#PAGE_PARAMS# #ADS_HEAD_SCRIPTS# #MICRODATA#

Nedd8 hydrolysis by UCH proteases in Plasmodium parasites


Autoři: Maryia Karpiyevich aff001;  Sophie Adjalley aff002;  Marco Mol aff001;  David B. Ascher aff003;  Bethany Mason aff001;  Gerbrand J. van der Heden van Noort aff005;  Heike Laman aff001;  Huib Ovaa aff005;  Marcus C. S. Lee aff002;  Katerina Artavanis-Tsakonas aff001
Působiště autorů: Department of Pathology, University of Cambridge, Cambridge, United Kingdom aff001;  Parasites and Microbes Programme, Wellcome Sanger Institute, Cambridge, United Kingdom aff002;  Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom aff003;  Department of Biochemistry, University of Melbourne, Melbourne, Australia aff004;  Oncode Institute and Department of Cell and Chemical Biology, Leiden University Medical Centre, Leiden, The Netherlands aff005
Vyšlo v časopise: Nedd8 hydrolysis by UCH proteases in Plasmodium parasites. PLoS Pathog 15(10): e32767. doi:10.1371/journal.ppat.1008086
Kategorie: Research Article
doi: https://doi.org/10.1371/journal.ppat.1008086

Souhrn

Plasmodium parasites are the causative agents of malaria, a disease with wide public health repercussions. Increasing drug resistance and the absence of a vaccine make finding new chemotherapeutic strategies imperative. Components of the ubiquitin and ubiquitin-like pathways have garnered increased attention as novel targets given their necessity to parasite survival. Understanding how these pathways are regulated in Plasmodium and identifying differences to the host is paramount to selectively interfering with parasites. Here, we focus on Nedd8 modification in Plasmodium falciparum, given its central role to cell division and DNA repair, processes critical to Plasmodium parasites given their unusual cell cycle and requirement for refined repair mechanisms. By applying a functional chemical approach, we show that deNeddylation is controlled by a different set of enzymes in the parasite versus the human host. We elucidate the molecular determinants of the unusual dual ubiquitin/Nedd8 recognition by the essential PfUCH37 enzyme and, through parasite transgenics and drug assays, determine that only its ubiquitin activity is critical to parasite survival. Our experiments reveal interesting evolutionary differences in how neddylation is controlled in higher versus lower eukaryotes, and highlight the Nedd8 pathway as worthy of further exploration for therapeutic targeting in antimalarial drug design.

Klíčová slova:

Crystal structure – Enzymes – Hydrolysis – Malarial parasites – Parasitic diseases – Plasmodium – Plasmodium falciparum – Proteasomes


Zdroje

1. Hershko A, Ciechanover A. The ubiquitin system. Annu Rev Biochem. 1998;67: 425–479. doi: 10.1146/annurev.biochem.67.1.425 9759494

2. Shabek N, Ciechanover A. Degradation of ubiquitin: the fate of the cellular reaper. Cell Cycle. 2010;9: 523–530. doi: 10.4161/cc.9.3.11152 20107325

3. Alan L. Schwartz MD, Aaron Ciechanover P. The ubiquitin-proteasome pathway and pathogenesis of human diseases. Annu Rev Med. 1999;50: 57–74. doi: 10.1146/annurev.med.50.1.57 10073263

4. Shen M, Schmitt S, Buac D, Dou QP. Targeting the ubiquitin-proteasome system for cancer therapy. Expert Opin Ther Targets. 2013;17: 1091–1108. doi: 10.1517/14728222.2013.815728 23822887

5. Ciechanover A, Schwartz AL. The ubiquitin system: pathogenesis of human diseases and drug targeting. Biochim Biophys Acta. 2004;1695: 3–17. doi: 10.1016/j.bbamcr.2004.09.018 15571805

6. Zhang J, Wu P, Hu Y. Clinical and marketed proteasome inhibitors for cancer treatment. Curr Med Chem. 2013;20: 2537–2551. doi: 10.2174/09298673113209990122 23531219

7. Kattenhorn LM, Korbel GA, Kessler BM, Spooner E, Ploegh HL. A deubiquitinating enzyme encoded by HSV-1 belongs to a family of cysteine proteases that is conserved across the family Herpesviridae. Mol Cell. 2005;19: 547–557. doi: 10.1016/j.molcel.2005.07.003 16109378

