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A Major Role for the ApiAP2 Protein PfSIP2 in Chromosome End Biology


The heterochromatic environment and physical clustering of chromosome ends at the nuclear periphery provide a functional and structural framework for antigenic variation and evolution of subtelomeric virulence gene families in the malaria parasite Plasmodium falciparum. While recent studies assigned important roles for reversible histone modifications, silent information regulator 2 and heterochromatin protein 1 (PfHP1) in epigenetic control of variegated expression, factors involved in the recruitment and organization of subtelomeric heterochromatin remain unknown. Here, we describe the purification and characterization of PfSIP2, a member of the ApiAP2 family of putative transcription factors, as the unknown nuclear factor interacting specifically with cis-acting SPE2 motif arrays in subtelomeric domains. Interestingly, SPE2 is not bound by the full-length protein but rather by a 60kDa N-terminal domain, PfSIP2-N, which is released during schizogony. Our experimental re-definition of the SPE2/PfSIP2-N interaction highlights the strict requirement of both adjacent AP2 domains and a conserved bipartite SPE2 consensus motif for high-affinity binding. Genome-wide in silico mapping identified 777 putative binding sites, 94% of which cluster in heterochromatic domains upstream of subtelomeric var genes and in telomere-associated repeat elements. Immunofluorescence and chromatin immunoprecipitation (ChIP) assays revealed co-localization of PfSIP2-N with PfHP1 at chromosome ends. Genome-wide ChIP demonstrated the exclusive binding of PfSIP2-N to subtelomeric SPE2 landmarks in vivo but not to single chromosome-internal sites. Consistent with this specialized distribution pattern, PfSIP2-N over-expression has no effect on global gene transcription. Hence, contrary to the previously proposed role for this factor in gene activation, our results provide strong evidence for the first time for the involvement of an ApiAP2 factor in heterochromatin formation and genome integrity. These findings are highly relevant for our understanding of chromosome end biology and variegated expression in P. falciparum and other eukaryotes, and for the future analysis of the role of ApiAP2-DNA interactions in parasite biology.


Vyšlo v časopise: A Major Role for the ApiAP2 Protein PfSIP2 in Chromosome End Biology. PLoS Pathog 6(2): e32767. doi:10.1371/journal.ppat.1000784
Kategorie: Research Article
prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.ppat.1000784

Souhrn

The heterochromatic environment and physical clustering of chromosome ends at the nuclear periphery provide a functional and structural framework for antigenic variation and evolution of subtelomeric virulence gene families in the malaria parasite Plasmodium falciparum. While recent studies assigned important roles for reversible histone modifications, silent information regulator 2 and heterochromatin protein 1 (PfHP1) in epigenetic control of variegated expression, factors involved in the recruitment and organization of subtelomeric heterochromatin remain unknown. Here, we describe the purification and characterization of PfSIP2, a member of the ApiAP2 family of putative transcription factors, as the unknown nuclear factor interacting specifically with cis-acting SPE2 motif arrays in subtelomeric domains. Interestingly, SPE2 is not bound by the full-length protein but rather by a 60kDa N-terminal domain, PfSIP2-N, which is released during schizogony. Our experimental re-definition of the SPE2/PfSIP2-N interaction highlights the strict requirement of both adjacent AP2 domains and a conserved bipartite SPE2 consensus motif for high-affinity binding. Genome-wide in silico mapping identified 777 putative binding sites, 94% of which cluster in heterochromatic domains upstream of subtelomeric var genes and in telomere-associated repeat elements. Immunofluorescence and chromatin immunoprecipitation (ChIP) assays revealed co-localization of PfSIP2-N with PfHP1 at chromosome ends. Genome-wide ChIP demonstrated the exclusive binding of PfSIP2-N to subtelomeric SPE2 landmarks in vivo but not to single chromosome-internal sites. Consistent with this specialized distribution pattern, PfSIP2-N over-expression has no effect on global gene transcription. Hence, contrary to the previously proposed role for this factor in gene activation, our results provide strong evidence for the first time for the involvement of an ApiAP2 factor in heterochromatin formation and genome integrity. These findings are highly relevant for our understanding of chromosome end biology and variegated expression in P. falciparum and other eukaryotes, and for the future analysis of the role of ApiAP2-DNA interactions in parasite biology.


