DOCSLIB.ORG

Complex Portal 2018: Extended Content and Enhanced Visualization Tools for Macromolecular Complexes Birgit H.M

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Complex Portal 2018: Extended Content and Enhanced Visualization Tools for Macromolecular Complexes Birgit H.M D550–D558 Nucleic Acids Research, 2019, Vol. 47, Database issue Published online 24 October 2018 doi: 10.1093/nar/gky1001 Complex Portal 2018: extended content and enhanced visualization tools for macromolecular complexes Birgit H.M. Meldal 1,*, Hema Bye-A-Jee1, Luka´sˇ Gajdosˇ 2, Zuzana Hammerova´ 2, Aneta Hora´ckovˇ a´ 2, Filip Melicher2, Livia Perfetto1, Daniel Pokorny´ 2, Milagros Rodriguez Lopez1,Alzbˇ etaˇ Turkov¨ a´ 2, Edith D. Wong3, Zengyan Xie4, Elisabeth Barrera Casanova 1, Noemi del-Toro1, Maximilian Koch1,5, Pablo Porras1, Henning Hermjakob1,6 and Sandra Orchard1 1European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK, 2Department of Biochemistry and National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno-Bohunice, Czech Republic, 3Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305-5477, USA, 4Chongqing Key Laboratory on Big Data for Bio Intelligence, Chongqing University of Posts and Telecommunications, No. 2 Chongwen Road, Nan’an District, Chongqing 400065, China, 5Novartis Institutes for BioMedical Research (NIBR), Basel, Canton of Basel-Stadt, Switzerland and 6State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Life Omics, Beijing 102206, China Received September 13, 2018; Revised October 05, 2018; Editorial Decision October 08, 2018; Accepted October 09, 2018 ABSTRACT INTRODUCTION The Complex Portal (www.ebi.ac.uk/complexportal) All biological processes rely on the interaction of proteins is a manually curated, encyclopaedic database that with other cellular components and in many cases these pro- collates and summarizes information on stable, teins function as part of macromolecular complexes. These complexes may be composed only of proteins or also con- macromolecular complexes of known function. It / captures complex composition, topology and func- tain nucleic acids and or small molecules. Complexes can be stable or transient in nature and vary in their function tion and links out to a large range of domain-specific and composition depending on the tissue type, developmen- resources that hold more detailed data, such as PDB tal stage and biological process. Many complexes have been or Reactome. We have made several significant im- well characterized by experimental methods while the exis- provements since our last update, including improv- tence or composition of other complexes has been inferred ing compliance to the FAIR data principles by pro- from related evidences. viding complex-specific, stable identifiers that in- The Complex Portal (www.ebi.ac.uk/complexportal)isa clude versioning. Protein complexes are now avail- manually curated, encyclopaedic resource that summarizes able from 20 species for download in standards- all functional aspects of stable macromolecular complexes compliant formats such as PSI-XML, MI-JSON and (1). Since our last update, we have improved the data struc- ComplexTAB or can be accessed via an improved ture by providing more data download formats, new iden- REST API. A component-based JS front-end frame- tifiers and expanded our data content in terms of both, the number of complexes curated and the species represented in work has been implemented to drive a new website the resource. We have significantly improved interoperabil- and this has allowed the use of APIs from linked ity with other resources, such as the Gene Ontology (2), and services to import and visualize information such updated the website to provide better data access and more as the 3D structure of protein complexes, its role visualization options, all making the Complex Portal more in reactions and pathways and the co-expression of fully compliant with the FAIR principles of Findability, Ac- complex components in the tissues of multi-cellular cessibility, Interoperability and Reusability (3). organisms. A first draft of the complete complex- The characterization of the complex composition in a ome of Saccharomyces cerevisiae is now available model organism can be used to predict the existence of sim- to browse and download. ilar complexes in other species (4). Such inferences can con- tribute to our understanding of evolutionary development *To whom correspondence should be addressed. Tel: +44 1223 494107; Email: [email protected] C The Author(s) 2018. Published by Oxford University Press on behalf of Nucleic Acids Research. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. Nucleic Acids Research, 2019, Vol. 47, Database issue D551 at the molecular level. We are currently developing a tool Quality control that can predict orthologous complexes in other species as All entries in the Complex Portal are manually annotated well as find homologous complexes that have already been and carefully checked by a second curator before publica- curated in the Complex Portal. tion. Entries are standards compliant, for example using stable identifiers (UniProt for proteins, ChEBI for small CONTENT molecules (9), RNAcentral for ncRNAs (10) and controlled Curation update vocabularies such as the Gene Ontology and PSI-MI ontol- ogy (11). Curators work to a detailed curation manual that The working definition of a protein complex is that it should is constantly updated and reviewed as we discover new data contain two or more macromolecules for which there is evi- concepts. A summary of our curation practices is available dence (experimental or inferred) that these molecules stably via the <Documentation> tile on the public website; this interact with each other and have a demonstrated molec- enables users to understand the annotation process. We have ular function. Each entry (Figure 1) describes the compo- implemented new syntax checks that are run before each sition, topology and function of a single complex from a release cycle, making the data more robust to human error. defined species and links out to external databases that pro- Following strict rules and quality control checks means that vide domain-specific information of the complex, such as our entries are consistent and of high quality. structural details from PDB (5) or the role of the complex in metabolic reactions or signalling pathways in Reactome (6). A complex is uniquely defined by its protein components us- Complex identifiers and versions ing canonical UniProt identifiers, i.e. the protein sequence The new complex-specific stable identifiers have a version selected as the reference sequence in a UniProtKB/Swiss- number that can be incrementally increased to indicate a Prot entry. Isoform-specific complex variants are only cre- major change to the underlying record, thus making the re- ated when the function of the complex is specific for a given source more fully compliant with the FAIR standard. Iden- isoform. The Cyclin L-CDK11 complexes provide interest- tifiers are of the type: CPX-xxxx.y, where xxxx is the run- ing examples where this is the case (CPX-341, CPX-343, ning number and y the version. The previously published CPX-344, CPX-347). Complex participants are described EBI-xxxxxxx identifiers are retained as secondary identi- using the UniProtKB identifiers for post-processed chains fiers and can still be retrieved as they remain in the down- when complexes are formed only by a specific cleavage load files and are indexed in the webservice. The new iden- product, for example the amyloid-beta protein 40/42 het- tifiers also provide an easy distinction from IntAct exper- erodimer (CPX-1062). Post-transcriptional modifications imental evidences with which they previously shared an are described only if they are essential to the formation of identifier space. A complex version will be incrementally in- the complex as, for example, in the case of the formation of creased if the composition of the complex has changed, for the SMAD1 homotrimer (CPX-144). example additional participants have been added. A change The Complex Portal currently focuses on curating stable in stoichiometry will currently not trigger reversioning. protein complexes from a limited number of model organ- If a complex has been obsoleted without replacement, the isms to provide a reference from which complexes in other accession number (AC) will no longer be searchable in the species can be inferred and the evolutionary development of current release files or the website but will remain accessi- a conserved functional unit can be traced. As of release 219 ble from the archive on our ftp