8. Zhang Y, Higashide WM, McCormick BA, Chen J, Zhou D. The inflammation-associated Salmonella SopA is a HECT-like E3 ubiquitin ligase. Mol Microbiol. 2006;62: 786–793. doi: 10.1111/j.1365-2958.2006.05407.x 17076670

9. Ye Z, Petrof EO, Boone D, Claud EC, Sun J. Salmonella effector AvrA regulation of colonic epithelial cell inflammation by deubiquitination. Am J Pathol. 2007;171: 882–892. doi: 10.2353/ajpath.2007.070220 17690189

10. Hashimoto M, Murata E, Aoki T. Secretory protein with RING finger domain (SPRING) specific to Trypanosoma cruzi is directed, as a ubiquitin ligase related protein, to the nucleus of host cells. Cell Microbiol. 2010;12: 19–30. doi: 10.1111/j.1462-5822.2009.01375.x 19702650

11. Bougdour A, Durandau E, Brenier-Pinchart M-P, Ortet P, Barakat M, Kieffer S, et al. Host cell subversion by Toxoplasma GRA16, an exported dense granule protein that targets the host cell nucleus and alters gene expression. Cell Host Microbe. 2013;13: 489–500. doi: 10.1016/j.chom.2013.03.002 23601110

12. Ponder EL, Bogyo M. Ubiquitin-like modifiers and their deconjugating enzymes in medically important parasitic protozoa. Eukaryot Cell. 2007;6: 1943–1952. doi: 10.1128/EC.00282-07 17905920

13. Pereira RV, de Gomes MS, Jannotti-Passos LK, Borges WC, Guerra-Sá R. Characterisation of the COP9 signalosome in Schistosoma mansoni parasites. Parasitol Res. 2013;112: 2245–2253. doi: 10.1007/s00436-013-3384-5 23519425

14. Chung D-WD, Ponts N, Prudhomme J, Rodrigues EM, Le Roch KG. Characterization of the Ubiquitylating Components of the Human Malaria Parasite’s Protein Degradation Pathway [Internet]. PLoS ONE. 2012. p. e43477. doi: 10.1371/journal.pone.0043477 22912882

15. Li H, O’Donoghue AJ, van der Linden WA, Xie SC, Yoo E, Foe IT, et al. Structure- and function-based design of Plasmodium-selective proteasome inhibitors. Nature. 2016;530: 233–236. doi: 10.1038/nature16936 26863983

16. Pereira PHS, Scarpelli Pereira PH, Curra C, Garcia CRS. Ubiquitin Proteasome System as a Potential Drug Target for Malaria [Internet]. Current Topics in Medicinal Chemistry. 2018. pp. 315–320. doi: 10.2174/1568026618666180427145308 29701143

17. Yoo E, Stokes BH, de Jong H, Vanaerschot M, Kumar T, Lawrence N, et al. Defining the Determinants of Specificity of Plasmodium Proteasome Inhibitors. J Am Chem Soc. 2018;140: 11424–11437. doi: 10.1021/jacs.8b06656 30107725

18. Frickel E-M, Quesada V, Muething L, Gubbels M-J, Spooner E, Ploegh H, et al. Apicomplexan UCHL3 retains dual specificity for ubiquitin and Nedd8 throughout evolution. Cell Microbiol. 2007;9: 1601–1610. doi: 10.1111/j.1462-5822.2007.00896.x 17371404

19. Artavanis-Tsakonas K, Misaghi S, Comeaux CA, Catic A, Spooner E, Duraisingh MT, et al. Identification by functional proteomics of a deubiquitinating/deNeddylating enzyme in Plasmodium falciparum. Mol Microbiol. 2006;61: 1187–1195. doi: 10.1111/j.1365-2958.2006.05307.x 16925553

20. Artavanis-Tsakonas K, Weihofen WA, Antos JM, Coleman BI, Comeaux CA, Duraisingh MT, et al. Characterization and structural studies of the Plasmodium falciparum ubiquitin and Nedd8 hydrolase UCHL3. J Biol Chem. 2010;285: 6857–6866. doi: 10.1074/jbc.M109.072405 20042598

21. Cope GA, Suh GSB, Aravind L, Schwarz SE, Zipursky SL, Koonin EV, et al. Role of predicted metalloprotease motif of Jab1/Csn5 in cleavage of Nedd8 from Cul1. Science. 2002;298: 608–611. doi: 10.1126/science.1075901 12183637

