Cryptic genetic variation enhances primate L1 retrotransposon survival by enlarging the functional coiled coil sequence space of ORF1p

Autoři: Anthony V. Furano aff001;  Charlie E. Jones aff001;  Vipul Periwal aff002;  Kathryn E. Callahan aff001;  Jean-Claude Walser aff001;  Pamela R. Cook aff001
Působiště autorů: Laboratory of Cellular and Molecular Biology, NIDDK, National Institutes of Health, Bethesda, Maryland, United States of America aff001;  Laboratory of Biological Modeling, NIDDK, National Institutes of Health, Bethesda, Maryland, United States of America aff002
Vyšlo v časopise: Cryptic genetic variation enhances primate L1 retrotransposon survival by enlarging the functional coiled coil sequence space of ORF1p. PLoS Genet 16(8): e32767. doi:10.1371/journal.pgen.1008991
Kategorie: Research Article
doi: 10.1371/journal.pgen.1008991


Accounting for continual evolution of deleterious L1 retrotransposon families, which can contain hundreds to thousands of members remains a major issue in mammalian biology. L1 activity generated upwards of 40% of some mammalian genomes, including humans where they remain active, causing genetic defects and rearrangements. L1 encodes a coiled coil-containing protein that is essential for retrotransposition, and the emergence of novel primate L1 families has been correlated with episodes of extensive amino acid substitutions in the coiled coil. These results were interpreted as an adaptive response to maintain L1 activity, however its mechanism remained unknown. Although an adventitious mutation can inactivate coiled coil function, its effect could be buffered by epistatic interactions within the coiled coil, made more likely if the family contains a diverse set of coiled coil sequences—collectively referred to as the coiled coil sequence space. Amino acid substitutions that do not affect coiled coil function (i.e., its phenotype) could be “hidden” from (not subject to) purifying selection. The accumulation of such substitutions, often referred to as cryptic genetic variation, has been documented in various proteins. Here we report that this phenomenon was in effect during the latest episode of primate coiled coil evolution, which occurred 30–10 MYA during the emergence of primate L1Pa7–L1Pa3 families. First, we experimentally demonstrated that while coiled coil function (measured by retrotransposition) can be eliminated by single epistatic mutations, it nonetheless can also withstand extensive amino acid substitutions. Second, principal component and cluster analysis showed that the coiled coil sequence space of each of the L1Pa7-3 families was notably increased by the presence of distinct, coexisting coiled coil sequences. Thus, sampling related networks of functional sequences rather than traversing discrete adaptive states characterized the persistence L1 activity during this evolutionary event.

Klíčová slova:

Amino acid substitution – Epistasis – Evolutionary genetics – Nucleic acids – Phylogenetic analysis – Primates – principal component analysis – Sequence alignment


1. Boissinot S, Sookdeo A. The Evolution of Line-1 in Vertebrates. Genome biology and evolution. 2016:3485–507. doi: 10.1093/gbe/evw247 28175298

2. IHGS-Consortium. Initial sequencing and analysis of the human genome. Nature. 2001;409(6822):860–921.

3. Skowronski J, Fanning TG, Singer MF. Unit-length line-1 transcripts in human teratocarcinoma cells. Mol Cell Biol. 1988;8(4):1385–97. doi: 10.1128/mcb.8.4.1385 2454389

4. Skowronski J, Singer MF. Expression of a cytoplasmic LINE-1 transcript is regulated in a human teratocarcinoma cell line. Proc Natl Acad Sci U S A. 1985;82(18):6050–4. doi: 10.1073/pnas.82.18.6050 2412228

5. Boissinot S, Chevret P, Furano AV. L1 (LINE-1) retrotransposon evolution and amplification in recent human history. Mol Biol Evol. 2000;17(6):915–28. doi: 10.1093/oxfordjournals.molbev.a026372 10833198

6. Boissinot S, Entezam A, Young L, Munson PJ, Furano AV. The Insertional History of an Active Family of L1 Retrotransposons in Humans. Genome Res. 2004;14:1221–31. doi: 10.1101/gr.2326704 15197167

7. Khan H, Smit A, Boissinot S. Molecular evolution and tempo of amplification of human LINE-1 retrotransposons since the origin of primates. Genome Res. 2006;16(1):78–87. doi: 10.1101/gr.4001406 16344559

8. Huang CRL, Schneider AM, Lu Y, Niranjan T, Shen P, Robinson MA, et al. Mobile Interspersed Repeats Are Major Structural Variants in the Human Genome. Cell. 2010;141(7):1171–82. doi: 10.1016/j.cell.2010.05.026 20602999

