Generated by SRI International Pathway Tools Version 25.0, Authors M

Total Page：16

File Type：pdf, Size：1020Kb

Generated by SRI International Pathway Tools Version 25.0, Authors M

Emticicia oligotrophica DSM 17448 NC_018748 by Pallavi Subhraveti1, Peter Midford, Ingrid Keseler1, Anamika Kothari1, Ron Caspi1, Peter D Karp1 --- 1SRI International Legend: Protein gene Transcription Start Adjacent genes drawn in the same color are within the same operon. This diagram was automatically generated by SRI International Pathway Tools version 25.0, authors M. Krummenacker and P.D. Karp. RNA gene Terminator Uncolored genes are not yet assigned to an operon. Pseudo-genes are crossed out with a big, diagonal X.

Copy Link

Recommended publications

(12) United States Patent (10) Patent No.: US 6,395,889 B1 Robison (45) Date of Patent: May 28, 2002
USOO6395889B1 (12) United States Patent (10) Patent No.: US 6,395,889 B1 Robison (45) Date of Patent: May 28, 2002 (54) NUCLEIC ACID MOLECULES ENCODING WO WO-98/56804 A1 * 12/1998 ........... CO7H/21/02 HUMAN PROTEASE HOMOLOGS WO WO-99/0785.0 A1 * 2/1999 ... C12N/15/12 WO WO-99/37660 A1 * 7/1999 ........... CO7H/21/04 (75) Inventor: fish E. Robison, Wilmington, MA OTHER PUBLICATIONS Vazquez, F., et al., 1999, “METH-1, a human ortholog of (73) Assignee: Millennium Pharmaceuticals, Inc., ADAMTS-1, and METH-2 are members of a new family of Cambridge, MA (US) proteins with angio-inhibitory activity', The Journal of c: - 0 Biological Chemistry, vol. 274, No. 33, pp. 23349–23357.* (*) Notice: Subject to any disclaimer, the term of this Descriptors of Protease Classes in Prosite and Pfam Data patent is extended or adjusted under 35 bases. U.S.C. 154(b) by 0 days. * cited by examiner (21) Appl. No.: 09/392, 184 Primary Examiner Ponnathapu Achutamurthy (22) Filed: Sep. 9, 1999 ASSistant Examiner William W. Moore (51) Int. Cl." C12N 15/57; C12N 15/12; (74) Attorney, Agent, or Firm-Alston & Bird LLP C12N 9/64; C12N 15/79 (57) ABSTRACT (52) U.S. Cl. .................... 536/23.2; 536/23.5; 435/69.1; 435/252.3; 435/320.1 The invention relates to polynucleotides encoding newly (58) Field of Search ............................... 536,232,235. identified protease homologs. The invention also relates to 435/6, 226, 69.1, 252.3 the proteases. The invention further relates to methods using s s s/ - - -us the protease polypeptides and polynucleotides as a target for (56) References Cited diagnosis and treatment in protease-mediated disorders.
[Show full text]
Serine Proteases with Altered Sensitivity to Activity-Modulating
(19) & (11) EP 2 045 321 A2 (12) EUROPEAN PATENT APPLICATION (43) Date of publication: (51) Int Cl.: 08.04.2009 Bulletin 2009/15 C12N 9/00 (2006.01) C12N 15/00 (2006.01) C12Q 1/37 (2006.01) (21) Application number: 09150549.5 (22) Date of filing: 26.05.2006 (84) Designated Contracting States: • Haupts, Ulrich AT BE BG CH CY CZ DE DK EE ES FI FR GB GR 51519 Odenthal (DE) HU IE IS IT LI LT LU LV MC NL PL PT RO SE SI • Coco, Wayne SK TR 50737 Köln (DE) •Tebbe, Jan (30) Priority: 27.05.2005 EP 05104543 50733 Köln (DE) • Votsmeier, Christian (62) Document number(s) of the earlier application(s) in 50259 Pulheim (DE) accordance with Art. 76 EPC: • Scheidig, Andreas 06763303.2 / 1 883 696 50823 Köln (DE) (71) Applicant: Direvo Biotech AG (74) Representative: von Kreisler Selting Werner 50829 Köln (DE) Patentanwälte P.O. Box 10 22 41 (72) Inventors: 50462 Köln (DE) • Koltermann, André 82057 Icking (DE) Remarks: • Kettling, Ulrich This application was filed on 14-01-2009 as a 81477 München (DE) divisional application to the application mentioned under INID code 62. (54) Serine proteases with altered sensitivity to activity-modulating substances (57) The present invention provides variants of ser- screening of the library in the presence of one or several ine proteases of the S1 class with altered sensitivity to activity-modulating substances, selection of variants with one or more activity-modulating substances. A method altered sensitivity to one or several activity-modulating for the generation of such proteases is disclosed, com- substances and isolation of those polynucleotide se- prising the provision of a protease library encoding poly- quences that encode for the selected variants.
