1887

Abstract

Diplomonad parasites of the genus have adapted to colonizing different hosts, most notably the intestinal tract of mammals. The human-pathogenic species, , has been extensively studied at the genome and gene expression level, but no such information is available for other species. Comparative data would be particularly valuable for , which colonizes mice and is commonly used as a prototypic model for investigating host responses to intestinal parasitic infection. Here we report the draft-genome of . We discovered a highly streamlined genome, amongst the most densely encoded ever described for a nuclear eukaryotic genome. and share many known or predicted virulence factors, including cysteine proteases and a large repertoire of cysteine-rich surface proteins involved in antigenic variation. Different to , maintains tandem arrays of pseudogenized surface antigens at the telomeres, whereas intact surface antigens are present centrally in the chromosomes. The two classes of surface antigens engage in genetic exchange. Reconstruction of metabolic pathways from the genome suggest significant metabolic differences to . Additionally, encodes proteins that might be used to modulate the prokaryotic microbiota. The responsible genes have been introduced in the genus via lateral gene transfer from prokaryotic sources. Our findings point to important evolutionary steps in the genus as it adapted to different hosts and it provides a powerful foundation for mechanistic exploration of host–pathogen interaction in the –mouse pathosystem.

Funding
This study was supported by the:
  • Staffan G Svärd , Vetenskapsrådet , (Award 2017-02918)
  • Lars Eckmann , National Institutes of Health , (Award P30 DK120515)
Loading

Article metrics loading...

/content/journal/mgen/10.1099/mgen.0.000402
2020-07-03
2020-09-19
Loading full text...

Full text loading...

/deliver/fulltext/mgen/6/8/mgen000402.html?itemId=/content/journal/mgen/10.1099/mgen.0.000402&mimeType=html&fmt=ahah

