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PLOS Neglected Tropical Diseases 2011

Gene Regulation in Giardia lambia Involves a Putative MicroRNA Derived from a Small Nucleolar RNA

DOI: 10.1371/journal.pntd.0001338

Wei Li,Ashesh A. Saraiya,Ching C. Wang

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Abstract:

Two core microRNA (miRNA) pathway proteins, Dicer and Argonaute, are found in Giardia lamblia, a deeply branching parasitic protozoan. There are, however, no apparent homologues of Drosha or Exportin5 in the genome. Here, we report a 26 nucleotide (nt) RNA derived from a 106 nt Box C/D snoRNA, GlsR2. This small RNA, designated miR5, localizes to the 3′ end of GlsR2 and has a 75 nt hairpin precursor. GlsR2 is processed by the Dicer from Giardia (GlDcr) and generated miR5. Immunoprecipitation of the Argonaute from Giardia (GlAgo) brought down miR5. When a Renilla Luciferase transcript with a 26 nt miR5 antisense sequence at the 3′-untranslated region (3′ UTR) was introduced into Giardia trophozoites, Luciferase expression was reduced ~25% when synthetic miR5 was also introduced. The Luciferase mRNA level remained, however, unchanged, suggesting translation repression by miR5. This inhibition was fully reversed by introducing also a 2′-O-methylated antisense inhibitor of miR5, suggesting that miR5 acts by interacting specifically with the antisense sequence in the mRNA. A partial antisense knock down of GlDcr or GlAgo in Giardia indicated that the former is needed for miR5 biogenesis whereas the latter is required for miR5-mediated translational repression. Potential targets for miR5 with canonical seed sequences were predicted bioinformatically near the stop codon of Giardia mRNAs. Four out of the 21 most likely targets were tested in the Luciferase reporter assay. miR5 was found to inhibit Luciferase expression (~20%) of transcripts carrying these potential target sites, indicating that snoRNA-derived miRNA can regulate the expression of multiple genes in Giardia.

