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. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . RNAi pathway components and function in Paramecium bursaria Finlay Maguire University of Exeter June 2, 2016

RNAi pathway components and function in Paramecium bursaria · 2021. 5. 20. · Paramecium tetaurelia Cid1 (Marker, 2014) [PTETP9100013001] Paramecium biaurelia [PBIGNP26212] Paramecium

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Page 1: RNAi pathway components and function in Paramecium bursaria · 2021. 5. 20. · Paramecium tetaurelia Cid1 (Marker, 2014) [PTETP9100013001] Paramecium biaurelia [PBIGNP26212] Paramecium

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RNAi pathway components and function inParamecium bursaria

Finlay Maguire

University of Exeter

June 2, 2016

Page 2: RNAi pathway components and function in Paramecium bursaria · 2021. 5. 20. · Paramecium tetaurelia Cid1 (Marker, 2014) [PTETP9100013001] Paramecium biaurelia [PBIGNP26212] Paramecium

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Overview

Motivation

RNAi in ciliates

Experimental RNAi induction in P. bursaria

RNAi pathway components in active P. bursaria transcriptome(s)

In-silico analysis of potential endosymbiont ‘cross-talk’

Conclusions

Page 3: RNAi pathway components and function in Paramecium bursaria · 2021. 5. 20. · Paramecium tetaurelia Cid1 (Marker, 2014) [PTETP9100013001] Paramecium biaurelia [PBIGNP26212] Paramecium

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Why is Paramecium bursariapotentially a good model for(secondary photosynthetic)

endosymbiosis?

Page 4: RNAi pathway components and function in Paramecium bursaria · 2021. 5. 20. · Paramecium tetaurelia Cid1 (Marker, 2014) [PTETP9100013001] Paramecium biaurelia [PBIGNP26212] Paramecium

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Broad diversity of plastid endosymbioses

Reproduced from [Arc09].

Page 5: RNAi pathway components and function in Paramecium bursaria · 2021. 5. 20. · Paramecium tetaurelia Cid1 (Marker, 2014) [PTETP9100013001] Paramecium biaurelia [PBIGNP26212] Paramecium

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Paramecium bursaria and its green algal endosymbionts

▶ 100 µm to 160 µm serial phagotrophic ciliate (nucleardimorphism).

▶ ∼ 300 endosymbiotic algae in stable heritable facultative(?)endosymbiosis.

▶ Multiple independent origins of these endosymbioses.▶ Single cell transcriptome and genome of P.

bursaria-Micractinium reisseri CCAP 1660/12.▶ P. bursaria bulk transcriptome Yad1g1N [KSD+14].

Page 6: RNAi pathway components and function in Paramecium bursaria · 2021. 5. 20. · Paramecium tetaurelia Cid1 (Marker, 2014) [PTETP9100013001] Paramecium biaurelia [PBIGNP26212] Paramecium

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RNAi pathways in the ciliates

Tetrahymena thermophila

Oxytricha trifallax

Paramecium bursaria

Paramecium caudatum

Paramecium multimicronucleatum

Paramecium sexaurelia

Paramecium primaurelia

Paramecium octaurelia

Paramecium tredecaurelia

Paramecium tetaurelia

Paramecium aureliaspecies complex

?

A good model needs a means to test hypotheses:▶ Ciliate specific scnRNA system [MG04, CMM13].▶ siRNA pathways present in Paramecium tetaurelia

[GS01, GS02] (and Tetrahymena thermophila [CL06, YC05]):1. Transgene inducible pathway [GS01].2. Exogenous dsRNA inducible pathway (feeding or injection)

[GS02].

Page 7: RNAi pathway components and function in Paramecium bursaria · 2021. 5. 20. · Paramecium tetaurelia Cid1 (Marker, 2014) [PTETP9100013001] Paramecium biaurelia [PBIGNP26212] Paramecium

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Transgene pathway

▶ Microinjection and transformation of MAC with high-copytransgenes lacking 3’ UTR [GS01]:

1. 23nt siRNA generated from transgene transcripts (Dcr1, Rdr2,Rdr3 and Cid2) [LNS+09, MCT+14].

2. mRNA cleavage (Ptiwi13 and Ptiwi14).

Page 8: RNAi pathway components and function in Paramecium bursaria · 2021. 5. 20. · Paramecium tetaurelia Cid1 (Marker, 2014) [PTETP9100013001] Paramecium biaurelia [PBIGNP26212] Paramecium

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Exogenous dsRNA pathway

Reproduced from [CGA+15].

