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Intrinsically Disordered Proteins As Crucial Constituents of Cellular Aqueous Two Phase Systems and Coacervates ⇑ Vladimir N
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Elsevier - Publisher Connector FEBS Letters 589 (2015) 15–22 journal homepage: www.FEBSLetters.org Hypothesis Intrinsically disordered proteins as crucial constituents of cellular aqueous two phase systems and coacervates ⇑ Vladimir N. Uversky a,b,c,d, , Irina M. Kuznetsova d,e, Konstantin K. Turoverov d,e, Boris Zaslavsky f a Department of Molecular Medicine and USF Health Byrd Alzheimer’s Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA b Institute for Biological Instrumentation, Russian Academy of Sciences, Pushchino, Moscow Region, Russian Federation c Biology Department, Faculty of Science, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia d Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russian Federation e St. Petersburg State Polytechnical University, St. Petersburg, Russian Federation f AnalizaDx Inc., 3615 Superior Ave., Suite 4407B, Cleveland, OH 44114, USA article info abstract Article history: Here, we hypothesize that intrinsically disordered proteins (IDPs) serve as important drivers of the Received 17 August 2014 intracellular liquid–liquid phase separations that generate various membrane-less organelles. This Revised 10 October 2014 hypothesis is supported by the overwhelming abundance of IDPs in these organelles. Assembly and Accepted 19 November 2014 disassembly of these organelles are controlled by changes in the concentrations of IDPs, their post- Available online 29 November 2014 translational modifications, binding of specific partners, and changes in the pH and/or temperature Edited by A. Valencia of the solution. -
A Putative Cystathionine Beta-Synthase Homolog of Mycolicibacterium Smegmatis Is Involved in De Novo Cysteine Biosynthesis
University of Arkansas, Fayetteville ScholarWorks@UARK Theses and Dissertations 5-2020 A Putative Cystathionine Beta-Synthase Homolog of Mycolicibacterium smegmatis is Involved in de novo Cysteine Biosynthesis Saroj Kumar Mahato University of Arkansas, Fayetteville Follow this and additional works at: https://scholarworks.uark.edu/etd Part of the Cell Biology Commons, Molecular Biology Commons, and the Pathogenic Microbiology Commons Citation Mahato, S. K. (2020). A Putative Cystathionine Beta-Synthase Homolog of Mycolicibacterium smegmatis is Involved in de novo Cysteine Biosynthesis. Theses and Dissertations Retrieved from https://scholarworks.uark.edu/etd/3639 This Thesis is brought to you for free and open access by ScholarWorks@UARK. It has been accepted for inclusion in Theses and Dissertations by an authorized administrator of ScholarWorks@UARK. For more information, please contact [email protected]. A Putative Cystathionine Beta-Synthase Homolog of Mycolicibacterium smegmatis is Involved in de novo Cysteine Biosynthesis A thesis submitted in partial fulfillment of the requirement for the degree of Master of Science in Cell and Molecular Biology by Saroj Kumar Mahato Purbanchal University Bachelor of Science in Biotechnology, 2016 May 2020 University of Arkansas This thesis is approved for recommendation to the Graduate Council. ___________________________________ Young Min Kwon, Ph.D. Thesis Director ___________________________________ ___________________________________ Suresh Thallapuranam, Ph.D. Inés Pinto, Ph.D. Committee Member Committee Member ABSTRACT Mycobacteria include serious pathogens of humans and animals. Mycolicibacterium smegmatis is a non-pathogenic model that is widely used to study core mycobacterial metabolism. This thesis explores mycobacterial pathways of cysteine biosynthesis by generating and study of genetic mutants of M. smegmatis. Published in vitro biochemical studies had revealed three independent routes to cysteine synthesis in mycobacteria involving separate homologs of cysteine synthase, namely CysK1, CysK2, and CysM. -
