Arabidopsis Thaliana Atypical Aspartic Proteases Involved in Primary Root Development and Lateral Root Formation

Total Page:16

File Type:pdf, Size:1020Kb

Arabidopsis Thaliana Atypical Aspartic Proteases Involved in Primary Root Development and Lateral Root Formation André Filipe Marques Soares RLR1 and RLR2, two novel Arabidopsis thaliana atypical aspartic proteases involved in primary root development and lateral root formation 2016 Thesis submitted to the Institute for Interdisciplinary Research of the University of Coimbra to apply for the degree of Doctor in Philosophy in the area of Experimental Biology and Biomedicine, specialization in Molecular, Cell and Developmental Biology This work was conducted at the Center for Neuroscience and Cell Biology (CNC) of University of Coimbra and at Biocant - Technology Transfer Association, under the scientific supervision of Doctor Isaura Simões and at the Department of Biochemistry of University of Massachusetts, Amherst, under the scientific supervision of Doctor Alice Y. Cheung. Part of this work was also performed at the Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna, under the scientific supervision of Doctor Herta Steinkellner and also at the Central Institute for Engineering, Electronics and Analytics, ZEA-3, Forschungszentrum Jülich, Jülich, under the schientific supervision of Doctor Pitter F. Huesgen. André Filipe Marques Soares was a student of the Doctoral Programme in Experimental Biology and Biomedicine coordinated by the Center for Neuroscience and Cell Biology (CNC) of the University of Coimbra and a recipient of the fellowship SFRH/BD/51676/2011 from the Portuguese Foundation for Science and Technology (FCT). The execution of this work was supported by a PPP grant of the German Academic Exchange Service with funding from the Federal Ministry of Education and Research (Project-ID 57128819 to PFH) and the Fundação para a Ciência e a Tecnologia (FCT) (grant: Scientific and Technological Bilateral Agreement 2015/2016 to IS) Agradecimentos/Acknowledgments Esta tese e todo o percurso que culminou na sua escrita não teriam sido possíveis sem o apoio, o carinho e a amizade de várias pessoas que ainda estão ou estiveram presentes na minha vida. Sem estas pessoas eu tenho a certeza que nada disto seria possível portanto aqui fica o meu muito obrigado por todo o apoio que me deram. Os próximos parágrafos são a expressão escrita de todo o meu agradecimento mas todas as palavras serão sempre poucas para vos agradecer! Em primeiro lugar, gostaria de agradecer ao Professor Doutor Carlos Faro e ao Professor Doutor Euclides Pires por terem proporcionado todas as condições necessárias para a realização deste trabalho quer na Unidade de Biotecnologia Molecular do Biocant, quer no Laboratório de Biotecnologia Molecular do Centro de Neurociências e Biologia Celular de Coimbra. Se nos agradecimentos da minha tese de Mestrado me faltaram as palavras para poder agradecer devidamente à Doutora Isaura Simões, nesta tese de Doutoramento todas as palavras serão sempre poucas para lhe agradecer tudo o que fez e continua a fazer por mim. Muito obrigado por voltar a apostar em mim Professora e por me ter acompanhado ao longo destes quase 5 anos! Obrigado por ter acreditado em mim quando eu próprio duvidava. Obrigado por toda a sua preocupação e por tudo o que me ensinou ao longo de todos estes anos que trabalhámos juntos. Se sou o cientista que sou neste momento devo-o a si e a tudo o que me ensinou! Tal como escrevi na minha tese de Mestrado, espero sinceramente não a ter desiludido Professora. To Dr. Alice Cheung and Dr. Hen-ming Wu I would like to thank the opportunity that they gave me to work in their lab at the University of Massachusetts, Amherst. Thank you for giving me all the conditions necessary to perform my work in your lab and for all the things that I learn during my stay. Especially I would like to express my deepest gratefulness to Dr. Alice for agreeing to be the co-supervisor of this thesis. Thank you for all the time and effort that you spent guiding me and discussing with me my results and ideas. Thank you very much. To Dr. Pitter Huesgen I would like to thank the opportunity of working with you in your laboratory at Forschungszentrum Jülich. Thank you very much for all the time that you spent and continue spending analyzing my data and for all the great ideas that you gave me. To Dr. Herta Steinkellner I also would like to thank the opportunity of working in your lab at BOKU University, Vienna. Thank you very much for allowing me in your lab and for giving me all the conditions to express both proteins in Nicotiana plants. It was a great opportunity for me and also a great experience! A todas as pessoas que fazem parte da Unidade de Biotecnologia Molecular do Biocant ou que por lá passaram enquanto eu lá trabalhei, o meu muito obrigado por tornarem o laboratório um sítio