DOCSLIB.ORG

The Sequence Pattern for the Glycosylphosphatidyl-Anchor Posttranslational Modification and Its Recognition in Proprotein Sequen

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
The Sequence Pattern for the Glycosylphosphatidyl-Anchor Posttranslational Modification and Its Recognition in Proprotein Sequen BGRS’ 2002 International Program Committee Nikolay Kolchanov, Institute of Cytology and Genetics, Novosibirsk, Russia (Chairman of the Conference) Ralf Hofestadt, University of Bielefeld, Germany (Co-Chairman of the Conference) Philip Bourne, SDSC, San-Diego, USA (Co-Chairman of the Conference) Nickolai Alexandrov, Ceres Inc., Malibu, USA Philipp Bucher, Swiss Institute for Experimental Cancer Research, Switzerland Julio Collado-Vides, National University of Mexico, Mexico Jim Fickett, AstraZeneca, Boston, USA Paolo Frasconi, University of Florence, Firenze, Italy Sergey Goncharov, Sobolev Institute of Mathematics, Novosibirsk, Russia Igor Goryanin, GlaxoSmithKline, UK Charlie Hodgman, GlaxoSmithKline, UK Elza Khusnutdinova, Institute of Biochemistry and Genetics, Ufa Sci. Centre RAS (Ufa), Russia Lev Kisselev, Engelhardt Institute of Molecular Biology, Moscow, Russia Boris Kovalerchuk, Central Washington University (Ellensburg), USA Luciano Milanesi, ITBA, Milan, Italy John Reinitz, The University at Stony Brook, N.Y., USA Akinori Sarai, RIKEN Tsukuba Life Science Center, Tsukuba, Japan Ilya Shindyalov, San Diego Supercomputer Center, USA Rustem Tchuraev, Institute of Biology, Ufa Sci. Centre RAS, Ufa, Russia Masaru Tomita, Institute for Advanced Biosciences, Keio University, Japan Edgar Wingender, GBF, Braunschweig, Germany Nikolay Yankovsky, Institute of General Genetics, Moscow, Russia Lev Zhivotovsky, Institute of General Genetics, Moscow, Russia Local Organizing Committee Dagmara Furman, Institute of Cytology and Genetics, Novosibirsk, Nadya Omelianchuk, Institute of Cytology and Genetics, Novosibirsk, Sergey Lavryushev, Institute of Cytology and Genetics, Novosibirsk, Galina Kiseleva, Institute of Cytology and Genetics, Novosibirsk, Elena Borovskikh , Institute of Cytology and Genetics, Novosibirsk, Nikolay Shkel, Institute of Cytology and Genetics, Novosibirsk, Andrey Kharkevich, Institute of Cytology and Genetics, Novosibirsk, The information about the Conference BGRS’ 2002 is presented at http://www.bionet.nsc.ru/meeting/bgrs2002/ 2 BGRS’ 2002 Our sponsors Organizers Institute of Cytology and Genetics, SB RAS Siberian Branch of the Russian Academy of Sciences Grants INTAS Conference Grant Glaxo Wellcome Inc. Russian Foundation for Basic Research Ministry of Industry, Science and Technologies of the Russian Federation Information sponsors San Diego Supercomputer Center, United States RIKEN Tsukuba Institute Bielefeld University, Faculty of Technology http://www.karger.com/ In Silico Biology Others KWESTA-group: computers, computer accessories, service 3 BGRS’ 2002 CONTENTS COMPARATIVE AND EVOLUTIONARY GENOMICS COMPARATIVE STUDY OF THE ORTHOPOXVIRUS GENES A27L, A56R, B8R, AND C11R Babkin I.V., Mikheev M.V., Shchelkunov S.N......................................................................................... 10 COMPARATIVE STUDY OF THE ORTHOPOXVIRUS GENES B19R AND B29R Mikheev M.V., Feshchenko M.V., Shchelkunov S.N.............................................................................. 13 ANALYSIS OF BACTERIAL RM-SYSTEMS THROUGH GENOME-SCALE ANALYSIS AND RELATED TAXONOMY ISSUES Vandenbogaert M., Makeev V................................................................................................................ 16 FNR/DNR/ANR-REGULON IN GAMMA-PROTEOBACTERIA Gerasimova A.V., Rodionov D.A., Mironov A.A., Gelfand M.S. ............................................................. 19 SEARCH FOR REGULATORY SIGNALS IN GROUPS OF ORTHOLOGOUS GENES OF GAMMA – PROTEOBACTERIA Danilova L.V., Gelfand M.S. ................................................................................................................... 