The minimal kinome of Giardia lamblia illuminates early kinase evolution and unique parasite biology
Tóm tắt
The major human intestinal pathogen Giardia lamblia is a very early branching eukaryote with a minimal genome of broad evolutionary and biological interest. To explore early kinase evolution and regulation of Giardia biology, we cataloged the kinomes of three sequenced strains. Comparison with published kinomes and those of the excavates Trichomonas vaginalis and Leishmania major shows that Giardia's 80 core kinases constitute the smallest known core kinome of any eukaryote that can be grown in pure culture, reflecting both its early origin and secondary gene loss. Kinase losses in DNA repair, mitochondrial function, transcription, splicing, and stress response reflect this reduced genome, while the presence of other kinases helps define the kinome of the last common eukaryotic ancestor. Immunofluorescence analysis shows abundant phospho-staining in trophozoites, with phosphotyrosine abundant in the nuclei and phosphothreonine and phosphoserine in distinct cytoskeletal organelles. The Nek kinase family has been massively expanded, accounting for 198 of the 278 protein kinases in Giardia. Most Neks are catalytically inactive, have very divergent sequences and undergo extensive duplication and loss between strains. Many Neks are highly induced during development. We localized four catalytically active Neks to distinct parts of the cytoskeleton and one inactive Nek to the cytoplasm. The reduced kinome of Giardia sheds new light on early kinase evolution, and its highly divergent sequences add to the definition of individual kinase families as well as offering specific drug targets. Giardia's massive Nek expansion may reflect its distinctive lifestyle, biphasic life cycle and complex cytoskeleton.
Tài liệu tham khảo
Holt LJ, Tuch BB, Villen J, Johnson AD, Gygi SP, Morgan DO: Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution. Science. 2009, 325: 1682–1686. 10.1126/science.1172867.
Adam RD: Biology of Giardia lamblia. Clin Microbiol Rev. 2001, 14: 447–475. 10.1128/CMR.14.3.447-475.2001.
Bingham AK, Meyer EA: Giardia excystation can be induced in vitro in acidic solutions. Nature. 1979, 277: 301–302. 10.1038/277301a0.
Boucher SE, Gillin FD: Excystation of in vitro-derived Giardia lamblia cysts. Infec Immun. 1990, 58: 3516–3522.
Bernander R, Palm JE, Svard SG: Genome ploidy in different stages of the Giardia lamblia life cycle. Cell Microbiol. 2001, 3: 55–62. 10.1046/j.1462-5822.2001.00094.x.
Elmendorf HG, Dawson SC, McCaffery JM: The cytoskeleton of Giardia lamblia. Int J Parasitol. 2003, 33: 3–28. 10.1016/S0020-7519(02)00228-X.
Dawson SC, House SA: Life with eight flagella: flagellar assembly and division in Giardia. Curr Opin Microbiol. 2010, 13: 480–490. 10.1016/j.mib.2010.05.014.
Morrison HG, McArthur AG, Gillin FD, Aley SB, Adam RD, Olsen GJ, Best AA, Cande WZ, Chen F, Cipriano MJ, Davids BJ, Dawson SC, Elmendorf HG, Hehl AB, Holder ME, Huse SM, Kim UU, Lasek-Nesselquist E, Manning G, Nigam A, Nixon JE, Palm D, Passamaneck NE, Prabhu A, Reich CI, Reiner DS, Samuelson J, Svard SG, Sogin ML: Genomic minimalism in the early diverging intestinal parasite Giardia lamblia. Science. 2007, 317: 1921–1926. 10.1126/science.1143837.
Franzen O, Jerlstrom-Hultqvist J, Castro E, Sherwood E, Ankarklev J, Reiner DS, Palm D, Andersson JO, Andersson B, Svard SG: Draft genome sequencing of Giardia intestinalis assemblage B isolate GS: is human Giardiasis caused by two different species?. PLoS Pathog. 2009, 5: e1000560-10.1371/journal.ppat.1000560.