References

  1. Poulin R, Randhawa HS. Evolution of parasitism along convergent lines: from ecology to genomics. Parasitology 2015; 142:S6–S15
    [Google Scholar]
  2. Hupalo DN, Bradic M, Carlton JM. The impact of genomics on population genetics of parasitic diseases. Curr Opin Microbiol 2015; 23:49–54
    [Google Scholar]
  3. Jackson AP, Otto TD, Aslett M, Armstrong SD, Bringaud F et al. Kinetoplastid phylogenomics reveals the evolutionary innovations associated with the origins of parasitism. Current Biology 2016; 26:161–172
    [Google Scholar]
  4. Einarsson E, Ma’ayeh S, Svärd SG. An up-date on Giardia and giardiasis. Curr Opin Microbiol 2016; 34:47–52
    [Google Scholar]
  5. Cacciò SM, Lalle M, Svärd SG. Host specificity in the Giardia duodenalis species complex. Infect. Genet. Evol 2018; 66:335–345
    [Google Scholar]
  6. Fink MY, Singer SM. The intersection of immune responses, microbiota, and pathogenesis in giardiasis. Trends in Parasitology 2017; 33:901–913
    [Google Scholar]
  7. Ma’ayeh SY, Knörr L, Sköld K, Granham A, Ansell BRE et al. Responses of the differentiated intestinal epithelial cell line Caco-2 to infection with the Giardia intestinalis Gs isolate. Front Cell Infect Microbiol 2018; 8:244
    [Google Scholar]
  8. Ma’ayeh SY, Liu J, Peirasmaki D, Hörnaeus K, Bergström Lind S et al. Characterization of the Giardia intestinalis secretome during interaction with human intestinal epithelial cells: the impact on host cells. PLOS Neglected Tropical Diseases 2017; 11:e0006120
    [Google Scholar]
  9. Nosala C, Hagen KD, Dawson SC. ‘Disc-o-Fever’: getting down with giardia’s groovy microtubule organelle. Trends in Cell Biology 2018; 28:99–112
    [Google Scholar]
  10. Nosala C, Dawson SC. The critical role of the cytoskeleton in the pathogenesis of Giardia. Clin Microbiol Rev Report 2015; 2:155–162
    [Google Scholar]
  11. McInally SG, Dawson SC. Eight unique basal bodies in the multi-flagellated diplomonad Giardia lamblia. Cilia 2016; 5:
    [Google Scholar]
  12. Liu J, Ma’ayeh S, Peirasmaki D, Lundström-Stadelmann B, Hellman L et al. Secreted Giardia intestinalis cysteine proteases disrupt intestinal epithelial cell junctional complexes and degrade chemokines. Virulence 2018; 9:879–894
    [Google Scholar]
  13. Ortega-Pierres G, Argüello-García R, Laredo-Cisneros MS, Fonseca-Linán R, Gómez-Mondragón M et al. Giardipain-1, a protease secreted by Giardia duodenalis trophozoites, causes junctional, barrier and apoptotic damage in epithelial cell monolayers. Int J Parasitol 2018; 48:621–639
    [Google Scholar]
  14. Amat CB, Motta J-P, Fekete E, Moreau F, Chadee K et al. Cysteine Protease–Dependent mucous disruptions and differential mucin gene expression in Giardia duodenalis infection. The American Journal of Pathology 2017; 187:2486–2498
    [Google Scholar]
  15. Cotton JA, Bhargava A, Ferraz JG, Yates RM, Beck PL et al. Giardia duodenalis cathepsin B proteases degrade intestinal epithelial interleukin-8 and attenuate interleukin-8-induced neutrophil chemotaxis. Infection and Immunity 2014; 82:2772–2787
    [Google Scholar]
  16. Cotton JA, Motta J-P, Schenck LP, Hirota SA, Beck PL et al. Giardia duodenalis infection reduces granulocyte infiltration in an in vivo model of bacterial toxin-induced colitis and attenuates inflammation in human intestinal tissue. PLoS ONE 2014; 9:e109087
    [Google Scholar]
  17. Allain T, Amat CB, Motta J-P, Manko A, Buret AG. Interactions of Giardia sp. with the intestinal barrier: epithelium, mucus, and microbiota. Tissue Barriers 2017; 5:e1274354
    [Google Scholar]
  18. Mendez TL, De Chatterjee A, Duarte T, De Leon J, Robles-Martinez L et al. And giardial encystation: the show must go on. Curr Trop Med Rep 2015; 2:136–143
    [Google Scholar]
  19. Stadelmann B, Merino MC, Persson L, Svärd SG. Arginine consumption by the intestinal parasite Giardia intestinalis reduces proliferation of intestinal epithelial cells. PLoS ONE 2012; 7:
    [Google Scholar]
  20. Eckmann L, Laurent F, Langford TD, Hetsko ML, Smith JR et al. Nitric oxide production by human intestinal epithelial cells and competition for arginine as potential determinants of host defense against the Lumen-Dwelling pathogen Giardia lamblia. J Immunol 2000; 164:1478–1487
    [Google Scholar]
  21. Helmy YA, Spierling NG, Schmidt S, Rosenfeld UM, Reil D et al. Occurrence and distribution of Giardia species in wild rodents in Germany. Parasites & Vectors 2018; 11:
    [Google Scholar]
  22. Friend DS. The fine structure of Giardia muris. J Cell Biol 1966; 29:317–332
    [Google Scholar]
  23. Dann SM, Le CHY HEM, Ross MC, Eckmann L. Giardia infection of the small intestine induces chronic colitis in genetically susceptible hosts. J Immunol 2018; 201:548–559
    [Google Scholar]
  24. Holberton DV. Fine structure of the ventral disk apparatus and the mechanism of attachment in the flagellate Giardia muris. J Cell Sci 1973; 13:11–41
    [Google Scholar]
  25. Schaefer FW, Rice EW, Hoff JC. Factors promoting in vitro excystation of Giardia muris cysts. Trans R Soc Trop Med Hyg 1984; 78:795–800
    [Google Scholar]
  26. Langford TD, Housley MP, Boes M, Chen J, Kagnoff MF et al. Central importance of immunoglobulin A in host defense against Giardia spp. Infect Immun 2002; 70:11–18
    [Google Scholar]
  27. Davids BJ, Palm JED, Housley MP, Smith JR, Andersen YS et al. Polymeric immunoglobulin receptor in intestinal immune defense against the lumen-dwelling protozoan parasite Giardia. J Immunol 2006; 177:6281–6290
    [Google Scholar]
  28. Dreesen L, De Bosscher K, Grit G, Staels B, Lubberts E et al. Giardia muris infection in mice is associated with a protective interleukin 17A response and induction of peroxisome proliferator-activated receptor alpha. Infect Immun 2014; 82:3333–3340
    [Google Scholar]
  29. Manko A, Motta J-P, Cotton JA, Feener T, Oyeyemi A et al. Giardia co-infection promotes the secretion of antimicrobial peptides beta-defensin 2 and trefoil factor 3 and attenuates attaching and effacing bacteria-induced intestinal disease. Plos One 2017; 12:e0178647
    [Google Scholar]
  30. Saghaug CS, Sørnes S, Peirasmaki D, Svärd S, Langeland N et al. Human memory CD4+ T cell immune responses against Giardia lamblia. Clinical and Vaccine Immunology 2016; 23:11–18
    [Google Scholar]
  31. Tanifuji G, Takabayashi S, Kume K, Takagi M, Nakayama T et al. The draft genome of Kipferlia bialata reveals reductive genome evolution in fornicate parasites. Plos One 2018; 13:e0194487
    [Google Scholar]
  32. Morrison HG, McArthur AG, Gillin FD, Aley SB, Adam RD et al. Genomic minimalism in the early diverging intestinal parasite Giardia lamblia. Science 2007; 317:1921–1926
    [Google Scholar]
  33. Franzén O, Jerlström-Hultqvist J, Castro E, Sherwood E, Ankarklev J et al. Draft genome sequencing of Giardia intestinalis assemblage B isolate Gs: is human giardiasis caused by two different species?. PLoS Pathog 2009; 5:e1000560
    [Google Scholar]
  34. Jerlström-Hultqvist J, Franzén O, Ankarklev J, Xu F, Nohýnková E et al. Genome analysis and comparative genomics of a Giardia intestinalis assemblage E isolate. BMC Genomics 2010; 11:543
    [Google Scholar]
  35. Xu F, Jerlström-Hultqvist J, Einarsson E, Á Ástvaldsson, Svärd SG et al. The genome of Spironucleus salmonicida highlights a fish pathogen adapted to fluctuating environments. PLoS Genetics 2014; 10:
    [Google Scholar]
  36. Campbell SR, van Keulen H, Erlandsen SL, Senturia JB, Jarroll EL. Giardia sp.: comparison of electrophoretic karyotypes. Experimental Parasitology 1990; 71:470–482
    [Google Scholar]
  37. Prabhu A, Morrison HG, Martinez CR, Adam RD. Characterisation of the subtelomeric regions of Giardia lamblia genome isolate WBC6. Int. J. Parasitol 2007; 37:503–513