21 TRANSCRIPTIONAL REGULATION OF A NEW BACTERIOCIN-PRODUCING SYSTEM IN STREPTOCOCCUS EQUI. Kotelnikova E.A., Gelfand M.S. .............................................................................................................. 23 SYSTEMATIC PREDICTION OF REGULATORY INTERACTIONS IN THE LACI FAMILY OF TRANSCRIPTIONAL REGULATORS Laikova O.N............................................................................................................................................ 26 PREDICTION OF NEW ENZYME INVOLVED IN PEPTIDOGLYCAN RECYCLING Panina E.M., Vassieva O., Gelfand M.S., Overbeek R. ......................................................................... 29 BIOINFORMATICS APPROACH TO ANALYSIS OF REGULATION OF AROMATIC AMINO ACIDS BIOSYNTHESIS IN BACILLUS/CLOSTRIDIUM GROUP Panina E., Vitrehschak A., Mironov A., Gelfand M................................................................................. 32 REGULATION OF THE HEAT SHOCK RESPONSE OF β-, γ- AND ε-PROTEOBACTERIA Permina E.A., Gelfand M.S. ................................................................................................................... 35 PURINE REGULON OF GAMMA-PROTEOBACTERIA Ravcheyev D.A., Gelfand M.S., Mironov A.A., Rakhmaninova A.B....................................................... 38 COMPUTATIONAL ANALYSIS OF THE BIOTIN REGULON IN BACTERIAL GENOMES Rodionov D.A., Mironov A.A., Gelfand M.S............................................................................................ 40 REGULATION OF BACTERIAL RIBOFLAVIN GENES BY A CONSERVED RNA STRUCTURAL ELEMENT Vitreschak A.G., Rodionov D.A., Mironov A.A., Gelfand M.S. ............................................................... 44 MCMC METHOD FOR IDENTIFICATION OF ALLELIC PATTERNS IN DATA WITH QUANTITATIVELY DESCRIBABLE PHENOTYPIC FEATURES Favorov A.V., Ochs M.F.......................................................................................................................... 47 S-RNASES IN THREE PLANT FAMILIES WITH GAMETOPHYTIC SELF-INCOMPATIBILITY: PHYLOGENY RELATED TO A PUTATIVE NUMBER OF S-LOCI IN ROSACEAE Alexeyenko A.V. ..................................................................................................................................... 50 SURVEY OF HUMAN NON-SYNONYMOUS SNPs Ramensky V.E., Bork P., Sunyaev S.R.................................................................................................. 53 COMPUTATIONAL BIOLOGY AND ANALYSIS OF HUMAN POPULATIONS WITH USE OF DNA MARKERS Zhivotovsky L.A. ..................................................................................................................................... 56 4 BGRS’ 2002 THE CHANNEL CAPACITY OF SELECTIVE BREEDING: ULTIMATE LIMITS ON THE AMOUNT OF INFORMATION MAINTAINABLE IN THE GENOME Watkins C.J.C.H. .................................................................................................................................... 58 METHOD OF HORIZONTAL GENE TRANSFER DETERMINATION USING PHYLOGENETIC DATA Lyubetsky V.A., V’yugin V.V................................................................................................................... 61 MINIMAL TREES IN PHYLOGENETIC SPACES Ivanov A.O., Tuzhilin A.A........................................................................................................................ 64 COMPARATIVE ANALYSIS OF CODING SEQUENCES OF APETALA1 HOMOLOGUES Omelyanchuk N.A., Gusev V.D., Nemytikova L.A., Aksenovich A.V. .................................................... 67 SYSTEM COMPUTATIONAL BIOLOGY: ANALYSIS AND MODELLING OF GENE NETWORKS AND METABOLIC PATHWAYS GENENET SYSTEM: ITS STATUS IN 2002 Ananko E.A., Podkolodny N.L., Ignatieva E.V., Podkolodnaya O.A., Stepanenko I.L., Kolchanov N.A.72 MOLECULAR-GENETICAL MECHANISMS OF ADIPOCYTE REGULATION: REPRESENTATION IN GENENET DATABASE Proscura A.L., Ignatieva E.V. ................................................................................................................. 