onde não só se trabalhava à séria mas onde também era possível dar umas boas gargalhadas! Apesar de ter andado a saltitar de um lado para o outro ao longo deste doutoramento, era no nosso laboratório que eu mais me sentia em casa e agora que parto tenho a certeza que vou sentir sempre a vossa falta! Queria agradecer também à Dona Alda, à Dona Adelaide e à Filipa todo o trabalho que tiveram comigo ao longo destes anos, por todas as provetas, frascos e fraquinhos que tiveram de lavar à minha conta! Muito obrigado por todo o apoio que me deram, por todas as gargalhadas partilhadas e pela forma incansável com que não só me apoiavam a mim mas também ao resto das pessoas do Biocant. Aproveito também para agradecer a todos os meus amigos que ainda estão ou já estiveram no Biocant e que ajudaram a fazer do Biocant muito mais do que um simples local de trabalho. Muito obrigado! To the people from the Amherst, Vienna and Jülich Laboratories, I thank you for the very good environment that I experience during my stay in your labs and for all the help that you were always willing to give me! A especial thanks to Yanjao (Amherst lab) for helping me taking my first baby steps in plant/pollen research, to Andreas and Alexandra (Vienna Lab) for all the help and advices, and finally to Stefan (Jülich lab) for all the time that you spent (and continue spending) doing my proteomics experiments and analyzing my data! Thank you very very much for everything! A todos os meus amigos da X edição do BEB, Catarina, Tânia, Sara, Joana, Dominique, Mariline, Sofia, Patrícia, António, Marcelo e Ribas, o meu muito obrigado por serem os amigos que são. O primeiro ano do Programa Doutoral foi sem dúvida o melhor ano que passei em Coimbra e se assim foi, devo-o a todos vós! Deixo um agradecimento especial à Nina e à Tânia pela vossa amizade e por estarem sempre presentes e dispostas a dois dedos de conversa sobre tudo ou mesmo sobre nada! Aos restantes amigos de Coimbra e arredores, o meu muito obrigado por todo o apoio que me têm dado! Deixo aqui também um agradecimento especial à Tábata e à Kaline, duas pessoas que tive a sorte de conhecer em Amherst e que tornaram a minha estadia naquele canto do mundo bastante mais alegre. Meninas, eu se calhar devia escrever este agradecimento em inglês porque eu não sei se vocês vão perceber este meu “Old Portuguese” mas o dicionário existe para essas coisas! Eheh! To the people that I met during my stay in Vienna, thank you very much for making those 3 months that I spent there unforgettable. A special thanks to my great friend Kemo, a.k.a. “The Bosnian Guy”, and to Anja and Heidi! Those last two months that I spent in your company were truly great and I will never forget them! Aos meus Pais, Avós e Irmã agradeço todo o incansável apoio que me deram ao longo de toda a minha vida. Eu posso andar sempre de um lado para o outro, a saltitar de país em país mas sei que terei sempre o vosso apoio e o vosso carinho! Muito obrigado por terem estado sempre presentes na minha vida, mesmo quando era eu que parecia estar mais ausente! O meu último e mais especial agradecimento vai para a Maria. Nós só nos conhecemos a meio desta jornada mas sem ti tudo isto teria sido bem mais difícil. Muito obrigado por toda a força que me deste especialmente quando estávamos separados por todo um oceano. Muito obrigado por acreditares sempre em mim mesmo quando eu próprio duvidava! Acima de tudo, muito obrigado por fazeres parte da minha vida desta forma tão especial. Abstract ................................................................................................... I Resumo .................................................................................................. V Abbreviations ......................................................................................... IX Chapter I - Introduction ........................................................................... 1 1.1 Plant Atypical and Nucellin-like Aspartic Proteases ................................................ 4 Primary structure organization ................................................................................................... 4 Cleavage Specificity and Inhibition ............................................................................................. 7 Distribution and localization ..................................................................................................... 10 1.2 Biological functions of plant atypical and nucellin-like APs ................................... 12 Protein degradation as a nitrogen source ................................................................................. 12 Chloroplast homeostasis and protein turnover ......................................................................... 13 Defense against biotic injury ....................................................................................................