site (ftp://ftp.ebi.ac.uk/pub/ (8 October 2018), 2472 complexes have been curated and databases/intact/complex/current). If a complex is split into released. several new entries the original AC will be retained as a sec- Recent curation priorities have included: ondary AC on the new complexes and, similarly, if two com- plexes are merged, the original AC from one complex be- a. Mammalian complexes with available 3D structures. comes a secondary AC on the retained and updated com- This is a long-term program in collaboration with plex. The website only displays the current AC whilst pre- CEITEC and PDBe. 297 curated mammalian complexes vious entry versions and obsoleted ACs are stored in the have crystal structures, 248
Load more

Recommended publications
  • Enhanced Representation of Natural Product Metabolism in Uniprotkb
    H OH metabolites OH Article Diverse Taxonomies for Diverse Chemistries: Enhanced Representation of Natural Product Metabolism in UniProtKB Marc Feuermann 1,* , Emmanuel Boutet 1,* , Anne Morgat 1 , Kristian B. Axelsen 1, Parit Bansal 1, Jerven Bolleman 1 , Edouard de Castro 1, Elisabeth Coudert 1, Elisabeth Gasteiger 1,Sébastien Géhant 1, Damien Lieberherr 1, Thierry Lombardot 1,†, Teresa B. Neto 1, Ivo Pedruzzi 1, Sylvain Poux 1, Monica Pozzato 1, Nicole Redaschi 1 , Alan Bridge 1 and on behalf of the UniProt Consortium 1,2,3,4,‡ 1 Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, CMU, 1 Michel-Servet, CH-1211 Geneva 4, Switzerland; [email protected] (A.M.); [email protected] (K.B.A.); [email protected] (P.B.); [email protected] (J.B.); [email protected] (E.d.C.); [email protected] (E.C.); [email protected] (E.G.); [email protected] (S.G.); [email protected] (D.L.); [email protected] (T.L.); [email protected] (T.B.N.); [email protected] (I.P.); [email protected] (S.P.); [email protected] (M.P.); [email protected] (N.R.); [email protected] (A.B.); [email protected] (U.C.) 2 European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK 3 Protein Information Resource, University of Delaware, 15 Innovation Way, Suite 205, Newark, DE 19711, USA 4 Protein Information Resource, Georgetown University Medical Center, 3300 Whitehaven Street NorthWest, Suite 1200, Washington, DC 20007, USA * Correspondence: [email protected] (M.F.); [email protected] (E.B.); Tel.: +41-22-379-58-75 (M.F.); +41-22-379-49-10 (E.B.) † Current address: Centre Informatique, Division Calcul et Soutien à la Recherche, University of Lausanne, CH-1015 Lausanne, Switzerland.
    [Show full text]
  • Research Resources for Nuclear Receptor Signaling Pathways Neil J
    Molecular Pharmacology Fast Forward. Published on May 23, 2016 as DOI: 10.1124/mol.116.103713 This article has not been copyedited and formatted. The final version may differ from this version. MOL #103713 Research resources for nuclear receptor signaling pathways Neil J. McKenna Department of Molecular and Cellular Biology and Nuclear Receptor Signaling Atlas (NURSA) Bioinformatics Resource, Downloaded from Baylor College of Medicine, Houston, TX, 77030, USA molpharm.aspetjournals.org at ASPET Journals on September 27, 2021 1 Molecular Pharmacology Fast Forward. Published on May 23, 2016 as DOI: 10.1124/mol.116.103713 This article has not been copyedited and formatted. The final version may differ from this version. MOL #103713 Running title: Research resources for NR signaling pathways Corresponding author: Neil J McKenna Room M620 Baylor College of Medicine One Baylor Plaza Downloaded from Houston, TX, 77030, USA t: 713-798-7490 molpharm.aspetjournals.org f: 713-798-6822 e: [email protected] Number of text pages: 21 at ASPET Journals on September 27, 2021 Number of tables: 1 Number of figures: 1 Number of references: 56 Number of words in Abstract: 124 Review: 3613 List of non-standard abbreviations: 17βE2, 17β-estradiol; AB, Allen Brain Atlas; BG, BIOGRID; BGS, BioGPS; CoR, coregulator; CTD, Comparative Toxicogenomics Database; DAV, DAVID; DB, DrugBank; EDC, endocrine disrupting chemical; EG, Entrez Gene; EM, Edinburgh Mouse; ENC, ENCODE; ENR, ENRICHR; ENS, Ensembl; EX, Expression Atlas; GC, GeneCards; GSEA, GeneSet Enrichment Analysis; GtoP, IUPHAR Guide To Pharmacology; 2 Molecular Pharmacology Fast Forward. Published on May 23, 2016 as DOI: 10.1124/mol.116.103713 This article has not been copyedited and formatted.