76 GENE NETWORK OF GLUTATHIONE HOMEOSTASIS: A RESPONSE TO OXIDATIVE STRESS Kudryavtseva A.N., Stepanenko I.L. ...................................................................................................... 80 MOLECULAR GENETIC MECHANISMS REGULATING THE THYROID SYSTEM: DESCRIPTION IN THE TRRD AND GENENET DATABASES Suslov V.V., Ignat’eva E.V...................................................................................................................... 83 INTERPRETATION OF GENE NETWORKS IN THE CONTEXT OF ANOKHIN’S THEORY OF FUNCTIONAL SYSTEMS Suslov V.V., Vityaev E.E., Ignatieva E.V. ............................................................................................... 87 ORGANIZATION OF THE GENE NETWORK OF APOPTOSIS Stepanenko I.L., Grigor’ev S.A............................................................................................................... 91 GENE NETWORK OF MACROPHAGE ACTIVATION UNDER THE ACTION OF INTERFERON-GAMMA AND LIPOPOLYSACCARIDES Nedosekina E.A., Ananko E.A................................................................................................................ 94 GENE NETWORK ON CELL CYCLE CONTROL Turnaev I.I., Podkolodnaya О.А. ............................................................................................................ 97 VARIABILITY OF FLOWER DEVELOPMENT GENE NETWORKS IN SEVERAL PLANT SPECIES Aksenovich A.V. ................................................................................................................................... 101 NEGATIVE REGULATION OF PLANT PHOTOMORPHOGENESIS Smirnova O.G., Ibragimova S.S., Shavrukov Yu.N., Stepanenko I.L. ................................................. 104 A HYBRID NETWORK OF NITROGEN-FIXING NODULES: INTERGENOMIC INTERACTIONS OF BACTERIA AND HOST PLANT Ibragimova S.S., Smirnova O.G., Shavrukov Yu.N., Stepanenko I.L. ................................................
Load more

Recommended publications
  • Pneumoniae CG43
    YjcC, a c-di-GMP Phosphodiesterase Protein, Regulates the Oxidative Stress Response and Virulence of Klebsiella pneumoniae CG43 Ching-Jou Huang1, Zhe-Chong Wang2, Hsi-Yuan Huang3, Hsien-Da Huang2,3, Hwei-Ling Peng1,2* 1 Institute of Molecular Medicine and Biological Technology, National Chiao Tung University, Hsin Chu, Taiwan, Republic of China, 2 Department of Biological Science and Technology, National Chiao Tung University, Hsin Chu, Taiwan, Republic of China, 3 Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsin Chu, Taiwan, Republic of China Abstract This study shows that the expression of yjcC, an in vivo expression (IVE) gene, and the stress response regulatory genes soxR, soxS, and rpoS are paraquat inducible in Klebsiella pneumoniae CG43. The deletion of rpoS or soxRS decreased yjcC expression, implying an RpoS- or SoxRS-dependent control. After paraquat or H2O2 treatment, the deletion of yjcC reduced bacterial survival. These effects could be complemented by introducing the DyjcC mutant with the YjcC-expression plasmid pJR1. The recombinant protein containing only the YjcC-EAL domain exhibited phosphodiesterase (PDE) activity; overexpression of yjcC has lower levels of cyclic di-GMP. The yjcC deletion mutant also exhibited increased reactive oxygen species (ROS) formation, oxidation damage, and oxidative stress scavenging activity. In addition, the yjcC deletion reduced capsular polysaccharide production in the bacteria, but increased the LD50 in mice, biofilm formation, and type 3 fimbriae major pilin MrkA production. Finally, a comparative transcriptome analysis showed 34 upregulated and 29 downregulated genes with the increased production of YjcC. The activated gene products include glutaredoxin I, thioredoxin, heat shock proteins, chaperone, and MrkHI, and proteins for energy metabolism (transporters, cell surface structure, and transcriptional regulation).