Dissertation Inês Silva ITQB.Pdf
The Role of Small RNAs and Ribonucleases in the Control of Gene Expression in Salmonella Typhimurium Inês de Jesus de Almeida e Silva Insert here an image with rounded corners Dissertation presented to obtain the Ph.D degree in Biology Instituto de Tecnologia Química e Biológica | Universidade Nova de Lisboa Oeiras, December, 2012 The Role of Small RNAs and Ribonucleases in the Control of Gene Expression in Salmonella Typhimurium Inês de Jesus de Almeida e Silva Dissertation presented to obtain the Ph.D degree in Biology Instituto de Tecnologia Química e Biológica Universidade Nova de Lisboa Oeiras, December, 2012 Financial Support from Fundação para a Ciência e Tecnologia (FCT) – Ph.D: grant - SFRH / BD / 43211 / 2008. Work performed at: Control of Gene Expression Laboratory Instituto de Tecnologia Química e Biológica Av. da República (EAN) 2781-901 Oeiras – Portugal Tel: +351-21-4469548 Fax: +351-21-4469549 Supervisor : Professora Doutora Cecília Maria Pais de Faria de Andrade Arraiano – Investigadora Coordenadora, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa. (Head of the Laboratory of Control of Gene Expression, where the work of this Dissertation was performed) Co-supervisor : Doutora Sandra Cristina de Oliveira Viegas – Investigadora Pós-Doutorada, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa. (Post-doc Fellow in the Laboratory of Control of Gene Expression, where the work of this Dissertation was performed) President of the Jury : Doutora Claudina Amélia Marques Rodrigues Pousada – Professora Catedrática Convidada do Instituto de Tecnologia Química e Biológica da Universidade Nova de Lisboa, por delegação; iii Examiners: Professor Doutor Iñigo Lasa Uzcudun – Head of Microbial Biofilm Research Group, Instituto de Agrobiotecnología, Pamplona (Principal Examiner). -
Generated by SRI International Pathway Tools Version 25.0, Authors S
An online version of this diagram is available at BioCyc.org. Biosynthetic pathways are positioned in the left of the cytoplasm, degradative pathways on the right, and reactions not assigned to any pathway are in the far right of the cytoplasm. Transporters and membrane proteins are shown on the membrane. Periplasmic (where appropriate) and extracellular reactions and proteins may also be shown. Pathways are colored according to their cellular function. Gcf_005222025Cyc: Escherichia coli 121 Cellular Overview Connections between pathways are omitted for legibility. pro a dicarboxylate a dicarboxylate an amino putrescine putrescine thiosulfate a hexose 6- glycine betaine glycine succinate γ-butyrobetaine L-ascorbate acid a dipeptide a dipeptide a dipeptide poly-β-1,6- 1-(β-D O-acetyl-L-serine O-acetyl-L-serine spermidine spermidine D-mannitol galactitol sulfate phosphate phosphate phosphate betaine Fe 3+ an amino an amino D-cellobiose an aromatic an aromatic a dipeptide 6 phosphate phosphate N-acetyl-D- thiamine cys cys spermidine spermidine protoheme 2+ citrate N -(D-fructosyl)-L-lysine L-proline betaine glutamate L-proline betaine L-carnitine acid an amino acid an amino an amino an amino an amino a tripeptide a tripeptide a tripeptide amino acid amino acid ribofuranosyl) (R)- putrescine Fe N-acetyl-D- molybdate phosphate a hydroxamate 3+ 3+ arbutin shikimate enterobactin 2-oxoglutarate N 6 -(D-psicosyl)-L-lysine D-sorbitol D-glucosamine D-mannitol galactitol N-acetylneuraminate N-acetylneuraminate sulfate sulfate sulfate glycine betaine -
(Helianthus Annuus L.) Plastidial Lipoyl Synthases Genes Expression In