[Show full text]
Expression of Treponema Denticola Oligopeptidase B in Escherichia Coli
CURRENT MICROBIOLOGY Vol. 48 (2004), pp. 379–382 DOI: 10.1007/s00284-003-4168-4 Current Microbiology An International Journal © Springer-Verlag New York LLC 2004 Expression of Treponema denticola Oligopeptidase B in Escherichia coli Si Young Lee,1,2 J. Christopher Fenno2 1Department of Oral Microbiology, College of Dentistry, Research Institute of Oral Science, Kangnung National University, Kangnung, 201- 702, Korea 2Department of Biologic and Materials Sciences, School of Dentistry, University of Michigan, Ann Arbor, MI 48109-1078, USA Received: 4 June 2003 / Accepted: 16 September 2003 Abstract. Treponema denticola is a small anaerobic spirochete often isolated from periodontal lesions and closely associated with periodontal diseases. This bacterium possesses a particular arginine peptidase activity (previously called “BANA-peptidase” or “trypsin-like enzyme”) that is common to the three cultivable bacterial species most highly associated with severe periodontal disease. We recently reported the identiﬁcation of the opdB locus that encodes the BANA-peptidase activity of T. denticola through DNA sequencing and mutagenesis studies. In the present study, we report expression of T. denticola OpdB peptidase in Escherichia coli. The opdB PCR product was cloned into pET30b and then transformed into the E. coli BL21 (DE3)/pLysS expression strain. Assays of enzymatic activities in E. coli containing T. denticola opdB showed BANA-peptidase activity similar to that of T. denticola. Availability of this recombinant expression system producing active peptidase will facilitate character- ization of the potential role of this peptidase in periodontal disease etiology. A speciﬁc complex of three cultivable anaerobic organ- bacterium expresses several virulence behaviors, such as isms including Treponema denticola, Porphyromonas adherence, cytotoxicity, iron sequestration, and locomo- gingivalis, and Bacteroides forsythus is associated with tion, which are likely to contribute to the periodontal periodontal disease severity [11].
[Show full text]
(12) Patent Application Publication (10) Pub. No.: US 2004/0081648A1 Afeyan Et Al
US 2004.008 1648A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2004/0081648A1 Afeyan et al. (43) Pub. Date: Apr. 29, 2004 (54) ADZYMES AND USES THEREOF Publication Classification (76) Inventors: Noubar B. Afeyan, Lexington, MA (51) Int. Cl." ............................. A61K 38/48; C12N 9/64 (US); Frank D. Lee, Chestnut Hill, MA (52) U.S. Cl. ......................................... 424/94.63; 435/226 (US); Gordon G. Wong, Brookline, MA (US); Ruchira Das Gupta, Auburndale, MA (US); Brian Baynes, (57) ABSTRACT Somerville, MA (US) Disclosed is a family of novel protein constructs, useful as Correspondence Address: drugs and for other purposes, termed “adzymes, comprising ROPES & GRAY LLP an address moiety and a catalytic domain. In Some types of disclosed adzymes, the address binds with a binding site on ONE INTERNATIONAL PLACE or in functional proximity to a targeted biomolecule, e.g., an BOSTON, MA 02110-2624 (US) extracellular targeted biomolecule, and is disposed adjacent (21) Appl. No.: 10/650,592 the catalytic domain So that its affinity Serves to confer a new Specificity to the catalytic domain by increasing the effective (22) Filed: Aug. 27, 2003 local concentration of the target in the vicinity of the catalytic domain. The present invention also provides phar Related U.S. Application Data maceutical compositions comprising these adzymes, meth ods of making adzymes, DNA's encoding adzymes or parts (60) Provisional application No. 60/406,517, filed on Aug. thereof, and methods of using adzymes, Such as for treating 27, 2002. Provisional application No. 60/423,754, human Subjects Suffering from a disease, Such as a disease filed on Nov.