    [Show full text]
  • Download Via Github on RNA-Seq and Chip-Seq Data Analysis and the University of And/Or Bioconductor [33–35, 38–40]
    Kumka and Bauer BMC Genomics (2015) 16:895 DOI 10.1186/s12864-015-2162-4 RESEARCH ARTICLE Open Access Analysis of the FnrL regulon in Rhodobacter capsulatus reveals limited regulon overlap with orthologues from Rhodobacter sphaeroides and Escherichia coli Joseph E. Kumka and Carl E. Bauer* Abstract Background: FNR homologues constitute an important class of transcription factors that control a wide range of anaerobic physiological functions in a number of bacterial species. Since FNR homologues are some of the most pervasive transcription factors, an understanding of their involvement in regulating anaerobic gene expression in different species sheds light on evolutionary similarity and differences. To address this question, we used a combination of high throughput RNA-Seq and ChIP-Seq analysis to define the extent of the FnrL regulon in Rhodobacter capsulatus and related our results to that of FnrL in Rhodobacter sphaeroides and FNR in Escherichia coli. Results: Our RNA-seq results show that FnrL affects the expression of 807 genes, which accounts for over 20 % of the Rba. capsulatus genome. ChIP-seq results indicate that 42 of these genes are directly regulated by FnrL. Importantly, this includes genes involved in the synthesis of the anoxygenic photosystem. Similarly, FnrL in Rba. sphaeroides affects 24 % of its genome, however, only 171 genes are differentially expressed in common between two Rhodobacter species, suggesting significant divergence in regulation. Conclusions: We show that FnrL in Rba. capsulatus activates photosynthesis while in Rba. sphaeroides FnrL regulation reported to involve repression of the photosystem. This analysis highlights important differences in transcriptional control of photosynthetic events and other metabolic processes controlled by FnrL orthologues in closely related Rhodobacter species.
    [Show full text]
  • The Escherichia Coli Narl Receiver Domain Regulates Transcription
    Katsir et al. BMC Microbiology (2015) 15:174 DOI 10.1186/s12866-015-0502-9 RESEARCH ARTICLE Open Access The Escherichia coli NarL receiver domain regulates transcription through promoter specific functions Galit Katsir1,3,4, Michael Jarvis2,5, Martin Phillips1, Zhongcai Ma2,6 and Robert P. Gunsalus2,3* Abstract Background: The Escherichia coli response regulator NarL controls transcription of genes involved in nitrate respiration during anaerobiosis. NarL consists of two domains joined by a linker that wraps around the interdomain interface. Phosphorylation of the NarL N-terminal receiver domain (RD) releases the, otherwise sequestered, C-terminal output domain (OD) that subsequently binds specific DNA promoter sites to repress or activate gene expression. The aim of this study is to investigate the extent to which the NarL OD and RD function independently to regulate transcription, and the affect of the linker on OD function. Results: NarL OD constructs containing different linker segments were examined for their ability to repress frdA-lacZ or activate narG-lacZ reporter fusion genes. These in vivo expression assays revealed that the NarL OD, in the absence or presence of linker helix α6, constitutively repressed frdA-lacZ expression regardless of nitrate availability. However, the presence of the linker loop α5-α6reversedthisrepressionandalsoshowedimpairedDNAbindingin vitro.The OD alone could not activate narG-lacZ expression; this activity required the presence of the NarL RD. A footprint assay demonstrated that the NarL OD only partially bound recognition sites at the narG promoter, and the binding affinity was increased by the presence of the phosphorylated RD. Analytical ultracentrifugation used to examine domain oligomerization showed that the NarL RD forms dimers in solution while the OD is monomeric.