Impact of sunflower (Helianthus annuus L.) plastidial lipoyl synthases genes expression in glycerolipids composition of transgenic Arabidopsis plants Raquel Martins-Noguerol, Antonio Javier Moreno-Pérez, Acket Sebastien, Manuel Adrián Troncoso-Ponce, Rafael Garcés, Brigitte Thomasset, Joaquín Salas, Enrique Martínez-Force To cite this version: Raquel Martins-Noguerol, Antonio Javier Moreno-Pérez, Acket Sebastien, Manuel Adrián Troncoso- Ponce, Rafael Garcés, et al.. Impact of sunflower (Helianthus annuus L.) plastidial lipoyl synthases genes expression in glycerolipids composition of transgenic Arabidopsis plants. Scientific Reports, Nature Publishing Group, 2020, 10, pp.3749. 10.1038/s41598-020-60686-z. hal-02881038 HAL Id: hal-02881038 https://hal.archives-ouvertes.fr/hal-02881038 Submitted on 25 Jun 2020 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. www.nature.com/scientificreports OPEN Impact of sunfower (Helianthus annuus L.) plastidial lipoyl synthases genes expression in glycerolipids composition of transgenic Arabidopsis plants Raquel Martins-Noguerol1,2, Antonio Javier Moreno-Pérez 1,2, Acket Sebastien2, Manuel Adrián Troncoso-Ponce2, Rafael Garcés1, Brigitte Thomasset2, Joaquín J. Salas1 & Enrique Martínez-Force 1* Lipoyl synthases are key enzymes in lipoic acid biosynthesis, a co-factor of several enzyme complexes involved in central metabolism. -
Crystallographic Snapshots of Sulfur Insertion by Lipoyl Synthase
Crystallographic snapshots of sulfur insertion by lipoyl synthase Martin I. McLaughlina,b,1, Nicholas D. Lanzc, Peter J. Goldmana, Kyung-Hoon Leeb, Squire J. Bookerb,c,d, and Catherine L. Drennana,e,f,2 aDepartment of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139; bDepartment of Chemistry, The Pennsylvania State University, University Park, PA 16802; cDepartment of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802; dHoward Hughes Medical Institute, The Pennsylvania State University, University Park, PA 16802; eDepartment of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139; and fHoward Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139 Edited by Vern L. Schramm, Albert Einstein College of Medicine, Bronx, NY, and approved July 5, 2016 (received for review March 8, 2016) Lipoyl synthase (LipA) catalyzes the insertion of two sulfur atoms substrate and at an intermediate stage in the reaction, just after at the unactivated C6 and C8 positions of a protein-bound octanoyl insertion of the C6 sulfur atom but before sulfur insertion at C8. chain to produce the lipoyl cofactor. To activate its substrate for sulfur insertion, LipA uses a [4Fe-4S] cluster and S-adenosylmethio- Results nine (AdoMet) radical chemistry; the remainder of the reaction The crystal structure of LipA from M. tuberculosis was de- mechanism, especially the source of the sulfur, has been less clear. termined to 1.64-Å resolution by iron multiwavelength anoma- One controversial proposal involves the removal of sulfur from a lous dispersion phasing (Table S1). The overall fold of LipA consists second (auxiliary) [4Fe-4S] cluster on the enzyme, resulting in de- of a (β/α)6 partial barrel common to most AdoMet radical enzymes struction of the cluster during each round of catalysis. -
Proteome Cold-Shock Response in the Extremely Acidophilic Archaeon, Cuniculiplasma Divulgatum
microorganisms Article Proteome Cold-Shock Response in the Extremely Acidophilic Archaeon, Cuniculiplasma divulgatum Rafael Bargiela 1 , Karin Lanthaler 1,2, Colin M. Potter 1,2 , Manuel Ferrer 3 , Alexander F. Yakunin 1,2, Bela Paizs 1,2, Peter N. Golyshin 1,2 and Olga V. Golyshina 1,2,* 1 School of Natural Sciences, Bangor University, Deiniol Rd, Bangor LL57 2UW, UK; [email protected] (R.B.); [email protected] (K.L.); [email protected] (C.M.P.); [email protected] (A.F.Y.); [email protected] (B.P.); [email protected] (P.N.G.) 2 Centre for Environmental Biotechnology, Bangor University, Deiniol Rd, Bangor LL57 2UW, UK 3 Systems Biotechnology Group, Department of Applied Biocatalysis, CSIC—Institute of Catalysis, Marie Curie 2, 28049 Madrid, Spain; [email protected] * Correspondence: [email protected]; Tel.: +44-1248-388607; Fax: +44-1248-382569 Received: 27 April 2020; Accepted: 15 May 2020; Published: 19 May 2020 Abstract: The archaeon Cuniculiplasma divulgatum is ubiquitous in acidic environments with low-to-moderate temperatures. However, molecular mechanisms underlying its ability to thrive at lower temperatures