References

[1]	Ankarklev J, Jerlstr？m-Hultqvist J, Ringqvist E, Troell K, Sv？rd SG (2010) Behind the smile: cell biology and disease mechanisms of Giardia species. Nat Rev Microbiol 8: 413–422. doi: 10.1038/nrmicro2317
[2]	Best AA, Morrison HG, McArthur AG, Sogin ML, Olsen GJ (2004) Evolution of eukaryotic transcription: insights from the genome of Giardia lamblia. Genome Res 14: 1537–1547. doi: 10.1101/gr.2256604
[3]	Adam RD (2001) Biology of Giardia lamblia. Clin Microbiol Rev 14: 447–475. doi: 10.1128/CMR.14.3.447-475.2001
[4]	Li L, Wang CC (2004) Capped mRNA with a single nucleotide leader is optimally translated in a primitive eukaryote, Giardia lamblia. J Biol Chem 279: 14656–14664. doi: 10.1074/jbc.M309879200
[5]	Miller RL, Wang AL, Wang CC (1988) Purification and characterization of the Giardia lamblia double-stranded RNA virus. Mol Biochem Parasitol 28: 189–195. doi: 10.1016/0166-6851(88)90003-5
[6]	Rivero MR, Kulakova L, Touz MC (2010) Long double-stranded RNA produces specific gene downregulation in Giardia lamblia. J Parasitol 96: 815–819. doi: 10.1645/GE-2406.1
[7]	Ambros V (2004) The functions of animal microRNAs. Nature 431: 350–355. doi: 10.1038/nature02871
[8]	Bartel DP (2009) MicroRNAs: target recognition and regulatory functions. Cell 136: 215–233. doi: 10.1016/j.cell.2009.01.002
[9]	Kim VN, Han J, Siomi MC (2009) Biogenesis of small RNAs in animals. Nat Rev Mol Cell Biol 10: 126–139. doi: 10.1038/nrm2632
[10]	Cai X, Hagedorn CH, Cullen BR (2004) Human microRNAs are processed from capped, polyadenylated transcripts that can also function as mRNAs. RNA 10: 1957–1966. doi: 10.1261/rna.7135204
[11]	Winter J, Jung S, Keller S, Gregory RI, Diederichs S (2009) Many roads to maturity: microRNA biogenesis pathways and their regulation. Nat Cell Biol 11: 228–234. doi: 10.1038/ncb0309-228
[12]	Lund E, Güttinger S, Calado A, Dahlberg JE, Kutay U (2004) Nuclear export of microRNA precursors. Science 303: 95–98. doi: 10.1126/science.1090599
[13]	Hutvágner G, McLachlan J, Pasquinelli AE, Balint E, Tuschl T, et al. (2001) A cellular function for the RNA-interference enzyme Dicer in the maturation of the let-7 small temporal RNA. Science 293: 834–838. doi: 10.1126/science.1062961
[14]	Knight SW, Bass BL (2001) A role for the RNase III enzyme DCR-1 in RNA interference and germ line development in Caenorhabditis elegans. Science 293: 2269–2271. doi: 10.1126/science.1062039
[15]	Hutvágner G, Zamore PD (2002) A microRNA in a multiple-turnover RNAi enzyme complex. Science 297: 2056–2060. doi: 10.1126/science.1073827
[16]	Mourelatos Z, Dostie J, Paushkin S, Sharma A, Charroux B, et al. (2002) miRNPs: a novel class of ribonucleoproteins containing numerous microRNAs. Genes Dev 16: 720–728. doi: 10.1101/gad.974702
[17]	Macrae IJ, Zhou K, Li F, Repic A, Brooks AN, et al. (2006) Structural basis for double-stranded RNA processing by Dicer. Science 311: 195–198. doi: 10.1126/science.1121638
[18]	Saraiya AA, Wang CC (2008) snoRNA, a novel precursor of microRNA in Giardia lamblia. PLoS Pathog 4: e1000224. doi: 10.1371/journal.ppat.1000224
[19]	Yang CY, Zhou H, Luo J, Qu LH (2005) Identification of 20 snoRNA-like RNAs from the primitive eukaryote, Giardia lamblia. Biochem Biophys Res Commun 328: 1224–1231. doi: 10.1016/j.bbrc.2005.01.077
[20]	Keister DB (1983) Axenic culture of Giardia lamblia in TYI-S-33 medium supplemented with bile. Trans R Soc Trop Med Hyg 77: 487–488. doi: 10.1016/0035-9203(83)90120-7
[21]	Saraiya AA, Wang CC (2011) A newly identified microRNA that regulates variant surface protein gene expression in Giardia lamblia. RNA. (in revision). doi: 10.1261/rna.028118.111
[22]	Rajewsky N, Socci ND (2004) Computational identification of microRNA targets. Dev Biol 267: 529–535. doi: 10.1016/j.ydbio.2003.12.003
[23]	Horwich MD, Zamore PD (2008) Design and delivery of antisense oligonucleotides to block microRNA function in cultured Drosophila and human cells. Nat Protoc 3: 1537–1549. doi: 10.1038/nprot.2008.145
[24]	Carthew RW, Sontheimer EJ (2009) Origins and Mechanisms of miRNAs and siRNAs. Cell 136: 642–655. doi: 10.1016/j.cell.2009.01.035
[25]	Baek D, Villen J, Shin C, Camargo FD, Gygi SP, et al. (2008) The impact of microRNAs on protein output. Nature 455: 64–71. doi: 10.1038/nature07242
[26]	Selbach M, Schwanh？usser B, Thierfelder N, Fang Z, Khanin R, et al. (2008) Widespread changes in protein synthesis induced by microRNAs. Nature 455: 58–63. doi: 10.1038/nature07228
[27]	John B, Enright AJ, Aravin A, Tuschl T, Sander C, et al. (2005) miRanda algorithm : Human MicroRNA targets. PLoS Biol 3: e264. doi: 10.1371/journal.pbio.0030264
[28]	Forman JJ, Legesse-Miller A, Coller HA (2008) A search for conserved sequences in coding regions reveals that the let-7 microRNA targets Dicer within its coding sequence. Proc Natl Acad Sci USA 105: 14879–14884. doi: 10.1073/pnas.0803230105
[29]	Tay Y, Zhang J, Thomson AM, Lim B, Rigoutsos I (2008) MicroRNAs to Nanog, Oct4 and Sox2 coding regions modulate embryonic stem cell differentiation. Nature 455: 1124–1128. doi: 10.1038/nature07299