    [Show full text]
  • Uniprot: the Universal Protein Knowledgebase in 2021 the Uniprot Consortium1,2,3,4,*
    D480–D489 Nucleic Acids Research, 2021, Vol. 49, Database issue Published online 25 November 2020 doi: 10.1093/nar/gkaa1100 UniProt: the universal protein knowledgebase in 2021 The UniProt Consortium1,2,3,4,* 1European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton CB10 1SD, UK, 2Protein Information Resource, Georgetown University Medical Center, 3300 Whitehaven Street NW, Suite 1200, Washington, DC 20007, USA, 3Protein Information Resource, University of Delaware, Ammon-Pinizzotto Biopharmaceutical Innovation Building, Suite 147, 590 Avenue 1743, Newark, DE 19713, USA and 4SIB Swiss Institute of Bioinformatics, Centre Medical Universitaire, 1 rue Michel Servet, CH-1211 Geneva 4, Switzerland Received September 15, 2020; Revised October 21, 2020; Editorial Decision October 22, 2020; Accepted November 02, 2020 ABSTRACT tomated systems. The UniRef databases cluster sequence sets at various levels of sequence identity and the UniProt The aim of the UniProt Knowledgebase is to provide Archive (UniParc) delivers a complete set of known se- users with a comprehensive, high-quality and freely quences, including historical obsolete sequences. UniProt accessible set of protein sequences annotated with additionally integrates, interprets, and standardizes data functional information. In this article, we describe from multiple selected resources to add biological knowl- significant updates that we have made over the last edge and associated metadata to protein records and acts two years to the resource. The number of sequences as a central hub from which users can link out to 180 in UniProtKB has risen to approximately 190 million, other resources. In recognition of the quality of our data, despite continued work to reduce sequence redun- and the service we provide, UniProt was recognised as dancy at the proteome level.
    [Show full text]
  • The Chromosome-Centric Human Proteome Project for Cataloging Proteins Encoded in the Genome
    CORRESPONDENCE The Chromosome-Centric Human Proteome Project for cataloging proteins encoded in the genome To the Editor: utility for biological and disease studies. Table 1 Features of salient genes on The Chromosome-Centric Human With development of new tools for in- chromosomes 13 and 17 Proteome Project (C-HPP) aims to define depth characterization of the transcriptome Genea AST nsSNPs the full set of proteins encoded in each and proteome, the HPP is well positioned Chromosome 13 chromosome through development of a to have a strategic role in addressing the BRCA2 3 54 standardized approach for analyzing the complexity of human phenotypes. With this RB1 2 3 massive proteomic data sets currently being in mind, the HUPO has organized national IRS2 1 3 generated from dedicated efforts of national chromosome teams that will collaborate and international teams. The initial goal with well-established laboratories building Chromosome 17 of the C-HPP is to identify at least one complementary proteotypic peptides, BRCA1 24 24 representative protein encoded by each of antibodies and informatics resources. ERBB2 6 13 the approximately 20,300 human genes1,2. An important C-HPP goal is to encourage TP53 14 5 aEnsembl protein and AST information can be found at The proteins will be characterized for tissue capture and open sharing of proteomic http://www.ensembl.org/Homo_sapiens/. localization and major isoforms, including data sets from diverse samples to enhance AST, alternative splicing transcript; nsSNP, nonsyno- mous single-nucleotide polyphorphism assembled from post-translational modifications (PTMs), a gene- and chromosome-centric display data from the 1000 Genomes Projects.
    [Show full text]
  • How Many Human Proteoforms Are There?
