increasingly used in modern medicine to supplement synthetic drugs. First, we present a review of the currently known effects of triterpene saponins-saikosaponins of Bupleurum species. The putative biosynthetic pathway of saikosaponins in Bupleurum species is summarized, followed by discussions on identification and characterization of genes involved in the biosynthesis of saikosaponins. The purpose is to provide a brief review of gene extraction, functional characterization of isolated genes and assessment of expression patterns of genes encoding enzymes in the process of saikosaponin production in Bupleurum species, mainly B. kaoi. We focus on the effects of MeJA on saikosaponin production, transcription patterns of genes involved in biosynthesis and on functional depiction. -
The Structure of Neurospora Crassa 3-Carboxy-Cis,Cis-Muconate Lactonizing Enzyme, a  Propeller Cycloisomerase
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Elsevier - Publisher Connector Structure, Vol. 10, 483–492, April, 2002, 2002 Elsevier Science Ltd. All rights reserved. PII S0969-2126(02)00744-X The Structure of Neurospora crassa 3-Carboxy-cis,cis-Muconate Lactonizing Enzyme, a  Propeller Cycloisomerase Tommi Kajander,1 Michael C. Merckel,1 ing the structural basis for different alternatives for catal- Andrew Thompson,2 Ashley M. Deacon,3 ysis in MLEs could therefore aid in understanding and Paul Mazur,4 John W. Kozarich,4,6 engineering enzymes for degradation of xenobiotic pol- and Adrian Goldman1,5 lutants, such as fluoroaromatics. 1 Institute of Biotechnology MLEs convert cis,cis-muconates to muconolactones Research Program in Structural Biology in soil microbes as part of the -ketoadipate pathway. and Biophysics This aerobic catabolic pathway converts aromatics, such University of Helsinki as the breakdown products of lignin, through catechol FIN-00014 Helsinki and protocatechuate to citric acid cycle intermediates. Finland The two major branches of the -ketoadipate pathway 2 EMBL are the catechol branch, with cis,cis-muconate lactoniz- Grenoble Outstation ing enzymes, and the protocatechuate branch (Figure 38024 Grenoble 1), with carboxy-cis,cis-muconate lactonizing enzymes France (CMLEs). 3 Stanford Synchrotron Radiation Laboratory The evolutionary origins of these enzymes are surpris- Menlo Park, California 94025 ingly divergent, both in terms of sequence similarity and 4 Merck Research Laboratories functional properties (Table 1). Three different classes of Rahway, New Jersey 07065 lactonizing enzymes can be distinguished. The bacterial MLEs contain an unusual TIM barrel [3] and are closely related to mandelate racemase [4]. -
Syntenic Gene and Genome Duplication Drives Diversification of Plant Secondary Metabolism and Innate Immunity in Flowering Plants
Genomics 4.0 - Syntenic Gene and Genome Duplication Drives Diversification of Plant Secondary Metabolism and Innate Immunity in Flowering Plants - Advanced Pattern Analytics in Duplicate Genomes - Johannes A. Hofberger Thesis committee Promotor Prof. Dr M. Eric Schranz Professor of Experimental Biosystematics Wageningen University Other members Prof. Dr Bart P.H.J. Thomma, Wageningen University Prof. Dr Berend Snel, Utrecht University Dr Klaas Vrieling, Leiden University Dr Gabino F. Sanchez, Wageningen University This research was conducted under the auspices of the Graduate School of Experimental Plant Sciences. Genomics 4.0 - Syntenic Gene and Genome Duplication Drives Diversification of Plant Secondary Metabolism and Innate Immunity in Flowering Plants - Advanced Pattern Analytics in Duplicate Genomes - Johannes A. Hofberger Thesis submitted in fulfilment of the requirements for the degree of doctor at Wageningen University by the authority of the Rector Magnificus Prof. Dr M.J. Kropff, in the presence of the Thesis Committee appointed by the Academic Board to be defended in public on Monday 18 May 2015 at 4 p.m. in the Aula. Johannes A. Hofberger Genomics 4.0 - Syntenic Gene and Genome Duplication Drives Diversification of Plant Secondary Metabolism and Innate Immunity in Flowering Plants 83 pages. PhD thesis, Wageningen University, Wageningen, NL (2015) With references, with summaries in Dutch and English ISBN: 978-94-6257-314-7 PROPOSITIONS 1. Ohnolog over-retention following ancient polyploidy facilitated diversification of the glucosinolate biosynthetic inventory in the mustard family. (this thesis) 2. Resistance protein conserved in structurally stable parts of plant genomes confer pleiotropic effects and expanded functions in plant innate immunity. (this thesis) 3. -
SI Appendix Index 1