Jerlstrom-Hultqvist J, Franzen O, Ankarklev J, Xu F, Nohynkova E, Andersson JO, Svard SG, Andersson B: Genome analysis and comparative genomics of a Giardia intestinalis assemblage E isolate. BMC Genomics. 2010, 11: 543-10.1186/1471-2164-11-543.
Parsons M, Valentine M, Carter V: Protein kinases in divergent eukaryotes: identification of protein kinase activities regulated during trypanosome development. Proc Natl Acad Sci USA. 1993, 90: 2656–2660. 10.1073/pnas.90.7.2656.
Alvarado ME, Wasserman M: Analysis of phosphorylated proteins and inhibition of kinase activity during Giardia intestinalis excystation. Parasitol Int. 2010, 59: 54–61. 10.1016/j.parint.2009.10.005.
Abel ES, Davids BJ, Robles LD, Loflin CE, Gillin FD, Chakrabarti R: Possible roles of protein kinase A in cell motility and excystation of the early diverging eukaryote Giardia lamblia. J Biol Chem. 2001, 276: 10320–10329. 10.1074/jbc.M006589200.
Gibson C, Schanen B, Chakrabarti D, Chakrabarti R: Functional characterisation of the regulatory subunit of cyclic AMP-dependent protein kinase A homologue of Giardia lamblia: differential expression of the regulatory and catalytic subunits during encystation. Int J Parasitol. 2006, 36: 791–799. 10.1016/j.ijpara.2005.11.008.
Lauwaet T, Davids BJ, Torres-Escobar A, Birkeland SR, Cipriano MJ, Preheim SP, Palm D, Svard SG, McArthur AG, Gillin FD: Protein phosphatase 2A plays a crucial role in Giardia lamblia differentiation. Mol Biochem Parasitol. 2007, 152: 80–89. 10.1016/j.molbiopara.2006.12.001.
Ellis JGt, Davila M, Chakrabarti R: Potential involvement of extracellular signal-regulated kinase 1 and 2 in encystation of a primitive eukaryote, Giardia lamblia. Stage-specific activation and intracellular localization. J Biol Chem. 2003, 278: 1936–1945. 10.1074/jbc.M209274200.
Aurrecoechea C, Brestelli J, Brunk BP, Carlton JM, Dommer J, Fischer S, Gajria B, Gao X, Gingle A, Grant G, Harb OS, Heiges M, Innamorato F, Iodice J, Kissinger JC, Kraemer E, Li W, Miller JA, Morrison HG, Nayak V, Pennington C, Pinney DF, Roos DS, Ross C, Stoeckert CJ, Sullivan S, Treatman C, Wang H: GiardiaDB and TrichDB: integrated genomic resources for the eukaryotic protist pathogens Giardia lamblia and Trichomonas vaginalis. Nucleic Acids Res. 2009, 37: D526–530. 10.1093/nar/gkn631.
KinBase. [https://doi.org/kinase.com/kinbase/]
Eisen JA, Coyne RS, Wu M, Wu D, Thiagarajan M, Wortman JR, Badger JH, Ren Q, Amedeo P, Jones KM, Tallon LJ, Delcher AL, Salzberg SL, Silva JC, Haas BJ, Majoros WH, Farzad M, Carlton JM, Smith RK, Garg J, Pearlman RE, Karrer KM, Sun L, Manning G, Elde NC, Turkewitz AP, Asai DJ, Wilkes DE, Wang Y, Cai H, et al: Macronuclear genome sequence of the ciliate Tetrahymena thermophila, a model eukaryote. PLoS Biol. 2006, 4: e286-10.1371/journal.pbio.0040286.
Goldberg JM, Manning G, Liu A, Fey P, Pilcher KE, Xu Y, Smith JL: The Dictyostelium kinome--analysis of the protein kinases from a simple model organism. PLoS Genet. 2006, 2: e38-10.1371/journal.pgen.0020038.
Manning G, Plowman GD, Hunter T, Sudarsanam S: Evolution of protein kinase signaling from yeast to man. Trends Biochem Sci. 2002, 27: 514–520. 10.1016/S0968-0004(02)02179-5.
