Retention and Loss of RNA Interference Pathways in Trypanosomatid Protozoans

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RNA interference (RNAi) pathways are widespread in metaozoans but the genes required show variable occurrence or activity in eukaryotic microbes, including many pathogens. While some Leishmania lack RNAi activity and Argonaute or Dicer genes, we show that Leishmania braziliensis and other species within the Leishmania subgenus Viannia elaborate active RNAi machinery. Strong attenuation of expression from a variety of reporter and endogenous genes was seen. As expected, RNAi knockdowns of the sole Argonaute gene implicated this protein in RNAi. The potential for functional genetics was established by testing RNAi knockdown lines lacking the paraflagellar rod, a key component of the parasite flagellum. This sets the stage for the systematic manipulation of gene expression through RNAi in these predominantly diploid asexual organisms, and may also allow selective RNAi-based chemotherapy. Functional evolutionary surveys of RNAi genes established that RNAi activity was lost after the separation of the Leishmania subgenus Viannia from the remaining Leishmania species, a divergence associated with profound changes in the parasite infectious cycle and virulence. The genus Leishmania therefore offers an accessible system for testing hypothesis about forces that may select for the loss of RNAi during evolution, such as invasion by viruses, changes in genome plasticity mediated by transposable elements and gene amplification (including those mediating drug resistance), and/or alterations in parasite virulence.

Vyšlo v časopise: Retention and Loss of RNA Interference Pathways in Trypanosomatid Protozoans. PLoS Pathog 6(10): e32767. doi:10.1371/journal.ppat.1001161
Kategorie: Research Article
prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.ppat.1001161

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Zdroje

1. CeruttiH

Casas-MollanoJA

2006 On the origin and functions of RNA-mediated silencing: from protists to man. Curr Genet 50 81 99

2. UlluE

TschudiC

ChakrabortyT

2004 RNA interference in protozoan parasites. Cell Microbiol 6 509 519

3. MilitelloKT

RefourP

ComeauxCA

DuraisinghMT

2008 Antisense RNA and RNAi in protozoan parasites: working hard or hardly working? Mol Biochem Parasitol 157 117 126

4. BaumJ

PapenfussAT

MairGR

JanseCJ

VlachouD

2009 Molecular genetics and comparative genomics reveal RNAi is not functional in malaria parasites. Nucleic Acids Res 37 3788 3798

5. BraunL

CannellaD

OrtetP

BarakatM

SautelCF

2010 A complex small RNA repertoire is generated by a plant/fungal-like machinery and effected by a metazoan-like Argonaute in the single-cell human parasite Toxoplasma gondii. PLoS Pathog 6 e1000920

6. LinfordAS

MorenoH

GoodKR

ZhangH

SinghU

2009 Short hairpin RNA-mediated knockdown of protein expression in Entamoeba histolytica. BMC Microbiol 9 38

7. PruccaCG

SlavinI

QuirogaR

EliasEV

RiveroFD

2008 Antigenic variation in Giardia lamblia is regulated by RNA interference. Nature 456 750 754

8. BanulsAL

HideM

PrugnolleF

2007 Leishmania and the leishmaniases: a parasite genetic update and advances in taxonomy, epidemiology and pathogenicity in humans. Adv Parasitol 64 1 109

9. ShiH

TschudiC

UlluE

2006 An unusual Dicer-like1 protein fuels the RNA interference pathway in Trypanosoma brucei. RNA 12 2063 2072

10. PatrickKL

ShiH

KolevNG

ErsfeldK

TschudiC

2009 Distinct and overlapping roles for two Dicer-like proteins in the RNA interference pathways of the ancient eukaryote Trypanosoma brucei. Proc Natl Acad Sci U S A 106 17933 17938

11. RobinsonKA

BeverleySM

2003 Improvements in transfection efficiency and tests of RNA interference (RNAi) approaches in the protozoan parasite Leishmania. Mol Biochem Parasitol 128 217 228

12. DaRochaWD

OtsuK

TeixeiraSM

DonelsonJE

2004 Tests of cytoplasmic RNA interference (RNAi) and construction of a tetracycline-inducible T7 promoter system in Trypanosoma cruzi. Mol Biochem Parasitol 133 175 186

