RNA binding protein 24 regulates the translation and replication of hepatitis C virus

Abstract

The secondary structures of hepatitis C virus (HCV) RNA and the cellular proteins that bind to them are important for modulating both translation and RNA replication. However, the sets of RNA-binding proteins involved in the regulation of HCV translation, replication and encapsidation remain unknown. Here, we identified RNA binding motif protein 24 (RBM24) as a host factor participated in HCV translation and replication. Knockdown of RBM24 reduced HCV propagation in Huh7.5.1 cells. An enhanced translation and delayed RNA synthesis during the early phase of infection was observed in RBM24 silencing cells. However, both overexpression of RBM24 and recombinant human RBM24 protein suppressed HCV IRES-mediated translation. Further analysis revealed that the assembly of the 80S ribosome on the HCV IRES was interrupted by RBM24 protein through binding to the 5′-UTR. RBM24 could also interact with HCV Core and enhance the interaction of Core and 5′-UTR, which suppresses the expression of HCV. Moreover, RBM24 enhanced the interaction between the 5′- and 3′-UTRs in the HCV genome, which probably explained its requirement in HCV genome replication. Therefore, RBM24 is a novel host factor involved in HCV replication and may function at the switch from translation to replication.

Key words： RNA binding protein; RBM24; hepatitis C virus; translation; replication

References

1 Ali N, Pruijn GJ, Kenan DJ, Keene JD, Siddiqui A (2000) Human La antigen is required for the hepatitis C virus internal ribosome entry site-mediated translation. J Biol Chem 275:27531–27540

2 Astier-Gin T, Bellecave P, Litvak S, Ventura M (2005) Template requirements and binding of hepatitis C virus NS5B polymerase during in vitro RNA synthesis from the 3’-end of virus minusstrand RNA. FEBS J 272:3872–3886

3 Bai Y, Zhou K, Doudna JA (2013) Hepatitis C virus 3’UTR regulates viral translation through direct interactions with the host translation machinery. Nucleic Acids Res 41:7861–7874

4 Bhat P, Shwetha S, Sharma DK, Joseph AP, Srinivasan N, Das S (2015) The beta hairpin structure within ribosomal protein S5 mediates interplay between domains II and IV and regulates HCV IRES function. Nucleic Acids Res 43:2888–2901

5 Boehringer D, Thermann R, Ostareck-Lederer A, Lewis JD, Stark H (2005) Structure of the hepatitis C virus IRES bound to the human 80S ribosome: remodeling of the HCV IRES. Structure 13:1695–1706

6 Cao H, Zhu W, Han Q, Pei R, Chen X (2014) Construction of a chimeric hepatitis C virus replicon based on a strain isolated from a chronic hepatitis C patient. Virol Sin 29:61–70

7 Chang KS, Luo G (2006) The polypyrimidine tract-binding protein (PTB) is required for efficient replication of hepatitis C virus (HCV) RNA. Virus Res 115:1–8

8 Cheng JC, Chang MF, Chang SC (1999) Specific interaction between the hepatitis C virus NS5B RNA polymerase and the 3’ end of the viral RNA. J Virol 73:7044–7049

9 Filbin ME, Kieft JS (2011) HCV IRES domain IIb affects the configuration of coding RNA in the 40S subunit’s decoding groove. RNA 17:1258–1273

10 Filbin ME, Vollmar BS, Shi D, Gonen T, Kieft JS (2013) HCV IRES manipulates the ribosome to promote the switch from translation initiation to elongation. Nat Struct Mol Biol 20:150–158

11 Fontanes V, Raychaudhuri S, Dasgupta A (2009) A cell-permeable peptide inhibits hepatitis C virus replication by sequestering IRES transacting factors. Virology 394:82–90

12 Friebe P, Boudet J, Simorre JP, Bartenschlager R (2005) Kissingloop interaction in the 3’ end of the hepatitis C virus genome essential for RNA replication. J Virol 79:380–392

