Adaptive evolution among cytoplasmic piRNA proteins leads to decreased genomic auto-immunity

Autoři: Luyang Wang aff001;  Daniel A. Barbash aff002;  Erin S. Kelleher aff001
Působiště autorů: Dept. Biology & Biochemistry, University of Houston, Houston, Texas, United States of America aff001;  Dept. Molecular Biology & Genetics, Cornell University, Ithaca, New York, United States of America aff002
Vyšlo v časopise: Adaptive evolution among cytoplasmic piRNA proteins leads to decreased genomic auto-immunity. PLoS Genet 16(6): e32767. doi:10.1371/journal.pgen.1008861
Kategorie: Research Article
doi: 10.1371/journal.pgen.1008861


In metazoan germlines, the piRNA pathway acts as a genomic immune system, employing small RNA-mediated silencing to defend host DNA from the harmful effects of transposable elements (TEs). Expression of genomic TEs is proposed to initiate self regulation by increasing the production of repressive piRNAs, thereby “adapting” piRNA-mediated control to the most active TE families. Surprisingly, however, piRNA pathway proteins, which execute piRNA biogenesis and enforce silencing of targeted sequences, evolve rapidly and adaptively in animals. If TE silencing is ensured through piRNA biogenesis, what necessitates changes in piRNA pathway proteins? Here we used interspecific complementation to test for functional differences between Drosophila melanogaster and D. simulans alleles of three adaptively evolving piRNA pathway proteins: Armitage, Aubergine and Spindle-E. In contrast to piRNA-mediated transcriptional regulators examined in previous studies, these three proteins have cytoplasmic functions in piRNA maturation and post-transcriptional silencing. Across all three proteins we observed interspecific divergence in the regulation of only a handful of TE families, which were more robustly silenced by the heterospecific piRNA pathway protein. This unexpected result suggests that unlike transcriptional regulators, positive selection has not acted on cytoplasmic piRNA effector proteins to enhance their function in TE repression. Rather, TEs may evolve to “escape” silencing by host proteins. We further discovered that D. simulans alleles of aub and armi exhibit enhanced off-target effects on host transcripts in a D. melanogaster background, as well as modest reductions in the efficiency of piRNA biogenesis, suggesting that promiscuous binding of D. simulans Aub and Armi proteins to host transcripts reduces their participation in piRNA production. Avoidance of genomic auto-immunity may therefore be a critical target of selection. Our observations suggest that piRNA effector proteins are subject to an evolutionary trade-off between defending the host genome from the harmful effect of TEs while also minimizing collateral damage to host genes.

Klíčová slova:

Biosynthesis – Drosophila – Drosophila melanogaster – Evolutionary adaptation – Gene expression – Invertebrate genomics – Messenger RNA – RNA sequencing


1. Chalitchagorn K, Shuangshoti S, Hourpai N, Kongruttanachok N, Tangkijvanich P, Thong-ngam D, et al. Distinctive pattern of LINE-1 methylation level in normal tissues and the association with carcinogenesis. Oncogene. 2004;23: 8841–8846. doi: 10.1038/sj.onc.1208137 15480421

2. Howard G, Eiges R, Gaudet F, Jaenisch R, Eden A. Activation and transposition of endogenous retroviral elements in hypomethylation induced tumors in mice. Oncogene. 2008;27: 404–408. doi: 10.1038/sj.onc.1210631 17621273

3. Kidwell MG, Novy JB. Hybrid Dysgenesis in DROSOPHILA MELANOGASTER: Sterility Resulting from Gonadal Dysgenesis in the P-M System. Genetics. 1979;92: 1127–1140. 17248943

4. Vilà MR, Gelpí C, Nicolás A, Morote J, Schwartz S, Schwartz S, et al. Higher processing rates of Alu-containing sequences in kidney tumors and cell lines with overexpressed Alu-mRNAs. Oncol Rep. 2003;10: 1903–1909. 14534716

5. Czech B, Hannon GJ. One Loop to Rule Them All: The Ping-Pong Cycle and piRNA-Guided Silencing. Trends Biochem Sci. 2016;41: 324–337. doi: 10.1016/j.tibs.2015.12.008 26810602

6. Anxolabéhère D, Kidwell MG, Periquet G. Molecular characteristics of diverse populations are consistent with the hypothesis of a recent invasion of Drosophila melanogaster by mobile P elements. Mol Biol Evol. 1988;5: 252–269. doi: 10.1093/oxfordjournals.molbev.a040491 2838720