[30]	Chi SW, Zang JB, Mele A, Darnell RB (2009) Argonaute HITS-CLIP decodes microRNA-mRNA interaction maps. Nature 460: 479–486. doi: 10.1038/nature08170
[31]	McArthur AG, Morrison HG, Nixon JE, Passamaneck NQ, Kim U, et al. (2000) The Giardia genome project database. FEMS Microbiol. Lett 189: 271–273. doi: 10.1016/s0378-1097(00)00299-8
[32]	Aurrecoechea C, Brestelli J, Brunk BP, Carlton JM, Dommer J, et al. (2009) GiardiaDB and TrichDB: integrated genomic resources for the eukaryotic protist pathogens Giardia lamblia and Trichomonas vaginalis. Nucleic Acids Res 37: D526–530. doi: 10.1093/nar/gkn631
[33]	Yang JH, Shao P, Zhou H, Chen YQ, Qu LH (2010) deepBase: a database for deeply annotating and mining deep sequencing data. Nucleic Acids Res 38: D123–D130. doi: 10.1093/nar/gkp943
[34]	Franzén O, Jerlstr？m-Hultqvist J, Castro E, Sherwood E, Ankarklev J, et al. (2009) Draft genome sequencing of giardia intestinalis assemblage B isolate GS: is human giardiasis caused by two different species? PLoS Pathog 5: e1000560. doi: 10.1371/journal.ppat.1000560
[35]	Liang WQ, Clark JA, Fournier MJ (1997) The rRNA processing function of the yeast U14 small nucleolar RNA can be rescued by a conserved RNA helicase-like protein. Mol Cell Biol 17: 4124–4132.
[36]	Prucca CG, Slavin I, Quiroga R, Elías EV, Rivero FD, et al. (2008) Antigenic variation in Giardia lamblia is regulated by RNA interference. Nature 456: 750–754. doi: 10.1038/nature07585
[37]	Watkins NJ, Lemm I, Ingelfinger D, Schneider C, Hossbach M, et al. (2004) Assembly and maturation of the U3 snoRNP in the nucleoplasm in a large dynamic multiprotein complex. Mol Cell 16: 789–798. doi: 10.1016/j.molcel.2004.11.012
[38]	Peculis BA (2001) SnoRNA nuclear import and potential for cotranscriptional function in pre-rRNA processing. RNA 7: 207–219. doi: 10.1017/S1355838201001625
[39]	Watkins NJ, Lemm I, Lührmann R (2007) Involvement of nuclear import and export factors in U8 box C/D snoRNP biogenesis. Mol Cell Biol 27: 7018–7027. doi: 10.1128/MCB.00516-07
[40]	Chen LM, Chern Y, Ong SJ, Tai JH (1994) Molecular cloning and characterization of a ras-related gene of ran/tc4/spi1 subfamily in Giardia lamblia. J Biol Chem 269: 17297–17304.
[41]	Castanotto D, Lingeman R, Riggs AD, Rossi JJ (2009) CRM1 mediates nuclear-cytoplasmic shuttling of mature microRNAs. Proc Natl Acad Sci USA 106: 21655–21659. doi: 10.1073/pnas.0912384106
[42]	Lau NC, Lim LP, Weinstein EG, Bartel DP (2001) An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans. Science 294: 858–862. doi: 10.1126/science.1065062
[43]	Faehnle CR, Joshua-Tor L (2007) Argonautes confront new small RNAs. Curr Opin Chem Biol 11: 569–577. doi: 10.1016/j.cbpa.2007.08.032
[44]	Zhang H, Ehrenkaufer GM, Pompey JM, Hackney JA, Singh U (2008) Small RNAs with 5′-polyphosphate termini associate with a Piwi-related protein and regulate gene expression in the single-celled eukaryote Entamoeba histolytica. PLoS Pathog 4: e1000219. doi: 10.1371/journal.ppat.1000219
[45]	Huang Y, Ji L, Huang Q, Vassylyev DG, Chen X, et al. (2009) Structural insights into mechanisms of the small RNA methyltransferase HEN1. Nature 461: 823–827. doi: 10.1038/nature08433
[46]	Li J, Yang Z, Yu B, Liu J, Chen X (2005) Methylation protects miRNAs and siRNAs from a 39-end uridylation activity in Arabidopsis. Curr Biol 15: 1501–1507. doi: 10.1016/j.cub.2005.07.029
[47]	Ramachandran V, Chen X (2008) Degradation of microRNAs by a family of exoribonucleases in Arabidopsis. Science 321: 1490–1492. doi: 10.1126/science.1163728
[48]	Yang Z, Ebright YW, Yu B, Chen X (2006) HEN1 recognizes 21–24 nt small RNA duplexes and deposits a methyl group onto the 2′ OH of the 3′ terminal nucleotide. Nucleic Acids Res 34: 667–675. doi: 10.1093/nar/gkj474
[49]	Friedman RC, Farh KK, Burge CB, Bartel DP (2009) Most mammalian mRNAs are conserved targets of microRNAs. Genome Res 19: 92–105. doi: 10.1101/gr.082701.108
[50]	Lewis BP, Burge CB, Bartel DP (2005) Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 120: 15–20. doi: 10.1016/j.cell.2004.12.035
[51]	Lim LP, Lau NC, Garrett-Engele P, Grimson A, Schelter JM, et al. (2005) Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs. Nature 433: 769–773. doi: 10.1038/nature03315
[52]	Rajewsky N (2006) microRNA target predictions in animals. Nat Genet 38: S8–S13. doi: 10.1038/ng1798
[53]	Wu S, Huang S, Ding J, Zhao Y, Liang L, et al. (2010) Multiple microRNAs modulate p21Cip1/Waf1 expression by directly targeting its 3′ untranslated region. Oncogene 29: 2302–2308. doi: 10.1038/onc.2010.34
[54]	Shi H, Chamond N, Djikeng A, Tschudi C, Ullu E (2009) RNA interference in Trypanosoma brucei: role of the n-terminal RGG domain and the polyribosome association of Argonaute. J Biol Chem 284: 36511–36520. doi: 10.1074/jbc.M109.073072
[55]	Yao MC, Chao JL (2005) RNA-guided DNA deletion in Tetrahymena: an RNAi-based mechanism for programmed genome rearrangements. Annu Rev Genet 39: 537–559. doi: 10.1146/annurev.genet.39.073003.095906
[56]	Sharp PA (1999) RNAi and double-strand RNA. Genes Dev 13: 139–141. doi: 10.1101/gad.13.2.139

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