A New Role for the GARP Complex in MicroRNA-Mediated Gene Regulation
Many core components of the microRNA pathway have been elucidated and knowledge of their mechanisms of action actively progresses. In contrast, factors with modulatory roles on the pathway are just starting to become known and understood. Using a genetic screen in Caenorhabditis elegans, we identify a component of the GARP (Golgi Associated Retrograde Protein) complex, vps-52, as a novel genetic interactor of the microRNA pathway. The loss of vps-52 in distinct sensitized genetic backgrounds induces the enhancement of defective microRNA-mediated gene silencing. It synergizes with the core microRNA components, alg-1 Argonaute and ain-1 (GW182), in enhancing seam cell defects and exacerbates the gene silencing defects of the let-7 family and lsy-6 microRNAs in the regulation of seam cell, vulva and ASEL neuron development. Underpinning the observed genetic interactions, we found that VPS-52 impinges on the abundance of the GW182 proteins as well as the levels of microRNAs including the let-7 family. Altogether, we demonstrate that GARP complex fulfills a positive modulatory role on microRNA function and postulate that acting through GARP, vps-52 participates in a membrane-related process of the microRNA pathway.
Vyšlo v časopise:
A New Role for the GARP Complex in MicroRNA-Mediated Gene Regulation. PLoS Genet 9(11): e32767. doi:10.1371/journal.pgen.1003961
Kategorie:
Research Article
prolekare.web.journal.doi_sk:
https://doi.org/10.1371/journal.pgen.1003961
Souhrn
Many core components of the microRNA pathway have been elucidated and knowledge of their mechanisms of action actively progresses. In contrast, factors with modulatory roles on the pathway are just starting to become known and understood. Using a genetic screen in Caenorhabditis elegans, we identify a component of the GARP (Golgi Associated Retrograde Protein) complex, vps-52, as a novel genetic interactor of the microRNA pathway. The loss of vps-52 in distinct sensitized genetic backgrounds induces the enhancement of defective microRNA-mediated gene silencing. It synergizes with the core microRNA components, alg-1 Argonaute and ain-1 (GW182), in enhancing seam cell defects and exacerbates the gene silencing defects of the let-7 family and lsy-6 microRNAs in the regulation of seam cell, vulva and ASEL neuron development. Underpinning the observed genetic interactions, we found that VPS-52 impinges on the abundance of the GW182 proteins as well as the levels of microRNAs including the let-7 family. Altogether, we demonstrate that GARP complex fulfills a positive modulatory role on microRNA function and postulate that acting through GARP, vps-52 participates in a membrane-related process of the microRNA pathway.
Zdroje
1. KrolJ, LoedigeI, FilipowiczW (2010) The widespread regulation of microRNA biogenesis, function and decay. Nature reviews Genetics 11: 597–610.
2. FabianMR, SonenbergN (2012) The mechanics of miRNA-mediated gene silencing: a look under the hood of miRISC. Nature structural & molecular biology 19: 586–593.
3. BaccariniA, ChauhanH, GardnerTJ, JayaprakashAD, SachidanandamR, et al. (2011) Kinetic analysis reveals the fate of a microRNA following target regulation in mammalian cells. Current biology 21: 369–376.
4. GibbingsDJ, CiaudoC, ErhardtM, VoinnetO (2009) Multivesicular bodies associate with components of miRNA effector complexes and modulate miRNA activity. Nat Cell Biol 11: 1143–1149.
5. GibbingsD, VoinnetO (2010) Control of RNA silencing and localization by endolysosomes. Trends Cell Biol 20: 491–501.
6. AmeresSL, HorwichMD, HungJH, XuJ, GhildiyalM, et al. (2010) Target RNA-directed trimming and tailing of small silencing RNAs. Science 328: 1534–1539.
7. ChatterjeeS, FaslerM, BussingI, GrosshansH (2011) Target-mediated protection of endogenous microRNAs in C. elegans. Developmental Cell 20: 388–396.