    [Google Scholar]
  38. Xu F, Jex A, Svärd SG. A chromosome-scale reference genome for Giardia intestinalis WB. Sci Data 2020; 7:38
    [Google Scholar]
  39. Franzén O, Jerlström-Hultqvist J, Einarsson E, Ankarklev J, Ferella M et al. Transcriptome profiling of Giardia intestinalis using strand-specific RNA-Seq. PLoS Computational Biology 2013; 9:e1003000
    [Google Scholar]
  40. Einarsson E, Troell K, Hoeppner MP, Grabherr M, Ribacke U et al. Coordinated changes in gene expression throughout encystation of Giardia intestinalis. PLOS Neglected Tropical Diseases 2016; 10:e0004571
    [Google Scholar]
  41. Morf L, Spycher C, Rehrauer H, Fournier CA, Morrison HG et al. The transcriptional response to encystation stimuli in Giardia lamblia is restricted to a small set of genes. Eukaryotic Cell 2010; 9:1566–1576
    [Google Scholar]
  42. Barash NR, Nosala C, Pham JK, McInally SG, Gourguechon S et al. Giardia Colonizes and Encysts in high-density foci in the murine small intestine. mSphere 2017; 2:
    [Google Scholar]
  43. Pham JK, Nosala C, Scott EY, Nguyen KF, Hagen KD et al. Transcriptomic profiling of high-density Giardia foci encysting in the murine proximal intestine. Front Cell Infect Mi 2017; 7:
    [Google Scholar]
  44. Hudson AJ, Moore AN, Elniski D, Joseph J, Yee J et al. Evolutionarily divergent spliceosomal snRNAs and a conserved non-coding RNA processing motif in Giardia lamblia. Nucleic Acids Res 2012; 40:10995–11008
    [Google Scholar]
  45. Kamikawa R, Inagaki Y, Tokoro M, Roger AJ, Hashimoto T. Split introns in the genome of Giardia intestinalis are excised by spliceosome-mediated trans-splicing. Current Biology 2011; 21:311–315
    [Google Scholar]
  46. William Roy S. Transcriptomic analysis of diplomonad parasites reveals a trans-spliced intron in a helicase gene in Giardia. Peer J 2017; 5:e2861
    [Google Scholar]
  47. Touz MC, Conrad JT, Nash TE. A novel palmitoyl acyl transferase controls surface protein palmitoylation and cytotoxicity in Giardia lamblia VSP palmitoylation. Mol Microbiol 2005; 58:999–1011
    [Google Scholar]
  48. Touz MC, Ropolo AS, Rivero MR, Vranych CV, Conrad JT et al. Arginine deiminase has multiple regulatory roles in the biology of Giardia lamblia. Journal of Cell Science 2008; 121:2930–2938
    [Google Scholar]
  49. Davids BJ, Reiner DS, Birkeland SR, Preheim SP, Cipriano MJ et al. A new family of giardial cysteine-rich non-VSP protein genes and a novel cyst protein. PLoS ONE 2006; 1:e44
    [Google Scholar]
  50. Ringqvist E, Avesson L, Söderbom F, Svärd SG. Transcriptional changes in Giardia during host-parasite interactions. Int J Parasitol 2011; 41:277–285
    [Google Scholar]
  51. Manning G, Reiner DS, Lauwaet T, Dacre M, Smith A et al. The minimal kinome of Giardia lamblia illuminates early kinase evolution and unique parasite biology. Gen Bio 2011; 12:R66
    [Google Scholar]
  52. Gargantini PR, Serradell M del C, Ríos DN, Tenaglia AH, Luján HD. Antigenic variation in the intestinal parasite Giardia lamblia. Curr Opin Microbiol 2016; 32:52–58
    [Google Scholar]
  53. Palm JED, Weiland ME-L, Griffiths WJ, Ljungström I, Svärd SG. Identification of immunoreactive proteins during acute human giardiasis. J. Infect. Dis 2003; 187:1849–1859
    [Google Scholar]
  54. Liu J, Svärd SG, Klotz C. Giardia intestinalis cystatin is a potent inhibitor of papain, parasite cysteine proteases and, to a lesser extent, human cathepsin B. FEBS Letters 2019; 593:1313–1325
    [Google Scholar]
  55. DuBois KN, Abodeely M, Sakanari J, Craik CS, Lee M et al. Identification of the major cysteine protease of Giardia and its role in encystation. J. Biol. Chem 2008; 283:18024–18031
    [Google Scholar]
  56. Ansell BRE, McConville MJ, Baker L, Korhonen PK, Young ND et al. Time-Dependent transcriptional changes in axenic Giardia duodenalis trophozoites. PLoS Neglected Tropical Diseases 2015; 9:1–24