9. Beck CR, Collier P, Macfarlane C, Malig M, Kidd JM, Eichler EE, et al. LINE-1 Retrotransposition Activity in Human Genomes. Cell. 2010;141(7):1159–70. doi: 10.1016/j.cell.2010.05.021 20602998

10. Iskow RC, McCabe MT, Mills RE, Torene S, Pittard WS, Neuwald AF, et al. Natural mutagenesis of human genomes by endogenous retrotransposons. Cell. 2010;141(7):1253–61. doi: 10.1016/j.cell.2010.05.020 20603005

11. Bourc’his D, Bestor TH. Meiotic catastrophe and retrotransposon reactivation in male germ cells lacking Dnmt3L. Nature. 2004;431(7004):96–9. doi: 10.1038/nature02886 15318244

12. Soper SFC, van der Heijden GW, Hardiman TC, Goodheart M, Martin SL, de Boer P, et al. Mouse Maelstrom, a Component of Nuage, Is Essential for Spermatogenesis and Transposon Repression in Meiosis. Dev Cell. 2008;15(2):285–97. doi: 10.1016/j.devcel.2008.05.015 18694567

13. Yang F, Wang PJ. Multiple LINEs of retrotransposon silencing mechanisms in the mammalian germline. Semin Cell Dev Biol. 2016;59:118–25. doi: 10.1016/j.semcdb.2016.03.001 26957474

14. Boissinot S, Entezam A, Furano AV. Selection against deleterious LINE-1-containing loci in the human lineage. Mol Biol Evol. 2001;18(6):926–35. doi: 10.1093/oxfordjournals.molbev.a003893 11371580

15. Boissinot S, Davis J, Entezam A, Petrov D, Furano AV. Fitness cost of LINE-1 (L1) activity in humans. Proc Natl Acad Sci USA. 2006;103(25):9590–4. doi: 10.1073/pnas.0603334103 16766655

16. Myers S, Bottolo L, Freeman C, McVean G, Donnelly P. A fine-scale map of recombination rates and hotspots across the human genome. Science. 2005;310(5746):321–4. doi: 10.1126/science.1117196 16224025

17. Goodier JL. Restricting retrotransposons: a review. Mob DNA. 2016;7:16. doi: 10.1186/s13100-016-0070-z 27525044

18. Schichman SA, Severynse DM, Edgell MH, Hutchison CAI. Strand-specific LINE-1 transcription in mouse F9 cells originates from the youngest phylogenetic subgroup of LINE-1 elements. J Mol Biol. 1992;224(3):559–74. doi: 10.1016/0022-2836(92)90544-t 1314898

19. Adey NB, Schichman SA, Graham DK, Peterson SN, Edgell MH, Hutchison CAI. Rodent L1 evolution has been driven by a single dominant lineage that has repeatedly acquired new transcriptional regulatory sequences. Mol Biol Evol. 1994;11(5):778–89. doi: 10.1093/oxfordjournals.molbev.a040158 7968491

20. Cabot EL, Angeletti B, Usdin K, Furano AV. Rapid evolution of a young L1 (LINE-1) clade in recently speciated Rattus taxa. J Mol Evol. 1997;45(4):412–23. doi: 10.1007/pl00006246 9321420

21. Furano AV. The biological properties and evolutionary dynamics of mammalian LINE-1 retrotransposons. Progress in Nucleic Acids Research & Molecular Biology. 2000;64:255–94.

22. Saxton JA, Martin SL. Recombination between subtypes creates a mosaic lineage of LINE-1 that is expressed and actively retrotransposing in the mouse genome. J Mol Biol. 1998;280(4):611–22. doi: 10.1006/jmbi.1998.1899 9677292

23. Sookdeo A, Hepp C, McClure M, Boissinot S. Revisiting the evolution of mouse LINE-1 in the genomic era. Mob DNA. 2013;4(1):3. doi: 10.1186/1759-8753-4-3 23286374

24. Jacobs FM, Greenberg D, Nguyen N, Haeussler M, Ewing AD, Katzman S, et al. An evolutionary arms race between KRAB zinc-finger genes ZNF91/93 and SVA/L1 retrotransposons. Nature. 2014.

25. Naufer MN, Furano AV, Williams MC. Protein-nucleic acid interactions of LINE-1 ORF1p. Seminars in Cell & Developmental Biology. 2019;86:140–9.

