Translation Enhancing ACA Motifs and Their Silencing by a Bacterial Small Regulatory RNA

English version České info

GcvB is an archetypal multi-target small RNA regulator of genes involved in amino acid uptake or metabolism in enteric bacteria. Included in the GcvB regulon is the yifK locus, encoding a conserved putative amino acid transporter. GcvB inhibits yifK mRNA translation by pairing with a sequence immediately upstream from the Shine-Dalgarno motif. Surprisingly, we found that some target sequence mutations that disrupt pairing, and thus were expected to relieve repression, actually lower yifK expression and cause it not to respond to GcvB variants carrying the corresponding compensatory changes. Work prompted by these observations revealed that the GcvB target sequence in yifK mRNA includes elements that stimulate translation initiation. Replacing each base of an ACA trinucleotide near the center of the target sequence, by any other base, caused yifK expression to decrease. Effects were additive, with some triple replacements causing up to a 90% reduction. The enhancer activity did not require the ACA motif to be strictly positioned relative to the Shine-Dalgarno sequence, nor did it depend on a particular spacing between the latter and the initiating AUG. The dppA mRNA, another GcvB target, contains four ACA motifs at the target site. Quite strikingly, replacement of all four ACAs by random trinucleotide sequences yielded variants showing over 100-fold reduction in expression, virtually inactivating the gene. Altogether, these data identify the ACA motif as a translation-enhancing module and show that GcvB's ability to antagonize the enhancer function in target mRNAs is quintessential to the regulatory effectiveness of this sRNA.

Vyšlo v časopise: Translation Enhancing ACA Motifs and Their Silencing by a Bacterial Small Regulatory RNA. PLoS Genet 10(1): e32767. doi:10.1371/journal.pgen.1004026
Kategorie: Research Article
prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.pgen.1004026

Souhrn

Zdroje

1. GottesmanS, StorzG (2011) Bacterial Small RNA Regulators: Versatile Roles and Rapidly Evolving Variations. Cold Spring Harb Perspect Biol doi:10.1101/cshperspect.a003798

2. StorzG, VogelJ, WassarmanKM (2011) Regulation by small RNAs in bacteria: expanding frontiers. Mol Cell 43 : 880–891.

3. VogelJ, LuisiBF (2011) Hfq and its constellation of RNA. Nat Rev Microbiol 9 : 578–589.

4. JacquesJF, JangS, PrevostK, DesnoyersG, DesmaraisM, et al. (2006) RyhB small RNA modulates the free intracellular iron pool and is essential for normal growth during iron limitation in Escherichia coli. Mol Microbiol 62 : 1181–1190.

5. MasséE, EscorciaFE, GottesmanS (2003) Coupled degradation of a small regulatory RNA and its mRNA targets in Escherichia coli. Genes Dev 17 : 2374–2383.

6. MasséE, GottesmanS (2002) A small RNA regulates the expression of genes involved in iron metabolism in Escherichia coli. Proc Natl Acad Sci U S A 99 : 4620–4625.

7. MasséE, VanderpoolCK, GottesmanS (2005) Effect of RyhB small RNA on global iron use in Escherichia coli. J Bacteriol 187 : 6962–6971.

8. PrevostK, DesnoyersG, JacquesJF, LavoieF, MasséE (2011) Small RNA-induced mRNA degradation achieved through both translation block and activated cleavage. Genes Dev 25 : 385–396.

9. BalbontínR, FioriniF, Figueroa-BossiN, CasadesúsJ, BossiL (2010) Recognition of heptameric seed sequence underlies multi-target regulation by RybB small RNA in Salmonella enterica. Mol Microbiol 78 : 380–394.

10. GogolEB, RhodiusVA, PapenfortK, VogelJ, GrossCA (2011) Small RNAs endow a transcriptional activator with essential repressor functions for single-tier control of a global stress regulon. Proc Natl Acad Sci U S A 108 : 12875–12880.

11. JohansenJ, RasmussenAA, OvergaardM, Valentin-HansenP (2006) Conserved small non-coding RNAs that belong to the σE regulon: role in down-regulation of outer membrane proteins. J Mol Biol 364 : 1–8.

12. PapenfortK, PfeifferV, MikaF, LucchiniS, HintonJC, et al. (2006) σE-dependent small RNAs of Salmonella respond to membrane stress by accelerating global omp mRNA decay. Mol Microbiol 62 : 1674–1688.