Manning G, Whyte DB, Martinez R, Hunter T, Sudarsanam S: The protein kinase complement of the human genome. Science. 2002, 298: 1912–1934. 10.1126/science.1075762.
Banks Jea: The compact Selaginella genome identifies changes in gene content associated with the evolution of vascular plants. Science. 2011, 332: 960–963. 10.1126/science.1203810.
Bazan-Tejeda ML, Arguello-Garcia R, Bermudez-Cruz RM, Robles-Flores M, Ortega-Pierres G: Protein kinase C isoforms from Giardia duodenalis: identification and functional characterization of a beta-like molecule during encystment. Arch Microbiol. 2007, 187: 55–66.
Lujan HD, Mowatt MR, Helman LJ, Nash TE: Insulin-like growth factors stimulate growth and L-cysteine uptake by the intestinal parasite Giardia lamblia. J Biol Chem. 1994, 269: 13069–13072.
Carlton JM, Hirt RP, Silva JC, Delcher AL, Schatz M, Zhao Q, Wortman JR, Bidwell SL, Alsmark UC, Besteiro S, Sicheritz-Ponten T, Noel CJ, Dacks JB, Foster PG, Simillion C, Van de Peer Y, Miranda-Saavedra D, Barton GJ, Westrop GD, Muller S, Dessi D, Fiori PL, Ren Q, Paulsen I, Zhang H, Bastida-Corcuera FD, Simoes-Barbosa A, Brown MT, Hayes RD, Mukherjee M, et al: Draft genome sequence of the sexually transmitted pathogen Trichomonas vaginalis. Science. 2007, 315: 207–212. 10.1126/science.1132894.
Naula C, Parsons M, Mottram JC: Protein kinases as drug targets in trypanosomes and Leishmania. Biochim Biophys Acta. 2005, 1754: 151–159.
Baldauf SL: The deep roots of eukaryotes. Science. 2003, 300: 1703–1706. 10.1126/science.1085544.
Ankarklev J, Jerlstrom-Hultqvist J, Ringqvist E, Troell K, Svard SG: Behind the smile: cell biology and disease mechanisms of Giardia species. Nat Rev. 2010, 8: 413–422.
Hampl V, Hug L, Leigh JW, Dacks JB, Lang BF, Simpson AG, Roger AJ: Phylogenomic analyses support the monophyly of Excavata and resolve relationships among eukaryotic "supergroups". Proc Natl Acad Sci USA. 2009, 106: 3859–3864. 10.1073/pnas.0807880106.
Regoes A, Zourmpanou D, Leon-Avila G, van der Giezen M, Tovar J, Hehl AB: Protein import, replication, and inheritance of a vestigial mitochondrion. J Biol Chem. 2005, 280: 30557–30563. 10.1074/jbc.M500787200.
Reiner DS, McCaffery JM, Gillin FD: Reversible interruption of Giardia lamblia cyst wall protein transport in a novel regulated secretory pathway. Cell Microbiol. 2001, 3: 459–472. 10.1046/j.1462-5822.2001.00129.x.
Sagolla MS, Dawson SC, Mancuso JJ, Cande WZ: Three-dimensional analysis of mitosis and cytokinesis in the binucleate parasite Giardia intestinalis. J Cell Sci. 2006, 119: 4889–4900. 10.1242/jcs.03276.
Yang J, Yu Y, Hamrick HE, Duerksen-Hughes PJ: ATM, ATR and DNA-PK: initiators of the cellular genotoxic stress responses. Carcinogenesis. 2003, 24: 1571–1580. 10.1093/carcin/bgg137.
Groth A, Lukas J, Nigg EA, Sillje HH, Wernstedt C, Bartek J, Hansen K: Human Tousled like kinases are targeted by an ATM- and Chk1-dependent DNA damage checkpoint. EMBO J. 2003, 22: 1676–1687. 10.1093/emboj/cdg151.
Hofstetrova K, Uzlikova M, Tumova P, Troell K, Svard SG, Nohynkova E: Giardia intestinalis: aphidicolin influence on the trophozoite cell cycle. Exp Parasitol. 2010, 124: 159–166. 10.1016/j.exppara.2009.09.004.