22. Gong L, Kamitani T, Millas S, Yeh ETH. Identification of a Novel Isopeptidase with Dual Specificity for Ubiquitin- and NEDD8-conjugated Proteins. J Biol Chem. 2000;275: 14212–14216. doi: 10.1074/jbc.275.19.14212 10799498

23. Gan-Erdene T, Nagamalleswari K, Yin L, Wu K, Pan Z-Q, Wilkinson KD. Identification and characterization of DEN1, a deneddylase of the ULP family. J Biol Chem. 2003;278: 28892–28900. doi: 10.1074/jbc.M302890200 12759362

24. Mendoza HM, Shen L-N, Botting C, Lewis A, Chen J, Ink B, et al. NEDP1, a highly conserved cysteine protease that deNEDDylates Cullins. J Biol Chem. 2003;278: 25637–25643. doi: 10.1074/jbc.M212948200 12730221

25. Wu K, Yamoah K, Dolios G, Gan-Erdene T, Tan P, Chen A, et al. DEN1 is a dual function protease capable of processing the C terminus of Nedd8 and deconjugating hyper-neddylated CUL1. J Biol Chem. 2003;278: 28882–28891. doi: 10.1074/jbc.M302888200 12759363

26. Wada H, Kito K, Caskey LS, Yeh ET, Kamitani T. Cleavage of the C-terminus of NEDD8 by UCH-L3. Biochem Biophys Res Commun. 1998;251: 688–692. doi: 10.1006/bbrc.1998.9532 9790970

27. Johnston SC, Larsen CN, Cook WJ, Wilkinson KD, Hill CP. Crystal structure of a deubiquitinating enzyme (human UCH-L3) at 1.8 A resolution. EMBO J. 1997;16: 3787–3796. doi: 10.1093/emboj/16.13.3787 9233788

28. Misaghi S, Galardy PJ, Meester WJN, Ovaa H, Ploegh HL, Gaudet R. Structure of the ubiquitin hydrolase UCH-L3 complexed with a suicide substrate. J Biol Chem. 2005;280: 1512–1520. doi: 10.1074/jbc.M410770200 15531586

29. Popp MW, Artavanis-Tsakonas K, Ploegh HL. Substrate filtering by the active site crossover loop in UCHL3 revealed by sortagging and gain-of-function mutations. J Biol Chem. 2009;284: 3593–3602. doi: 10.1074/jbc.M807172200 19047059

30. Borodovsky A, Kessler BM, Casagrande R, Overkleeft HS, Wilkinson KD, Ploegh HL. A novel active site-directed probe specific for deubiquitylating enzymes reveals proteasome association of USP14. EMBO J. 2001;20: 5187–5196. doi: 10.1093/emboj/20.18.5187 11566882

31. Hemelaar J, Galardy PJ, Borodovsky A, Kessler BM, Ploegh HL, Ovaa H. Chemistry-based functional proteomics: mechanism-based activity-profiling tools for ubiquitin and ubiquitin-like specific proteases. J Proteome Res. 2004;3: 268–276. 15113103

32. Shin Y-C, Chen J-H, Chang S-C. The molecular determinants for distinguishing between ubiquitin and NEDD8 by USP2. Sci Rep. 2017;7: 2304. doi: 10.1038/s41598-017-02322-x 28536428

33. Shen L-N, Liu H, Dong C, Xirodimas D, Naismith JH, Hay RT. Structural basis of NEDD8 ubiquitin discrimination by the deNEDDylating enzyme NEDP1. EMBO J. 2005;24: 1341–1351. doi: 10.1038/sj.emboj.7600628 15775960

34. Ekkebus R, van Kasteren SI, Kulathu Y, Scholten A, Berlin I, Geurink PP, et al. On terminal alkynes that can react with active-site cysteine nucleophiles in proteases. J Am Chem Soc. 2013;135: 2867–2870. doi: 10.1021/ja309802n 23387960

35. Zhang M, Wang C, Otto TD, Oberstaller J, Liao X, Adapa SR, et al. Uncovering the essential genes of the human malaria parasite Plasmodium falciparum by saturation mutagenesis. Science. 2018;360. doi: 10.1126/science.aap7847 29724925

36. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004;32: 1792–1797. doi: 10.1093/nar/gkh340 15034147

37. White RR, Miyata S, Papa E, Spooner E, Gounaris K, Selkirk ME, et al. Characterisation of the Trichinella spiralis deubiquitinating enzyme, TsUCH37, an evolutionarily conserved proteasome interaction partner. PLoS Negl Trop Dis. 2011;5: e1340. doi: 10.1371/journal.pntd.0001340 22013496