8. RueggerS, GrosshansH (2012) MicroRNA turnover: when, how, and why. Trends in biochemical sciences 37: 436–446.
9. GibbingsD, MostowyS, JayF, SchwabY, CossartP, et al. (2012) Selective autophagy degrades DICER and AGO2 and regulates miRNA activity. Nature cell biology 14: 1314–1321.
10. DerrienB, BaumbergerN, SchepetilnikovM, ViottiC, De CilliaJ, et al. (2012) Degradation of the antiviral component ARGONAUTE1 by the autophagy pathway. Proceedings of the National Academy of Sciences of the United States of America 109: 15942–15946.
11. ZhangP, ZhangH (2013) Autophagy modulates miRNA-mediated gene silencing and selectively degrades AIN-1/GW182 in C. elegans. EMBO reports 14: 568–576.
12. WarfMB, JohnsonWE, BassBL (2011) Improved annotation of C. elegans microRNAs by deep sequencing reveals structures associated with processing by Drosha and Dicer. RNA 17: 563–577.
13. ZhangL, DingL, CheungTH, DongMQ, ChenJ, et al. (2007) Systematic identification of C. elegans miRISC proteins, miRNAs, and mRNA targets by their interactions with GW182 proteins AIN-1 and AIN-2. Molecular Cell 28: 598–613.
14. DingL, SpencerA, MoritaK, HanM (2005) The developmental timing regulator AIN-1 interacts with miRISCs and may target the argonaute protein ALG-1 to cytoplasmic P bodies in C. elegans. Molecular Cell 19: 437–447.
15. GrishokA, PasquinelliAE, ConteD, LiN, ParrishS, et al. (2001) Genes and mechanisms related to RNA interference regulate expression of the small temporal RNAs that control C. elegans developmental timing. Cell 106: 23–34.
16. KnightSW, BassBL (2001) A role for the RNase III enzyme DCR-1 in RNA interference and germ line development in Caenorhabditis elegans. Science 293: 2269–2271.
17. DenliAM, TopsBB, PlasterkRH, KettingRF, HannonGJ (2004) Processing of primary microRNAs by the Microprocessor complex. Nature 432: 231–235.
18. Vasquez-RifoA, JannotG, ArmisenJ, LabouesseM, BukhariSI, et al. (2012) Developmental characterization of the microRNA-specific C. elegans Argonautes alg-1 and alg-2. PLoS One 7: e33750.
19. BukhariSI, Vasquez-RifoA, GagnéD, PaquetER, ZetkaM, et al. (2012) The microRNA pathway controls germ cell proliferation and differentiation in C. elegans. Cell Res 22: 1034–1045.
20. BouaskerS, SimardMJ (2012) The slicing activity of miRNA-specific Argonautes is essential for the miRNA pathway in C. elegans. Nucleic acids research 40: 10452–10462.
21. FayDS, KeenanS, HanM (2002) fzr-1 and lin-35/Rb function redundantly to control cell proliferation in C. elegans as revealed by a nonbiased synthetic screen. Genes & development 16: 503–517.
22. ConibearE, StevensTH (2000) Vps52p, Vps53p, and Vps54p form a novel multisubunit complex required for protein sorting at the yeast late Golgi. Mol Biol Cell 11: 305–323.
23. LiewenH, Meinhold-HeerleinI, OliveiraV, SchwarzenbacherR, LuoG, et al. (2005) Characterization of the human GARP (Golgi associated retrograde protein) complex. Experimental cell research 306: 24–34.
24. LuoL, HannemannM, KoenigS, HegermannJ, AilionM, et al. (2011) The Caenorhabditis elegans GARP complex contains the conserved Vps51 subunit and is required to maintain lysosomal morphology. Mol Biol Cell 22: 2564–2578.
25. AmbrosV, HorvitzHR (1984) Heterochronic mutants of the nematode Caenorhabditis elegans. Science 226: 409–416.
26. AbbottAL, Alvarez-SaavedraE, MiskaEA, LauNC, BartelDP, et al. (2005) The let-7 MicroRNA family members mir-48, mir-84, and mir-241 function together to regulate developmental timing in Caenorhabditis elegans. Developmental Cell 9: 403–414.