    [Show full text]
  • Pleuropneumoniae Gene Expression
    Global Effects of Catecholamines on Actinobacillus pleuropneumoniae Gene Expression Lu Li, Zhuofei Xu, Yang Zhou, Lili Sun, Ziduo Liu, Huanchun Chen, Rui Zhou* Division of Animal Infectious Diseases in State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China Abstract Bacteria can use mammalian hormones to modulate pathogenic processes that play essential roles in disease development. Actinobacillus pleuropneumoniae is an important porcine respiratory pathogen causing great economic losses in the pig industry globally. Stress is known to contribute to the outcome of A. pleuropneumoniae infection. To test whether A. pleuropneumoniae could respond to stress hormone catecholamines, gene expression profiles after epinephrine (Epi) and norepinephrine (NE) treatment were compared with those from untreated bacteria. The microarray results showed that 158 and 105 genes were differentially expressed in the presence of Epi and NE, respectively. These genes were assigned to various functional categories including many virulence factors. Only 18 genes were regulated by both hormones. These genes included apxIA (the ApxI toxin structural gene), pgaB (involved in biofilm formation), APL_0443 (an autotransporter adhesin) and genes encoding potential hormone receptors such as tyrP2, the ygiY-ygiX (qseC-qseB) operon and narQ-narP (involved in nitrate metabolism). Further investigations demonstrated that cytotoxic activity was enhanced by Epi but repressed by NE in accordance with apxIA gene expression changes. Biofilm formation was not affected by either of the two hormones despite pgaB expression being affected. Adhesion to host cells was induced by NE but not by Epi, suggesting that the hormones affect other putative adhesins in addition to APL_0443. This study revealed that A.
    [Show full text]
  • Prokaryotic Genome Regulation: a Revolutionary Paradigm
    No. 9] Proc. Jpn. Acad., Ser. B 88 (2012) 485 Review Prokaryotic genome regulation: A revolutionary paradigm † By Akira ISHIHAMA*1, (Communicated by Tasuku HONJO, M.J.A.) Abstract: After determination of the whole genome sequence, the research frontier of bacterial molecular genetics has shifted to reveal the genome regulation under stressful conditions in nature. The gene selectivity of RNA polymerase is modulated after interaction with two groups of regulatory proteins, 7 sigma factors and 300 transcription factors. For identification of regulation targets of transcription factors in Escherichia coli, we have developed Genomic SELEX system and subjected to screening the binding sites of these factors on the genome. The number of regulation targets by a single transcription factor was more than those hitherto recognized, ranging up to hundreds of promoters. The number of transcription factors involved in regulation of a single promoter also increased to as many as 30 regulators. The multi-target transcription factors and the multi-factor promoters were assembled into complex networks of transcription regulation. The most complex network was identified in the regulation cascades of transcription of two master regulators for planktonic growth and biofilm formation. Keywords: transcription regulation, genome regulation, transcription factor, regulation network, genomic SELEX, Escherichia coli developed and employed to reveal the expression of 1. Introduction the whole set of genes on the genome (the tran- In the early stage of molecular biology, Esche- scriptome) under a given culture condition. The high- richia coli served as a model organism of biochemical, throughput microarray has made a break-through biophysical, molecular genetic and biotechnological for providing transcription patterns of the whole set studies.