SI Appendix Index Calculating chemical attributes using EC-BLAST ................................................................................ 2 Chemical attributes in isomerase reactions ............................................................................................ 3 Bond changes …..................................................................................................................................... 3 Reaction centres …................................................................................................................................. 5 Substrates and products …..................................................................................................................... 6 Comparative analysis …........................................................................................................................ 7 Racemases and epimerases (EC 5.1) ….................................................................................................. 7 Intramolecular oxidoreductases (EC 5.3) …........................................................................................... 8 Intramolecular transferases (EC 5.4) ….................................................................................................. 9 Supporting references …....................................................................................................................... 10 Fig. S1. Overview …............................................................................................................................ -
Mortierellaceae Phylogenomics and Tripartite Plant-Fungal-Bacterial Symbiosis of Mortierella Elongata
MORTIERELLACEAE PHYLOGENOMICS AND TRIPARTITE PLANT-FUNGAL-BACTERIAL SYMBIOSIS OF MORTIERELLA ELONGATA By Natalie Vandepol A DISSERTATION Submitted to Michigan State University in partial fulfillment of the requirements for the degree of Microbiology & Molecular Genetics – Doctor of Philosophy 2020 ABSTRACT MORTIERELLACEAE PHYLOGENOMICS AND TRIPARTITE PLANT-FUNGAL-BACTERIAL SYMBIOSIS OF MORTIERELLA ELONGATA By Natalie Vandepol Microbial promotion of plant growth has great potential to improve agricultural yields and protect plants against pathogens and/or abiotic stresses. Soil fungi in Mortierellaceae are non- mycorrhizal plant associates that frequently harbor bacterial endosymbionts. My research focused on resolving the Mortierellaceae phylogeny and on characterizing the effect of Mortierella elongata and its bacterial symbionts on Arabidopsis thaliana growth and molecular functioning. Early efforts to classify Mortierellaceae were based on morphology, but phylogenetic studies with ribosomal DNA (rDNA) markers have demonstrated conflicting taxonomic groupings and polyphyletic genera. In this study, I applied two approaches: low coverage genome (LCG) sequencing and high-throughput targeted amplicon sequencing to generate multi-locus sequence data. I combined these datasets to generate a well-supported genome-based phylogeny having broad sampling depth from the amplicon dataset. Resolving the Mortierellaceae phylogeny into monophyletic groups led to the definition of 14 genera, 7 of which are newly proposed. Mortierellaceae are broadly considered plant associates, but the underlying mechanisms of association are not well understood. In this study, I focused on the symbiosis between M. elongata, its endobacteria, and A. thaliana. I measured aerial plant growth and seed production and used transcriptomics to characterize differentially expressed plant genes (DEGs) while varying fungal treatments. M. elongata was shown to promote aerial plant growth and affect seed production independent of endobacteria. -
Functional and Physiological Discovery in the Mannonate Dehydratase Subgroup of the Enolase Superfamily
FUNCTIONAL AND PHYSIOLOGICAL DISCOVERY IN THE MANNONATE DEHYDRATASE SUBGROUP OF THE ENOLASE SUPERFAMILY BY DANIEL JOSEPH WICHELECKI DISSERTATION Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Biochemistry in the Graduate College of the University of Illinois at Urbana-Champaign, 2014 Urbana, Illinois Doctoral Committee: Professor John Gerlt, Chair Professor John Cronan Professor Scott Silverman Professor Wilfred van der Donk ABSTRACT In the current post-genomic world, the exponential amassing of protein sequences is overwhelming the scientific community’s ability to experimentally assign each protein’s function. The use of automated, homology-based annotations has allowed a reprieve from this efflux of data, but has led to widespread misannotation and nonannotation in protein sequence databases. This dissertation details the functional and physiological characterization of the mannonate dehydratase subgroup (ManD) of the enolase superfamily (ENS). The outcome affirms the dangers of homology-based annotations while discovering novel metabolic pathways. Furthermore, the experimental verification of these pathways ( in vitro and in vivo ) has provided a platform to test the general strategies for