7. Yang H-P, Barbash DA. Abundant and species-specific DINE-1 transposable elements in 12 Drosophila genomes. Genome Biol. 2008;9: R39. doi: 10.1186/gb-2008-9-2-r39 18291035

8. de la Chaux N, Wagner A. BEL/Pao retrotransposons in metazoan genomes. BMC Evol Biol. 2011;11: 154. doi: 10.1186/1471-2148-11-154 21639932

9. Lu C, Chen J, Zhang Y, Hu Q, Su W, Kuang H. Miniature inverted-repeat transposable elements (MITEs) have been accumulated through amplification bursts and play important roles in gene expression and species diversity in Oryza sativa. Mol Biol Evol. 2012;29: 1005–1017. doi: 10.1093/molbev/msr282 22096216

10. Lu J, Clark AG. Population dynamics of PIWI-interacting RNAs (piRNAs) and their targets in Drosophila. Genome Res. 2010;20: 212–227. doi: 10.1101/gr.095406.109 19948818

11. Malone CD, Hannon GJ. Molecular evolution of piRNA and transposon control pathways in Drosophila. Cold Spring Harb Symp Quant Biol. 2009;74: 225–234. doi: 10.1101/sqb.2009.74.052 20453205

12. Kolaczkowski B, Hupalo DN, Kern AD. Recurrent adaptation in RNA interference genes across the Drosophila phylogeny. Mol Biol Evol. 2011;28: 1033–1042. doi: 10.1093/molbev/msq284 20971974

13. Obbard DJ, Gordon KHJ, Buck AH, Jiggins FM. The evolution of RNAi as a defence against viruses and transposable elements. Philos Trans R Soc Lond B Biol Sci. 2009;364: 99–115. doi: 10.1098/rstb.2008.0168 18926973

14. Palmer WH, Hadfield JD, Obbard DJ. RNA-Interference Pathways Display High Rates of Adaptive Protein Evolution in Multiple Invertebrates. Genetics. 2018;208: 1585–1599. doi: 10.1534/genetics.117.300567 29437826

15. Simkin A, Wong A, Poh Y-P, Theurkauf WE, Jensen JD. Recurrent and recent selective sweeps in the piRNA pathway. Evolution. 2013;67: 1081–1090. doi: 10.1111/evo.12011 23550757

16. Yi M, Chen F, Luo M, Cheng Y, Zhao H, Cheng H, et al. Rapid evolution of piRNA pathway in the teleost fish: implication for an adaptation to transposon diversity. Genome Biol Evol. 2014;6: 1393–1407. doi: 10.1093/gbe/evu105 24846630

17. Vermaak D, Henikoff S, Malik HS. Positive selection drives the evolution of rhino, a member of the heterochromatin protein 1 family in Drosophila. PLoS Genet. 2005;1: 96–108. doi: 10.1371/journal.pgen.0010009 16103923

18. Senti K-A, Brennecke J. The piRNA pathway: a fly’s perspective on the guardian of the genome. Trends Genet. 2010;26: 499–509. doi: 10.1016/j.tig.2010.08.007 20934772

19. Blumenstiel JP, Erwin AA, Hemmer LW. What Drives Positive Selection in the Drosophila piRNA Machinery? The Genomic Autoimmunity Hypothesis. Yale J Biol Med. 2016;89: 499–512. 28018141

20. Parhad SS, Tu S, Weng Z, Theurkauf WE. Adaptive Evolution Leads to Cross-Species Incompatibility in the piRNA Transposon Silencing Machinery. Dev Cell. 2017;43: 60–70.e5. doi: 10.1016/j.devcel.2017.08.012 28919205

21. Castillo DM, Mell JC, Box KS, Blumenstiel JP. Molecular evolution under increasing transposable element burden in Drosophila: a speed limit on the evolutionary arms race. BMC Evol Biol. 2011;11: 258. doi: 10.1186/1471-2148-11-258 21917173

22. Yu B, Lin YA, Parhad SS, Jin Z, Ma J, Theurkauf WE, et al. Structural insights into Rhino-Deadlock complex for germline piRNA cluster specification. EMBO Rep. 2018;19. doi: 10.15252/embr.201745418 29858487

23. Parhad SS, Yu T, Zhang G, Rice NP, Weng Z, Theurkauf WE. Adaptive evolution targets a piRNA precursor transcription network. bioRxiv. 2019. p. 678227. doi: 10.1101/678227

