#PAGE_PARAMS# #ADS_HEAD_SCRIPTS# #MICRODATA#

Base Pairing Interaction between 5′- and 3′-UTRs Controls mRNA Translation in


The presence of regulatory sequences in the 3′ untranslated region (3′-UTR) of eukaryotic mRNAs controlling RNA stability and translation efficiency is widely recognized. In contrast, the relevance of 3′-UTRs in bacterial mRNA functionality has been disregarded. Here, we report evidences showing that around one-third of the mapped mRNAs of the major human pathogen Staphylococcus aureus carry 3′-UTRs longer than 100-nt and thus, potential regulatory functions. We selected the long 3′-UTR of icaR, which codes for the repressor of the main exopolysaccharidic compound of the S. aureus biofilm matrix, to evaluate the role that 3′-UTRs may play in controlling mRNA expression. We showed that base pairing between the 3′-UTR and the Shine-Dalgarno (SD) region of icaR mRNA interferes with the translation initiation complex and generates a double-stranded substrate for RNase III. Deletion or substitution of the motif (UCCCCUG) within icaR 3′-UTR was sufficient to abolish this interaction and resulted in the accumulation of IcaR repressor and inhibition of biofilm development. Our findings provide a singular example of a new potential post-transcriptional regulatory mechanism to modulate bacterial gene expression through the interaction of a 3′-UTR with the 5′-UTR of the same mRNA.


Vyšlo v časopise: Base Pairing Interaction between 5′- and 3′-UTRs Controls mRNA Translation in. PLoS Genet 9(12): e32767. doi:10.1371/journal.pgen.1004001
Kategorie: Research Article
prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.pgen.1004001

Souhrn

The presence of regulatory sequences in the 3′ untranslated region (3′-UTR) of eukaryotic mRNAs controlling RNA stability and translation efficiency is widely recognized. In contrast, the relevance of 3′-UTRs in bacterial mRNA functionality has been disregarded. Here, we report evidences showing that around one-third of the mapped mRNAs of the major human pathogen Staphylococcus aureus carry 3′-UTRs longer than 100-nt and thus, potential regulatory functions. We selected the long 3′-UTR of icaR, which codes for the repressor of the main exopolysaccharidic compound of the S. aureus biofilm matrix, to evaluate the role that 3′-UTRs may play in controlling mRNA expression. We showed that base pairing between the 3′-UTR and the Shine-Dalgarno (SD) region of icaR mRNA interferes with the translation initiation complex and generates a double-stranded substrate for RNase III. Deletion or substitution of the motif (UCCCCUG) within icaR 3′-UTR was sufficient to abolish this interaction and resulted in the accumulation of IcaR repressor and inhibition of biofilm development. Our findings provide a singular example of a new potential post-transcriptional regulatory mechanism to modulate bacterial gene expression through the interaction of a 3′-UTR with the 5′-UTR of the same mRNA.


Zdroje

1. MazumderB, SeshadriV, FoxPL (2003) Translational control by the 3′-UTR: the ends specify the means. Trends Biochem Sci 28: 91–98 doi:10.1016/S0968-0004(03)00002-1

2. BrodersenP, VoinnetO (2009) Revisiting the principles of microRNA target recognition and mode of action. Nat Rev Mol Cell Biol 10: 141–148 doi:10.1038/nrm2619

3. MangusDA, EvansMC, JacobsonA (2003) Poly(A)-binding proteins: multifunctional scaffolds for the post-transcriptional control of gene expression. Genome Biol 4: 223 doi:10.1186/gb-2003-4-7-223

4. GarneauNL, WiluszJ, WiluszCJ (2007) The highways and byways of mRNA decay. Nat Rev Mol Cell Biol 8: 113–126 doi:10.1038/nrm2104

5. MatoulkovaE, MichalovaE, VojtesekB, HrstkaR (2012) The role of the 3′ untranslated region in post-transcriptional regulation of protein expression in mammalian cells. RNA Biol 9: 563–576 doi:10.4161/rna.20231

6. NakamotoT (2009) Evolution and the universality of the mechanism of initiation of protein synthesis. Gene 432: 1–6 doi:10.1016/j.gene.2008.11.001

7. BeuzónCR, MarquésS, CasadesúsJ (1999) Repression of IS200 transposase synthesis by RNA secondary structures. Nucleic Acids Research 27: 3690–3695.

8. ChenLH, EmorySA, BrickerAL, BouvetP, BelascoJG (1991) Structure and function of a bacterial mRNA stabilizer: analysis of the 5′ untranslated region of ompA mRNA. Journal of Bacteriology 173: 4578–4586.