13 Guan W, Cheng F, Huang Q, Kleiboeker S, Qiu J (2011) Inclusion of the central exon of parvovirus B19 precursor mRNA is determined by multiple splicing enhancers in both the exon and the downstream intron. J Virol 85:2463–2468

14 Guo M, Pei R, Yang Q, Cao H, Wang Y, Wu C, Chen J, Zhou Y, Hu X, Lu M (2014) Phosphatidylserine-specific phospholipase A1 is involved in hepatitis C Virus Assembly through NS2 complex formation. J Virol 89:2367–2377

15 Heise T, Guidotti LG, Chisari FV (1999) La autoantigen specifically recognizes a predicted stem-loop in hepatitis B virus RNA. J Virol 73:5767–5776

16 Horke S, Reumann K, Rang A, Heise T (2002) Molecular characterization of the human La protein.hepatitis B virus RNA.B interaction in vitro. J Biol Chem 277:34949–34958

17 Ito T, Lai MM (1997) Determination of the secondary structure of and cellular protein binding to the 3’-untranslated region of the hepatitis C virus RNA genome. J Virol 71:8698–8706

18 Jin D, Hidaka K, Shirai M, Morisaki T (2010) RNA-binding motif protein 24 regulates myogenin expression and promotes myogenic differentiation. Genes Cells 15:1158–1167

19 Jones DM, Atoom AM, Zhang X, Kottilil S, Russell RS (2011) A genetic interaction between the core and NS3 proteins of hepatitis C virus is essential for production of infectious virus. J Virol 85:12351–12361

20 Kaminski A, Jackson RJ (1998) The polypyrimidine tract binding protein (PTB) requirement for internal initiation of translation of cardiovirus RNAs is conditional rather than absolute. RNA 4:626–638

21 Keene JD, Komisarow JM, Friedersdorf MB (2006) RIP-Chip: the isolation and identification of mRNAs, microRNAs and protein components of ribonucleoprotein complexes from cell extracts. Nat Protoc 1:302–307

22 Kim SM, Jeong YS (2006) Polypyrimidine tract-binding protein interacts with the 3’ stem-loop region of Japanese encephalitis virus negative-strand RNA. Virus Res 115:131–140

23 Kim YK, Kim CS, Lee SH, Jang SK (2002) Domains I and II in the 5’ nontranslated region of the HCV genome are required for RNA replication. Biochem Biophys Res Commun 290:105–112

24 Kim JH, Paek KY, Ha SH, Cho S, Choi K, Kim CS, Ryu SH, Jang SK (2004) A cellular RNA-binding protein enhances internal ribosomal entry site-dependent translation through an interaction downstream of the hepatitis C virus polyprotein initiation codon. Mol Cell Biol 24:7878–7890

25 Kumar A, Ray U, Das S (2013) Human La protein interaction with GCAC near the initiator AUG enhances hepatitis C Virus RNA replication by promoting linkage between 5’ and 3’ untranslated regions. J Virol 87:6713–6726

26 Li D, Takyar ST, Lott WB, Gowans EJ (2003) Amino acids 1-20 of the hepatitis C virus (HCV) core protein specifically inhibit HCV IRES-dependent translation in HepG2 cells, and inhibit both HCV IRES- and cap-dependent translation in HuH7 and CV-1 cells. J Gen Virol 84:815–825

27 Liu HM, Aizaki H, Choi KS, Machida K, Ou JJ, Lai MM (2009) SYNCRIP (synaptotagmin-binding, cytoplasmic RNA-interactingprotein) is a host factor involved in hepatitis C virus RNA replication. Virology 386:249–256

28 Locker N, Easton LE, Lukavsky PJ (2007) HCV and CSFV IRES domain II mediate eIF2 release during 80S ribosome assembly. EMBO J 26:795–805

29 Lukavsky PJ (2009) Structure and function of HCV IRES domains. Virus Res 139:166–171

30 Mahias K, Ahmed-El-Sayed N, Masante C, Bitard J, Staedel C, Darfeuille F, Ventura M, Astier-Gin T (2010) Identification of a structural element of the hepatitis C virus minus strand RNA involved in the initiation of RNA synthesis. Nucleic Acids Res 38:4079–4091