[Show full text]
Protein Turnover and Differentiation in Leishmania
International Journal for Parasitology 37 (2007) 1063–1075 www.elsevier.com/locate/ijpara Invited Review Protein turnover and differentiation in Leishmania Se´bastien Besteiro a,1,2, Roderick A.M. Williams a,2, Graham H. Coombs b, Jeremy C. Mottram a,* a Wellcome Centre for Molecular Parasitology and Division of Infection & Immunity, Institute of Biomedical and Life Sciences, University of Glasgow, 120 University Place, Glasgow G12 8TA, UK b Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow G4 0NR, UK Received 18 February 2007; accepted 16 March 2007 Abstract Leishmania occurs in several developmental forms and thus undergoes complex cell differentiation events during its life-cycle. Those are required to allow the parasite to adapt to the different environmental conditions. The sequencing of the genome of L. major has facil- itated the identification of the parasite’s vast arsenal of proteolytic enzymes, a few of which have already been carefully studied and found to be important for the development and virulence of the parasite. This review focuses on these peptidases and their role in the cellular differentiation of Leishmania through their key involvement in a variety of degradative pathways in the lysosomal and autophagy networks. Ó 2007 Australian Society for Parasitology Inc. Published by Elsevier Ltd. All rights reserved. Keywords: Leishmania; Differentiation; Protease; Peptidase; Genome 1. Introduction are present in the insect’s midgut; non-dividing, but mam- malian-infective, metacyclic promastigotes in the thoracic Leishmania are protozoan parasites with a complex life- midgut and proboscis of the sandfly. The metacyclic prom- cycle, involving several developmental forms (Fig.
[Show full text]
Prolyl Endopeptidase Enzyme Inhibitors of Plant Origin
FABAD J. Pharm. Sci., 27, 231-237; 2002 SCIENTIFIC REVIEWS Prolyl Endopeptidase Enzyme Inhibitors of Plant Origin 0 İlkay ORHAN* , Gürdal ORHAN**, Bilge ŞENER* ltıhibitors Plaııt Prolyl Endopeptidase Enzyme of Origin Bitkisel Kaynaklı Prolil Endopeptidaz Enzim İnhibitörleri Summary : Prolyl endopeptidase (PEP) is a serine protease Özet : Prolil endopeptidaz (PEP), öğrenme ve hafıza sü• which is known ta play a role in degradation of proline recinde etkili prolin içerikli nöropeptitlerin yıkılnıasında rol containing neııropeptides involved in the processes of learn oynadığı bilinen bir serin proteazdır. PEP inhibitörlerinin ing and nıenıory. PEP inhibitors are expected to exert their sinirleri hasar ve hücre ölümüne karşı korıjyan, tanıma beneficial effects by increasing the brain levels of those neu fonksiyonlarını yeniden yapılandırıp iyileştirebilen nö• ropeptides ıvhich may improve and restore cognitive func ropeptitlerin beyin düzeylerini artırarak yararlı olnıaları tions and protect vulnerable nerves against damage and celi beklenir. Bugüne kadar, sentetik eşdeğerleri olduğu kadar, death. Therefore, they are considered to have therapeutic Alzheimer hastalığına karşı terapötik bir potansiyele sahip potential against Alzheimer's Disease. To date many com pounds have been isolated from natura! sources including PEP inhibitör aktiviteli pek çok bileşik, bitkiler, mantarlar plants, fungi and bacteria. Their synthetic counterparts have ve bakteriler de dahil olmak üzere doğal kaynaklardan izole been alsa studied. This revie1v covers
[Show full text]
Studies on Oligopeptidase B of Leishmania Major