    [Show full text]
  • Full Text Document (Pdf)
    Kent Academic Repository Full text document (pdf) Citation for published version Dolata, Katarzyna M. and Montero, Isabel Guerrero and Miller, Wayne and Sievers, Susanne and Sura, Thomas and Wolff, Christian and Schlüter, Rabea and Riedel, Katharina and Robinson, Colin (2019) Far-reaching cellular consequences of tat deletion in Escherichia coli revealed by comprehensive proteome analyses. Microbiological Research, 218 . pp. 97-107. ISSN 0944-5013. DOI https://doi.org/10.1016/j.micres.2018.10.008 Link to record in KAR https://kar.kent.ac.uk/70187/ Document Version Publisher pdf Copyright & reuse Content in the Kent Academic Repository is made available for research purposes. Unless otherwise stated all content is protected by copyright and in the absence of an open licence (eg Creative Commons), permissions for further reuse of content should be sought from the publisher, author or other copyright holder. Versions of research The version in the Kent Academic Repository may differ from the final published version. Users are advised to check http://kar.kent.ac.uk for the status of the paper. Users should always cite the published version of record. Enquiries For any further enquiries regarding the licence status of this document, please contact: [email protected] If you believe this document infringes copyright then please contact the KAR admin team with the take-down information provided at http://kar.kent.ac.uk/contact.html Microbiological Research 218 (2019) 97–107 Contents lists available at ScienceDirect Microbiological Research journal homepage: www.elsevier.com/locate/micres Far-reaching cellular consequences of tat deletion in Escherichia coli revealed by comprehensive proteome analyses T Katarzyna M.
    [Show full text]
  • 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).
    [Show full text]
  • Transcription Regulation of the Expression of the Plasmid Encoded Toxin of Enteroaggregative Escherichia Coli
    TRANSCRIPTION REGULATION OF THE EXPRESSION OF THE PLASMID ENCODED TOXIN OF ENTEROAGGREGATIVE ESCHERICHIA COLI by Jacob Henry Duddy A thesis submitted to The University of Birmingham for the degree of MASTER OF PHILOSOPHY February 2013 School of Biosciences The University of Birmingham University of Birmingham Research Archive e-theses repository This unpublished thesis/dissertation is copyright of the author and/or third parties. The intellectual property rights of the author or third parties in respect of this work are as defined by The Copyright Designs and Patents Act 1988 or as modified by any successor legislation. Any use made of information contained in this thesis/dissertation must be in accordance with that legislation and must be properly acknowledged. Further distribution or reproduction in any format is prohibited without the permission of the copyright holder. Abstract The pathogenic properties of Enteroaggregative Escherichia coli strain 042 results from the synchronised expression of virulence factors, which include the Plasmid Encoded Toxin. Pet is a member of the serine protease autotransporter of the Enterobacteriaceae family and contributes to infection by cleaving α-fodrin, disrupting the actin cytoskeleton of host cells. The expression of Pet is induced by global transcription factor CRP with further enhancement by the nucleoid associated protein Fis. This study identifies the residues of RNA polymerase, Fis and CRP required for the induction of transcription, thereby clarifying the mechanism of activation employed by the transcription factors. Fis activates transcription from the Fis binding site via a direct interaction with RNA polymerase, facilitated by protein specific determinants. This interaction is dependent on the position of the Fis binding site on the DNA and it subsequent orientation on the helical face of the DNA.
    [Show full text]
  • CTP Synthase Sulfolobus Solfataricus
    CTP Synthase from Sulfolobus solfataricus Master Thesis in Biochemistry Iben Havskov Lauritsen June 2010 University of Copenhagen, Department of Biology Supervisor: Kaj Frank Jensen PREFACE This work represents my master thesis in Biochemistry at the University of Copenhagen. Most of the work was carried out at the Department of Biological Chemistry, Institute of Molecular Biology, University of Copenhagen under supervision by Kaj Frank Jensen. Crystallization was carried out at Centre for Crystallographic Studies, Department of Chemistry, University of Copenhagen under supervision by Eva Johansson. The preliminary work I did on solving the structure was done at Department of Chemistry, Technical University of Denmark under supervision by Pernille Harris. She later finished solving the structure, and a paper on the work is about to be submitted. I thank Eva Johansson and Pernille Harris for teaching me how to make protein crystals and how to solve the structure of them. That has been a very exciting part of the project for me. I also thank Lise Schack for endless help and good company in the laboratory. Finally I thank Kaj Frank Jensen for encouraging supervision. _____________________________________________ Iben Havskov Lauritsen June 2010, Copenhagen ABSTRACT CTP synthase from the extreme thermoacidophilic archaeon Sulfolobus solfataricus has been investigated in several ways in this study. CTP synthase is responsible for de novo synthesis of CTP from UTP. The first part of the reaction is the deamination of glutamine to generate ammonia for the second part of the reaction, the CTP synthesis. This work is mostly focused on the kinetics of the first part of the reaction.