remain unexplored. Using mass spectrometry (MS)-based proteomics, we analysed the effect of short-term (3 h) exposure to cold. The C. divulgatum genome encodes 2016 protein-coding genes, from which 819 proteins were identified in the cells grown under optimal conditions. In line with the peptidolytic lifestyle of C. divulgatum, its intracellular proteome revealed the abundance of proteases, ABC transporters and cytochrome C oxidase. From 747 quantifiable polypeptides, the levels of 582 proteins showed no change after the cold shock, whereas 104 proteins were upregulated suggesting that they might be contributing to cold adaptation. -
SUPLEMENTARY MATERIAL 1) Comparative Analysis of The
1 SUPLEMENTARY MATERIAL 2 1) Comparative analysis of the different differential expression methods applied to the 3 transcriptome of Vanilla planifolia Jacks. 4 5 6 7 8 9 10 11 12 13 14 2dpi 10dpi 15 16 Supplemental Figure S1. Venn diagram showing the comparison of the differentially 17 expressed unigenes obtained with the methods DESeq2, EdgeR, NOISeq, and DESeq. At the 18 center of the diagram we observed that the EdgeR method comprises the great majority of 19 genes determined by the other methods. The right panel corresponds to 2 dpi, while the left 20 panel corresponds to 10 dpi. 21 22 23 24 25 26 2) Global expression profiles in response to infection caused by Fusarium 27 oxysporum f. sp. vanillae in vanilla. 28 . 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 2dpi 10dpi 51 Supplemental Figure S2. Heat map that contrasts the global vanilla response to 52 Fusarium oxysporum f. sp. vanillae. On the right we observe the early response 53 (2dpi); while in the left panel it presents the response to 10dpi. All differentially 54 expressed unigenes are included. 55 56 3) Expression profiles related to biotic stress, in the late response (10dpi) of 57 vanilla to Fusarium oxysporum f. sp. vanillae 58 59 60 61 62 63 64 65 66 67 68 69 70 71 Supplemental Figure S3. Heat map indicating the expression profiles of the annotated DEG 72 unigenes, corresponding to 10dpi. The numbers in the figure correspond to different 73 categories of gene ontology, as described below: 25 C1-metabolism, 11 lipid metabolism, 3 74 minor CHO metabolism, 13 amino acid metabolism, 16 secondary metabolism, 26 misc, 17 75 hormone metabolism, 30 signalling, 31 cell, 23 nucleotide metabolism, 27 RNA, 28 DNA, 76 33 development, 24 Biodegradation of Xenobiotics, 18 Co-factor and vitamine metabolism, 77 35 not assigned, 34 transport, 29 protein, 20 stress, 2 major CHO metabolism, 10 cell wall. -
Supplemental Methods
Supplemental Methods: Sample Collection Duplicate surface samples were collected from the Amazon River plume aboard the R/V Knorr in June 2010 (4 52.71’N, 51 21.59’W) during a period of high river discharge. The collection site (Station 10, 4° 52.71’N, 51° 21.59’W; S = 21.0; T = 29.6°C), located ~ 500 Km to the north of the Amazon River mouth, was characterized by the presence of coastal diatoms in the top 8 m of the water column. Sampling was conducted between 0700 and 0900 local time by gently impeller pumping (modified Rule 1800 submersible sump pump) surface water through 10 m of tygon tubing (3 cm) to the ship's deck where it then flowed through a 156 µm mesh into 20 L carboys. In the lab, cells were partitioned into two size fractions by sequential filtration (using a Masterflex peristaltic pump) of the pre-filtered seawater through a 2.0 µm pore-size, 142 mm diameter polycarbonate (PCTE) membrane filter (Sterlitech Corporation, Kent, CWA) and a 0.22 µm pore-size, 142 mm diameter Supor membrane filter (Pall, Port Washington, NY). Metagenomic and non-selective metatranscriptomic analyses were conducted on both pore-size filters; poly(A)-selected (eukaryote-dominated) metatranscriptomic analyses were conducted only on the larger pore-size filter (2.0 µm pore-size). All filters were immediately submerged in RNAlater (Applied Biosystems, Austin, TX) in sterile 50 mL conical tubes, incubated at room temperature overnight and then stored at -80oC until extraction. Filtration and stabilization of each sample was completed within 30 min of water collection. -