▶ Exogenous dsRNA viafeeding (or microinjection)[GS02].

▶ 1◦ siRNA targeted cleavage(Ptiwi13) [BGK+11].

▶ Undefined role in MAC for2◦ siRNA (Ptiwi12, Ptiwi15)[MCT+14, CGA+15,BGK+11].

▶ Pds1 involved in uptake ofdsRNA from vacuole?[CGA+15].

▶ Activated at low levels byssRNA from normal foodbacteria [CGA+15].

Page 9: RNAi pathway components and function in Paramecium bursaria · 2021. 5. 20. · Paramecium tetaurelia Cid1 (Marker, 2014) [PTETP9100013001] Paramecium biaurelia [PBIGNP26212] Paramecium

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So, can we experimentally induceRNAi in P. bursaria?

Page 10: RNAi pathway components and function in Paramecium bursaria · 2021. 5. 20. · Paramecium tetaurelia Cid1 (Marker, 2014) [PTETP9100013001] Paramecium biaurelia [PBIGNP26212] Paramecium

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Experimental feeding vector

L4440

2790 bp

698

466

233

2790

2558

2325

2093

1860

1628

1396

1163

931

pBR322_origin

ORF frame 2

Ampicillin

AmpR_promoter

f1_origin

lacZ_a

T7_promoter

T7_promoterInsert

Transformed into E. coli with IPTG-inducible T7 polymerase andRNAse III deficiency.

Page 11: RNAi pathway components and function in Paramecium bursaria · 2021. 5. 20. · Paramecium tetaurelia Cid1 (Marker, 2014) [PTETP9100013001] Paramecium biaurelia [PBIGNP26212] Paramecium

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Construct inserts

Gene Function RNAi phenotype in P. tetaureliaepi2 Epiplasmin “Monstrous” cellsNSF Membrane fusion factor Lethal

bug22 Basal body/ciliary protein Slow swimming and death

Page 12: RNAi pathway components and function in Paramecium bursaria · 2021. 5. 20. · Paramecium tetaurelia Cid1 (Marker, 2014) [PTETP9100013001] Paramecium biaurelia [PBIGNP26212] Paramecium

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RNAi feeding had mixed results

0

500

1000

1500

2000C

ells

per

ml

Construct = Control Construct = bug22

0 2 4 6 8 10Day

0

500

1000

1500

2000

Cells

per

ml

Construct = epi2

0 2 4 6 8 10Day

Construct = NSF

Organism

P. tetaurelia

CCAP 1660/12

Yad1g1N

HA1

186b

Page 13: RNAi pathway components and function in Paramecium bursaria · 2021. 5. 20. · Paramecium tetaurelia Cid1 (Marker, 2014) [PTETP9100013001] Paramecium biaurelia [PBIGNP26212] Paramecium

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Are all the known RNAi pathwaycomponents present in the active

transcriptome(s)?

Page 14: RNAi pathway components and function in Paramecium bursaria · 2021. 5. 20. · Paramecium tetaurelia Cid1 (Marker, 2014) [PTETP9100013001] Paramecium biaurelia [PBIGNP26212] Paramecium

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Summary of known RNAi components

Pathway Component Functiontransgene-induced siRNA Rdr3 RdRP

Ptiwi14 Piwiboth pathways Rdr2 RdRP

Dcr1 DicerPtiwi13 PiwiCid2 Nucleotidyl transferase

exogenous dsRNA-induced siRNA Rdr1 RdRPCid1 Nucleotidyl transferase

Ptiwi12 PiwiPtiwi15 PiwiPds1 Import of dsRNA?

Page 15: RNAi pathway components and function in Paramecium bursaria · 2021. 5. 20. · Paramecium tetaurelia Cid1 (Marker, 2014) [PTETP9100013001] Paramecium biaurelia [PBIGNP26212] Paramecium

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Cid ancestorCid

Tetrahymena thermophila [XP̲001012854.1]

Tetrahymena thermophila [XP̲001012858.1]

Paramecium bursaria SW1 [comp3906̲seq0̲m.68533]

Paramecium bursaria SW1 [comp3906̲seq0̲m.68531]

Paramecium bursaria Yad1g [TR17851̲c0̲g1̲i8̲m.235761]

Paramecium bursaria Yad1g [TR432̲c1̲g1̲i2̲m.4057]

80.7%/0.93

Paramecium biaurelia [PBIGNP33303]

Paramecium tetaurelia Cid3 [GSPATP00025353001]

Paramecium sexaurelia [PSEXPNG26288]