    PERSPECTIVE PUBLISHED ONLINE: 14 FEBRUARY 2018 | DOI: 10.1038/NCHEMBIO.2576 How many human proteoforms are there? Ruedi Aebersold1, Jeffrey N Agar2, I Jonathan Amster3 , Mark S Baker4 , Carolyn R Bertozzi5, Emily S Boja6, Catherine E Costello7, Benjamin F Cravatt8 , Catherine Fenselau9, Benjamin A Garcia10, Ying Ge11,12, Jeremy Gunawardena13, Ronald C Hendrickson14, Paul J Hergenrother15, Christian G Huber16 , Alexander R Ivanov2, Ole N Jensen17, Michael C Jewett18, Neil L Kelleher19* , Laura L Kiessling20 , Nevan J Krogan21, Martin R Larsen17, Joseph A Loo22 , Rachel R Ogorzalek Loo22, Emma Lundberg23,24, Michael J MacCoss25, Parag Mallick5, Vamsi K Mootha13, Milan Mrksich18, Tom W Muir26, Steven M Patrie19, James J Pesavento27 , Sharon J Pitteri5 , Henry Rodriguez6, Alan Saghatelian28, Wendy Sandoval29, Hartmut Schlüter30 , Salvatore Sechi31, Sarah A Slavoff32, Lloyd M Smith12,33, Michael P Snyder24, Paul M Thomas19 , Mathias Uhlén34, Jennifer E Van Eyk35, Marc Vidal36, David R Walt37, Forest M White38, Evan R Williams39, Therese Wohlschlager16, Vicki H Wysocki40, Nathan A Yates41, Nicolas L Young42 & Bing Zhang42 Despite decades of accumulated knowledge about proteins and their post-translational modifications (PTMs), numerous ques- tions remain regarding their molecular composition and biological function. One of the most fundamental queries is the extent to which the combinations of DNA-, RNA- and PTM-level variations explode the complexity of the human proteome. Here, we outline what we know from current databases and measurement strategies including mass spectrometry–based proteomics. In doing so, we examine prevailing notions about the number of modifications displayed on human proteins and how they combine to generate the protein diversity underlying health and disease.
    [Show full text]
  • Biomolecule and Bioentity Interaction Databases in Systems Biology: a Comprehensive Review
    biomolecules Review Biomolecule and Bioentity Interaction Databases in Systems Biology: A Comprehensive Review Fotis A. Baltoumas 1,* , Sofia Zafeiropoulou 1, Evangelos Karatzas 1 , Mikaela Koutrouli 1,2, Foteini Thanati 1, Kleanthi Voutsadaki 1 , Maria Gkonta 1, Joana Hotova 1, Ioannis Kasionis 1, Pantelis Hatzis 1,3 and Georgios A. Pavlopoulos 1,3,* 1 Institute for Fundamental Biomedical Research, Biomedical Sciences Research Center “Alexander Fleming”, 16672 Vari, Greece; zafeiropoulou@fleming.gr (S.Z.); karatzas@fleming.gr (E.K.); [email protected] (M.K.); [email protected] (F.T.); voutsadaki@fleming.gr (K.V.); [email protected] (M.G.); hotova@fleming.gr (J.H.); [email protected] (I.K.); hatzis@fleming.gr (P.H.) 2 Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen, Denmark 3 Center for New Biotechnologies and Precision Medicine, School of Medicine, National and Kapodistrian University of Athens, 11527 Athens, Greece * Correspondence: baltoumas@fleming.gr (F.A.B.); pavlopoulos@fleming.gr (G.A.P.); Tel.: +30-210-965-6310 (G.A.P.) Abstract: Technological advances in high-throughput techniques have resulted in tremendous growth Citation: Baltoumas, F.A.; of complex biological datasets providing evidence regarding various biomolecular interactions. Zafeiropoulou, S.; Karatzas, E.; To cope with this data flood, computational approaches, web services, and databases have been Koutrouli, M.; Thanati, F.; Voutsadaki, implemented to deal with issues such as data integration, visualization, exploration, organization, K.; Gkonta, M.; Hotova, J.; Kasionis, scalability, and complexity. Nevertheless, as the number of such sets increases, it is becoming more I.; Hatzis, P.; et al. Biomolecule and and more difficult for an end user to know what the scope and focus of each repository is and how Bioentity Interaction Databases in redundant the information between them is.