Zdroje

1. PrydeFE

GorhamHC

LouisEJ

1997 Chromosome ends: all the same under their caps. Curr Opin Genet Dev 7 822 828

2. TaddeiA

HedigerF

NeumannFR

GasserSM

2004 The function of nuclear architecture: a genetic approach. Annu Rev Genet 38 305 345

3. LouisEJ

VershininAV

2005 Chromosome ends: different sequences may provide conserved functions. Bioessays 27 685 697

4. ThamWH

ZakianVA

2002 Transcriptional silencing at Saccharomyces telomeres: implications for other organisms. Oncogene 21 512 521

5. MoazedD

2001 Common themes in mechanisms of gene silencing. Mol Cell 8 489 498

6. BarryJD

GingerML

BurtonP

McCullochR

2003 Why are parasite contingency genes often associated with telomeres? Int J Parasitol 33 29 45

7. SnowRW

GuerraCA

NoorAM

MyintHY

HaySI

2005 The global distribution of clinical episodes of Plasmodium falciparum malaria. Nature 434 214 217

8. BaruchDI

GormelyJA

MaC

HowardRJ

PasloskeBL

1996 Plasmodium falciparum erythrocyte membrane protein 1 is a parasitized erythrocyte receptor for adherence to CD36, thrombospondin, and intercellular adhesion molecule 1. Proc Natl Acad Sci U S A 93 3497 3502

9. GardnerJP

PinchesRA

RobertsDJ

NewboldCI

1996 Variant antigens and endothelial receptor adhesion in Plasmodium falciparum. Proc Natl Acad Sci U S A 93 3503 3508

10. RoweJA

MouldsJM

NewboldCI

MillerLH

1997 P. falciparum rosetting mediated by a parasite-variant erythrocyte membrane protein and complement-receptor 1. Nature 388 292 295

11. ReederJC

CowmanAF

DavernKM

BeesonJG

ThompsonJK

1999 The adhesion of Plasmodium falciparum-infected erythrocytes to chondroitin sulfate A is mediated by P. falciparum erythrocyte membrane protein 1. Proc Natl Acad Sci U S A 96 5198 5202

12. PongponratnE

RigantiM

PunpoowongB

AikawaM

1991 Microvascular sequestration of parasitized erythrocytes in human falciparum malaria: a pathological study. Am J Trop Med Hyg 168 175

13. MacPhersonGG

WarrellMJ

WhiteNJ

LooareesuwanS

WarrellDA

1985 Human cerebral malaria. A quantitative ultrastructural analysis of parasitized erythrocyte sequestration. Am J Pathol 119 385 401

14. BeesonJG

DuffyPE

2005 The immunology and pathogenesis of malaria during pregnancy. Curr Top Microbiol Immunol 297 187 227

15. BaruchDI

PasloskeBL

SinghHB

BiX

MaXC

1995 Cloning the P. falciparum gene encoding PfEMP1, a malarial variant antigen and adherence receptor on the surface of parasitized human erythrocytes. Cell 82 77 87

16. SuXZ

HeatwoleVM

WertheimerSP

GuinetF

HerrfeldtJA

1995 The large diverse gene family var encodes proteins involved in cytoadherence and antigenic variation of Plasmodium falciparum-infected erythrocytes. Cell 82 89 100

17. SmithJD

ChitnisCE

CraigAG

RobertsDJ

Hudson-TaylorDE

1995 Switches in expression of Plasmodium falciparum var genes correlate with changes in antigenic and cytoadherent phenotypes of infected erythrocytes. Cell 82 101 110

18. GardnerMJ

HallN

FungE

WhiteO

BerrimanM

2002 Genome sequence of the human malaria parasite Plasmodium falciparum. Nature 419 498 511

19. ScherfA

Hernandez-RivasR

BuffetP

BottiusE

BenatarC

1998 Antigenic variation in malaria: in situ switching, relaxed and mutually exclusive transcription of var genes during intra-erythrocytic development in Plasmodium falciparum. EMBO J 17 5418 5426

20. Freitas-JuniorLH

Hernandez-RivasR

RalphSA

Montiel-CondadoD

Ruvalcaba-SalazarOK

2005 Telomeric heterochromatin propagation and histone acetylation control mutually exclusive expression of antigenic variation genes in malaria parasites. Cell 121 25 36

21. Lopez-RubioJJ

GontijoAM

NunesMC

IssarN

HernandezRR

2007 5′ flanking region of var genes nucleate histone modification patterns linked to phenotypic inheritance of virulence traits in malaria parasites. Mol Microbiol 66 1296 1305