13. ThompsonKM, RhodiusVA, GottesmanS (2007) σE regulates and is regulated by a small RNA in Escherichia coli. J Bacteriol 189 : 4243–4256.

14. BeiselCL, StorzG (2011) The base-pairing RNA spot 42 participates in a multioutput feedforward loop to help enact catabolite repression in Escherichia coli. Mol Cell 41 : 286–297.

15. PulvermacherSC, StaufferLT, StaufferGV (2009) Role of the sRNA GcvB in regulation of cycA in Escherichia coli. Microbiology 155 : 106–114.

16. SharmaCM, DarfeuilleF, PlantingaTH, VogelJ (2007) A small RNA regulates multiple ABC transporter mRNAs by targeting C/A-rich elements inside and upstream of ribosome-binding sites. Genes Dev 21 : 2804–2817.

17. SharmaCM, PapenfortK, PernitzschSR, MollenkopfHJ, HintonJC, et al. (2011) Pervasive post-transcriptional control of genes involved in amino acid metabolism by the Hfq-dependent GcvB small RNA. Mol Microbiol 81 : 1144–1165.

18. UrbanowskiML, StaufferLT, StaufferGV (2000) The gcvB gene encodes a small untranslated RNA involved in expression of the dipeptide and oligopeptide transport systems in Escherichia coli. Mol Microbiol 37 : 856–868.

19. StaufferLT, StaufferGV (2005) GcvA interacts with both the alpha and sigma subunits of RNA polymerase to activate the Escherichia coli gcvB gene and the gcvTHP operon. FEMS Microbiol Lett 242 : 333–338.

20. CoornaertA, ChiaruttiniC, SpringerM, GuillierM (2013) Post-Transcriptional Control of the Escherichia coli PhoQ-PhoP Two-Component System by Multiple sRNAs Involves a Novel Pairing Region of GcvB. PLoS Genet 9: e1003156.

21. Figueroa-BossiN, LemireS, MaloriolD, BalbontínR, CasadesúsJ, et al. (2006) Loss of Hfq activates the σE-dependent envelope stress response in Salmonella enterica. Mol Microbiol 62 : 838–852.

22. DesnoyersG, MasséE (2012) Noncanonical repression of translation initiation through small RNA recruitment of the RNA chaperone Hfq. Genes Dev 26 : 726–739.

23. BrennanRG, LinkTM (2007) Hfq structure, function and ligand binding. Curr Opin Microbiol 10 : 125–133.

24. BossiL, SmithDM (1984) Conformational change in the DNA associated with an unusual promoter mutation in a tRNA operon of Salmonella. Cell 39 : 643–652.

25. ZhangA, WassarmanKM, RosenowC, TjadenBC, StorzG, et al. (2003) Global analysis of small RNA and mRNA targets of Hfq. Mol Microbiol 50 : 1111–1124.

26. ModiSR, CamachoDM, KohanskiMA, WalkerGC, CollinsJJ Functional characterization of bacterial sRNAs using a network biology approach. Proc Natl Acad Sci U S A 108 : 15522–15527.

27. ShultzabergerRK, BucheimerRE, RuddKE, SchneiderTD (2001) Anatomy of Escherichia coli ribosome binding sites. J Mol Biol 313 : 215–228.

28. Figueroa-BossiN, ValentiniM, MalleretL, FioriniF, BossiL (2009) Caught at its own game: regulatory small RNA inactivated by an inducible transcript mimicking its target. Genes Dev 23 : 2004–2015.

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

30. DreyfusM (1988) What constitutes the signal for the initiation of protein synthesis on Escherichia coli mRNAs? J Mol Biol 204 : 79–94.

31. CalvoJM, MatthewsRG (1994) The leucine-responsive regulatory protein, a global regulator of metabolism in Escherichia coli. Microbiol Rev 58 : 466–490.

32. Martin-FarmerJ, JanssenGR (1999) A downstream CA repeat sequence increases translation from leadered and unleadered mRNA in Escherichia coli. Mol Microbiol 31 : 1025–1038.

33. YarchukO, JacquesN, GuillerezJ, DreyfusM (1992) Interdependence of translation, transcription and mRNA degradation in the lacZ gene. J Mol Biol 226 : 581–596.

34. KomarovaAV, TchufistovaLS, SupinaEV, BoniIV (2002) Protein S1 counteracts the inhibitory effect of the extended Shine-Dalgarno sequence on translation. RNA 8 : 1137–1147.