Studies on Oligopeptidase B of Leishmania major Jane Claire Munday BSc (Hons) MSc A thesis submitted in the fulfillment of the requirement for the degree of Doctor of Philosophy in the Faculty of Veterinary Medicine, University of Glasgow Wellcome Centre for Molecular Parasitology Glasgow Biomedical Research Centre University of Glasgow United Kingdom May 2008 Jane Claire Munday 2008 ii Abstract Peptidases of Leishmania are acknowledged virulence factors. It is hypothesised that peptidases are crucial for the survival of Leishmania in its hosts and that many could be potential targets for new antileishmanial drugs. As such, the investigation of peptidase activity in live Leishmania promastigotes was proposed as a valuable approach by which to increase knowledge on particular peptidases. In order to complete this investigation, it was decided to use short peptidyl fluorogenic substrates, which only fluoresce once the bond linking the peptide to the fluorescent moiety is cleaved. These allow detection of peptidase activity by quantifying the release of the fluorescent moiety. Detection of peptidase activity in live Leishmania using the fluorogenic substrate Bz-R-AMC proved fruitful, enabling study of the activity of the serine peptidase oligopeptidase B (OPB) in live L. major promastigotes. OPB is a member of the Family S9 peptidases, the prolyl-oligopeptidases, which are taxonomically restricted to plants, bacteria and trypanosomatid flagellates. In African and American trypanosomes, OPB has been shown to have important roles: OPB is a virulence factor in Trypanosoma cruzi , mediating entry into host cells, and OPB is released into the serum by African trypanosomes, where it cleaves host blood factors. In this study, the inhibition profile of L.
[Show full text]
Cell Signalling and Trypanosoma Cruzi Invasionb
Blackwell Science, LtdOxford, UKCMICellular Microbiology Cellular Microbiology 1462-5814Blackwell Science, 20024Review ArticleCell signalling and Trypanosoma cruzi invasionB. A. Burleigh and A. M. Woolsey Cellular Microbiology (2002) 4(11), 701–711 Microreview Cell signalling and Trypanosoma cruzi invasion Barbara A. Burleigh* and Aaron M. Woolsey cycle takes 3–5 days, after which infective trypomastig- Department of Immunology and Infectious Diseases, otes, released into the bloodstream of the host, are dis- Harvard School of Public Health, 665 Huntington Ave, seminated throughout the body and infect tissues at distal Bldg I Rm 713, Boston, MA 02115, USA. sites. Thus, the ability to infect and replicate within a variety of cell types is an essential feature of the T. cruzi life cycle in the mammalian host. Whereas parasites are Summary eventually cleared from most tissues and parasitaemia is Mammalian cell invasion by the protozoan pathogen no longer detectable in the post-acute stages of infection, Trypanosoma cruzi is critical to its survival in the low-level persistence, particularly in the myocardium and host. To promote its entry into a wide variety of non- smooth muscle, contributes to the pathology associated professional phagocytic cells, infective trypomastig- with chronic Chagas’ disease. Presently, several determi- otes exploit an arsenal of heterogenous surface nants of host cell invasion have been uncovered, but the glycoproteins, secreted proteases and signalling molecular requirements for intracellular growth and para- agonists to actively manipulate multiple host cell site persistence remain poorly understood. The resulting signalling pathways. Signals initiated in the parasite complex interplay between T. cruzi-dependent modulation upon contact with mammalian cells also function as of the host cell environment and immune avoidance critical regulators of the invasion process.