Structure of Soybean Serine Acetyltransferase
THE JOURNAL OF BIOLOGICAL CHEMISTRY VOL. 288, NO. 51, pp. 36463–36472, December 20, 2013 Published in the U.S.A. Structure of Soybean Serine Acetyltransferase and Formation of the Cysteine Regulatory Complex as a Molecular Chaperone* Received for publication, October 14, 2013, and in revised form, November 4, 2013 Published, JBC Papers in Press, November 13, 2013, DOI 10.1074/jbc.M113.527143 Hankuil Yi‡1, Sanghamitra Dey§1, Sangaralingam Kumaran¶, Soon Goo Leeʈ, Hari B. Krishnan**, and Joseph M. Jezʈ2 From the ‡Department of Biological Sciences, Chungnam National University, 220 Gung-Dong, Yuseong-Gu, Daejeon 305-764,Korea, the §Department of Biological Sciences, Presidency University, Kolkata, West Bengal 700073, India, the ¶Council of Scientific and Industrial Research, Institute of Microbial Technology, Sector 39-A, Chandigarh 160036, India, the ʈDepartment of Biology, Washington University, St. Louis, Missouri 63130, and the **Plant Genetics Research Unit, United States Department of Agriculture- Agricultural Research Service, Department of Agronomy, University of Missouri, Columbia, Missouri 65211 Background: Serine acetyltransferase (SAT) catalyzes the limiting step in cysteine biosynthesis. Results: Analysis of soybean SAT provides insight into catalysis and protein-protein interactions. Downloaded from Conclusion: Key structural features are required for catalysis and formation of a stable macromolecular complex. Significance: A new role for protein complex formation in plant cysteine biosynthesis is proposed. Serine acetyltransferase (SAT) catalyzes the limiting reaction sis plays a central role in fixing inorganic sulfur from the envi- in plant and microbial biosynthesis of cysteine. In addition to its ronment into the metabolic precursor for cellular thiol-con- http://www.jbc.org/ enzymatic function, SAT forms a macromolecular complex with taining compounds (3–6). -
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). -
Ribonuclease E Organizes the Protein Interactions in the Escherichia Coli RNA Degradosome
Downloaded from genesdev.cshlp.org on September 26, 2021 - Published by Cold Spring Harbor Laboratory Press Ribonuclease E organizes the protein interactions in the Escherichia coli RNA degradosome Nathalie F. Vanzo,1 Yeun Shan Li,2 Be´atrice Py,2,3 Erwin Blum,2 Christopher F. Higgins,2,4 Lelia C. Raynal,1 Henry M. Krisch,1 and Agamemnon J. Carpousis1,5 1Laboratoire de Microbiologie et Ge´ne´tique Mole´culaire, UPR 9007, Centre National de la Recherche Scientifique (CNRS), 31062 Toulouse Cedex, France; 2Nuffield Department of Clinical Biochemistry and Imperial Cancer Research Fund Laboratories, Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK The Escherichia coli RNA degradosome is the prototype of a recently discovered family of multiprotein machines involved in the processing and degradation of RNA. The interactions between the various protein components of the RNA degradosome were investigated by Far Western blotting, the yeast two-hybrid assay, and coimmunopurification experiments. Our results demonstrate that the carboxy-terminal half (CTH) of ribonuclease E (RNase E) contains the binding sites for the three other major degradosomal components, the DEAD-box RNA helicase RhlB, enolase, and polynucleotide phosphorylase (PNPase). The CTH of RNase E acts as the scaffold of the complex upon which the other degradosomal components are assembled. Regions for oligomerization were detected in the amino-terminal and central regions of RNase E. Furthermore, polypeptides derived from the highly charged region of RNase E, containing the RhlB binding site, stimulate RhlB activity at least 15-fold, saturating at one polypeptide per RhlB molecule. A model for the regulation of the RhlB RNA helicase activity is presented.