35. McCarthyJE, SchairerHU, SebaldW (1985) Translational initiation frequency of atp genes from Escherichia coli: identification of an intercistronic sequence that enhances translation. EMBO J 4 : 519–526.

36. TzarevaNV, MakhnoVI, BoniIV (1994) Ribosome-messenger recognition in the absence of the Shine-Dalgarno interactions. FEBS Lett 337 : 189–194.

37. RingquistS, JonesT, SnyderEE, GibsonT, BoniI, et al. (1995) High-affinity RNA ligands to Escherichia coli ribosomes and ribosomal protein S1: comparison of natural and unnatural binding sites. Biochemistry 34 : 3640–3648.

38. DubeyAK, BakerCS, RomeoT, BabitzkeP (2005) RNA sequence and secondary structure participate in high-affinity CsrA-RNA interaction. RNA 11 : 1579–1587.

39. VesperO, AmitaiS, BelitskyM, ByrgazovK, KaberdinaAC, et al. (2011) Selective translation of leaderless mRNAs by specialized ribosomes generated by MazF in Escherichia coli. Cell 147 : 147–157.

40. LilleengenK (1948) Typing of Salmonella typhimurium by means of bacteriophage. Acta Pathol Microbiol Scand 77 : 2–125.

41. Figueroa-BossiN, CoissacE, NetterP, BossiL (1997) Unsuspected prophage-like elements in Salmonella typhimurium. Mol Microbiol 25 : 161–173.

42. BertaniG (2004) Lysogeny at mid-twentieth century: P1, P2, and other experimental systems. J Bacteriol 186 : 595–600.

43. MaloySR, RothJR (1983) Regulation of proline utilization in Salmonella typhimurium: characterization of put::Mu d(Ap, lac) operon fusions. J Bacteriol 154 : 561–568.

44. MacconkeyA (1905) Lactose-Fermenting Bacteria in Faeces. J Hyg (Lond) 5 : 333–379.

45. SchmiegerH (1972) Phage P22-mutants with increased or decreased transduction abilities. Mol Gen Genet 119 : 75–88.

46. LemireS, Figueroa-BossiN, BossiL (2011) Bacteriophage crosstalk: coordination of prophage induction by trans-acting antirepressors. PLoS Genet 7: e1002149.

47. DatsenkoKA, WannerBL (2000) One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proc Natl Acad Sci U S A 97 : 6640–6645.

48. MurphyKC, CampelloneKG, PoteeteAR (2000) PCR-mediated gene replacement in Escherichia coli. Gene 246 : 321–330.

49. YuD, EllisHM, LeeEC, JenkinsNA, CopelandNG, et al. (2000) An efficient recombination system for chromosome engineering in Escherichia coli. Proc Natl Acad Sci U S A 97 : 5978–5983.

50. BossiL, Figueroa-BossiN (2007) A small RNA downregulates LamB maltoporin in Salmonella. Mol Microbiol 65 : 799–810.

51. BossiL, SchwartzA, GuillemardetB, BoudvillainM, Figueroa-BossiN (2012) A role for Rho-dependent polarity in gene regulation by a noncoding small RNA. Genes Dev 26 : 1864–1873.

52. BochnerBR, HuangHC, SchievenGL, AmesBN (1980) Positive selection for loss of tetracycline resistance. J Bacteriol 143 : 926–933.

53. UzzauS, Figueroa-BossiN, RubinoS, BossiL (2001) Epitope tagging of chromosomal genes in Salmonella. Proc Natl Acad Sci U S A 98 : 15264–15269.

54. DarfeuilleF, UnosonC, VogelJ, WagnerEG (2007) An antisense RNA inhibits translation by competing with standby ribosomes. Mol Cell 26 : 381–392.

55. Miller JH (1992) A Short Course in Bacterial Genetics. A Laboratory Manual and Handbook for Escherichia coli and Related Bacteria. Cold Spring Harbor, New York: Cold Spring Harbor Laboratory Press.

56. CamachoEM, CasadesúsJ (2002) Conjugal transfer of the virulence plasmid of Salmonella enterica is regulated by the leucine-responsive regulatory protein and DNA adenine methylation. Mol Microbiol 44 : 1589–1598.

57. EllermeierCD, JanakiramanA, SlauchJM (2002) Construction of targeted single copy lac fusions using lambda Red and FLP-mediated site-specific recombination in bacteria. Gene 290 : 153–161.