[Show full text]
Structural and Kinetic Analysis of Escherichia Coli Signal Peptide Peptidase A
Structural and Kinetic Analysis of Escherichia coli Signal Peptide Peptidase A by Apollos C. Kim B.A. (Psychology), Simon Fraser University, 2001 B.Sc. (Biology), Seoul National University, Korea, 1992 Thesis Submitted in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy in the Department of Molecular Biology and Biochemistry Faculty of Science Apollos C. Kim 2013 SIMON FRASER UNIVERSITY Summer 2013 All rights reserved. However, in accordance with the Copyright Act of Canada, this work may be reproduced, without authorization, under the conditions for “Fair Dealing.” Therefore, limited reproduction of this work for the purposes of private study, research, criticism, review and news reporting is likely to be in accordance with the law, particularly if cited appropriately. Approval Name: Apollos C. Kim Degree: Doctor of Philosophy (Molecular Biology and Biochemistry) Title of Thesis: Structural and kinetic analysis of Escherichia coli signal peptide peptidase A Examining Committee: Chair: Frederic Pio, Associate Professor Mark Paetzel Senior Supervisor Associate Professor Nicholas Harden Supervisor Professor Edgar C. Young Supervisor Associate Professor Dipankar Sen Internal Examiner Professor Ross MacGillivray External Examiner Professor Department of Biochemistry and Molecular Biology University of British Columbia Date Defended/Approved: June 19, 2013 ii Partial Copyright Licence iii Abstract Secretory proteins contain a signal peptide at their N-terminus. The signal peptide functions to guide proteins to the membrane and is cleaved off by signal peptidase. The remnant signal peptides must be removed from the membrane to prevent their accumulation which can lead to membrane destabilization. Escherichia coli signal peptide peptidase A (SppAEC) has been identified as a major enzyme that processes the remnant signal peptide to smaller fragments.
[Show full text]
A Serine Protease from a Detergent-Soluble
A Serine Protease from a Detergent-soluble Extract of Leishmania (Leishmania) amazonensis Raquel Elisa da Silva Lopeza,* and Salvatore Giovanni De Simonea,b a Laborato´ rio de Bioquı´mica de Proteı´nas e Peptı´deos, Departamento de Bioquı´mica e Biologia Molecular, Instituto Oswaldo Cruz, FIOCRUZ, Av. Brasil 4365, 21045-900, Rio de Janeiro, RJ, Brasil. Fax: +55215903495. E-mail: [email protected] b Departamento de Biologia Celular e Molecular, Instituto de Biologia, Universidade Federal Fluminense, Nitero´ i, RJ, Brasil * Author for correspondence and reprint requests Z. Naturforsch. 59c, 590Ð598 (2004); January 22/March 18, 2004 Proteases mediate important crucial functions in parasitic diseases, and their characteriza- tion contributes to the understanding of host-parasite interaction. A serine protease was purified about 43-fold with a total recovery of 60% from a detergent-soluble extract of pro- mastigotes of Leishmania amazonensis. The purification procedures included aprotinin-agar- ose affinity chromatography and gel filtration high performance liquid chromatography. The molecular mass of active enzyme was 110 kDa by native gel filtration HPLC and by SDS- PAGE gelatin under non-reducing conditions. Under conditions of reduction using SDS- PAGE gelatin analyses the activity of enzyme was observed in two proteins of 60 and 45 kDa, suggesting that the enzyme may be considered as a dimer. The Leishmania protease was not glycosylated, and its isoelectric point (pI) was around 4.8. The maximal protease activity was α ρ at pH 7.0 and 28 ∞C, using -N- -tosyl-L-arginyl-methyl ester (l-TAME) as substrate. Assays of thermal stability indicated that this enzyme was totally denatured after pre-treatment at 42 ∞C for 12 min and preserved only 20% of its activity after pre-treatment at 37 ∞C for 24 h, in the absence of substrate.