13. BeverleySM

2003 Protozomics: trypanosomatid parasite genetics comes of age. Nat Rev Genet 4 11 19

14. IvensAC

PeacockCS

WortheyEA

MurphyL

AggarwalG

2005 The genome of the kinetoplastid parasite, Leishmania major. Science 309 436 442

15. PeacockCS

SeegerK

HarrisD

MurphyL

RuizJC

2007 Comparative genomic analysis of three Leishmania species that cause diverse human disease. Nat Genet 39 839 847

16. DjikengA

ShiH

TschudiC

UlluE

2001 RNA interference in Trypanosoma brucei: cloning of small interfering RNAs provides evidence for retroposon-derived 24–26-nucleotide RNAs. RNA 7 1522 1530

17. ShiH

DjikengA

TschudiC

UlluE

2004 Argonaute protein in the early divergent eukaryote Trypanosoma brucei: control of small interfering RNA accumulation and retroposon transcript abundance. Mol Cell Biol 24 420 427

18. LeBowitzJH

CoburnCM

McMahon-PrattD

BeverleySM

1990 Development of a stable Leishmania expression vector and application to the study of parasite surface antigen genes. Proc Natl Acad Sci USA 87 9736 9740

19. CapulAA

BarronT

DobsonDE

TurcoSJ

BeverleySM

2007 Two functionally divergent UDP-Gal nucleotide sugar transporters participate in phosphoglycan synthesis in Leishmania major. J Biol Chem 282 14006 14017

20. ClaytonCE

2002 Life without transcriptional control? From fly to man and back again. EMBO J 21 1881 1888

21. NgoH

TschudiC

GullK

UlluE

1998 Double-stranded RNA induces mRNA degradation in Trypanosoma brucei. Proc Natl Acad Sci USA 95 14687 14692

22. TurcoSJ

SpäthGF

BeverleySM

2001 Is lipophosphoglycan a virulence factor? A surprising diversity between Leishmania species. Trends Parasitol 17 223 226

23. MagaJA

SherwinT

FrancisS

GullK

LeBowitzJH

1999 Genetic dissection of the Leishmania paraflagellar rod, a unique flagellar cytoskeleton structure. J Cell Sci 112 Pt 16 2753 2763

24. ChangT

MilneKG

GutherML

SmithTK

FergusonMA

2002 Cloning of Trypanosoma brucei and Leishmania major genes encoding the GlcNAc-phosphatidylinositol de-N-acetylase of glycosylphosphatidylinositol biosynthesis that is essential to the African sleeping sickness parasite. J Biol Chem 277 50176 50182

25. de SouzaW

Souto-PadronT

1980 The paraxial structure of the flagellum of trypanosomatidae. J Parasitol 66 229 236

26. BastinP

SherwinT

GullK

1998 Paraflagellar rod is vital for trypanosome motility. Nature 391 548

27. SchlaeppiK

DeflorinJ

SeebeckT

1989 The major component of the paraflagellar rod of Trypanosoma brucei is a helical protein that is encoded by two identical, tandemly linked genes. J Cell Biol 109 1695 1709

28. BastinP

MatthewsKR

GullK

1996 The paraflagellar rod of kinetoplastida: solved and unsolved questions. Parasitol Today 12 302 307

29. BernsteinE

CaudyAA

HammondSM

HannonGJ

2001 Role for a bidentate ribonuclease in the initiation step of RNA interference. Nature 409 363 366

30. DudleyNR

LabbeJC

GoldsteinB

2002 Using RNA interference to identify genes required for RNA interference. Proc Natl Acad Sci USA 99 4191 4196

31. KimJK

GabelHW

KamathRS

TewariM

PasquinelliA

2005 Functional genomic analysis of RNA interference in C. elegans. Science 308 1164 1167

32. BerrimanM

GhedinE

Hertz-FowlerC

BlandinG

RenauldH

2005 The genome of the African trypanosome Trypanosoma brucei. Science 309 416 422

33. DrinnenbergIA

WeinbergDE

XieKT

MowerJP

WolfeKH

2009 RNAi in budding yeast. Science 326 544 550

34. PattersonJL

1993 The current status of Leishmania RNA virus I. Parasitol Today 9 135 136

35. TarrPI

AlineRFJr

SmileyBL

SchollerJ

KeithlyJ

1988 LR1: a candidate RNA virus of Leishmania. Proc Natl Acad Sci USA 85 9572 9575

36. WidmerG

ComeauAM

FurlongDB

WirthDF

PattersonJL

1989 Characterization of a RNA virus from the parasite Leishmania. Proc Natl Acad Sci USA 86 5979 5982

37. GuilbrideL

MylerPJ

StuartK

1992 Distribution and sequence divergence of LRV1 viruses among different Leishmania species. Mol Biochem Parasitol 54 101 104

38. RoYT

ScheffterSM

PattersonJL

1997 Hygromycin B resistance mediates elimination of Leishmania virus from persistently infected parasites. J Virol 71 8991 8998