    [Google Scholar]
  57. Stadelmann B, Merino MC, Persson L, Svärd SG. Arginine consumption by the intestinal parasite Giardia intestinalis reduces proliferation of intestinal epithelial cells. PLoS ONE 2012; 7:e45325
    [Google Scholar]
  58. Mastronicola D, Testa F, Forte E, Bordi E, Pucillo LP et al. Flavohemoglobin and nitric oxide detoxification in the human protozoan parasite Giardia intestinalis. Biochem Biophys Res Commun 2010; 399:654–658
    [Google Scholar]
  59. Das P, Lahiri A, Lahiri A, Chakravortty D. Modulation of the arginase pathway in the context of microbial pathogenesis: a metabolic enzyme moonlighting as an immune modulator. PLoS Pathogens 2010; 6:
    [Google Scholar]
  60. Krasity BC, Troll JV, Weiss JP, McFall-Ngai MJ. LBP/BPI proteins and their relatives: conservation over evolution and roles in mutualism. Biochem Soc Trans 2011; 39:1039–1044
    [Google Scholar]
  61. Ankarklev J, Franzén O, Peirasmaki D, Jerlström-Hultqvist J, Lebbad M et al. Comparative genomic analyses of freshly isolated Giardia intestinalis assemblage a isolates. BMC Genomics 2015; 16:
    [Google Scholar]
  62. Lee J-H, Wood TK. Lee J. Roles of indole as an interspecies and Interkingdom signaling molecule. Trends in Microbiology 2015; 23:707–718
    [Google Scholar]
  63. Russell AB, Singh P, Brittnacher M, Bui NK, Hood RD et al. A widespread bacterial type VI secretion effector superfamily identified using a heuristic approach. Cell Host & Microbe 2012; 11:538–549
    [Google Scholar]
  64. Sana TG, Flaugnatti N, Lugo KA, Lam LH, Jacobson A et al. Salmonella typhimurium utilizes a T6SS-mediated antibacterial weapon to establish in the host gut. Proceedings of the National Academy of Sciences 2016; 113:E5044–E5051
    [Google Scholar]
  65. Kim MH, Choi W-C, Kang HO, Lee JS, Kang BS et al. The molecular structure and catalytic mechanism of a quorum-quenching N-acyl-L-homoserine lactone hydrolase. Proceedings of the National Academy of Sciences 2005; 102:17606–17611
    [Google Scholar]
  66. Leckenby A, Hall N. Genomic changes during evolution of animal parasitism in eukaryotes. Curr Opin Genet Dev 2015; 35:86–92
    [Google Scholar]
  67. Peyretaillade E, Boucher D, Parisot N, Gasc C, Butler R et al. Exploiting the architecture and the features of the microsporidian genomes to investigate diversity and impact of these parasites on ecosystems. Heredity 2015; 114:441–449
    [Google Scholar]
  68. Singer SM, Nash TE. The Role of Normal Flora in Giardia lamblia Infections in Mice. Int J Infect Dis 2000; 181:1510–1512
    [Google Scholar]
  69. Singer SM, Nash TE. T-Cell-Dependent control of acute Giardia lamblia infections in mice. Infect Immun 2000; 68:170–175
    [Google Scholar]
  70. Ropolo AS, Saura A, Carranza PG, Lujan HD. Identification of variant-specific surface proteins in Giardia muris trophozoites. Infect Immun 2005; 73:5208–5211
    [Google Scholar]
  71. Adam RD, Nigam A, Seshadri V, Martens CA, Farneth GA et al. The Giardia lamblia VSP gene repertoire: characteristics, genomic organization, and evolution. BMC Genomics 2010; 11:424
    [Google Scholar]
  72. Schmid-Siegert E, Richard S, Luraschi A, Mühlethaler K, Pagni M et al. Mechanisms of surface antigenic variation in the human pathogenic fungus Pneumocystis jirovecii. mBio 2017; 8:
    [Google Scholar]
  73. Mugnier MR, Stebbins CE, Papavasiliou FN. Masters of disguise: antigenic variation and the VSG coat in Trypanosoma brucei. PLoS Pathog 2016; 12:e1005784
    [Google Scholar]
  74. Husnik F, McCutcheon JP. Functional horizontal gene transfer from bacteria to eukaryotes. Nat Rev Microbiol 2018; 16:67–79
    [Google Scholar]
  75. Alsmark C, Foster PG, Sicheritz-Ponten T, Nakjang S, Martin Embley T et al. Patterns of prokaryotic lateral gene transfers affecting parasitic microbial eukaryotes. Genome Biology 2013; 14:R19
    [Google Scholar]