[Show full text]
Serine Proteases and Vaccines Against Leishmaniasis: a Dual Role
ccines & a V f V a o c l c i a n n a r t u i o o n J Chaves et al., J Vaccines Vaccin 2015, 6:1 Journal of Vaccines & Vaccination DOI: 10.4172/2157-7560.1000264 ISSN: 2157-7560 Review Article Open Access Serine Proteases and Vaccines against Leishmaniasis: A Dual Role Suzana Passos Chaves3, Daniel Claudio Oliveira Gomes4, Salvatore Giovanni De-Simone6,7, Bartira Rossi-Bergmann5, and Herbert Leonel de Matos Guedes1,2,* 1Laboratório de Inflamação, Grupo de Imunologia e Vacinologia, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, 21941-902 Rio de Janeiro, RJ, Brazil 2Núcleo Multidisciplinar de Pesquisa UFRJ – Xerém em Biologia (NUMPEXBIO), Polo Avançado de Xerém-Universidade Federal do Rio de Janeiro, 25245-390 Duque de Caxias, RJ, Brazil 3Laboratório de Imunoparasitologia, Universidade do Rio de Janeiro, Campus Macaé, 27965-045, Macaé, RJ. Brazil 4Laboratório de Imunobiologia, Núcleo de Doenças Infecciosas/ Núcleo de Biotecnologia, Universidade Federal do Espírito Santo, 29043-900 Vitória- ES, Brazil 5Laboratório de Imunofarmacologia, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, 21941-902 Rio de Janeiro, RJ, Brazil 6Centro de Desenvolvimento Tecnológico em Saúde (CDTS)/Instituto Nacional de Ciencia e Tecnologia de Inovação em Doenças de Populações Negligenciadas (INCT-IDPN), 21045-900 Rio de Janeiro, RJ, Brazil 7Laboratório de Bioquímica de Proteínas e Peptídeos Instituto Oswaldo cruz (IOC). Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro, RJ, Brazil *Corresponding author: Herbert Leonel de Matos Guedes, 1Laboratório de Inflamação, Grupo de Imunologia e Vacinologia, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, 21941-902 Rio de Janeiro, RJ, Brazil, Tel: 02139386507; E-mail: [email protected] Received date: 21 October 2014; Accepted date: 16 January 2015; Published date: 20 January 2015 Copyright: © 2015 Chaves SP, et al.
[Show full text]
On the Activities of Pancreatic Proteases and Alpha-1 Proteinase Inhibitor in Meat-Type Chicken
Open Journal of Animal Sciences, 2017, 7, 289-296 http://www.scirp.org/journal/ojas ISSN Online: 2161-7627 ISSN Print: 2161-7597 On the Activities of Pancreatic Proteases and Alpha-1 Proteinase Inhibitor in Meat-Type Chicken Vladimir G. Vertiprakhov*, Alena A. Grozina, Ivan A. Egorov, Tatiana N. Lenkova, Vardges A. Manukyan, Tatiana A. Egorova Federal Scientific Center, “All-Russian Research and Technological Poultry Institute” of Russian Academy of Sciences, Moscow, Russia How to cite this paper: Vertiprakhov, Abstract V.G., Grozina, A.A., Egorov, I.A., Lenkova, T.N., Manukyan, V.A. and Egorova, T.A. The study was aimed at the evaluation of the effects of breed, age, different (2017) On the Activities of Pancreatic Pro- digestion stimulators, and dietary crude protein (CP) level on the activities of teases and Alpha-1 Proteinase Inhibitor in proteolytic enzymes in pancreatic tissue and duodenal chymus (in vivo), se- Meat-Type Chicken. Open Journal of Animal Sciences, 7, 289-296. rum trypsin and α1-proteinase inhibitor (A1PI) concentrations in meat-type https://doi.org/10.4236/ojas.2017.73022 chicks. The study of age dynamics of trypsin and A1PI concentrations was performed on the chicks of hybrid cross “Smena-8” and two parental lines Received: May 11, 2017 Accepted: July 9, 2017 (Plymouth Rock and Cornish) fed standard commercial corn-wheat-SBM di- Published: July 12, 2017 ets. Twenty birds per breed were euthanized at 1, 7, 14, 21, 28 and 35 days of age to obtain blood samples and pancreatic homogenate. Experiments on the Copyright © 2017 by authors and effects of different digestion promotors (probiotic, acidifier, phytobiotic, en- Scientific Research Publishing Inc.
[Show full text]