38. Johnston SC, Riddle SM, Cohen RE, Hill CP. Structural basis for the specificity of ubiquitin C-terminal hydrolases. EMBO J. 1999;18: 3877–3887. doi: 10.1093/emboj/18.14.3877 10406793

39. Muralidharan V, Goldberg DE. Asparagine repeats in Plasmodium falciparum proteins: good for nothing? PLoS Pathog. 2013;9: e1003488. doi: 10.1371/journal.ppat.1003488 23990777

40. Muralidharan V, Oksman A, Iwamoto M, Wandless TJ, Goldberg DE. Asparagine repeat function in a Plasmodium falciparum protein assessed via a regulatable fluorescent affinity tag. Proc Natl Acad Sci U S A. 2011;108: 4411–4416. doi: 10.1073/pnas.1018449108 21368162

41. Pires DEV, Ascher DB, Blundell TL. mCSM: predicting the effects of mutations in proteins using graph-based signatures. Bioinformatics. 2014;30: 335–342. doi: 10.1093/bioinformatics/btt691 24281696

42. Al-Shami A, Jhaver KG, Vogel P, Wilkins C, Humphries J, Davis JJ, et al. Regulators of the proteasome pathway, Uch37 and Rpn13, play distinct roles in mouse development. PLoS One. 2010;5: e13654. doi: 10.1371/journal.pone.0013654 21048919

43. Gomes AR, Bushell E, Schwach F, Girling G, Anar B, Quail MA, et al. A genome-scale vector resource enables high-throughput reverse genetic screening in a malaria parasite. Cell Host Microbe. 2015;17: 404–413. doi: 10.1016/j.chom.2015.01.014 25732065

44. O’Donoghue JE, Bech-Otschir D, Larsen IB, Wallace M, Hartmann-Petersen R, Gordon C. Nedd8 processing enzymes in Schizosaccharomyces pombe. BMC Biochem. 2013;14: 8. doi: 10.1186/1471-2091-14-8 23496905

45. Guan J, Yu S, Zheng X. NEDDylation antagonizes ubiquitination of proliferating cell nuclear antigen and regulates the recruitment of polymerase η in response to oxidative DNA damage. Protein Cell. 2018;9: 365–379. doi: 10.1007/s13238-017-0455-x 28831681

46. Keuss MJ, Hjerpe R, Hsia O, Gourlay R, Burchmore R, Trost M, et al. Unanchored tri-NEDD8 inhibits PARP-1 to protect from oxidative stress-induced cell death. EMBO J. 2019;38. doi: 10.15252/embj.2018100024 30804002

47. Bett JS, Ritorto MS, Ewan R, Jaffray EG, Virdee S, Chin JW, et al. Ubiquitin C-terminal hydrolases cleave isopeptide-and peptide-linked ubiquitin from structured proteins but do not edit ubiquitin homopolymers. Biochem J. 2015;466: 489–498. doi: 10.1042/BJ20141349 25489924

48. Tateishi K, Omata M, Tanaka K, Chiba T. The NEDD8 system is essential for cell cycle progression and morphogenetic pathway in mice. J Cell Biol. 2001;155: 571–579. doi: 10.1083/jcb.200104035 11696557

49. Dharmasiri S, Dharmasiri N, Hellmann H, Estelle M. The RUB/Nedd8 conjugation pathway is required for early development in Arabidopsis. EMBO J. 2003;22: 1762–1770. doi: 10.1093/emboj/cdg190 12682009

50. Ou C-Y, Lin Y-F, Chen Y-J, Chien C-T. Distinct protein degradation mechanisms mediated by Cul1 and Cul3 controlling Ci stability in Drosophila eye development. Genes Dev. 2002;16: 2403–2414. doi: 10.1101/gad.1011402 12231629

51. Jones D, Candido EP. The NED-8 conjugating system in Caenorhabditis elegans is required for embryogenesis and terminal differentiation of the hypodermis. Dev Biol. 2000;226: 152–165. doi: 10.1006/dbio.2000.9847 10993680

52. Osaka F, Saeki M, Katayama S, Aida N, Toh‐e A, Kominami K, et al. Covalent modifier NEDD8 is essential for SCF ubiquitin‐ligase in fission yeast. EMBO J. 2000;19: 3475–3484. doi: 10.1093/emboj/19.13.3475 10880460