24. Gunawardane LS, Saito K, Nishida KM, Miyoshi K, Kawamura Y, Nagami T, et al. A slicer-mediated mechanism for repeat-associated siRNA 5’ end formation in Drosophila. Science. 2007;315: 1587–1590. doi: 10.1126/science.1140494 17322028

25. Brennecke J, Aravin AA, Stark A, Dus M, Kellis M, Sachidanandam R, et al. Discrete small RNA-generating loci as master regulators of transposon activity in Drosophila. Cell. 2007;128: 1089–1103. doi: 10.1016/j.cell.2007.01.043 17346786

26. Malone CD, Brennecke J, Dus M, Stark A, McCombie WR, Sachidanandam R, et al. Specialized piRNA pathways act in germline and somatic tissues of the Drosophila ovary. Cell. 2009;137: 522–535. doi: 10.1016/j.cell.2009.03.040 19395010

27. Haase AD, Fenoglio S, Muerdter F, Guzzardo PM, Czech B, Pappin DJ, et al. Probing the initiation and effector phases of the somatic piRNA pathway in Drosophila. Genes Dev. 2010;24: 2499–2504. doi: 10.1101/gad.1968110 20966049

28. Andress A, Bei Y, Fonslow BR, Giri R, Wu Y, Yates JR 3rd, et al. Spindle-E cycling between nuage and cytoplasm is controlled by Qin and PIWI proteins. J Cell Biol. 2016;213: 201–211. doi: 10.1083/jcb.201411076 27091448

29. Pandey RR, Homolka D, Chen K-M, Sachidanandam R, Fauvarque M-O, Pillai RS. Recruitment of Armitage and Yb to a transcript triggers its phased processing into primary piRNAs in Drosophila ovaries. PLoS Genet. 2017;13: e1006956. doi: 10.1371/journal.pgen.1006956 28827804

30. Ge DT, Wang W, Tipping C, Gainetdinov I, Weng Z, Zamore PD. The RNA-Binding ATPase, Armitage, Couples piRNA Amplification in Nuage to Phased piRNA Production on Mitochondria. Mol Cell. 2019;74: 982–995.e6. doi: 10.1016/j.molcel.2019.04.006 31076285

31. Kelleher ES, Edelman NB, Barbash DA. Drosophila Interspecific Hybrids Phenocopy piRNA-Pathway Mutants. PLoS Biol. 2012;10. doi: 10.1371/journal.pbio.1001428 23189033

32. Li C, Vagin VV, Lee S, Xu J, Ma S, Xi H, et al. Collapse of germline piRNAs in the absence of Argonaute3 reveals somatic piRNAs in flies. Cell. 2009;137: 509–521. doi: 10.1016/j.cell.2009.04.027 19395009

33. Mohn F, Handler D, Brennecke J. piRNA-guided slicing specifies transcripts for Zucchini-dependent, phased piRNA biogenesis. Science. 2015;348: 812–817. doi: 10.1126/science.aaa1039 25977553

34. Han BW, Wang W, Li C, Weng Z, Zamore PD. Noncoding RNA. piRNA-guided transposon cleavage initiates Zucchini-dependent, phased piRNA production. Science. 2015;348: 817–821. doi: 10.1126/science.aaa1264 25977554

35. Wang W, Han BW, Tipping C, Ge DT, Zhang Z, Weng Z, et al. Slicing and Binding by Ago3 or Aub Trigger Piwi-Bound piRNA Production by Distinct Mechanisms. Mol Cell. 2015;59: 819–830. doi: 10.1016/j.molcel.2015.08.007 26340424

36. Vourekas A, Zheng K, Fu Q, Maragkakis M, Alexiou P, Ma J, et al. The RNA helicase MOV10L1 binds piRNA precursors to initiate piRNA processing. Genes Dev. 2015;29: 617–629. doi: 10.1101/gad.254631.114 25762440

37. Ishizu H, Kinoshita T, Hirakata S, Komatsuzaki C, Siomi MC. Distinct and Collaborative Functions of Yb and Armitage in Transposon-Targeting piRNA Biogenesis. Cell Rep. 2019;27: 1822–1835.e8. doi: 10.1016/j.celrep.2019.04.029 31067466

38. Adams MD, Celniker SE, Holt RA, Evans CA, Gocayne JD, Amanatides PG, et al. The genome sequence of Drosophila melanogaster. Science. 2000;287: 2185–2195. doi: 10.1126/science.287.5461.2185 10731132