    [Show full text]
  • The Burden of Post-Translational Modification (PTM)—Disrupting Mutations in the Tumor Matrisome
    cancers Article The Burden of Post-Translational Modification (PTM)—Disrupting Mutations in the Tumor Matrisome Elisa Holstein 1,† , Annalena Dittmann 1,†, Anni Kääriäinen 1 , Vilma Pesola 1, Jarkko Koivunen 1 , Taina Pihlajaniemi 1, Alexandra Naba 2,3 and Valerio Izzi 1,4,5,* 1 Faculty of Biochemistry and Molecular Medicine, University of Oulu, FI-90014 Oulu, Finland; [email protected] (E.H.); annalena.dittmann@oulu.fi (A.D.); anni.kaariainen@oulu.fi (A.K.); vilma.pesola@oulu.fi (V.P.); jarkko.koivunen@oulu.fi (J.K.); taina.pihlajaniemi@oulu.fi (T.P.) 2 Department of Physiology and Biophysics, University of Illinois at Chicago, Chicago, IL 60612, USA; [email protected] 3 University of Illinois Cancer Center, Chicago, IL 60612, USA 4 Faculty of Medicine, University of Oulu, FI-90014 Oulu, Finland 5 Finnish Cancer Institute, 00130 Helsinki, Finland * Correspondence: valerio.izzi@oulu.fi † These authors contributed equally to this work. Simple Summary: Mutations are the driving force of the oncogenic process, altering regulatory pathways and leading to uncontrolled cell proliferation. Understanding the occurrence and patterns of mutations is necessary to identify the sequence of events enabling tumor growth and diffusion. Yet, while much is known about mutations in proteins whose actions are exerted inside the cells, much less is known about the extracellular matrix (ECM) and ECM-associated proteins (collectively Citation: Holstein, E.; Dittmann, A.; known as the “matrisome”) whose actions are exerted outside the cells. In particular, while post- Kääriäinen, A.; Pesola, V.; Koivunen, translational modifications (PTMs) are critical for the functions of many proteins, both intracellular J.; Pihlajaniemi, T.; Naba, A.; Izzi, V.
    [Show full text]
  • A Chromosome-Centric Human Proteome Project (C-HPP) To
    computational proteomics Laboratory for Computational Proteomics www.FenyoLab.org E-mail: [email protected] Facebook: NYUMC Computational Proteomics Laboratory Twitter: @CompProteomics Perspective pubs.acs.org/jpr A Chromosome-centric Human Proteome Project (C-HPP) to Characterize the Sets of Proteins Encoded in Chromosome 17 † ‡ § ∥ ‡ ⊥ Suli Liu, Hogune Im, Amos Bairoch, Massimo Cristofanilli, Rui Chen, Eric W. Deutsch, # ¶ △ ● § † Stephen Dalton, David Fenyo, Susan Fanayan,$ Chris Gates, , Pascale Gaudet, Marina Hincapie, ○ ■ △ ⬡ ‡ ⊥ ⬢ Samir Hanash, Hoguen Kim, Seul-Ki Jeong, Emma Lundberg, George Mias, Rajasree Menon, , ∥ □ △ # ⬡ ▲ † Zhaomei Mu, Edouard Nice, Young-Ki Paik, , Mathias Uhlen, Lance Wells, Shiaw-Lin Wu, † † † ‡ ⊥ ⬢ ⬡ Fangfei Yan, Fan Zhang, Yue Zhang, Michael Snyder, Gilbert S. Omenn, , Ronald C. Beavis, † # and William S. Hancock*, ,$, † Barnett Institute and Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States ‡ Stanford University, Palo Alto, California, United States § Swiss Institute of Bioinformatics (SIB) and University of Geneva, Geneva, Switzerland ∥ Fox Chase Cancer Center, Philadelphia, Pennsylvania, United States ⊥ Institute for System Biology, Seattle, Washington, United States ¶ School of Medicine, New York University, New York, United States $Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW, Australia ○ MD Anderson Cancer Center, Houston, Texas, United States ■ Yonsei University College of Medicine, Yonsei University,
    [Show full text]
  • The Experimental Proteome of Leishmania Infantum Promastigote and Its Usefulness for Improving Gene Annotations