39. DingSW

VoinnetO

2007 Antiviral immunity directed by small RNAs. Cell 130 413 426

40. OggMM

CarrionRJr

BotelhoAC

MayrinkW

Correa-OliveiraR

2003 Short report: quantification of leishmaniavirus RNA in clinical samples and its possible role in pathogenesis. Am J Trop Med Hyg 69 309 313

41. GuptaV

DeepA

2007 An insight into the Leishmania RNA virus. Indian J Med Microbiol 25 7 9

42. ShiH

ChamondN

TschudiC

UlluE

2004 Selection and characterization of RNA interference-deficient trypanosomes impaired in target mRNA degradation. Eukaryot Cell 3 1445 1453

43. PatrickKL

LuzPM

RuanJP

ShiH

UlluE

2008 Genomic rearrangements and transcriptional analysis of the spliced leader-associated retrotransposon in RNA interference-deficient Trypanosoma brucei. Mol Microbiol 67 435 447

44. GirardA

HannonGJ

2008 Conserved themes in small-RNA-mediated transposon control. Trends Cell Biol 18 136 148

45. BeverleySM

1991 Gene amplification in Leishmania. Annu Rev Microbiol 45 417 444

46. BorstP

OuelletteM

1995 New mechanisms of drug resistance in parasitic protozoa. Annu Rev Microbiol 49 427 460

47. de LafailleMAC

LabanA

WirthDF

1992 Gene expression in Leishmania: analysis of essential 5′ DNA sequences. Proc Natl Acad Sci USA 89 2703 2707

48. DiasFC

RuizJC

LopesWC

SquinaFM

RenziA

2007 Organization of H locus conserved repeats in Leishmania (Viannia) braziliensis correlates with lack of gene amplification and drug resistance. Parasitol Res 101 667 676

49. PatnaikPK

KulkarniSK

CrossGA

1993 Autonomously replicating single-copy episomes in Trypanosoma brucei show unusual stability. EMBO J 12 2529 2538

50. RathodPK

McErleanT

LeePC

1997 Variations in frequencies of drug resistance in Plasmodium falciparum. Proc Natl Acad Sci USA 94 9389 9393

51. DenamurE

MaticI

2006 Evolution of mutation rates in bacteria. Mol Microbiol 60 820 827

52. StevensJR

NoyesHA

SchofieldCJ

GibsonW

2001 The molecular evolution of Trypanosomatidae. Adv Parasitol 48 1 56

53. BatesPA

2007 Transmission of Leishmania metacyclic promastigotes by phlebotomine sand flies. Int J Parasitol 37 1097 1106

54. DornerS

LumL

KimM

ParoR

BeachyPA

2006 A genomewide screen for components of the RNAi pathway in Drosophila cultured cells. Proc Natl Acad Sci USA 103 11880 11885

55. Martinez-CalvilloS

YanS

NguyenD

FoxM

StuartK

2003 Transcription of Leishmania major Friedlin chromosome 1 initiates in both directions within a single region. Mol Cell 11 1291 1299

56. BelliSI

MonneratS

SchaffC

MasinaS

NollT

2003 Sense and antisense transcripts in the histone H1 (HIS-1) locus of Leishmania major. Int J Parasitol 33 965 975

57. KaplerGM

BeverleySM

1989 Transcriptional mapping of the amplified region encoding the dihydrofolate reductase-thymidylate synthase of Leishmania major reveals a high density of transcripts, including overlapping and antisense RNAs. Mol Cell Biol 9 3959 3972

58. BeverleySM

2003 Genetic and genomic approaches to the analysis of Leishmania virulence.

MarrJM

NilsenT

KomunieckiR

Molecular & Medical Parasitology New York Academic Press

59. TimmonsL

FireA

1998 Specific interference by ingested dsRNA. Nature 395 854

60. KaplerGM

CoburnCM

BeverleySM

1990 Stable transfection of the human parasite Leishmania major delineates a 30-kilobase region sufficient for extrachromosomal replication and expression. Mol Cell Biol 10 1084 1094

61. OrlandiPAJr

TurcoSJ

1987 Structure of the lipid moiety of the Leishmania donovani lipophosphoglycan. J Biol Chem 262 10384 10391

62. SoaresRP

CardosoTL

BarronT

AraujoMS

PimentaPF

2005 Leishmania braziliensis: a novel mechanism in the lipophosphoglycan regulation during metacyclogenesis. Int J Parasitol 35 245 253

63. DjikengA

ShiH

TschudiC