31 Malygin AA, Kossinova OA, Shatsky IN, Karpova GG (2013) HCV IRES interacts with the 18S rRNA to activate the 40S ribosome for subsequent steps of translation initiation. Nucleic Acids Res 41:8706–8714

32 Measey TJ, Smith KB, Decatur SM, Zhao L, Yang G, Schweitzer-Stenner R (2009) Self-aggregation of a polyalanine octamer promoted by its C-terminal tyrosine and probed by a strongly enhanced vibrational circular dichroism signal. J Am Chem Soc 131:18218–18219

33 Miyamoto S, Hidaka K, Jin D, Morisaki T (2009) RNA-binding proteins Rbm38 and Rbm24 regulate myogenic differentiation via p21-dependent and-independent regulatory pathways. Genes Cells 14:1241–1252

34 Park SM, Paek KY, Hong KY, Jang CJ, Cho S, Park JH, Kim JH, Jan E, Jang SK (2011) Translation-competent 48S complex formation on HCV IRES requires the RNA-binding protein NSAP1. Nucleic Acids Res 39:7791–7802

35 Pietschmann T, Kaul A, Koutsoudakis G, Shavinskaya A, Kallis S, Steinmann E, Abid K, Negro F, Dreux M, Cosset FL (2006) Construction and characterization of infectious intragenotypic and intergenotypic hepatitis C virus chimeras. Proc Natl Acad Sci USA 103:7408–7413

36 Poon KL, Tan KT, Wei YY, Ng CP, Colman A, Korzh V,Xu XQ (2012) RNA-binding protein RBM24 is required for sarcomere assembly and heart contractility. Cardiovasc Res 94:418–427

37 Ranjith-Kumar CT, Kao CC (2006) Biochemical activities of the HCV NS5B RNA-dependent RNA polymerase. Hepatitis C viruses: genomes and molecular biology. Chapter 10. Horizon Bioscience, Norfolk, UK

38 Ray U, Das S (2011) Interplay between NS3 protease and human La protein regulates translation-replication switch of Hepatitis C virus. Sci Rep 1:1

39 Reigadas S, Ventura M, Sarih-Cottin L, Castroviejo M, Litvak S, Astier-Gin T (2001) HCV RNA-dependent RNA polymerase replicates in vitro the 3’ terminal region of the minus-strand viral RNA more efficiently than the 3’ terminal region of the plus RNA. Eur J Biochem 268:5857–5867

40 Romero-Lopez C, Berzal-Herranz A (2009) A long-range RNA-RNA interaction between the 5’ and 3’ ends of the HCV genome. RNA 15:1740–1752

41 Romero-Lopez C, Berzal-Herranz A (2012) The functional RNA domain 5BSL3.2 within the NS5B coding sequence influences hepatitis C virus IRES-mediated translation. Cell Mol Life Sci 69:103–113

42 Schuster C, Isel C, Imbert I, Ehresmann C, Marquet R, Kieny MP (2002) Secondary structure of the 3’ terminus of hepatitis C virus minus-strand RNA. J Virol 76:8058–8068

43 Shetty S, Kim S, Shimakami T, Lemon SM, Mihailescu MR (2010) Hepatitis C virus genomic RNA dimerization is mediated via a kissing complex intermediate. RNA 16:913–925

44 Shetty S, Stefanovic S, Mihailescu MR (2013) Hepatitis C virus RNA: molecular switches mediated by long-range RNA-RNA interactions? Nucleic Acids Res 41:2526–2540

45 Shi ST, Lai MMC (2006) HCV 5′ and 3′ UTR: when translation meets replication. Hepatitis C Viruses: genomes and molecular biology. Chapter 2. Horizon Bioscience, Norfolk, UK

46 Shimoike T, Mimori S, Tani H, Matsuura Y, Miyamura T (1999) Interaction of hepatitis C virus core protein with viral sense RNA and suppression of its translation. J Virol 73:9718–9725