9. AgaisseH, LereclusD (1996) STAB-SD: a Shine-Dalgarno sequence in the 5′ untranslated region is a determinant of mRNA stability. Mol Microbiol 20: 633–643.

10. WatersLS, StorzG (2009) Regulatory RNAs in bacteria. Cell 136: 615–628 doi:10.1016/j.cell.2009.01.043

11. BabitzkeP, BakerCS, RomeoT (2009) Regulation of translation initiation by RNA binding proteins. Annu Rev Microbiol 63: 27–44 doi:10.1146/annurev.micro.091208.073514

12. GeissmannT, MarziS, RombyP (2009) The role of mRNA structure in translational control in bacteria. RNA Biol 6: 153–160.

13. NarberhausF (2010) Translational control of bacterial heat shock and virulence genes by temperature-sensing mRNAs. RNA Biol 7: 84–89.

14. KortmannJ, NarberhausF (2012) Bacterial RNA thermometers: molecular zippers and switches. Nat Rev Micro 10: 255–265 doi:10.1038/nrmicro2730

15. WinklerWC, BreakerRR (2005) Regulation of bacterial gene expression by riboswitches. Annu Rev Microbiol 59: 487–517 doi:10.1146/annurev.micro.59.030804.121336

16. SerganovA, NudlerE (2013) A decade of riboswitches. Cell 152: 17–24 doi:10.1016/j.cell.2012.12.024

17. BelascoJG (2010) All things must pass: contrasts and commonalities in eukaryotic and bacterial mRNA decay. Nat Rev Mol Cell Biol 11: 467–478 doi:10.1038/nrm2917

18. ArraianoCM, AndradeJM, DominguesS, GuinoteIB, MaleckiM, et al. (2010) The critical role of RNA processing and degradation in the control of gene expression. FEMS Microbiology Reviews 34: 883–923 doi:10.1111/j.1574-6976.2010.00242.x

19. RasmussenS, NielsenHB, JarmerH (2009) The transcriptionally active regions in the genome of Bacillus subtilis. Mol Microbiol 73: 1043–1057 doi:10.1111/j.1365-2958.2009.06830.x

20. Toledo-AranaA, DussurgetO, NikitasG, SestoN, Guet-RevilletH, et al. (2009) The Listeria transcriptional landscape from saprophytism to virulence. Nature 459: 950–956 doi:10.1038/nature08080

21. GripenlandJ, NetterlingS, LohE, TiensuuT, Toledo-AranaA, et al. (2010) RNAs: regulators of bacterial virulence. Nat Rev Micro 8: 857–866 doi:10.1038/nrmicro2457

22. LasaI, Toledo-AranaA, DobinA, VillanuevaM, de los MozosIR, et al. (2011) Genome-wide antisense transcription drives mRNA processing in bacteria. Proceedings of the National Academy of Sciences 108: 20172–20177 doi:10.1073/pnas.1113521108

23. LasaI, Toledo-AranaA, GingerasTR (2012) An effort to make sense of antisense transcription in bacteria. RNA Biol 9: 1039–44 doi:10.4161/rna.21167

24. KawanoM, ReynoldsAA, Miranda-RiosJ, StorzG (2005) Detection of 5′- and 3′-UTR-derived small RNAs and cis-encoded antisense RNAs in Escherichia coli. Nucleic Acids Research 33: 1040–1050 doi:10.1093/nar/gki256

25. ChaoY, PapenfortK, ReinhardtR, SharmaCM, VogelJ (2012) An atlas of Hfq-bound transcripts reveals 3′ UTRs as a genomic reservoir of regulatory small RNAs. EMBO J 31: 4005–4019 doi:10.1038/emboj.2012.229

26. SittkaA, LucchiniS, PapenfortK, SharmaCM, RolleK, et al. (2008) Deep sequencing analysis of small noncoding RNA and mRNA targets of the global post-transcriptional regulator, Hfq. PLoS Genet 4: e1000163 doi:10.1371/journal.pgen.1000163

27. LioliouE, SharmaCM, CaldelariI, HelferAC, FechterP, et al. (2012) Global Regulatory Functions of the Staphylococcus aureus Endoribonuclease III in Gene Expression. PLoS Genet 8: e1002782 doi:10.1371/journal.pgen.1002782.t001

28. ArciolaCR, CampocciaD, SpezialePietro, MontanaroL, CostertonJW (2012) Biofilm formation in Staphylococcus implant infections. A review of molecular mechanisms and implications for biofilm-resistant materials. Biomaterials 33: 5967–5982 doi:10.1016/j.biomaterials.2012.05.031

29. CramtonSE, GerkeC, SchnellNF, NicholsWW, GötzF (1999) The intercellular adhesion (ica) locus is present in Staphylococcus aureus and is required for biofilm formation. Infection and Immunity 67: 5427–5433.