89.8%/0.94

Paramecium multimicronucleatum [PMMNP07604]

99.8%/1.00

Paramecium caudatum [PCAUDP10462]

91%/0.93

Paramecium tetaurelia Cid1 (Marker, 2014) [PTETP9100013001]

Paramecium biaurelia [PBIGNP26212]

Paramecium primaurelia [PPRIMP23072]

5%/0.51

Paramecium sexaurelia [PSEXPNG26738]

42%/0.71

Paramecium multimicronucleatum [PMMNP02964]

98.9%/0.99

Paramecium caudatum [PCAUDP15935]

55.4%/0.63

99.7%/1.00

59.5%/0.67

100%/1.00

97.9%/1.00

Paramecium caudatum [PSEXPNG26858]

Paramecium multimicronucleatum [PMMNP03007]

Paramecium sexaurelia [PSEXPNG26858]

Paramecium primaurelia [PPRIMP27560]

Paramecium biaurelia [PBIGNP11073]

Paramecium tetaurelia Cid2 (Marker, 2014) [PTETP13400003001]84.1%/0.91

83%/0.88

95.3%/0.96

83.9%/0.88

59.1%/0.54

99.7%/1.00

86.7%/0.69

100%/1.00

0.2

Cid2

Cid1

Cid3

Cid1-3Ancestor?

Tetrahymena thermophila

Oxytricha trifallax

Paramecium bursaria

Paramecium caudatum

Paramecium multimicronucleatum

Paramecium sexaurelia

Paramecium primaurelia

Paramecium octaurelia

Paramecium tredecaurelia

Paramecium tetaurelia

?

Page 16: RNAi pathway components and function in Paramecium bursaria · 2021. 5. 20. · Paramecium tetaurelia Cid1 (Marker, 2014) [PTETP9100013001] Paramecium biaurelia [PBIGNP26212] Paramecium

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Pds1 absent

Pds1

0.2

Paramecium caudatum [PCAUDP0810]

Paramecium sexaurelia [PSEXPNG04218]

Paramecium tetaurelia Psd1 (Marker, 2014) [PTETP600032001]

Paramecium primaurelia [PPRIMP00625]

Paramecium multimicronucleatum [PMMNP02700]

Paramecium biaurelia [PBIGNP01684]

Paramecium multimicronucleatum [PMMNP02686]

100%/1.0

99.5%/0.99

31.2%/0.64

87.2%/0.93

Tetrahymena thermophila

Oxytricha trifallax

Paramecium bursaria

Paramecium caudatum

Paramecium multimicronucleatum

Paramecium sexaurelia

Paramecium primaurelia

Paramecium octaurelia

Paramecium tredecaurelia

Paramecium tetaurelia

?

Page 17: RNAi pathway components and function in Paramecium bursaria · 2021. 5. 20. · Paramecium tetaurelia Cid1 (Marker, 2014) [PTETP9100013001] Paramecium biaurelia [PBIGNP26212] Paramecium

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Presence/absence of known pathway components

Paramecium sexaurelia

Paramecium biaurelia

Paramecium caudatum

Paramecium multimicronucleatum

Paramecium primaurelia

Paramecium tetaurelia

Paramecium bursaria

Rdr3

Rdr2

Ptiwi14

Cid1Rdr1Pds1

Ptiwi12

Ptiwi15

Presence of homologue

Absence of homologue

Unresolved

Putative unduplicated ancestral orthologue

Ptiwi13

Dcr1

Cid2

Exogenous dsRNA factors

Transgene dsRNA

Required by both

Page 18: RNAi pathway components and function in Paramecium bursaria · 2021. 5. 20. · Paramecium tetaurelia Cid1 (Marker, 2014) [PTETP9100013001] Paramecium biaurelia [PBIGNP26212] Paramecium

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Putative RNAi component evolution scenario

Duplication of Cid1-Cid3 ancestor into Cid1 and Cid3

Duplication of ancestral Rdr into Rdr1 and Rdr2

Whole genome duplication

AB?C

Duplication of ancestral Cid into Cid2 and Cid1-Cid3 ancestor

Tetrahymena thermophila

Oxytricha trifallax

Paramecium bursaria

Paramecium caudatum

Paramecium multimicronucleatum

Paramecium sexaurelia

Paramecium primaureliaParamecium tetaurelia

Paramecium aureliaspecies complex

? Paramecium biaurelia

Dcr1Ancestral RdrAncestral Cid

Ancestral PiwisB?A

Rdr3

Pds1B? C

Page 19: RNAi pathway components and function in Paramecium bursaria · 2021. 5. 20. · Paramecium tetaurelia Cid1 (Marker, 2014) [PTETP9100013001] Paramecium biaurelia [PBIGNP26212] Paramecium

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Could having a eukaryoticendosymbiont and RNAi activated bydsRNA in vacuoles be deleterious?