27. ReinhartBJ, SlackFJ, BassonM, PasquinelliAE, BettingerJC, et al. (2000) The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans. Nature 403: 901–906.
28. AbrahanteJE, DaulAL, LiM, VolkML, TennessenJM, et al. (2003) The Caenorhabditis elegans hunchback-like gene lin-57/hbl-1 controls developmental time and is regulated by microRNAs. Developmental Cell 4: 625–637.
29. LeeRC, FeinbaumRL, AmbrosV (1993) The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 75: 843–854.
30. WightmanB, HaI, RuvkunG (1993) Posttranscriptional regulation of the heterochronic gene lin-14 by lin-4 mediates temporal pattern formation in C. elegans. Cell 75: 855–862.
31. MossEG, LeeRC, AmbrosV (1997) The cold shock domain protein LIN-28 controls developmental timing in C. elegans and is regulated by the lin-4 RNA. Cell 88: 637–646.
32. SlackFJ, BassonM, LiuZ, AmbrosV, HorvitzHR, et al. (2000) The lin-41 RBCC gene acts in the C. elegans heterochronic pathway between the let-7 regulatory RNA and the LIN-29 transcription factor. Molecular Cell 5: 659–669.
33. GrosshansH, JohnsonT, ReinertKL, GersteinM, SlackFJ (2005) The temporal patterning microRNA let-7 regulates several transcription factors at the larval to adult transition in C. elegans. Developmental Cell 8: 321–330.
34. BussingI, YangJS, LaiEC, GrosshansH (2010) The nuclear export receptor XPO-1 supports primary miRNA processing in C. elegans and Drosophila. The EMBO journal 29: 1830–1839.
35. JannotG, BajanS, GiguèreNJ, BouaskerS, BanvilleIH, et al. (2011) The ribosomal protein RACK1 is required for microRNA function in both C. elegans and humans. EMBO reports 12: 581–586.
36. HammellCM, LubinI, BoagPR, BlackwellTK, AmbrosV (2009) nhl-2 Modulates microRNA activity in Caenorhabditis elegans. Cell 136: 926–938.
37. ParryDH, XuJ, RuvkunG (2007) A whole-genome RNAi Screen for C. elegans miRNA pathway genes. Curr Biol 17: 2013–2022.
38. BaggaS, BrachtJ, HunterS, MassirerK, HoltzJ, et al. (2005) Regulation by let-7 and lin-4 miRNAs results in target mRNA degradation. Cell 122: 553–563.
39. VellaMC, ChoiEY, LinSY, ReinertK, SlackFJ (2004) The C. elegans microRNA let-7 binds to imperfect let-7 complementary sites from the lin-41 3′UTR. Genes Dev 18: 132–137.
40. SternbergPW, HorvitzHR (1986) Pattern formation during vulval development in C. elegans. Cell 44: 761–772.
41. BeitelGJ, ClarkSG, HorvitzHR (1990) Caenorhabditis elegans ras gene let-60 acts as a switch in the pathway of vulval induction. Nature 348: 503–509.
42. HanM, AroianRV, SternbergPW (1990) The let-60 locus controls the switch between vulval and nonvulval cell fates in Caenorhabditis elegans. Genetics 126: 899–913.
43. JohnsonSM, GrosshansH, ShingaraJ, ByromM, JarvisR, et al. (2005) RAS is regulated by the let-7 microRNA family. Cell 120: 635–647.
44. JohnstonRJ, HobertO (2003) A microRNA controlling left/right neuronal asymmetry in Caenorhabditis elegans. Nature 426: 845–849.
45. SarinS, O'MearaMM, FlowersEB, AntonioC, PooleRJ, et al. (2007) Genetic screens for Caenorhabditis elegans mutants defective in left/right asymmetric neuronal fate specification. Genetics 176: 2109–2130.
46. BonifacinoJS, HierroA (2011) Transport according to GARP: receiving retrograde cargo at the trans-Golgi network. Trends Cell Biol 21: 159–167.