  76. Liu J, Fu Z, Hellman L, Svärd SG. Cleavage specificity of recombinant Giardia intestinalis cysteine proteases: degradation of immunoglobulins and defensins. Molecular and Biochemical Parasitology 2019; 227:29–38
    [Google Scholar]
  77. Feely DE, Gardner MD, Hardin EL. Excystation of Giardia muris induced by a phosphate-bicarbonate medium: localization of acid phosphatase. J. Parasitol 1991; 77:441–448
    [Google Scholar]
  78. Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G et al. Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol 2010; 28:511–515
    [Google Scholar]
  79. Kanehisa M, Sato Y, Morishima K. BlastKOALA and GhostKOALA: KEGG tools for functional characterization of genome and metagenome sequences. J Mol Bio 2016; 428:726–731
    [Google Scholar]
  80. Kanehisa M, Furumichi M, Tanabe M, Sato Y, Morishima K. KEGG: new perspectives on genomes, pathways, diseases and drugs. Nucleic Acids Res 2017; 45:D353–D361
    [Google Scholar]
  81. Karp PD, Latendresse M, Paley SM, Krummenacker M, Ong QD et al. Pathway tools version 19.0 update: software for pathway/genome informatics and systems biology. Brief. Bioinformatics 2016; 17:877–890
    [Google Scholar]
  82. Aurrecoechea C, Brestelli J, Brunk BP, Carlton JM, Dommer J et al. GiardiaDB and TrichDB: integrated genomic resources for the eukaryotic protist pathogens Giardia lamblia and Trichomonas vaginalis. Nucleic Acids Res 2009; 37:D526–530
    [Google Scholar]
  83. Green ML, Karp PD. A Bayesian method for identifying missing enzymes in predicted metabolic pathway databases. BMC Bioinformatics 2004; 5:76
    [Google Scholar]
  84. Lee TJ, Paulsen I, Karp P. Annotation-based inference of transporter function. Bioinformatics 2008; 24:i259–267
    [Google Scholar]
  85. Marchler-Bauer A, Bryant SH. CD-Search: protein domain annotations on the fly. Nucleic Acids Res 2004; 32:W327–331
    [Google Scholar]
  86. Katoh K, Misawa K, Kuma K, Miyata T. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic acids research 2002; 30:3059–3066
    [Google Scholar]
  87. CB D, Mahabhashyam MSP, Brudno M, Batzoglou S. ProbCons: probabilistic consistency-based multiple sequence alignment. Genome research 2005; 15:330–340
    [Google Scholar]
  88. Notredame C, Higgins DG, Heringa J. T-Coffee: a novel method for fast and accurate multiple sequence alignment. J. Mol. Biol 2000; 302:205–217
    [Google Scholar]
  89. Criscuolo A, BMGE GS. Block mapping and Gathering with Entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments. BMC Evol Biol 2010; 10:210
    [Google Scholar]
  90. Nguyen L-T, Schmidt HA, von Haeseler A, Minh BQ. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol. Biol. Evol 2015; 32:268–274
    [Google Scholar]
  91. Kalyaanamoorthy S, Minh BQ, Wong TKF, von Haeseler A, Jermiin LS. ModelFinder: fast model selection for accurate phylogenetic estimates. Nat. Methods 2017; 14:587–589
    [Google Scholar]
  92. Hoang DT, Chernomor O, von Haeseler A, Minh BQ, Vinh LS. UFBoot2: improving the ultrafast bootstrap approximation. Mol. Biol. Evol 2018; 35:518–522
    [Google Scholar]
  93. Guindon S, Dufayard J-F, Lefort V, Anisimova M, Hordijk W et al. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst. Biol 2010; 59:307–321
    [Google Scholar]
  94. Gu Z, Gu L, Eils R, Schlesner M, Brors B. circlize implements and enhances circular visualization in R. Bioinformatics 2014; 30:2811–2812
    [Google Scholar]
  95. Guy L, Kultima JR, Andersson SGE. genoPlotR: comparative gene and genome visualization in R. Bioinformatics 2010; 26:2334–2335
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/mgen/10.1099/mgen.0.000402
Loading
/content/journal/mgen/10.1099/mgen.0.000402
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Supplementary material 2

EXCEL

Most cited this month Most Cited RSS feed

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error