Recommended publications
  • IUB No. Enzyme Name Source Approved in EC 1,4-Alpha-Glucan Bacillus Subtilis JECFA, Denmark, France, Brazil, 2.4.1.18 Branching Enzyme USA (GRAS Notice No
    IUB No. Enzyme name Source Approved in EC 1,4-alpha-glucan Bacillus subtilis JECFA, Denmark, France, Brazil, 2.4.1.18 branching enzyme USA (GRAS Notice No. GRN 00274) Alpha-acetolactate Bacillus subtilis expressed in USA 21 CFR 173.115 decarboxylase Bacillus brevis EC 3.2.1.1 Alpha amylase Aspergillus niger Australia/New Zealand, Canada, France, Brazil, Mexico, USA (GRN 89) Aspergillus oryzae Australia/New Zealand, Canada, France, Brazil, Mexico, USA (GRN 90) Bacillus amyloliquefaciens Australia and New Zealand, Canada, Mexico, Brazil, USA 21 CFR 184.1148 Bacillus licheniformis Belgium, France, China, Japan, Denmark, Australia and New Zealand, Canada, Mexico, Brazil Bacillus licheniformis expressed Australia/New Zealand, Canada, in Bacillus licheniformis France, Brazil, Denmark, Mexico, USA GRAS Notice No. GRN 000079, JECFA Bacillus licheniformis and GRAS Notice No. GRN 00022, Bacillus amyloliquefaciens Brazil, Mexico expressed in Bacillus licheniformis Bacillus amyloliquefaciens Brazil, Denmark, France expressed in Bacillus licheniformis Bacillus megaterium expressed JECFA, Canada, Brazil, Mexico in Bacillus subtilis Bacillus stearothermophilus JECFA, Canada, Brazil, Mexico, USA 21 CFR 184.1012 Bacillus stearothermophilus Australia/New Zealand, Canada, expressed in Bacillus France, Brazil, Denmark, Mexico, licheniformis Japan, GRAS Notice No. GRN 000024 Bacillus stearothermophilus Australia/New Zealand, Canada, expressed in Bacillus subtilis France, Brazil, Denmark, Mexico Bacillus stearothermophilus Australia/New Zealand, Canada, (Geobacillus France, Europa, Brazil, Mexico, stearothermophilus) USA (GRN 594) Bacillus subtilis Australia and New Zealand, Canada, Mexico, Brazil, USA 21 CFR 184.1148 Rhizopus delemar Brazil Rhizopus oryzae Brazil, Mexico, USA GRAS Notice No. GRN 000090 Thermoccocales expressed in Brazil, USA (GRN126) Pseudomonas fluorecens Rhizomucor pusillus expressed Brazil, Denmark, France, Mexico, in Aspergillus niger Australia and New Zealand.