30. GötzF (2002) Staphylococcus and biofilms. Mol Microbiol 43: 1367–1378.

31. JeffersonKK, CramtonSE, GötzF, PierGB (2003) Identification of a 5-nucleotide sequence that controls expression of the ica locus in Staphylococcus aureus and characterization of the DNA-binding properties of IcaR. Mol Microbiol 48: 889–899.

32. KingsfordCL, AyanbuleK, SalzbergSL (2007) Rapid, accurate, computational discovery of Rho-independent transcription terminators illuminates their relationship to DNA uptake. Genome Biol 8: R22 doi:10.1186/gb-2007-8-2-r22

33. WassarmanKM, RepoilaF, RosenowC, StorzG, GottesmanS (2001) Identification of novel small RNAs using comparative genomics and microarrays. Genes & Development 15: 1637–1651 doi:10.1101/gad.901001

34. FeldenB, VandeneschF, BoulocP, RombyP (2011) The Staphylococcus aureus RNome and its commitment to virulence. PLoS Pathog 7: e1002006 doi:10.1371/journal.ppat.1002006

35. ZukerM (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Research 31: 3406–3415.

36. BoissetS, GeissmannT, HuntzingerE, FechterP, BendridiN, et al. (2007) Staphylococcus aureus RNAIII coordinately represses the synthesis of virulence factors and the transcription regulator Rot by an antisense mechanism. Genes & Development 21: 1353–1366 doi:10.1101/gad.423507

37. GeissmannT, ChevalierC, CrosM-J, BoissetS, FechterP, et al. (2009) A search for small noncoding RNAs in Staphylococcus aureus reveals a conserved sequence motif for regulation. Nucleic Acids Research 37: 7239–7257 doi:10.1093/nar/gkp668

38. JacksonRJ, HellenCUT, PestovaTV (2010) The mechanism of eukaryotic translation initiation and principles of its regulation. Nat Rev Mol Cell Biol 11: 113–127 doi:10.1038/nrm2838

39. TomekW, WollenhauptK (2012) The “closed loop model” in controlling mRNA translation during development. Animal Reproduction Science 134: 2–8 doi:10.1016/j.anireprosci.2012.08.005

40. GuoL, AllenEM, MillerWA (2001) Base-pairing between untranslated regions facilitates translation of uncapped, nonpolyadenylated viral RNA. Molecular Cell 7: 1103–1109.

41. AlvarezDE, LodeiroMF, LudueñaSJ, PietrasantaLI, GamarnikAV (2005) Long-range RNA-RNA interactions circularize the dengue virus genome. J Virol 79: 6631–6643 doi:10.1128/JVI.79.11.6631-6643.2005

42. Møller-JensenJ, FranchT, GerdesK (2001) Temporal translational control by a metastable RNA structure. J Biol Chem 276: 35707–35713 doi:10.1074/jbc.M105347200

43. PaillartJC, Shehu-XhilagaM, MarquetR, MakJ (2004) Dimerization of retroviral RNA genomes: An inseparable pair. Nat Rev Micro 2: 461–472 doi:10.1038/nrmicro903

44. FerrandonD, KochI, WesthofE, Nüsslein-VolhardC (1997) RNA-RNA interaction is required for the formation of specific bicoid mRNA 3′ UTR-STAUFEN ribonucleoprotein particles. EMBO J 16: 1751–1758 doi:10.1093/emboj/16.7.1751

45. WagnerC, PalaciosI, JaegerL, St JohnstonD, EhresmannB, et al. (2001) Dimerization of the 3′UTR of bicoid mRNA involves a two-step mechanism. Journal of Molecular Biology 313: 511–524 doi:10.1006/jmbi.2001.5057

46. GuoP, ZhangC, ChenC, GarverK, TrottierM (1998) Inter-RNA interaction of phage phi29 pRNA to form a hexameric complex for viral DNA transportation. Molecular Cell 2: 149–155.

47. GuoP (2005) RNA nanotechnology: engineering, assembly and applications in detection, gene delivery and therapy. J Nanosci Nanotechnol 5: 1964–1982.

48. BalabanN, NovickRP (1995) Translation of RNAIII, the Staphylococcus aureus agr regulatory RNA molecule, can be activated by a 3′-end deletion. FEMS Microbiology Letters 133: 155–161.