Page 20: RNAi pathway components and function in Paramecium bursaria · 2021. 5. 20. · Paramecium tetaurelia Cid1 (Marker, 2014) [PTETP9100013001] Paramecium biaurelia [PBIGNP26212] Paramecium

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Higher level of collisions with eukaryotes

Page 21: RNAi pathway components and function in Paramecium bursaria · 2021. 5. 20. · Paramecium tetaurelia Cid1 (Marker, 2014) [PTETP9100013001] Paramecium biaurelia [PBIGNP26212] Paramecium

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Collisions are a function of transcriptome size

Page 22: RNAi pathway components and function in Paramecium bursaria · 2021. 5. 20. · Paramecium tetaurelia Cid1 (Marker, 2014) [PTETP9100013001] Paramecium biaurelia [PBIGNP26212] Paramecium

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Conclusions

▶ RNAi phenotypes not inducible in most P. bursaria strains viafeeding.

▶ P. bursaria lacks Pds1 (in active transcriptome) thus may beunable to take up RNA from digestive vacuoles.

▶ High levels of 23-mer collisions between P. bursaria andeukaryotic endosymbiont transcriptomes may lead todeactivation of dsRNA uptake from vacuoles.

▶ Presence of other factors in active transcriptomes of P.bursaria indicate transgene and microinjected exogenousdsRNA pathways may function.

Page 23: RNAi pathway components and function in Paramecium bursaria · 2021. 5. 20. · Paramecium tetaurelia Cid1 (Marker, 2014) [PTETP9100013001] Paramecium biaurelia [PBIGNP26212] Paramecium

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Acknowledgements

▶ Ben Jenkins (feeding experiments)▶ David Milner (labwork)▶ Tom Richards (PI)▶ NHM-UCL PhD Studentship (main funding)

Page 24: RNAi pathway components and function in Paramecium bursaria · 2021. 5. 20. · Paramecium tetaurelia Cid1 (Marker, 2014) [PTETP9100013001] Paramecium biaurelia [PBIGNP26212] Paramecium

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References[Arc09] John M Archibald. The puzzle of plastid evolution. Curr. Biol., 19(2):R81–8, January 2009.

[BGK+11] K. Bouhouche, J.-F. Gout, a. Kapusta, M. Betermier, and E. Meyer. Functionalspecialization of Piwi proteins in Paramecium tetraurelia from post-transcriptional genesilencing to genome remodelling. Nucleic Acids Res., 39(10):4249–4264, 2011.

[CGA+15] Q. Carradec, U. Gotz, O. Arnaiz, J. Pouch, M. Simon, E. Meyer, and S. Marker. Primaryand secondary siRNA synthesis triggered by RNAs from food bacteria in the ciliateParamecium tetraurelia. Nucleic Acids Res., 43(3):1818–1833, 2015.

[CL06] Kathleen Collins and Suzanne R Lee. Two classes of endogenous small RNAs inTetrahymena thermophila. Genes Dev., 20:28–33, 2006.

[CMM13] Douglas L Chalker, E. Meyer, and Kazufumi Mochizuki. Epigenetics of ciliates. Cold SpringHarb. Prespectives Epigenetics, 5:a017764, 2013.

[GS01] Angélique Galvani and Linda Sperling. Transgene-mediated post-transcriptional genesilencing is inhibited by 3 non-coding sequences in Paramecium. Nucleic Acids Res.,29(21):4387–4394, 2001.

[GS02] Angélique Galvani and Linda Sperling. RNA interference by feeding in Paramecium. TrendsGenet., 18(1):11–2, January 2002.

[KSD+14] Yuuki Kodama, Haruo Suzuki, Hideo Dohra, Manabu Sugii, Tatsuya Kitazume, KatsushiYamaguchi, Shuji Shigenobu, and Masahiro Fujishima. Comparison of gene expression ofParamecium bursaria with and without Chlorella variabilis symbionts. BMC Genomics,15:183, 2014.

[LNS+09] G. Lepere, M. Nowacki, V. Serrano, J.-F. Gout, G. Guglielmi, S. Duharcourt, and E. Meyer.Silencing-associated and meiosis-specific small RNA pathways in Paramecium tetraurelia.Nucleic Acids Res., 37(3):903–915, 2009.