    [Show full text]
  • (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]
  • In Vitro Inhibition of HIV-1 Proteinase by Cerulenin
    View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Elsevier - Publisher Connector Volume 261, number 2, 373-377 FEBS 08165 February 1990 In vitro inhibition of HIV-1 proteinase by cerulenin Karin Moelling, Thomas Schulze, Marie-Theres Knoop, John Kay +, Raymond Jupp +, George Nicolaou* and Laurence H. Pearl* Max-Planck lnstitut fiir Molekular Genetik, lhnestrasse 73, D-IO00 Berlin 33, FRG, +Department of Biochemistry, University College of Wales, PO Box 903, Cardiff CFl 1ST, UK and *Department of Biochemistry, University College London, Gower Street, London WCIE 6BT, UK Received 13 October 1989; revised version received 18 December 1989 Retroviruses encode proteinases necessary for the proteolytic processing of the viral gag and gag-pol precursor proteins. These enzymes have been shown to be structurally and functionally related to aspartyl proteinases such as pepsin and renin. Cerulenin is a naturally occurring antibiotic, commonly used as an inhibitor of fatty acid synthesis. Cerulenin has been observed to inhibit production of Rous sarcoma virus and murine leukae- mia virus by infected cells, possibly by interfering with proteolytic processing of viral precursor proteins. We show here that cerulenin inhibits the action of the HIV-1 proteinase in vitro, using 3 substrates: a synthetic heptapeptide (SQNYPIV) which corresponds to the sequence at the HIV-I gag p17/p24 junction, a bacterially expressed gag precursor, and purified 66 kDa reverse transcriptase. Inhibition of cleavage by HIV-1 proteinase required preincubation with cerulenin. Cerulenin also inactivates endothiapepsin, a well-characterised fungal aspartyl proteinase, sug- gesting that the action of cerulenin is a function of the common active site structure of the retroviral and aspartic proteinases.
    [Show full text]
  • Chymotrypsin-Like Peptidases in Insects
    Chymotrypsin-like peptidases in insects Dissertation zur Erlangung des akademischen Grades Doctor rerum naturalium (Dr. rer. nat.) Fachbereich Biologie/Chemie der Universität Osnabrück vorgelegt von Gunnar Bröhan Osnabrück, Mai 2010 TABLE OF CONTENTS I Table of contents 1. Introduction 1 1.1. Serine endopeptidases 1 1.2. The structure of S1A chymotrypsin-like peptidases 2 1.3. Catalytic mechanism of chymotrypsin-like peptidases 6 1.4. Insect chymotrypsin-like peptidases 9 1.4.1. Chymotrypsin-like peptidases in insect immunity 9 1.4.2. Role of chymotrypsin-like peptidases in digestion 14 1.4.3. Involvement of chymotrypsin-like peptidases in molt 16 1.5. Objective of the work 18 2. Material and Methods 20 2.1. Material 20 2.1.1. Culture Media 20 2.1.2. Insects 20 2.2. Molecular biological methods 20 2.2.1. Tissue preparations for total RNA isolation 20 2.2.2. Total RNA isolation 21 2.2.3. Reverse transcription 21 2.2.4. Quantification of nucleic acids 21 2.2.5. Chemical competent Escherichia coli 21 2.2.6. Ligation and transformation in E. coli 21 2.2.7. Preparation of plasmid DNA 22 2.2.8. Restriction enzyme digestion of DNA 22 2.2.9. DNA gel-electrophoresis and DNA isolation 22 2.2.10. Polymerase-chain-reaction based methods 23 2.2.10.1. RACE-PCR 23 2.2.10.2. Quantitative Realtime PCR 23 2.2.10.3. Megaprimer PCR 24 2.2.11. Cloning of insect CTLPs 25 2.2.12. Syntheses of Digoxigenin-labeled DNA and RNA probes 26 2.2.13.