26. Naufer MN, Callahan KE, Cook PR, Perez-Gonzalez CE, Williams MC, Furano AV. L1 retrotransposition requires rapid ORF1p oligomerization, a novel coiled coil-dependent property conserved despite extensive remodeling. Nucleic Acids Res. 2016;44(1):281–93. doi: 10.1093/nar/gkv1342 26673717

27. Boissinot S, Furano AV. Adaptive evolution in LINE-1 retrotransposons. Mol Biol Evol. 2001;18(12):2186–94. doi: 10.1093/oxfordjournals.molbev.a003765 11719568

28. Hayden EJ, Ferrada E, Wagner A. Cryptic genetic variation promotes rapid evolutionary adaptation in an RNA enzyme. Nature. 2011;474:92. doi: 10.1038/nature10083 21637259

29. Wagner A. Robustness and evolvability: a paradox resolved. Proceedings of the Royal Society B: Biological Sciences. 2008;275(1630):91–100.

30. Hou J, van Leeuwen J, Andrews BJ, Boone C. Genetic Network Complexity Shapes Background-Dependent Phenotypic Expression. Trends in Genetics. 2018;34(8):578–86. doi: 10.1016/j.tig.2018.05.006 29903533

31. Montville R, Froissart R, Remold SK, Tenaillon O, Turner PE. Evolution of Mutational Robustness in an RNA Virus. PLoS Biol. 2005;3(11):e381. doi: 10.1371/journal.pbio.0030381 16248678

32. Burch CL, Chao L. Epistasis and its relationship to canalization in the RNA virus phi 6. Genetics. 2004;167(2):559–67. doi: 10.1534/genetics.103.021196 15238511

33. Desai MM, Weissman D, Feldman MW. Evolution Can Favor Antagonistic Epistasis. Genetics. 2007;177(2):1001–10. doi: 10.1534/genetics.107.075812 17720923

34. Baier F, Hong N, Yang G, Pabis A, Miton CM, Barrozo A, et al. Cryptic genetic variation shapes the adaptive evolutionary potential of enzymes. Elife. 2019;8:e40789. doi: 10.7554/eLife.40789 30719972

35. Lee J, Cordaux R, Han K, Wang J, Hedges DJ, Liang P, et al. Different evolutionary fates of recently integrated human and chimpanzee LINE-1 retrotransposons. Gene. 2007;390(1–2):18–27. doi: 10.1016/j.gene.2006.08.029 17055192

36. Hormozdiari F, Konkel MK, Prado-Martinez J, Chiatante G, Herraez IH, Walker JA, et al. Rates and patterns of great ape retrotransposition. Proc Nat Acad Sci. 2013;110(33):13457–62. doi: 10.1073/pnas.1310914110 23884656

37. Bershtein S, Serohijos AW, Shakhnovich EI. Bridging the physical scales in evolutionary biology: from protein sequence space to fitness of organisms and populations. Curr Opin Struct Biol. 2017;42:31–40. doi: 10.1016/ 27810574

38. de Visser JA, Krug J. Empirical fitness landscapes and the predictability of evolution. Nat Rev Genet. 2014;15(7):480–90. doi: 10.1038/nrg3744 24913663

39. Martin SL, Bushman D, Wang F, Li PWL, Walker A, Cummiskey J, et al. A single amino acid substitution in ORF1 dramatically decreases L1 retrotransposition and provides insight into nucleic acid chaperone activity. Nucleic Acids Research. 2008;36(18):5845–54. doi: 10.1093/nar/gkn554 18790804

40. Khazina E, Weichenrieder O. Human LINE-1 retrotransposition requires a metastable coiled coil and a positively charged N-terminus in L1ORF1p. Elife. 2018;7.

41. Grigoryan G, Keating AE. Structural specificity in coiled-coil interactions. Current Opinion in Structural Biology. 2008;18(4):477–83. doi: 10.1016/ 18555680

42. Hartmann MD, Mendler CT, Bassler J, Karamichali I, Ridderbusch O, Lupas AN, et al. α/β coiled coils. Elife. 2016;5:e11861. doi: 10.7554/eLife.11861 26771248

43. Hancks DC, Kazazian HH. Roles for retrotransposon insertions in human disease. Mob DNA. 2016;7(1):1–28.

44. Martin SL, Branciforte D, Keller D, Bain DL. Trimeric structure for an essential protein in L1 retrotransposition. Proc Natl Acad Sci U S A. 2003;100(24):13815–20. doi: 10.1073/pnas.2336221100 14615577

45. Khazina E, Truffault V, Buttner R, Schmidt S, Coles M, Weichenrieder O. Trimeric structure and flexibility of the L1ORF1 protein in human L1 retrotransposition. Nature structural & molecular biology. 2011;18(9):1006–U64.