Linden KG, Shin GA, Faubert G, Cairns W, Sobsey MD: UV disinfection of Giardia lamblia cysts in water. Environ Sci Technol. 2002, 36: 2519–2522. 10.1021/es0113403.
Guo Z, Stiller JW: Comparative genomics and evolution of proteins associated with RNA polymerase II C-terminal domain. Mol Biol Evol. 2005, 22: 2166–2178. 10.1093/molbev/msi215.
Lee JM, Greenleaf AL: CTD kinase large subunit is encoded by CTK1, a gene required for normal growth of Saccharomyces cerevisiae. Gene Expression. 1991, 1: 149–167.
Best AA, Morrison HG, McArthur AG, Sogin ML, Olsen GJ: Evolution of eukaryotic transcription: insights from the genome of Giardia lamblia. Genome Res. 2004, 14: 1537–1547. 10.1101/gr.2256604.
Wikinome: Dual Specificity Kinases. [https://doi.org/kinase.com/wiki/index.php/Dual-Specificity_Kinases]
Nett IR, Martin DM, Miranda-Saavedra D, Lamont D, Barber JD, Mehlert A, Ferguson MA: The phosphoproteome of bloodstream form Trypanosoma brucei, causative agent of African sleeping sickness. Mol Cell Proteomics. 2009, 8: 1527–1538. 10.1074/mcp.M800556-MCP200.
Manning G, Young SL, Miller WT, Zhai Y: The protist, Monosiga brevicollis, has a tyrosine kinase signaling network more elaborate and diverse than found in any known metazoan. Proc Natl Acad Sci USA. 2008, 105: 9674–9679. 10.1073/pnas.0801314105.
Lalle M, Salzano AM, Crescenzi M, Pozio E: The Giardia duodenalis 14-3-3 protein is post-translationally modified by phosphorylation and polyglycylation of the C-terminal tail. J Biol Chem. 2006, 281: 5137–5148.
Anamika K, Bhattacharya A, Srinivasan N: Analysis of the protein kinome of Entamoeba histolytica. Proteins. 2008, 71: 995–1006. 10.1002/prot.21790.
Scheeff ED, Eswaran J, Bunkoczi G, Knapp S, Manning G: Structure of the pseudokinase VRK3 reveals a degraded catalytic site, a highly conserved kinase fold, and a putative regulatory binding site. Structure. 2009, 17: 128–138. 10.1016/j.str.2008.10.018.
Kim KT, Mok MT, Edwards MR: Protein kinase B from Giardia intestinalis. Biochem Biophys Res Commun. 2005, 334: 333–341. 10.1016/j.bbrc.2005.06.106.
Hernandez Y, Zamora G, Ray S, Chapoy J, Chavez E, Valvarde R, Williams E, Aley SB, Das S: Transcriptional analysis of three major putative phosphatidylinositol kinase genes in a parasitic protozoan, Giardia lamblia. J Eukaryot Microbiol. 2007, 54: 29–32. 10.1111/j.1550-7408.2006.00142.x.
Cox SS, van der Giezen M, Tarr SJ, Crompton MR, Tovar J: Evidence from bioinformatics, expression and inhibition studies of phosphoinositide-3 kinase signalling in Giardia intestinalis. BMC Microbiol. 2006, 6: 45-10.1186/1471-2180-6-45.
Morrison HG, Zamora G, Campbell RK, Sogin ML: Inferring protein function from genomic sequence: Giardia lamblia expresses a phosphatidylinositol kinase-related kinase similar to yeast and mammalian TOR. Comp Biochem Physiol B Biochem Mol Biol. 2002, 133: 477–491. 10.1016/S1096-4959(02)00218-X.
Ward P, Equinet L, Packer J, Doerig C: Protein kinases of the human malaria parasite Plasmodium falciparum: the kinome of a divergent eukaryote. BMC Genomics. 2004, 5: 79-10.1186/1471-2164-5-79.