    [Show full text]
  • Concentration of Tissue Angiotensin II Increases with Severity of Experimental Pancreatitis
    MOLECULAR MEDICINE REPORTS 8: 335-338, 2013 Concentration of tissue angiotensin II increases with severity of experimental pancreatitis HIROYUKI FURUKAWA1, ATSUSHI SHINMURA1, HIDEHIRO TAJIMA1, TOMOYA TSUKADA1, SHIN-ICHI NAKANUMA1, KOICHI OKAMOTO1, SEISHO SAKAI1, ISAMU MAKINO1, KEISHI NAKAMURA1, HIRONORI HAYASHI1, KATSUNOBU OYAMA1, MASAFUMI INOKUCHI1, HISATOSHI NAKAGAWARA1, TOMOHARU MIYASHITA1, HIDETO FUJITA1, HIROYUKI TAKAMURA1, ITASU NINOMIYA1; HIROHISA KITAGAWA1, SACHIO FUSHIDA1, TAKASHI FUJIMURA1, TETSUO OHTA1, TOMOHIKO WAKAYAMA2 and SHOICHI ISEKI2 1Department of Gastroenterological Surgery, Division of Cancer Medicine; 2Department of Histology and Embryology, Graduate School of Medical Science, Kanazawa University, Kanazawa, Ishikawa 920-8641, Japan Received January 23, 2013; Accepted May 30, 2013 DOI: 10.3892/mmr.2013.1509 Abstract. Necrotizing pancreatitis is a serious condition that Introduction is associated with high morbidity and mortality. Although vasospasm is reportedly involved in necrotizing pancreatitis, Acute pancreatitis, particularly the necrotizing type, is the underlying mechanism is not completely clear. In addition, associated with high morbidity and mortality. Necrotizing the local renin-angiotensin system has been hypothesized to pancreatitis is characterized by parenchymal non-enhance- be involved in the progression of pancreatitis and trypsin has ment on contrast-enhanced computed tomography images (1). been shown to generate angiotensin II under weakly acidic Although necrosis is irreversible, certain patients exhibiting conditions. However, to the best of our knowledge, no studies this pancreatic parenchymal non-enhancement recover have reported elevated angiotensin II levels in tissue with with normal pancreatic conditions (2). Vasospasm has been pancreatitis. In the present study, the concentration of pancre- implicated in the development of pancreatic ischemia and atic angiotensin II in rats with experimentally induced acute necrosis (3); however, the precise underlying mechanism is pancreatitis was measured.
    [Show full text]
  • In Escherichia Coli (Synthetic Oligonucleotide/Gene Expression/Industrial Enzyme) J
    Proc. Nati Acad. Sci. USA Vol. 80, pp. 3671-3675, June 1983 Biochemistry Synthesis of calf prochymosin (prorennin) in Escherichia coli (synthetic oligonucleotide/gene expression/industrial enzyme) J. S. EMTAGE*, S. ANGALt, M. T. DOELt, T. J. R. HARRISt, B. JENKINS*, G. LILLEYt, AND P. A. LOWEt Departments of *Molecular Genetics, tMolecular Biology, and tFermentation Development, Celltech Limited, 250 Bath Road, Slough SL1 4DY, Berkshire, United Kingdom Communicated by Sydney Brenner, March 23, 1983 ABSTRACT A gene for calf prochymosin (prorennin) has been maturation conditions and remained insoluble on neutraliza- reconstructed from chemically synthesized oligodeoxyribonucleo- tion, it was possible that purification as well as activation could tides and cloned DNA copies of preprochymosin mRNA. This gene be achieved. has been inserted into a bacterial expression plasmid containing We describe here the construction of E. coli plasmids de- the Escherichia coli tryptophan promoter and a bacterial ribo- signed to express the prochymosin gene from the trp promoter some binding site. Induction oftranscription from the tryptophan and the isolation and conversion of this prochymosin to en- promoter results in prochymosin synthesis at a level of up to 5% active of total protein. The enzyme has been purified from bacteria by zymatically chymosin. extraction with urea and chromatography on DEAE-celiulose and MATERIALS AND METHODS converted to enzymatically active chymosin by acidification and neutralization. Bacterially produced chymosin is as effective in Materials. DNase I, pepstatin A, and phenylmethylsulfonyl clotting milk as the natural enzyme isolated from calf stomach. fluoride were obtained from Sigma. Calf prochymosin (Mr 40,431) and chymosin (Mr 35,612) were purified from stomachs Chymosin (rennin) is an aspartyl proteinase found in the fourth from 1-day-old calves (1).