39. Clark AG, Eisen MB, Smith DR, Bergman CM, Oliver B, Markow TA, et al. Evolution of genes and genomes on the Drosophila phylogeny. Nature. 2007;450: 203–218. doi: 10.1038/nature06341 17994087

40. Mitchell AL, Attwood TK, Babbitt PC, Blum M, Bork P, Bridge A, et al. InterPro in 2019: improving coverage, classification and access to protein sequence annotations. Nucleic Acids Res. 2019;47: D351–D360. doi: 10.1093/nar/gky1100 30398656

41. Groth AC, Fish M, Nusse R, Calos MP. Construction of transgenic Drosophila by using the site-specific integrase from phage phiC31. Genetics. 2004;166: 1775–1782. doi: 10.1534/genetics.166.4.1775 15126397

42. Schüpbach T, Wieschaus E. Female sterile mutations on the second chromosome of Drosophila melanogaster. II. Mutations blocking oogenesis or altering egg morphology. Genetics. 1991;129: 1119–1136. 1783295

43. Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014;15: 550. doi: 10.1186/s13059-014-0550-8 25516281

44. Olivieri D, Senti K-A, Subramanian S, Sachidanandam R, Brennecke J. The Cochaperone Shutdown Defines a Group of Biogenesis Factors Essential for All piRNA Populations in Drosophila. Mol Cell. 2012. doi: 10.1016/j.molcel.2012.07.021 22902557

45. Barckmann B, Pierson S, Dufourt J, Papin C, Armenise C, Port F, et al. Aubergine iCLIP Reveals piRNA-Dependent Decay of mRNAs Involved in Germ Cell Development in the Early Embryo. Cell Rep. 2015;12: 1205–1216. doi: 10.1016/j.celrep.2015.07.030 26257181

46. Post C, Clark JP, Sytnikova YA, Chirn G-W, Lau NC. The capacity of target silencing byDrosophilaPIWI and piRNAs. RNA. 2014. pp. 1977–1986. doi: 10.1261/rna.046300.114 25336588

47. Sytnikova YA, Rahman R, Chirn G-W, Clark JP, Lau NC. Transposable element dynamics and PIWI regulation impacts lncRNA and gene expression diversity in Drosophila ovarian cell cultures. Genome Res. 2014;24: 1977–1990. doi: 10.1101/gr.178129.114 25267525

48. Lim AK, Tao L, Kai T. piRNAs mediate posttranscriptional retroelement silencing and localization to pi-bodies in the Drosophila germline. J Cell Biol. 2009;186: 333–342. doi: 10.1083/jcb.200904063 19651888

49. Rouget C, Papin C, Boureux A, Meunier A-C, Franco B, Robine N, et al. Maternal mRNA deadenylation and decay by the piRNA pathway in the early Drosophila embryo. Nature. 2010;467: 1128–1132. doi: 10.1038/nature09465 20953170

50. Levine MT, McCoy C, Vermaak D, Lee YCG, Hiatt MA, Matsen FA, et al. Phylogenomic analysis reveals dynamic evolutionary history of the Drosophila heterochromatin protein 1 (HP1) gene family. PLoS Genet. 2012;8: e1002729. doi: 10.1371/journal.pgen.1002729 22737079

51. Levine MT, Vander Wende HM, Hsieh E, Baker EP, Malik HS. Recurrent Gene Duplication Diversifies Genome Defense Repertoire in Drosophila. Mol Biol Evol. 2016;33: 1641–1653. doi: 10.1093/molbev/msw053 26979388

52. Cañizares J, Grau M, Paricio N, Moltó MD. Tirant is a new member of the gypsy family of retrotransposons in Drosophila melanogaster. Genome. 2000;43: 9–14. doi: 10.1139/g99-082 10701107

53. Fablet M, McDonald JF, Biémont C, Vieira C. Ongoing loss of the tirant transposable element in natural populations of Drosophila simulans. Gene. 2006;375: 54–62. doi: 10.1016/j.gene.2006.02.008 16626897

54. Kofler R, Nolte V, Schlötterer C. Tempo and Mode of Transposable Element Activity in Drosophila. PLoS Genet. 2015;11: e1005406. doi: 10.1371/journal.pgen.1005406 26186437

55. Parhad SS, Yu T, Zhang G, Rice NP, Weng Z, Theurkauf WE. Adaptive Evolution Targets a piRNA Precursor Transcription Network. Cell Rep. 2020;30: 2672–2685.e5.