Davids BJ, Williams S, Lauwaet T, Palanca T, Gillin FD: Giardia lamblia aurora kinase: a regulator of mitosis in a binucleate parasite. Int J Parasitol. 2008, 38: 353–369. 10.1016/j.ijpara.2007.08.012.
Pan J, Snell WJ: Regulated targeting of a protein kinase into an intact flagellum. An aurora/Ipl1p-like protein kinase translocates from the cell body into the flagella during gamete activation in chlamydomonas. J Biol Chem. 2000, 275: 24106–24114. 10.1074/jbc.M002686200.
O'Connell MJ, Krien MJ, Hunter T: Never say never. The NIMA-related protein kinases in mitotic control. Trends Cell Biol. 2003, 13: 221–228. 10.1016/S0962-8924(03)00056-4.
Mahjoub MR, Qasim Rasi M, Quarmby LM: A NIMA-related kinase, Fa2p, localizes to a novel site in the proximal cilia of Chlamydomonas and mouse kidney cells. Mol Biol Cell. 2004, 15: 5172–5186. 10.1091/mbc.E04-07-0571.
Liu S, Lu W, Obara T, Kuida S, Lehoczky J, Dewar K, Drummond IA, Beier DR: A defect in a novel Nek-family kinase causes cystic kidney disease in the mouse and in zebrafish. Development. 2002, 129: 5839–5846. 10.1242/dev.00173.
Wloga D, Camba A, Rogowski K, Manning G, Jerka-Dziadosz M, Gaertig J: Members of the NIMA-related kinase family promote disassembly of cilia by multiple mechanisms. Mol Biol Cell. 2006, 17: 2799–2810. 10.1091/mbc.E05-05-0450.
Stajich JE, Wilke SK, Ahren D, Au CH, Birren BW, Borodovsky M, Burns C, Canback B, Casselton LA, Cheng CK, Deng J, Dietrich FS, Fargo DC, Farman ML, Gathman AC, Goldberg J, Guigo R, Hoegger PJ, Hooker JB, Huggins A, James TY, Kamada T, Kilaru S, Kodira C, Kues U, Kupfer D, Kwan HS, Lomsadze A, Li W, Lilly WW, et al: Insights into evolution of multicellular fungi from the assembled chromosomes of the mushroom Coprinopsis cinerea (Coprinus cinereus). Proc Natl Acad Sci USA. 2010, 107: 11889–11894. 10.1073/pnas.1003391107.
Jimenez-Garcia LF, Zavala G, Chavez-Munguia B, Ramos-Godinez Mdel P, Lopez-Velazquez G, Segura-Valdez Mde L, Montanez C, Hehl AB, Arguello-Garcia R, Ortega-Pierres G: Identification of nucleoli in the early branching protist Giardia duodenalis. Int J Parasitol. 2008, 38: 1297–1304. 10.1016/j.ijpara.2008.04.012.
Birkeland SR, Preheim SP, Davids BJ, Cipriano MJ, Palm D, Reiner DS, Svard SG, Gillin FD, McArthur AG: Transcriptome analyses of the Giardia lamblia life cycle. Mol Biochem Parasitol. 2010, 174: 62–65. 10.1016/j.molbiopara.2010.05.010.
Pradel LC, Bonhivers M, Landrein N, Robinson DR: NIMA-related kinase TbNRKC is involved in basal body separation in Trypanosoma brucei. J Cell Sci. 2006, 119: 1852–1863. 10.1242/jcs.02900.
Shiba D, Manning DK, Koga H, Beier DR, Yokoyama T: Inv acts as a molecular anchor for Nphp3 and Nek8 in the proximal segment of primary cilia. Cytoskeleton. 2010, 67: 112–119.
Mahjoub MR, Montpetit B, Zhao L, Finst RJ, Goh B, Kim AC, Quarmby LM: The FA2 gene of Chlamydomonas encodes a NIMA family kinase with roles in cell cycle progression and microtubule severing during deflagellation. J Cell Sci. 2002, 115: 1759–1768.