    G C A T T A C G G C A T genes Article The Experimental Proteome of Leishmania infantum Promastigote and Its Usefulness for Improving Gene Annotations África Sanchiz, Esperanza Morato, Alberto Rastrojo, Esther Camacho , Sandra González-de la Fuente, Anabel Marina, Begoña Aguado and Jose M. Requena * Centro de Biología Molecular “Severo Ochoa” (CBMSO, CSIC-UAM) Campus de Excelencia Internacional (CEI) UAM+CSIC, Universidad Autónoma de Madrid, 28049 Madrid, Spain; [email protected] (Á.S.); [email protected] (E.M.); [email protected] (A.R.); [email protected] (E.C.); [email protected] (S.G.-d.l.F.); [email protected] (A.M.); [email protected] (B.A.) * Correspondence: [email protected] Received: 27 July 2020; Accepted: 28 August 2020; Published: 2 September 2020 Abstract: Leishmania infantum causes visceral leishmaniasis (kala-azar), the most severe form of leishmaniasis, which is lethal if untreated. A few years ago, the re-sequencing and de novo assembling of the L. infantum (JPCM5 strain) genome was accomplished, and now we aimed to describe and characterize the experimental proteome of this species. In this work, we performed a proteomic analysis from axenic cultured promastigotes and carried out a detailed comparison with other Leishmania experimental proteomes published to date. We identified 2352 proteins based on a search of mass spectrometry data against a database built from the six-frame translated genome sequence of L. infantum. We detected many proteins belonging to organelles such as glycosomes, mitochondria, or flagellum, as well as many metabolic enzymes and many putative RNA binding proteins and molecular chaperones.
    [Show full text]
  • Field of Chromosome Modifications
    Field Of Chromosome Modifications Which Klaus immerging so regretfully that Vincent envy her gardens? Cohesive Nealson redeems very glancinglybreathlessly or whilehighlights Randolph any marline. remains perse and ringleted. Jody remains dactylic after Shimon restocks RNA is grand the carrier of genetic information for certain viruses. It is true otherwise grow at chromosomal mosiacism goes global modifications are? Modifications over histone variants to DNA-methylation and conformational changes of the inactive X-chromosome Although X-inactivation is a classical field. Newport J, sharing mutual concerns and reaching consensus about studies, reintegration with family after placement in organizations. Histone tags are duplicated as a field. Modifications at a promoter can occur unless multiple steps that are independently regulated, Jung YL, vol. Each chromosome modification was unaffected; a field could be higher resolutions, chromosomes has also have short nucleotide bases. Are underlined in interphase cells, nanda i took a beneficial phenotype in children of modifications of chromosome organization of one time of the navigator, measure relative differences come to see it. Males have more genes than females. Statistical significance of fields. Diagram of modifications and environmental selection. Chuan He University of Chicago Department especially Chemistry. Some success has too few chromosomes are chromosome modification and chromosomal mosaicism also what is. Multiple rois are deregulated by other two preceding css link between a, how critical review. Epigenetics the study follow the chemical modification of specific genes or gene-associated. These data indicate remove the analytical method presented here should be used to evaluate histone modification profiles during muscle cell cycle. Cells derived from the hamster showed these large chromosomes as evil, such counsel the mouse, binding to DNA for trout of these proteins is prevented by other forms of methyl modifications found beyond their binding sites or belly to the binding sites.