47. Perez-VictoriaFJ, MardonesGA, BonifacinoJS (2008) Requirement of the human GARP complex for mannose 6-phosphate-receptor-dependent sorting of cathepsin D to lysosomes. Mol Biol Cell 19: 2350–2362.
48. MillerVJ, UngarD (2012) Re'COG'nition at the Golgi. Traffic 13: 891–897.
49. CikalukDE, TahbazN, HendricksLC, DiMattiaGE, HansenD, et al. (1999) GERp95, a membrane-associated protein that belongs to a family of proteins involved in stem cell differentiation. Mol Biol Cell 10: 3357–3372.
50. TahbazN, CarmichaelJB, HobmanTC (2001) GERp95 belongs to a family of signal-transducing proteins and requires Hsp90 activity for stability and Golgi localization. The Journal of biological chemistry 276: 43294–43299.
51. LiS, LiuL, ZhuangX, YuY, LiuX, et al. (2013) MicroRNAs Inhibit the Translation of Target mRNAs on the Endoplasmic Reticulum in Arabidopsis. Cell 153: 562–574.
52. StalderL, HeusermannW, SokolL, TrojerD, WirzJ, et al. (2013) The rough endoplasmatic reticulum is a central nucleation site of siRNA-mediated RNA silencing. The EMBO journal 32: 1115–1127.
53. LeeYS, PressmanS, AndressAP, KimK, WhiteJL, et al. (2009) Silencing by small RNAs is linked to endosomal trafficking. Nature cell biology 11: 1150–1156.
54. ShiZ, RuvkunG (2012) The mevalonate pathway regulates microRNA activity in Caenorhabditis elegans. Proc Natl Acad Sci U S A 109: 4568–4573.
55. BrodersenP, Sakvarelidze-AchardL, SchallerH, KhafifM, SchottG, et al. (2012) Isoprenoid biosynthesis is required for miRNA function and affects membrane association of ARGONAUTE 1 in Arabidopsis. Proc Natl Acad Sci U S A 109: 1778–1783.
56. ChenX, LiangH, ZhangJ, ZenK, ZhangCY (2012) Secreted microRNAs: a new form of intercellular communication. Trends in cell biology 22: 125–132.
57. ZhangH, FireAZ (2010) Cell autonomous specification of temporal identity by Caenorhabditis elegans microRNA lin-4. Developmental biology 344: 603–610.
58. YaoB, LaLB, ChenYC, ChangLJ, ChanEK (2012) Defining a new role of GW182 in maintaining miRNA stability. EMBO reports 13: 1102–1108.
59. JiangZ, YuN, KuangP, ChenM, ShaoF, et al. (2012) Trinucleotide repeat containing 6a (Tnrc6a)-mediated microRNA function is required for development of yolk sac endoderm. J Biol Chem 287: 5979–5987.
60. BrennerS (1974) The genetics of Caenorhabditis elegans. Genetics 77: 71–94.
61. BosséGD, RueggerS, OwMC, Vasquez-RifoA, RondeauEL, et al. (2013) The Decapping Scavenger Enzyme DCS-1 Controls MicroRNA Levels in Caenorhabditis elegans. Molecular Cell 50: 281–287.
62. Frokjaer-JensenC, DavisMW, HopkinsCE, NewmanBJ, ThummelJM, et al. (2008) Single-copy insertion of transgenes in Caenorhabditis elegans. Nature genetics 40: 1375–1383.
63. WuE, ThiviergeC, FlamandM, MathonnetG, VashishtAA, et al. (2010) Pervasive and cooperative deadenylation of 3′UTRs by embryonic microRNA families. Molecular Cell 40: 558–570.
64. DuchaineTF, WohlschlegelJA, KennedyS, BeiY, ConteDJr, et al. (2006) Functional proteomics reveals the biochemical niche of C. elegans DCR-1 in multiple small-RNA-mediated pathways. Cell 124: 343–354.
65. DrinnenbergIA, WeinbergDE, XieKT, MowerJP, WolfeKH, et al. (2009) RNAi in budding yeast. Science 326: 544–550.
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