22. Perez-ToledoK

Rojas-MezaAP

Mancio-SilvaL

Hernandez-CuevasNA

DelgadilloDM

2009 Plasmodium falciparum heterochromatin protein 1 binds to tri-methylated histone 3 lysine 9 and is linked to mutually exclusive expression of var genes. Nucleic Acids Res 37 2596 2606

23. Lopez-RubioJJ

Mancio-SilvaL

ScherfA

2009 Genome-wide analysis of heterochromatin associates clonally variant gene regulation with perinuclear repressive centers in malaria parasites. Cell Host Microbe 5 179 190

24. VossTS

HealerJ

MartyAJ

DuffyMF

ThompsonJK

2006 A var gene promoter controls allelic exclusion of virulence genes in Plasmodium falciparum malaria. Nature 439 1004 1008

25. DuraisinghMT

VossTS

MartyAJ

DuffyMF

GoodRT

2005 Heterochromatin silencing and locus repositioning linked to regulation of virulence genes in Plasmodium falciparum. Cell 121 13 24

26. TonkinCJ

CarretCK

DuraisinghMT

VossTS

RalphSA

2009 Sir2 paralogues cooperate to regulate virulence genes and antigenic variation in Plasmodium falciparum. PLoS Biol 7 e84 doi:10.1371/journal.pbio.1000084

27. FlueckC

BartfaiR

VolzJ

NiederwieserI

Salcedo-AmayaAM

2009 Plasmodium falciparum heterochromatin protein 1 marks genomic loci linked to phenotypic variation of exported virulence factors. PLoS Pathog 5 e1000569 doi:10.1371/journal.ppat.1000569

28. ScherfA

FigueiredoLM

Freitas-JuniorLH

2001 Plasmodium telomeres: a pathogen's perspective. Curr Opin Microbiol 4 409 414

29. FigueiredoLM

PirritLA

ScherfA

2000 Genomic organisation and chromatin structure of Plasmodium falciparum chromosome ends. Mol Biochem Parasitol 106 169 174

30. Freitas-JuniorLH

BottiusE

PirritLA

DeitschKW

ScheidigC

2000 Frequent ectopic recombination of virulence factor genes in telomeric chromosome clusters of P. falciparum. Nature 407 1018 1022

31. MartyAJ

ThompsonJK

DuffyMF

VossTS

CowmanAF

2006 Evidence that Plasmodium falciparum chromosome end clusters are cross-linked by protein and are the sites of both virulence gene silencing and activation. Mol Microbiol 62 72 83

32. GasserSM

HedigerF

TaddeiA

NeumannFR

GartenbergMR

2004 The function of telomere clustering in yeast: the circe effect. Cold Spring Harb Symp Quant Biol 69 327 337

33. FigueiredoLM

Freitas-JuniorLH

BottiusE

Olivo-MarinJC

ScherfA

2002 A central role for Plasmodium falciparum subtelomeric regions in spatial positioning and telomere length regulation. EMBO J 21 815 824

34. NiangM

YanY, X

PreiserPR

2009 The Plasmodium falciparum STEVOR multigene family mediates antigenic variation of the infected erythrocyte. PLoS Pathog 5 e1000307 doi:10.1371/journal.ppat.1000307

35. LavazecC

SanyalS

TempletonTJ

2007 Expression switching in the stevor and Pfmc-2TM superfamilies in Plasmodium falciparum. Mol Microbiol 64 1621 1634

36. MokBW

RibackeU

WinterG

YipBH

TanCS

2007 Comparative transcriptomal analysis of isogenic Plasmodium falciparum clones of distinct antigenic and adhesive phenotypes. Mol Biochem Parasitol 151 184 192

37. Salcedo-AmayaAM

van DrielMA

AlakoBT

TrelleMB

van den ElzenAM

2009 Dynamic histone H3 epigenome marking during the intraerythrocytic cycle of Plasmodium falciparum. Proc Natl Acad Sci U S A 106 9655 9660

38. GrewalSI

JiaS

2007 Heterochromatin revisited. Nat Rev Genet 8 35 46

39. SinghPB

GeorgatosSD

2002 HP1: facts, open questions, and speculation. J Struct Biol 140 10 16

40. RalphSA

Scheidig-BenatarC

ScherfA

2005 Antigenic variation in Plasmodium falciparum is associated with movement of var loci between subnuclear locations. Proc Natl Acad Sci U S A 102 5414 5419