49. ThistedT, SorensenNS, GerdesK (1995) Mechanism of post-segregational killing: Secondary structure analysis of the entire Hok mRNA from plasmid R1 suggests a fold-back structure that prevents translation and antisense RNA binding. Journal of Molecular Biology 247: 859–873 doi:10.1006/jmbi.1995.0186

50. NovickRP, RossHF, ProjanSJ, KornblumJ, KreiswirthB, et al. (1993) Synthesis of staphylococcal virulence factors is controlled by a regulatory RNA molecule. EMBO J 12: 3967–3975.

51. BenitoY, KolbFA, RombyP, LinaG, EtienneJ, et al. (2000) Probing the structure of RNAIII, the Staphylococcus aureus agr regulatory RNA, and identification of the RNA domain involved in repression of protein A expression. RNA 6: 668–679.

52. HuntzingerE, BoissetS, SaveanuC, BenitoY, GeissmannT, et al. (2005) Staphylococcus aureus RNAIII and the endoribonuclease III coordinately regulate spa gene expression. EMBO J 24: 824–835 doi:10.1038/sj.emboj.7600572

53. EggenhoferF, TaferH, StadlerPF, HofackerIL (2011) RNApredator: fast accessibility-based prediction of sRNA targets. Nucleic Acids Research 39: W149–W154 doi:10.1093/nar/gkr467

54. AlbrechtM, SharmaCM, ReinhardtR, VogelJ, RudelT (2010) Deep sequencing-based discovery of the Chlamydia trachomatis transcriptome. Nucleic Acids Research 38: 868–877 doi:10.1093/nar/gkp1032

55. DornenburgJE, DevitaAM, PalumboMJ, WadeJT (2010) Widespread antisense transcription in Escherichia coli. mBio 1 pii. doi:10.1128/mBio.00024-10

56. SchmidtkeC, FindeissS, SharmaCM, KuhfußJ, HoffmannS, et al. (2012) Genome-wide transcriptome analysis of the plant pathogen Xanthomonas identifies sRNAs with putative virulence functions. Nucleic Acids Research 40: 2020–2031 doi:10.1093/nar/gkr904

57. SharmaCM, VogelJ (2009) Experimental approaches for the discovery and characterization of regulatory small RNA. Current Opinion in Microbiology 12: 536–546 doi:10.1016/j.mib.2009.07.006

58. MitschkeJ, GeorgJ, ScholzI, SharmaCM, DienstD, et al. (2011) An experimentally anchored map of transcriptional start sites in the model cyanobacterium Synechocystis sp. PCC6803. Proceedings of the National Academy of Sciences 108: 2124–2129 doi:10.1073/pnas.1015154108

59. MitschkeJ, VioqueA, HaasF, HessWR, Muro-PastorAM (2011) Dynamics of transcriptional start site selection during nitrogen stress-induced cell differentiation in Anabaena sp. PCC7120. Proceedings of the National Academy of Sciences 108: 20130–20135 doi:10.1073/pnas.1112724108

60. WurtzelO, SestoN, MellinJR, KarunkerI, EdelheitS, et al. (2012) Comparative transcriptomics of pathogenic and non-pathogenic Listeria species. Mol Syst Biol 8: 1–14 doi:10.1038/msb.2012.11

61. WurtzelO, Yoder-HimesDR, HanK, DandekarAA, EdelheitS, et al. (2012) The Single-Nucleotide Resolution Transcriptome of Pseudomonas aeruginosa Grown in Body Temperature. PLoS Pathog 8: e1002945 doi:10.1371/journal.ppat.1002945.g007

62. PesoleG, LiuniS, GrilloG, LicciulliF, MignoneF, et al. (2002) UTRdb and UTRsite: specialized databases of sequences and functional elements of 5″ and 3″ untranslated regions of eukaryotic mRNAs. Update 2002. Nucleic Acids Research 30: 335–340.

63. Broeke-Smits tenNJP, PronkTE, JongeriusI, BruningO, WittinkFR, et al. (2010) Operon structure of Staphylococcus aureus. Nucleic Acids Research 38: 3263–3274 doi:10.1093/nar/gkq058

64. PerocchiF, XuZ, Clauder-MünsterS, SteinmetzLM (2007) Antisense artifacts in transcriptome microarray experiments are resolved by actinomycin D. Nucleic Acids Research 35: e128 doi:10.1093/nar/gkm683

65. SeguraV, Toledo-AranaA, UzquedaM, LasaI, Muñoz-BarrutiaA (2012) Wavelet-based detection of transcriptional activity on a novel Staphylococcus aureus tiling microarray. BMC Bioinformatics 13: 222 doi:10.1186/1471-2105-13-222