47 Shimoike T, Koyama C, Murakami K, Suzuki R, Matsuura Y, Miyamura T, Suzuki T (2006) Down-regulation of the internal ribosome entry site (IRES)-mediated translation of the hepatitis C virus: critical role of binding of the stem-loop IIId domain of IRES and the viral core protein. Virology 345:434–445

48 Shwetha S, Kumar A, Mullick R, Vasudevan D, Mukherjee N, Das S (2015) HuR displaces PTB to facilitate La binding to the 3’ UTR and enhances HCV replication. J Virol 89:11356–11371

49 Spahn CM, Kieft JS, Grassucci RA, Penczek PA, Zhou K, Doudna JA, Frank J (2001) Hepatitis C virus IRES RNA-induced changes in the conformation of the 40s ribosomal subunit. Science 291:1959–1962

50 Spangberg K, Schwartz S (1999) Poly(C)-binding protein interacts with the hepatitis C virus 5’ untranslated region. J Gen Virol 80(Pt 6):1371–1376

51 Sun C, Querol-Audi J, Mortimer SA, Arias-Palomo E, Doudna JA, Nogales E, Cate JH (2013) Two RNA-binding motifs in eIF3 direct HCV IRES-dependent translation. Nucleic Acids Res 41:7512–7521

52 Tanaka Y, Shimoike T, Ishii K, Suzuki R, Suzuki T, Ushijima H, Matsuura Y, Miyamura T (2000) Selective binding of hepatitis C virus core protein to synthetic oligonucleotides corresponding to the 5’ untranslated region of the viral genome. Virology 270:229–236

53 Tsukiyama-Kohara K, Iizuka N, Kohara M, Nomoto A (1992) Internal ribosome entry site within hepatitis C virus RNA. J Virol 66:1476–1483

54 Vashist S, Anantpadma M, Sharma H, Vrati S (2009) La protein binds the predicted loop structures in the 3’ non-coding region of Japanese encephalitis virus genome: role in virus replication. J Gen Virol 90:1343–1352

55 Vashist S, Bhullar D, Vrati S (2011) La protein can simultaneously bind to both 3′- and 5′-noncoding regions of Japanese encephalitis virus genome. DNA Cell Biol 30:339–346

56 Wang L, Jeng KS, Lai MM (2011) Poly(C)-binding protein 2 interacts with sequences required for viral replication in the hepatitis C virus (HCV) 5’ untranslated region and directs HCV RNA replication through circularizing the viral genome. J Virol 85:7954–7964

57 Wood J, Frederickson RM, Fields S, Patel AH (2001) Hepatitis C virus 3’X region interacts with human ribosomal proteins. J Virol 75:1348–1358

58 Xu S, Pei R, Guo M, Han Q, Lai J, Wang Y, Wu C, Zhou Y, Lu M, Chen X (2012) Cytosolic phospholipase A2 gamma is involved in hepatitis C virus replication and assembly. J Virol 86:13025–13037

59 Xu E, Zhang J, Zhang M, Jiang Y, Cho SJ, Chen X (2014) RNAbinding protein RBM24 regulates p63 expression via mRNA stability. Mol Cancer Res 12:359–369

60 Yang J, Hung LH, Licht T, Kostin S, Looso M, Khrameeva E, Bindereif A, Schneider A, Braun T (2014) RBM24 is a major regulator of muscle-specific alternative splicing. Dev Cell 31:87–99

61 Zang WQ, Li B, Huang PY, Lai MM, Yen TS (2001) Role of polypyrimidine tract binding protein in the function of the hepatitis B virus posttranscriptional regulatory element. J Virol 75:10779–10786

62 Zhu W, Pei R, Jin R, Hu X, Zhou Y, Wang Y, Wu C, Lu M, Chen X (2014) Nuclear receptor 4 group A member 1 determines hepatitis C virus entry efficiency through the regulation of cellular receptor and apolipoprotein E expression. J Gen Virol 95:1510–1521