[MCT+14] Simone Marker, Quentin Carradec, Véronique Tanty, Olivier Arnaiz, and Eric Meyer. Aforward genetic screen reveals essential and non-essential RNAi factors in Parameciumtetraurelia. Nucleic Acids Res., 42(11):7268–7280, 2014.

[MG04] Kazufumi Mochizuki and Martin a. Gorovsky. Conjugation-specific small RNAs inTetrahymena have predicted properties of scan (scn) RNAs involved in genomerearrangement. Genes Dev., 18(Nanney 1974):2068–2073, 2004.

[YC05] Meng-Chao Yao and Ju-Lan Chao. RNA-guided DNA deletion in Tetrahymena: anRNAi-based mechanism for programmed genome rearrangements. Annu. Rev. Genet.,39:537–59, 2005.

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Microinjection proved difficult

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Dcr1

Paramecium bursaria SW1 [comp4263_seq4_m.73243]

Paramecium bursaria Yad1g [TR10970_c0_g1_i3_m.150314]

Paramecium multimicronucleatum [PMMNP06401]

Paramecium caudatum [PCAUDP17596]

Paramecium sexaurelia [PSEXPNG07454]

Paramecium primaurelia [PPRIMP21835]

Paramecium tetaurelia Dcr1 (Marker, 2014) [GSPATP00021751001]

Paramecium biaurelia [PBIGNP07629]

14.2%/0.41

100%/0.99

100%/1.00

30.8/50

100%/1.00

100%/1.00

Oxytricha trifallax [Contig17740.0.g110_protein]

Tetrahymena thermophila [gi_50897085_dbj_BAD34723.1]

100%/1.00

0.5Dcr1

Page 27: RNAi pathway components and function in Paramecium bursaria · 2021. 5. 20. · Paramecium tetaurelia Cid1 (Marker, 2014) [PTETP9100013001] Paramecium biaurelia [PBIGNP26212] Paramecium

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Rdr1 Rdr2

Rdr1 & Rdr2

Tetrahymena thermophila [XP_001026321.2]

Oxytricha trifallax [gi403346586]

Paramecium bursaria Yad1g [TR10997_c0_g2_i5_m.152701]

Paramecium bursaria SW1 [comp1394_seq3_m.27654]

Paramecium bursaria Yad1g [TR24504_c0_g1_i1_m.344314]

Paramecium bursaria SW1 [comp2093_seq0_m.40761]

Paramecium biaurelia [PBIGNP22852]

Paramecium primaurelia [PPRIMP16453]

Paramecium tetaurelia Rdr2 (Marker, 2014) [GSPATP00036857001]80.4%/0.82

Paramecium sexaurelia [PSEXPNG32890]

99.4%/0.97

Paramecium sexaurelia [PSEXPNG31119]

87.6%/0.83

Paramecium multimicronucleatum [PMMNP14096]

100%/1.00

Paramecium caudatum [PCAUDP11670]

93.3%/0.94

100%/1.00

100%/1.00

Paramecium biaurelia [PBIGNP28717]

Paramecium tetaurelia Rdr1 (Marker, 2014) [PTETP8500012001]

Paramecium primaurelia [PPRIMP21923]

64.1%/0.81

Paramecium sexaurelia [PSEXPNG23839]

98.5%/0.98

96.7%/0.99

Paramecium caudatum [PCAUDP07869]

Paramecium multimicronucleatum [PMMNP15732]24.6%/0.5

99.9%/1.00

100%/1.00

100%/1.00

76.7%/0.85

99.2%

0.2

/0.99

Rdr1

Rdr2

Rdr1?

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Rdr3

Paramecium bursaria Yad1g [TR463_c0_g2_i1_m.5849]

Paramecium bursaria SW1 [comp11757_seq0_m.132993]

Paramecium biaurelia [BIGNP03905]

Paramecium primaurelia [PPRIMP22734]

Paramecium tetaurelia Rdr3 (Marker, 2014) [GSPATP00006401001]

17.7%/0.50

Paramecium sexaurelia [PSEXPNG06491]

98.4%/0.96

Paramecium multimicronucleatum [PMMNP00936]

100%/1.00

Paramecium caudatum [PCAUDP10550]

96.6%/0.92

100%/1.00

0.2Rdr3

Page 29: RNAi pathway components and function in Paramecium bursaria · 2021. 5. 20. · Paramecium tetaurelia Cid1 (Marker, 2014) [PTETP9100013001] Paramecium biaurelia [PBIGNP26212] Paramecium

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Psd1 Structure