46. Callahan KE, Hickman AB, Jones CE, Ghirlando R, Furano AV. Polymerization and nucleic acid-binding properties of human L1 ORF1 protein. Nucleic Acids Res. 2012;40(2):813–27. doi: 10.1093/nar/gkr728 21937507

47. Sahakyan AB, Murat P, Mayer C, Balasubramanian S. G-quadruplex structures within the 3’ UTR of LINE-1 elements stimulate retrotransposition. Nat Struct Mol Biol. 2017;24(3):243–7. doi: 10.1038/nsmb.3367 28134931

48. Howell R, Usdin K. The ability to form intrastrand tetraplexes is an evolutionarily conserved feature of the 3' end of L1 retrotransposons. Mol Biol Evol. 1997;14(2):144–55. doi: 10.1093/oxfordjournals.molbev.a025747 9029792

49. Cook PR, Jones CE, Furano AV. Phosphorylation of ORF1p is required for L1 retrotransposition. Proc Natl Acad Sci U S A. 2015;112(14):4298–303. doi: 10.1073/pnas.1416869112 25831499

50. Pele J, Becu JM, Abdi H, Chabbert M. Bios2mds: an R package for comparing orthologous protein families by metric multidimensional scaling. BMC Bioinformatics. 2012;13:133. doi: 10.1186/1471-2105-13-133 22702410

51. Walser JC, Furano AV. The mutational spectrum of non-CpG DNA varies with CpG content. Genome Res. 2010;20(7):875–82. doi: 10.1101/gr.103283.109 20498119

52. Sassaman DM, Dombroski BA, Moran JV, Kimberland ML, Naas TP, DeBerardinis RJ, et al. Many human L1 elements are capable of retrotransposition. Nat Genet. 1997;16(1):37–43. doi: 10.1038/ng0597-37 9140393

53. Callahan KE. Structure and Function of the First Open Reading Frame (ORF1) Protein Encoded by the Human LINE-1 Retrotransposon. Washington DC: Georgetown 2012.

54. Kulpa DA, Moran JV. Cis-preferential LINE-1 reverse transcriptase activity in ribonucleoprotein particles. Nat Struct Mol Biol. 2006;13(7):655–60. doi: 10.1038/nsmb1107 16783376

55. Pichon X, Bastide A, Safieddine A, Chouaib R, Samacoits A, Basyuk E, et al. Visualization of single endogenous polysomes reveals the dynamics of translation in live human cells. The Journal of Cell Biology. 2016;214(6):769–81. doi: 10.1083/jcb.201605024 27597760

56. Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics. 2014;30(9):1312–3. doi: 10.1093/bioinformatics/btu033 24451623

57. Edgar RC. Search and clustering orders of magnitude faster than BLAST. Bioinformatics. 2010;26(19):2460–1. doi: 10.1093/bioinformatics/btq461 20709691

58. Moran JV, Holmes SE, Naas TP, DeBerardinis RJ, Boeke JD, Kazazian HH Jr. High frequency retrotransposition in cultured mammalian cells. Cell. 1996;87(5):917–27. doi: 10.1016/s0092-8674(00)81998-4 8945518

59. Guzman C, Bagga M, Kaur A, Westermarck J, Abankwa D. ColonyArea: an ImageJ plugin to automatically quantify colony formation in clonogenic assays. PLoS ONE. 2014;9(3):e92444. doi: 10.1371/journal.pone.0092444 24647355

60. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004;32(5):1792–7. doi: 10.1093/nar/gkh340 15034147

61. Gouy M, Guindon S, Gascuel O. SeaView version 4: A multiplatform graphical user interface for sequence alignment and phylogenetic tree building. Mol Biol Evol. 2010;27(2):221–4. doi: 10.1093/molbev/msp259 19854763

62. Armstrong CT, Vincent TL, Green PJ, Woolfson DN. SCORER 2.0: an algorithm for distinguishing parallel dimeric and trimeric coiled-coil sequences. Bioinformatics. 2011;27(14):1908–14. doi: 10.1093/bioinformatics/btr299 21576179

63. Walser JC, Ponger L, Furano AV. CpG dinucleotides and the mutation rate of non-CpG DNA. Genome Res. 2008;18(9):1403–14. doi: 10.1101/gr.076455.108 18550801

64. Crooks GE, Hon G, Chandonia JM, Brenner SE. WebLogo: a sequence logo generator. Genome Res. 2004;14(6):1188–90. doi: 10.1101/gr.849004 15173120

65. Huson DH, Scornavacca C. Dendroscope 3: An Interactive Tool for Rooted Phylogenetic Trees and Networks. Syst Biol. 2012;61(6):1061–7. doi: 10.1093/sysbio/sys062 22780991

Článek vyšel v časopise

PLOS Genetics

2020 Číslo 8
Nejčtenější tento týden
Nejčtenější v tomto čísle
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