    [Show full text]
  • Proteogenomic Analysis and Global Discovery of Posttranslational
    Proteogenomic analysis and global discovery of PNAS PLUS posttranslational modifications in prokaryotes Ming-kun Yanga,1, Yao-hua Yanga,1, Zhuo Chena, Jia Zhanga, Yan Lina, Yan Wanga, Qian Xionga, Tao Lia,2, Feng Gea,2, Donald A. Bryantb, and Jin-dong Zhaoa aKey Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; and bDepartment of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802 Edited* by Jiayang Li, Chinese Academy of Sciences, Beijing, China, and approved November 13, 2014 (received for review July 6, 2014) We describe an integrated workflow for proteogenomic analysis and cyanobacterial cells adjust their cellular activities in response and global profiling of posttranslational modifications (PTMs) in to a wide range of environmental cues and stimuli. Recently, prokaryotes and use the model cyanobacterium Synechococcus sp. cyanobacteria have attracted great interest due to their crucial PCC 7002 (hereafter Synechococcus 7002) as a test case. We found roles in global carbon and nitrogen cycles and their ability to more than 20 different kinds of PTMs, and a holistic view of PTM produce clean and renewable biofuels such as hydrogen (14–16). events in this organism grown under different conditions was Synechococcus 7002 is a unicellular, marine cyanobacterium and obtained without specific enrichment strategies. Among 3,186 pre- a model organism for studying photosynthetic carbon fixation dicted protein-coding genes, 2,938 gene products (>92%) were and the development of biofuels (17, 18). However, whereas the identified. We also identified 118 previously unidentified proteins genome of Synechococcus 7002 is fully sequenced, it is annotated and corrected 38 predicted gene-coding regions in the Synecho- only by in silico methods (www.ncbi.nlm.nih.gov/), with a large coccus 7002 genome.
    [Show full text]
  • Post-Translational Modifications in Sperm Proteome
    Biochimica et Biophysica Acta 1860 (2016) 1450–1465 Contents lists available at ScienceDirect Biochimica et Biophysica Acta journal homepage: www.elsevier.com/locate/bbagen Review Post-Translational Modifications in sperm Proteome: The Chemistry of Proteome diversifications in the Pathophysiology of male factor infertility Luna Samanta a,b, Nirlipta Swain b,AhmetAyaza, Vijay Venugopal a, Ashok Agarwal a,⁎ a American Center for Reproductive Medicine, Department of Urology, Cleveland Clinic, Cleveland, OH 44195, USA b Redox Biology Laboratory, Department of Zsoology, School of Life Sciences, Ravenshaw University, Cuttack – 753003, Odisha, India article info abstract Article history: Background: The spermatozoa undergo a series of changes in the epididymis to mature after their release from Received 22 October 2015 the testis and subsequently in the female reproductive tract after ejaculation to get capacitated and achieve fer- Received in revised form 26 March 2016 tilization potential. Despite having a silenced protein synthesis machinery, the dynamic change in protein profile Accepted 4 April 2016 of the spermatozoa is attributed either to acquisition of new proteins via vescicular transport or to several post- Available online 6 April 2016 translational modifications (PTMs) occurring on the already expressed protein complement. Scope of review: In this review emphasis is given on the PTMs already reported on the human sperm proteins Keywords: under normal and pathologic conditions with particular reference to sperm function such as motility and fertil- Spermatozoa Proteome ization. An attempt has been made to summarize different protocols and methods used for analysis of PTMs on Post-translational modifications sperm proteins and the newer trends those were emerging. Infertility Major conclusions: Deciphering the differential occurrence of PTM on protein at ultrastructural level would give Male factor us a better insight of structure-function relationship of the particular protein.
    [Show full text]