56. Hoskins RA, Carlson JW, Wan KH, Park S, Mendez I, Galle SE, et al. The Release 6 reference sequence of the Drosophila melanogaster genome. Genome Res. 2015;25: 445–458. doi: 10.1101/gr.185579.114 25589440

57. Hu TT, Eisen MB, Thornton KR, Andolfatto P. A second-generation assembly of the Drosophila simulans genome provides new insights into patterns of lineage-specific divergence. Genome Res. 2013;23: 89–98. doi: 10.1101/gr.141689.112 22936249

58. Maheshwari S, Barbash DA. Cis-by-Trans regulatory divergence causes the asymmetric lethal effects of an ancestral hybrid incompatibility gene. PLoS Genet. 2012;8: e1002597. doi: 10.1371/journal.pgen.1002597 22457639

59. Venken KJT, He Y, Hoskins RA, Bellen HJ. P[acman]: a BAC transgenic platform for targeted insertion of large DNA fragments in D. melanogaster. Science. 2006;314: 1747–1751. doi: 10.1126/science.1134426 17138868

60. Wickersheim ML, Blumenstiel JP. Terminator oligo blocking efficiently eliminates rRNA from Drosophila small RNA sequencing libraries. Biotechniques. 2013;55: 269–272. doi: 10.2144/000114102 24215643

61. Marioni JC, Mason CE, Mane SM, Stephens M, Gilad Y. RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays. Genome Res. 2008;18: 1509–1517. doi: 10.1101/gr.079558.108 18550803

62. Martin M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet.journal. 2011;17: 10–12.

63. Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 2009;10: R25. doi: 10.1186/gb-2009-10-3-r25 19261174

64. Gramates LS, Marygold SJ, Santos G dos, Urbano J-M, Antonazzo G, Matthews BB, et al. FlyBase at 25: looking to the future. Nucleic Acids Res. 2017;45: D663–D671. doi: 10.1093/nar/gkw1016 27799470

65. Bao W, Kojima KK, Kohany O. Repbase Update, a database of repetitive elements in eukaryotic genomes. Mob DNA. 2015;6: 11. doi: 10.1186/s13100-015-0041-9 26045719

66. Trapnell C, Pachter L, Salzberg SL. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics. 2009;25: 1105–1111. doi: 10.1093/bioinformatics/btp120 19289445

67. Anders S, Pyl PT, Huber W. HTSeq—A Python framework to work with high-throughput sequencing data. bioRxiv. 2014. p. 002824. doi: 10.1101/002824

68. Anders S, Huber W. Differential expression analysis for sequence count data. Genome Biol. 2010;11: R106. doi: 10.1186/gb-2010-11-10-r106 20979621

69. Brennecke J, Malone CD, Aravin AA, Sachidanandam R, Stark A, Hannon GJ. An epigenetic role for maternally inherited piRNAs in transposon silencing. Science. 2008;322: 1387–1392. doi: 10.1126/science.1165171 19039138

70. Teixeira FK, Okuniewska M, Malone CD, Coux R-X, Rio DC, Lehmann R. piRNA-mediated regulation of transposon alternative splicing in the soma and germ line. Nature. 2017;552: 268–272. doi: 10.1038/nature25018 29211718

71. Malone CD, Hannon GJ. Molecular evolution of piRNA and transposon control pathways in Drosophila. Cold Spring Harb Symp Quant Biol. 2009;74: 225–234. doi: 10.1101/sqb.2009.74.052 20453205

Článek vyšel v časopise

PLOS Genetics

2020 Číslo 6

Nejčtenější v tomto čísle

Tomuto tématu se dále věnují…


Zvyšte si kvalifikaci online z pohodlí domova

Nová éra v léčbě migrény
nový kurz
Autoři: MUDr. Eva Medová, MUDr. Tomáš Nežádal, Ph.D.

Význam nutraceutik u kardiovaskulárních onemocnění


White paper - jak vidíme optimální péči o zubní náhrady
Autoři: MUDr. Jindřich Charvát, CSc.

Faktory ovlivňující léčbu levotyroxinem

Všechny kurzy
Zapomenuté heslo

Nemáte účet?  Registrujte se

Zapomenuté heslo

Zadejte e-mailovou adresu se kterou jste vytvářel(a) účet, budou Vám na ni zaslány informace k nastavení nového hesla.


Nemáte účet?  Registrujte se