    [Show full text]
  • Membrane Proteins • Cofactors – Plimstex • Membranes • Dna • Small Molecules/Gas • Large Complexes
    Structural mass spectrometry hydrogen/deuterium exchange Petr Man Structural Biology and Cell Signalling Institute of Microbiology, Czech Academy of Sciences Structural biology methods Low-resolution methods High-resolution methods Rigid SAXS IR Raman CD ITC MST Cryo-EM AUC SPR MS X-ray crystallography Chemical cross-linking H/D exchange Native ESI + ion mobility Oxidative labelling Small Large NMR Dynamic Structural biology approaches Simple MS, quantitative MS Cross-linking, top-down, native MS+dissociation native MS+ion mobility Cross-linking Structural MS What can we get using mass spectrometry IM – ion mobility CXL – chemical cross-linking AP – afinity purification OFP – oxidative footprinting HDX – hydrogen/deuterium exchange ISOTOPE EXCHANGE IN PROTEINS 1H 2H 3H occurence [%] 99.988 0.0115 trace 5 …Kaj Ulrik Linderstrøm-Lang „Cartesian diver“ Proteins are migrating in tubes with density gradient until they stop at the point where the densities are equal 1H 2H 3H % 99.9885 0.0115 trace density [g/cm3] 1.000 1.106 1.215 Methods of detection IR: β-: NMR: 1 n = 1.6749 × 10-27 kg MS: 1H 2H 3H výskyt% [%] 99.9885 0.0115 trace hustotadensity vody [g/cm [g/cm3] 3] 1.000 1.106 1.215 jadernýspinspin ½+ 1+ ½+ mass [u] 1.00783 2.01410 3.01605 Factors affecting H/D exchange hydrogen bonding solvent accessibility Factors affecting H/D exchange Side chains (acidity, steric shielding) Bai et al.: Proteins (1993) Glasoe, Long: J. Phys. Chem. (1960) Factors affecting H/D exchange – side chain effects Inductive effect – electron density is Downward shift due to withdrawn from peptide steric hindrance effect of bond (S, O).
    [Show full text]
  • (12) Patent Application Publication (10) Pub. No.: US 2016/0346364 A1 BRUNS Et Al
    US 2016.0346364A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2016/0346364 A1 BRUNS et al. (43) Pub. Date: Dec. 1, 2016 (54) MEDICAMENT AND METHOD FOR (52) U.S. Cl. TREATING INNATE IMMUNE RESPONSE CPC ........... A61K 38/488 (2013.01); A61K 38/482 DISEASES (2013.01); C12Y 304/23019 (2013.01); C12Y 304/21026 (2013.01); C12Y 304/23018 (71) Applicant: DSM IPASSETS B.V., Heerlen (NL) (2013.01); A61K 9/0053 (2013.01); C12N 9/62 (2013.01); A23L 29/06 (2016.08); A2ID 8/042 (72) Inventors: Maaike Johanna BRUINS, Kaiseraugst (2013.01); A23L 5/25 (2016.08); A23V (CH); Luppo EDENS, Kaiseraugst 2002/00 (2013.01) (CH); Lenneke NAN, Kaiseraugst (CH) (57) ABSTRACT (21) Appl. No.: 15/101,630 This invention relates to a medicament or a dietary Supple (22) PCT Filed: Dec. 11, 2014 ment comprising the Aspergillus niger aspergilloglutamic peptidase that is capable of hydrolyzing plant food allergens, (86). PCT No.: PCT/EP2014/077355 and more particularly, alpha-amylase/trypsin inhibitors, thereby treating diseases due to an innate immune response S 371 (c)(1), in humans, and/or allowing to delay the onset of said (2) Date: Jun. 3, 2016 diseases. The present invention relates to the discovery that (30) Foreign Application Priority Data the Aspergillus niger aspergilloglutamic peptidase is capable of hydrolyzing alpha-amylase/trypsin inhibitors that are Dec. 11, 2013 (EP) .................................. 13196580.8 present in wheat and related cereals said inhibitors being strong inducers of innate immune response. Furthermore, Publication Classification the present invention relates to a method for hydrolyzing alpha-amylase/trypsin inhibitors comprising incubating a (51) Int.