Lauwaet T, Smith AJ, Reiner DS, Romijn EP, Wong CCL, Davids BJ, Shah SA, Yates JR, Gillin FD: Mining the Giardiagenome and proteome for conserved and unique basal body proteins. Int J Parasitol. 2011,
Miranda-Saavedra D, Stark MJ, Packer JC, Vivares CP, Doerig C, Barton GJ: The complement of protein kinases of the microsporidium Encephalitozoon cuniculi in relation to those of Saccharomyces cerevisiae and Schizosaccharomyces pombe. BMC Genomics. 2007, 8: 309-10.1186/1471-2164-8-309.
Kulakova L, Singer SM, Conrad J, Nash TE: Epigenetic mechanisms are involved in the control of Giardia lamblia antigenic variation. Mol Microbiol. 2006, 61: 1533–1542. 10.1111/j.1365-2958.2006.05345.x.
Nohynkova E, Tumova P, Kulda J: Cell division of Giardia intestinalis: flagellar developmental cycle involves transformation and exchange of flagella between mastigonts of a diplomonad cell. Eukaryotic cell. 2006, 5: 753–761. 10.1128/EC.5.4.753-761.2006.
Dawson SC: An insider's guide to the microtubule cytoskeleton of Giardia. Cell Microbiol. 2010, 12: 588–598. 10.1111/j.1462-5822.2010.01458.x.
GiardiaDB. [https://doi.org/Giardiadb.org/]
TrichDB. [https://doi.org/trichdb.org]
TriTrypDB. [https://doi.org/tritrypdb.org]
Sonnhammer EL, von Heijne G, Krogh A: A hidden Markov model for predicting transmembrane helices in protein sequences. Proc Int Conf Intell Syst Mol Biol. 1998, 6: 175–182.
Lupas A, Van Dyke M, Stock J: Predicting coiled coils from protein sequences. Science. 1991, 252: 1162–1164. 10.1126/science.252.5009.1162.
Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG: Clustal W and Clustal × version 2.0. Bioinformatics. 2007, 23: 2947–2948. 10.1093/bioinformatics/btm404.
Eddy SR: A new generation of homology search tools based on probabilistic inference. Genome Informatics. 2009, 23: 205–211.
Waterhouse AM, Procter JB, Martin DM, Clamp M, Barton GJ: Jalview Version 2--a multiple sequence alignment editor and analysis workbench. Bioinformatics. 2009, 25: 1189–1191. 10.1093/bioinformatics/btp033.
Diamond LS, Harlow DR, Cunnick CC: A new medium for the axenic cultivation of Entamoeba histolytica and other Entamoeba. Trans R Soc Trop Med Hyg. 1978, 72: 431–432. 10.1016/0035-9203(78)90144-X.
Keister DB: Axenic culture of Giardia lamblia in TYI-S-33 medium supplemented with bile. Trans R Soc Trop Med Hyg. 1983, 77: 487–488. 10.1016/0035-9203(83)90120-7.
Ward HD, Lev BI, Kane AV, Keusch GT, Pereira ME: Identification and characterization of taglin, a mannose 6-phosphate binding, trypsin-activated lectin from Giardia lamblia. Biochemistry. 1987, 26: 8669–8675. 10.1021/bi00400a027.
Weiland ME, Palm JE, Griffiths WJ, McCaffery JM, Svard SG: Characterisation of alpha-1 giardin: an immunodominant Giardia lamblia annexin with glycosaminoglycan-binding activity. Int J Parasitol. 2003, 33: 1341–1351. 10.1016/S0020-7519(03)00201-7.
Touz MC, Lujan HD, Hayes SF, Nash TE: Sorting of encystation-specific cysteine protease to lysosome-like peripheral vacuoles in Giardia lamblia requires a conserved tyrosine-based motif. J Biol Chem. 2003, 278: 6420–6426. 10.1074/jbc.M208354200.
Knodler LA, Svard SG, Silberman JD, Davids BJ, Gillin FD: Developmental gene regulation in Giardia lamblia: first evidence for an encystation-specific promoter and differential 5' mRNA processing. Mol Microbiol. 1999, 34: 327–340. 10.1046/j.1365-2958.1999.01602.x.