41. ChookajornT

DzikowskiR

FrankM

LiF

JiwaniAZ

2007 Epigenetic memory at malaria virulence genes. Proc Natl Acad Sci U S A 104 899 902

42. HorrocksP

WongE

RussellK

EmesRD

2009 Control of gene expression in Plasmodium falciparum - Ten years on. Mol Biochem Parasitol 164 9 25

43. CoulsonRM

HallN

OuzounisCA

2004 Comparative genomics of transcriptional control in the human malaria parasite Plasmodium falciparum. Genome Res 14 1548 1554

44. AravindL

IyerLM

WellemsTE

MillerLH

2003 Plasmodium biology: genomic gleanings. Cell 115 771 785

45. IyerLM

AnantharamanV

WolfMY

AravindL

2008 Comparative genomics of transcription factors and chromatin proteins in parasitic protists and other eukaryotes. Int J Parasitol 38 1 31

46. GissotM

BriquetS

RefourP

BoschetC

VaqueroC

2005 PfMyb1, a Plasmodium falciparum transcription factor, is required for intra-erythrocytic growth and controls key genes for cell cycle regulation. J Mol Biol 346 29 42

47. BalajiS

BabuMM

IyerLM

AravindL

2005 Discovery of the principal specific transcription factors of Apicomplexa and their implication for the evolution of the AP2-integrase DNA binding domains. Nucleic Acids Res 33 3994 4006

48. De SilvaEK

GehrkeAR

OlszewskiK

LeonI

ChahalJS

2008 Specific DNA-binding by apicomplexan AP2 transcription factors. Proc Natl Acad Sci U S A 105 8393 8398

49. YudaM

IwanagaS

ShigenobuS

MairGR

JanseCJ

2009 Identification of a transcription factor in the mosquito-invasive stage of malaria parasites. Mol Microbiol 71 1402 1414

50. VossTS

KaestliM

VogelD

BoppS

BeckHP

2003 Identification of nuclear proteins that interact differentially with Plasmodium falciparum var gene promoters. Mol Microbiol 48 1593 1607

51. GatlinCL

EngJK

CrossST

DetterJC

YatesJRIII

2000 Automated identification of amino acid sequence variations in proteins by HPLC/microspray tandem mass spectrometry. Anal Chem 72 757 763

52. BozdechZ

LlinasM

PulliamBL

WongED

ZhuJ

2003 The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum. PLoS Biol 1 e5 doi:10.1371/journal.pbio.0000005

53. LlinasM

BozdechZ

WongED

AdaiAT

DeRisiJL

2006 Comparative whole genome transcriptome analysis of three Plasmodium falciparum strains. Nucleic Acids Res 34 1166 1173

54. VossTS

TonkinCJ

MartyAJ

ThompsonJK

HealerJ

2007 Alterations in local chromatin environment are involved in silencing and activation of subtelomeric var genes in Plasmodium falciparum. Mol Microbiol 66 139 150

55. YoungJA

JohnsonJR

BennerC

YanSF

ChenK

2008 In silico discovery of transcription regulatory elements in Plasmodium falciparum. BMC Genomics 9 70

56. Ohme-TakagiM

ShinshiH

1995 Ethylene-inducible DNA binding proteins that interact with an ethylene-responsive element. Plant Cell 7 173 182

57. BakerSS

WilhelmKS

ThomashowMF

1994 The 5′-region of Arabidopsis thaliana cor15a has cis-acting elements that confer cold-, drought- and ABA-regulated gene expression. Plant Mol Biol 24 701 713

58. Nole-WilsonS

KrizekBA

2000 DNA binding properties of the Arabidopsis floral development protein AINTEGUMENTA. Nucleic Acids Res 28 4076 4082

59. ConradMN

WrightJH

WolfAJ

ZakianVA

1990 RAP1 protein interacts with yeast telomeres in vivo: overproduction alters telomere structure and decreases chromosome stability. Cell 63 739 750

60. ZakianVA

1996 Structure, function, and replication of Saccharomyces cerevisiae telomeres. Annu Rev Genet 30 141 172

61. SadaieM

NaitoT

IshikawaF

2003 Stable inheritance of telomere chromatin structure and function in the absence of telomeric repeats. Genes Dev 17 2271 2282