66. BrittonRA, WenT, SchaeferL, PellegriniO, UickerWC, et al. (2007) Maturation of the 5′ end of Bacillus subtilis 16S rRNA by the essential ribonuclease YkqC/RNase J1. Mol Microbiol 63: 127–138 doi:10.1111/j.1365-2958.2006.05499.x

67. Vergara-IrigarayM, ValleJ, MerinoN, LatasaC, GarcíaB, et al. (2009) Relevant role of fibronectin-binding proteins in Staphylococcus aureus biofilm-associated foreign-body infections. Infection and Immunity 77: 3978–3991 doi:10.1128/IAI.00616-09

68. ArnaudM, ChastanetA, DébarbouilléM (2004) New vector for efficient allelic replacement in naturally nontransformable, low-GC-content, Gram-positive bacteria. Applied and Environmental Microbiology 70: 6887–6891 doi:10.1128/AEM.70.11.6887-6891.2004

69. ValleJ, Toledo-AranaA, BerasainC, GhigoJ-M, AmorenaB, et al. (2003) SarA and not sigma B is essential for biofilm development by Staphylococcus aureus. Mol Microbiol 48: 1075–1087.

70. JoanneP, FalordM, ChesneauO, LacombeC, CastanoS, et al. (2009) Comparative study of two plasticins: specificity, interfacial behavior, and bactericidal activity. Biochemistry 48: 9372–9383 doi:10.1021/bi901222p

71. CharpentierE, AntonAI, BarryP, AlfonsoB, FangY, et al. (2004) Novel cassette-based shuttle vector system for Gram-positive bacteria. Applied and Environmental Microbiology 70: 6076–6085 doi:10.1128/AEM.70.10.6076-6085.2004

72. UdekwuKI, DarfeuilleF, VogelJ, ReimegårdJ, HolmqvistE, et al. (2005) Hfq-dependent regulation of OmpA synthesis is mediated by an antisense RNA. Genes & Development 19: 2355–2366 doi:10.1101/gad.354405

73. AmarasingheAK, Calin-JagemanI, HarmouchA, SunW, NicholsonAW (2001) Escherichia coli ribonuclease III: affinity purification of hexahistidine-tagged enzyme and assays for substrate binding and cleavage. Meth Enzymol 342: 143–158.

74. ChelladuraiBS, LiH, NicholsonAW (1991) A conserved sequence element in ribonuclease III processing signals is not required for accurate in vitro enzymatic cleavage. Nucleic Acids Research 19: 1759–1766.

75. SerganovA, RakA, GarberM, ReinboltJ, EhresmannB, et al. (1997) Ribosomal protein S15 from Thermus thermophilus. Cloning, sequencing, overexpression of the gene and RNA-binding properties of the protein. Eur J Biochem 246: 291–300.

76. FechterP, ChevalierC, YusupovaG, YusupovM, RombyP, et al. (2009) Ribosomal initiation complexes probed by toeprinting and effect of trans-acting translational regulators in bacteria. Methods Mol Biol 540: 247–263 doi:_10.1007/978-1-59745-558-9_18

77. Maira-LitránT, KropecA, GoldmannDA, PierGB (2005) Comparative opsonic and protective activities of Staphylococcus aureus conjugate vaccines containing native or deacetylated Staphylococcal Poly-N-acetyl-beta-(1–6)-glucosamine. Infection and Immunity 73: 6752–6762 doi:10.1128/IAI.73.10.6752-6762.2005

78. GhigoJM (2001) Natural conjugative plasmids induce bacterial biofilm development. Nature 412: 442–445 doi:10.1038/35086581

79. LaederachA, DasR, VicensQ, PearlmanSM, BrenowitzM, et al. (2008) Semiautomated and rapid quantification of nucleic acid footprinting and structure mapping experiments. Nat Protoc 3: 1395–1401 doi:10.1038/nprot.2008.134

Štítky
Genetika Reprodukčná medicína

Článok vyšiel v časopise

PLOS Genetics


2013 Číslo 12
Najčítanejšie tento týždeň
Najčítanejšie v tomto čísle
Kurzy

Zvýšte si kvalifikáciu online z pohodlia domova

Získaná hemofilie - Povědomí o nemoci a její diagnostika
nový kurz

Eozinofilní granulomatóza s polyangiitidou
Autori: doc. MUDr. Martina Doubková, Ph.D.

Všetky kurzy
Prihlásenie
Zabudnuté heslo

Zadajte e-mailovú adresu, s ktorou ste vytvárali účet. Budú Vám na ňu zasielané informácie k nastaveniu nového hesla.

Prihlásenie

Nemáte účet?  Registrujte sa

#ADS_BOTTOM_SCRIPTS#