    [Show full text]
  • Structure-Based Optimization of Inhibitors of the Aspartic Protease Endothiapepsin
    Int. J. Mol. Sci. 2015, 16, 19184-19194; doi:10.3390/ijms160819184 OPEN ACCESS International Journal of Molecular Sciences ISSN 1422-0067 www.mdpi.com/journal/ijms Article Structure-Based Optimization of Inhibitors of the Aspartic Protease Endothiapepsin Alwin M. Hartman 1,†, Milon Mondal 1,†, Nedyalka Radeva 2, Gerhard Klebe 2 and Anna K. H. Hirsch 1,* 1 Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands; E-Mails: [email protected] (A.M.H.); [email protected] (M.M.) 2 Institute of Pharmaceutical Chemistry, Philipps-University Marburg, Marbacher Weg 6, 35032 Marburg, Germany; E-Mails: [email protected] (N.R.); [email protected] (G.K.) † These authors contributed equally to this work. * Author to whom correspondence should be addressed; E-Mail: [email protected]; Fax: +31-50-363-4296. Academic Editor: John George Hardy Received: 1 May 2015 / Accepted: 6 July 2015 / Published: 14 August 2015 Abstract: Aspartic proteases are a class of enzymes that play a causative role in numerous diseases such as malaria (plasmepsins), Alzheimer’s disease (β-secretase), fungal infections (secreted aspartic proteases), and hypertension (renin). We have chosen endothiapepsin as a model enzyme of this class of enzymes, for the design, preparation and biochemical evaluation of a new series of inhibitors of endothiapepsin. Here, we have optimized a hit, identified by de novo structure-based drug design (SBDD) and DCC, by using structure-based design approaches focusing on the optimization of an amide–π interaction. Biochemical results are in agreement with SBDD.
    [Show full text]
  • Progress in the Field of Aspartic Proteinases in Cheese Manufacturing
    Progress in the field of aspartic proteinases in cheese manufacturing: structures, functions, catalytic mechanism, inhibition, and engineering Sirma Yegin, Peter Dekker To cite this version: Sirma Yegin, Peter Dekker. Progress in the field of aspartic proteinases in cheese manufacturing: structures, functions, catalytic mechanism, inhibition, and engineering. Dairy Science & Technology, EDP sciences/Springer, 2013, 93 (6), pp.565-594. 10.1007/s13594-013-0137-2. hal-01201447 HAL Id: hal-01201447 https://hal.archives-ouvertes.fr/hal-01201447 Submitted on 17 Sep 2015 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. Dairy Sci. & Technol. (2013) 93:565–594 DOI 10.1007/s13594-013-0137-2 REVIEW PAPER Progress in the field of aspartic proteinases in cheese manufacturing: structures, functions, catalytic mechanism, inhibition, and engineering Sirma Yegin & Peter Dekker Received: 25 February 2013 /Revised: 16 May 2013 /Accepted: 21 May 2013 / Published online: 27 June 2013 # INRA and Springer-Verlag France 2013 Abstract Aspartic proteinases are an important class of proteinases which are widely used as milk-coagulating agents in industrial cheese production. They are available from a wide range of sources including mammals, plants, and microorganisms.