53. Liao S, Hu H, Wang T, Tu X, Li Z. The Protein Neddylation Pathway in Trypanosoma brucei: functional characterization and substrate identification. J Biol Chem. 2017; Available: http://www.jbc.org/content/292/3/1081.short

54. Yao T, Song L, Xu W, DeMartino GN, Florens L, Swanson SK, et al. Proteasome recruitment and activation of the Uch37 deubiquitinating enzyme by Adrm1. Nat Cell Biol. 2006;8: 994–1002. doi: 10.1038/ncb1460 16906146

55. Trager W, Jensen JB. Human malaria parasites in continuous culture. Science. 1976;193: 673–675. doi: 10.1126/science.781840 781840

56. Schlieker C, Weihofen WA, Frijns E, Kattenhorn LM, Gaudet R, Ploegh HL. Structure of a herpesvirus-encoded cysteine protease reveals a unique class of deubiquitinating enzymes. Mol Cell. 2007;25: 677–687. doi: 10.1016/j.molcel.2007.01.033 17349955

57. Lim MY-X, LaMonte G, Lee MCS, Reimer C, Tan BH, Corey V, et al. UDP-galactose and acetyl-CoA transporters as Plasmodium multidrug resistance genes. Nat Microbiol. 2016; 16166. doi: 10.1038/nmicrobiol.2016.166 27642791

58. Baragaña B, Hallyburton I, Lee MCS, Norcross NR, Grimaldi R, Otto TD, et al. A novel multiple-stage antimalarial agent that inhibits protein synthesis. Nature. 2015;522: 315–320. doi: 10.1038/nature14451 26085270

59. Sali A, Blundell TL. Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol. 1993;234: 779–815. doi: 10.1006/jmbi.1993.1626 8254673

60. Eisenberg D, Lüthy R, Bowie JU. VERIFY3D: assessment of protein models with three-dimensional profiles. Methods Enzymol. 1997;277: 396–404. doi: 10.1016/s0076-6879(97)77022-8 9379925

61. Jubb H, Blundell TL, Ascher DB. Flexibility and small pockets at protein–protein interfaces: New insights into druggability. Prog Biophys Mol Biol. 2015;119: 2–9. doi: 10.1016/j.pbiomolbio.2015.01.009 25662442

62. Pires DEV, Ascher DB, Blundell TL. DUET: a server for predicting effects of mutations on protein stability using an integrated computational approach. Nucleic Acids Res. 2014;42: W314–9. doi: 10.1093/nar/gku411 24829462

63. Pires DEV, Chen J, Blundell TL, Ascher DB. In silico functional dissection of saturation mutagenesis: Interpreting the relationship between phenotypes and changes in protein stability, interactions and activity. Sci Rep. 2016;6: 19848. doi: 10.1038/srep19848 26797105

64. Jubb HC, Higueruelo AP, Ochoa-Montaño B, Pitt WR, Ascher DB, Blundell TL. Arpeggio: A Web Server for Calculating and Visualising Interatomic Interactions in Protein Structures. J Mol Biol. 2017;429: 365–371. doi: 10.1016/j.jmb.2016.12.004 27964945

Štítky
Hygiena a epidemiologie Infekční lékařství Laboratoř

Článek vyšel v časopise

PLOS Pathogens


2019 Číslo 10
Nejčtenější tento týden
Nejčtenější v tomto čísle
Kurzy

Zvyšte si kvalifikaci online z pohodlí domova

Svět praktické medicíny 1/2024 (znalostní test z časopisu)
nový kurz

Koncepce osteologické péče pro gynekology a praktické lékaře
Autoři: MUDr. František Šenk

Sekvenční léčba schizofrenie
Autoři: MUDr. Jana Hořínková

Hypertenze a hypercholesterolémie – synergický efekt léčby
Autoři: prof. MUDr. Hana Rosolová, DrSc.

Význam metforminu pro „udržitelnou“ terapii diabetu
Autoři: prof. MUDr. Milan Kvapil, CSc., MBA

Všechny kurzy
Kurzy Podcasty Doporučená témata Časopisy
Přihlášení
Zapomenuté heslo

Zadejte e-mailovou adresu, se kterou jste vytvářel(a) účet, budou Vám na ni zaslány informace k nastavení nového hesla.

Přihlášení

Nemáte účet?  Registrujte se

#ADS_BOTTOM_SCRIPTS#