    [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]
  • Supplementary Table S1: Early Sporulation Genes the Early
    Supplementary Table S1: Early sporulation Genes The early sporulation genes are listed. The average pattern (log2ratio) is plotted upon transfer to YPD (which was followed for 5, 20 and 40 minutes after the transfer). The genes in each group, along with a one line description, are indicated. Template genes used to create this group are: ZIP1, HOP1, HOP2 and SPO16. Average 1 expression: -1 SNC1; YAL030W Synaptobrevin (v-SNARE) homolog present on post-Golgi vesicles ACS1; FUN44; YAL054C Acetyl-CoA synthetase RFA1; BUF2; (RPA1); FUN3; SRR1; YAR007C DNA replication factor A, 69K subunit, binds single-stranded DNA NTH2; YBR0106; YBR001C Putative secondary neutral trehalase (alpha, alpha-trehalase), may catalyze conversion of trehalose to glucose MUM2; YBR0514; YBR057C; SPOT8 Protein required for premeiotic DNA synthesis and sporulation YBR090C; YBR0811b Protein of unknown function YBR113W; YBR0908e Protein of unknown function NPL4; YBR1231; YBR170C Nuclear pore protein UMP1; YBR1234; YBR173C Proteasome maturation factor chaperone involved in proteasome assembly YBR184W; YBR1306 Protein of unknown function PCH2; YBR1308; YBR186W Protein required for cell cycle arrest at the pachytene stage of meiosis in a zip1 mutant, has similarity to Rpt5p andNSF vesicular fusion protein and other members of the AAA family of ATPases POP4; YBR1725; YBR257W Protein component of both the RNase MRP and RNase P ribonucleoproteins, which are involved in rRNA and tRNAprocessing respectively YBR280C; YBR2017 Protein with similarity to Srm1p/Prp20p PRD1; YCL434; YCL057W
    [Show full text]
  • Phonology and Grammar of Modern West Frisian, with Phonetic Texts And
    SO CORNELL UNIVERSITY LIBRARY ENGLISH COLLECTION THE GIFT OF JAMES MORGAN HART PROFESSOR OF ENGLISH « Cornell University Library PF 1421.S61 Phonology and grammar of modern west Fri 3 1924 006 850 881 Cornell University Library The original of this book is in the Cornell University Library. There are no known copyright restrictions in the United States on the use of the text. http://www.archive.org/details/cu31924006850881 PREFACE On the publication of this book, it is a pleasant duty for me to express my sincere thanks, in the first place to the Philological Society for having considered it worthy of inclusion among its issues, and in the second place to the authorities of the Clarendon Press for the excellent manner in which it has been printed. But most of all I feel indebted to Dr. W. A. Craigie, President of the Philological Society, whose advice and assistance have made the publication of this work possible. He has revised the English of my manuscript, and has translated into English such Frisian words as are explained in the Phonology and Grammar. And lastly he has kindly lent a helping hand in the correction of the proof-sheets. May his example be followed by many in showing an interest in the study of my native language, which has been overlooked and neglected for too long a time. P. SIPMA. Sneek, Fkiesland, April, 1913. : : . : CONTENTS PAGE Introduction . ... 1 PART I. PHONOLOGY I Table of Frisian Speech-sounds . 8 Vowels General Remarks 9 Vowels in detail . .... 9 Diphthongs and Triphthongs General Remarks . .... .11 Diphthongs in detail ...
    [Show full text]