    [Show full text]
  • Discovery of Digestive Enzymes in Carnivorous Plants with Focus on Proteases
    A peer-reviewed version of this preprint was published in PeerJ on 5 June 2018. View the peer-reviewed version (peerj.com/articles/4914), which is the preferred citable publication unless you specifically need to cite this preprint. Ravee R, Mohd Salleh F‘, Goh H. 2018. Discovery of digestive enzymes in carnivorous plants with focus on proteases. PeerJ 6:e4914 https://doi.org/10.7717/peerj.4914 Discovery of digestive enzymes in carnivorous plants with focus on proteases Rishiesvari Ravee 1 , Faris ‘Imadi Mohd Salleh 1 , Hoe-Han Goh Corresp. 1 1 Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia Corresponding Author: Hoe-Han Goh Email address: [email protected] Background. Carnivorous plants have been fascinating researchers with their unique characters and bioinspired applications. These include medicinal trait of some carnivorous plants with potentials for pharmaceutical industry. Methods. This review will cover recent progress based on current studies on digestive enzymes secreted by different genera of carnivorous plants: Drosera (sundews), Dionaea (Venus flytrap), Nepenthes (tropical pitcher plants), Sarracenia (North American pitcher plants), Cephalotus (Australian pitcher plants), Genlisea (corkscrew plants), and Utricularia (bladderworts). Results. Since the discovery of secreted protease nepenthesin in Nepenthes pitcher, digestive enzymes from carnivorous plants have been the focus of many studies. Recent genomics approaches have accelerated digestive enzyme discovery. Furthermore, the advancement in recombinant technology and protein purification helped in the identification and characterisation of enzymes in carnivorous plants. Discussion. These different aspects will be described and discussed in this review with focus on the role of secreted plant proteases and their potential industrial applications.
    [Show full text]
  • A Label-Free Cellular Proteomics Approach to Decipher the Antifungal Action of Dimiq, a Potent Indolo[2,3- B]Quinoline Agent, Against Candida Albicans Biofilms
    A Label-Free Cellular Proteomics Approach to Decipher the Antifungal Action of DiMIQ, a Potent Indolo[2,3- b]Quinoline Agent, against Candida albicans Biofilms Robert Zarnowski 1,2*, Anna Jaromin 3*, Agnieszka Zagórska 4, Eddie G. Dominguez 1,2, Katarzyna Sidoryk 5, Jerzy Gubernator 3 and David R. Andes 1,2 1 Department of Medicine, School of Medicine & Public Health, University of Wisconsin-Madison, Madison, WI 53706, USA; [email protected] (E.G.D.); [email protected] (D.R.A.) 2 Department of Medical Microbiology, School of Medicine & Public Health, University of Wisconsin-Madison, Madison, WI 53706, USA 3 Department of Lipids and Liposomes, Faculty of Biotechnology, University of Wroclaw, 50-383 Wroclaw, Poland; [email protected] 4 Department of Medicinal Chemistry, Jagiellonian University Medical College, 30-688 Cracow, Poland; [email protected] 5 Department of Pharmacy, Cosmetic Chemicals and Biotechnology, Team of Chemistry, Łukasiewicz Research Network-Industrial Chemistry Institute, 01-793 Warsaw, Poland; [email protected] * Correspondence: [email protected] (R.Z.); [email protected] (A.J.); Tel.: +1-608-265-8578 (R.Z.); +48-71-3756203 (A.J.) Label-Free Cellular Proteomics of Candida albicans biofilms treated with DiMIQ Identified Proteins Accession # Alternate ID Gene names (ORF ) WT DIMIQ Z SCORE Proteins induced by DiMIQ Arginase (EC 3.5.3.1) A0A1D8PP00 CAR1 CAALFM_C504490CA 0.000 6.648 drug induced Glucan 1,3-beta-glucosidase BGL2 (EC 3.2.1.58) (Exo-1Q5AMT2 BGL2 CAALFM_C402250CA
    [Show full text]