improved functional and metabolic characterization being developed by the Enzyme Function Initiative (EFI). Prior to this study, one member of the ManD subgroup had been characterized and was shown to dehydrate D-mannonate to 2-keto-3-deoxy-D-gluconate. Forty-two additional members of the ManD, selected from across the sequence space of the subgroup, were screened for activity and kinetic constants were determined. The members of the once isofunctional subgroup were found to differ in both catalytic efficiency and substrate specificity: 1) high 3 4 -1 -1 efficiency (k cat /K M = 10 to 10 M s ) dehydration of D-mannonate, 2) low efficiency (k cat /K M = 10 1 to 10 2 M-1s-1) dehydration of D-mannonate and/or D-gluconate, and 3) no-activity with either D-mannonate or D-gluconate (or any other acid sugar tested). -
Proquest Dissertations
RICE UNIVERSITY Investigation of Triterpene Biosynthesis in Arabidopsis thaliana by Mariya D. Kolesnikova A THESIS SUBMITTED IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE Doctor of Philosophy APPROVED, THESIS COMMITTEE: Seircni P. T. Matsuda, Professor, Department Chair Department of Chemistry Department of Biochemistry and Cell Biology JU- Ronald J. Parry, Professor Department of Chemistry Department of Biochemistry and Cell Biology UL Jonatnan Silberg, ^gs&tant Profasabr Department of Biochemistry and Cell Biology HOUSTON, TEXAS May 2008 UMI Number: 3362344 INFORMATION TO USERS The quality of this reproduction is dependent upon the quality of the copy submitted. Broken or indistinct print, colored or poor quality illustrations and photographs, print bleed-through, substandard margins, and improper alignment can adversely affect reproduction. In the unlikely event that the author did not send a complete manuscript and there are missing pages, these will be noted. Also, if unauthorized copyright material had to be removed, a note will indicate the deletion. UMI® UMI Microform 3362344 Copyright 2009 by ProQuest LLC All rights reserved. This microform edition is protected against unauthorized copying under Title 17, United States Code. ProQuest LLC 789 East Eisenhower Parkway P.O. Box 1346 Ann Arbor, Ml 48106-1346 ii ABSTRACT Investigation of Triterpene Biosynthesis in Arabidopsis thaliana By Mariya D. Kolesnikova This thesis describes functional characterization of three oxidosqualene cyclase genes (Atlg78955, At3g45130, and At4gl5340) from the model plant Arabidopsis thaliana that encode enzymes with novel catalytic functions. Oxidosqualene cyclases are a family of membrane proteins that convert the acyclic substrate oxidosqualene into polycyclic products with many chiral centers. The complex mechanistic pathways and relevant catalytic motifs can be elucidated through judicious applications of mutagenesis, heterologous expression in combination with a genome mining approach, and protein modeling. -
Crystal Structure Analysis of a Bacterial Lysozyme at Very High Resolution
The crystal structure of a bacterial lysozyme at atomic resolution Dissertation zur Erlangung des akademischen Grades doctor rerum naturalium (Dr. rer. nat.) vorgelegt dem Rat der Chemisch-Geowissenschaftlichen Fakultät der Friedrich-Schiller-Universität Jena von Diplom-Chemikerin Astrid Rau geboren am 01.06.1974 in Saalfeld Gutachter: 1. Prof. Dr. R. Hilgenfeld 2. Prof. Dr. D. Klemm Tag der öffentlichen Verteidigung: 01.06.2005 TABLE OF CONTENTS 1. INTRODUCTION 1 1.1 Milestones in lysozyme research 1 1.2 Definition and classification of lysozymes 5 1.3 Catalytic mechanisms of lysozymes 7 1.4 Chalaropsis-type lysozymes 9 1.5 Cellosyl – a Ch-type lysozyme from Streptomyces coelicolor 12 1.7 Aim of the project 13 2. MATERIALS AND METHODS 14 2.1 Materials 14 2.1.1 Proteins 14 2.1.2 Carbohydrates 14 2.1.3 Chemicals 15 2.1.4 Crystallisation screens 15 2.1.5 Dialysing tools, assays, crystallisation materials and cryo-tools 15 2.1.6 Laboratory equipment and synchrotron facilities 16 2.2 Methods 17 2.2.1 Determination of protein purity 17 2.2.2 Determination of protein concentration 18 2.2.3 Dialysis 18 2.2.4 Sample concentration 18 2.2.5 Crystallisation 18 2.2.6 Heavy atom and polysaccharide soaks 19 2.2.7 Cryocooling 20 2.2.8 Data acquisition and processing 20 2.2.8.1 Native data collection on the monoclinic crystal form 21 2.2.8.2 Native data collection on the hexagonal crystal form 22 2.2.8.3 MAD data collection 22 2.2.8.4 Data collection on heavy-atom derivatised crystals 24 2.2.8.5 Collection and processing of atomic-resolution data 25 I 2.2.9 Phase determination 27 2.2.9.1 Molecular replacement 28 2.2.9.2 Multiple wavelength anomalous dispersion 29 2.2.9.3 Multiple isomorphous replacement with anomalous scattering 29 2.2.10 Model building and electron-density maps 31 2.2.11 Structure refinement 33 2.2.12 Validation of model quality 35 3.