62. KanohJ

SadaieM

UranoT

IshikawaF

2005 Telomere binding protein Taz1 establishes Swi6 heterochromatin independently of RNAi at telomeres. Curr Biol 15 1808 1819

63. CooperJP

NimmoER

AllshireRC

CechTR

1997 Regulation of telomere length and function by a Myb-domain protein in fission yeast. Nature 385 744 747

64. van SteenselB

de LangeT

1997 Control of telomere length by the human telomeric protein TRF1. Nature 385 740 743

65. DiffleyJF

StillmanB

1989 Similarity between the transcriptional silencer binding proteins ABF1 and RAP1. Science 246 1034 1038

66. YuS

SmirnovaJB

FriedbergEC

StillmanB

AkiyamaM

2009 ABF1-binding sites promote efficient global genome nucleotide excision repair. J Biol Chem 284 966 973

67. ReedSH

AkiyamaM

StillmanB

FriedbergEC

1999 Yeast autonomously replicating sequence binding factor is involved in nucleotide excision repair. Genes Dev 13 3052 3058

68. DiffleyJF

StillmanB

1988 Purification of a yeast protein that binds to origins of DNA replication and a transcriptional silencer. Proc Natl Acad Sci U S A 85 2120 2124

69. VendittiP

CostanzoG

NegriR

CamilloniG

1994 ABFI contributes to the chromatin organization of Saccharomyces cerevisiae ARS1 B-domain. Biochim Biophys Acta 1219 677 689

70. PrydeFE

LouisEJ

1999 Limitations of silencing at native yeast telomeres. EMBO J 18 2538 2550

71. BurgersPM

1998 Eukaryotic DNA polymerases in DNA replication and DNA repair. Chromosoma 107 218 227

72. MoserBA

SubramanianL

ChangYT

NoguchiC

NoguchiE

2009 Differential arrival of leading and lagging strand DNA polymerases at fission yeast telomeres. EMBO J 28 810 820

73. MossiR

HubscherU

1998 Clamping down on clamps and clamp loaders–the eukaryotic replication factor C. Eur J Biochem 254 209 216

74. ConawayRC

ConawayJW

2009 The INO80 chromatin remodeling complex in transcription, replication and repair. Trends Biochem Sci 34 71 77

75. CollinsN

PootRA

KukimotoI

Garcia-JimenezC

DellaireG

2002 An ACF1-ISWI chromatin-remodeling complex is required for DNA replication through heterochromatin. Nat Genet 32 627 632

76. Ehrenhofer-MurrayAE

KamakakaRT

RineJ

1999 A role for the replication proteins PCNA, RF-C, polymerase epsilon and Cdc45 in transcriptional silencing in Saccharomyces cerevisiae. Genetics 153 1171 1182

77. DrorV

WinstonF

2004 The Swi/Snf chromatin remodeling complex is required for ribosomal DNA and telomeric silencing in Saccharomyces cerevisiae. Mol Cell Biol 24 8227 8235

78. FrancoAA

LamWM

BurgersPM

KaufmanPD

2005 Histone deposition protein Asf1 maintains DNA replisome integrity and interacts with replication factor 1. Genes Dev 19 1365 1375

79. Van AttikumH

GasserSM

2005 ATP-dependent chromatin remodeling and DNA double-strand break repair. Cell Cycle 4 1011 1014

80. LabibK

HodgsonB

2007 Replication fork barriers: pausing for a break or stalling for time? EMBO Rep 8 346 353

81. MoonNS

PremdasP

TruscottM

LeduyL

BerubeG

2001 S phase-specific proteolytic cleavage is required to activate stable DNA binding by the CDP/Cut homeodomain protein. Mol Cell Biol 21 6332 6345

82. ClarkeDJ

2002 Proteolysis and the cell cycle. Cell Cycle 1 233 234

83. TragerW

JensonJB

1978 Cultivation of malarial parasites. Nature 273 621 622

84. LambrosC

VanderbergJP

1979 Synchronization of Plasmodium falciparum erythrocytic stages in culture. J Parasitol 65 418 420

85. CinquinO

ChristophersonRI

MenzRI

2001 A hybrid plasmid for expression of toxic malarial proteins in Escherichia coli. Mol Biochem Parasitol 117 245 247

86. HuG

LlinasM

LiJ

PreiserPR

BozdechZ

2007 Selection of long oligonucleotides for gene expression microarrays using weighted rank-sum strategy. BMC Bioinformatics 8 350

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