Elongation factor P (EF-P) is a well-conserved bacterial protein. Although it can enhance protein synthesis in vitro, it is generally regarded as an ancillary factor required for robust translation of transcripts with stretches of consecutive prolines. In this work we performed ribosome profiling to better understand the role of EF-P during translation. Our data confirmed that translational effects due to lack of EF-P are mainly confined to PPX–encoding genes. Wide variations in EF-P dependent translation of these PPXs led us to investigate the effect of sequences upstream of diproline-containing motifs. We found that amino acids encoded upstream of PPX play a key role in EF-P-dependent translation. Finally, comparison of ribosome profiling data to existing proteomic data indicates that although many PPX-containing patterns have increased ribosome occupancies, this does not necessarily lead to altered protein levels. Taken together these data show a direct role for EF-P during synthesis of PPX motifs, and indirect effects on other post-transcriptional regulators of gene expression.
Vyšlo v časopise: EF-P Dependent Pauses Integrate Proximal and Distal Signals during Translation. PLoS Genet 10(8): e32767. doi:10.1371/journal.pgen.1004553 Kategorie: Research Article prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.pgen.1004553
1. LiGW, OhE, WeissmanJS (2012) The anti-Shine-Dalgarno sequence drives translational pausing and codon choice in bacteria. Nature 484 : 538–541.
2. ItoK, ChibaS, PoglianoK (2010) Divergent stalling sequences sense and control cellular physiology. Biochem Biophys Res Commun 393 : 1–5.
3. LuJ, DeutschC (2008) Electrostatics in the ribosomal tunnel modulate chain elongation rates. J Mol Biol 384 : 73–86.
4. WoolstenhulmeCJ, ParajuliS, HealeyDW, ValverdeDP, PetersenEN, et al. (2013) Nascent peptides that block protein synthesis in bacteria. Proc Natl Acad Sci U S A 110: E878–887.
5. YapMN, BernsteinHD (2009) The plasticity of a translation arrest motif yields insights into nascent polypeptide recognition inside the ribosome tunnel. Mol Cell 34 : 201–211.
6. KomarAA, LesnikT, ReissC (1999) Synonymous codon substitutions affect ribosome traffic and protein folding during in vitro translation. FEBS Lett 462 : 387–391.
7. TsaiCJ, SaunaZE, Kimchi-SarfatyC, AmbudkarSV, GottesmanMM, et al. (2008) Synonymous mutations and ribosome stalling can lead to altered folding pathways and distinct minima. J Mol Biol 383 : 281–291.
8. DoerfelLK, WohlgemuthI, KotheC, PeskeF, UrlaubH, et al. (2013) EF-P is essential for rapid synthesis of proteins containing consecutive proline residues. Science 339 : 85–88.
9. UdeS, LassakJ, StarostaAL, KraxenbergerT, WilsonDN, et al. (2013) Translation elongation factor EF-P alleviates ribosome stalling at polyproline stretches. Science 339 : 82–85.
10. PeilL, StarostaAL, LassakJ, AtkinsonGC, VirumaeK, et al. (2013) Distinct XPPX sequence motifs induce ribosome stalling, which is rescued by the translation elongation factor EF-P. Proc Natl Acad Sci U S A 110 : 15265–15270.
11. HerschSJ, WangM, ZouSB, MoonKM, FosterLJ, et al. (2013) Divergent protein motifs direct elongation factor P-mediated translational regulation in Salmonella enterica and Escherichia coli. MBio 4: e00180–00113.
12. Hanawa-SuetsuguK, SekineS, SakaiH, Hori-TakemotoC, TeradaT, et al. (2004) Crystal structure of elongation factor P from Thermus thermophilus HB8. Proc Natl Acad Sci U S A 101 : 9595–9600.
13. YanagisawaT, SumidaT, IshiiR, TakemotoC, YokoyamaS (2010) A paralog of lysyl-tRNA synthetase aminoacylates a conserved lysine residue in translation elongation factor P. Nat Struct Mol Biol 17 : 1136–1143.
14. BlahaG, StanleyRE, SteitzTA (2009) Formation of the first peptide bond: the structure of EF-P bound to the 70S ribosome. Science 325 : 966–970.
15. RoyH, ZouSB, BullwinkleTJ, WolfeBS, GilreathMS, et al. (2011) The tRNA synthetase paralog PoxA modifies elongation factor-P with (R)-beta-lysine. Nat Chem Biol 7 : 667–669.
16. PeilL, StarostaAL, VirumaeK, AtkinsonGC, TensonT, et al. (2012) Lys34 of translation elongation factor EF-P is hydroxylated by YfcM. Nat Chem Biol 8 : 695–697 doi:10.1038/nchembio.1001
17. BullwinkleTJ, ZouSB, RajkovicA, HerschSJ, ElgamalS, et al. (2013) (R)-beta-lysine-modified elongation factor P functions in translation elongation. J Biol Chem 288 : 4416–4423.
18. GutierrezE, ShinBS, WoolstenhulmeCJ, KimJR, SainiP, et al. (2013) eIF5A promotes translation of polyproline motifs. Mol Cell 51 : 35–45.
19. ParkMH (2006) The post-translational synthesis of a polyamine-derived amino acid, hypusine, in the eukaryotic translation initiation factor 5A (eIF5A). J Biochem 139 : 161–169.
20. IngoliaNT, BrarGA, RouskinS, McGeachyAM, WeissmanJS (2012) The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments. Nat Protoc 7 : 1534–1550.
21. IngoliaNT, GhaemmaghamiS, NewmanJR, WeissmanJS (2009) Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling. Science 324 : 218–223.
22. OhE, BeckerAH, SandikciA, HuberD, ChabaR, et al. (2011) Selective ribosome profiling reveals the cotranslational chaperone action of trigger factor in vivo. Cell 147 : 1295–1308.
23. LorenzR, BernhartSH, Höner Zu SiederdissenC, TaferH, FlammC, et al. (2011) ViennaRNA Package 2.0. Algorithms Mol Biol 6 : 26.
24. FredrickK, IbbaM (2010) How the sequence of a gene can tune its translation. Cell 141 : 227–229.
25. Cruz-VeraLR, Magos-CastroMA, Zamora-RomoE, GuarnerosG (2004) Ribosome stalling and peptidyl-tRNA drop-off during translational delay at AGA codons. Nucleic Acids Res 32 : 4462–4468.
26. RamuH, Vazquez-LaslopN, KlepackiD, DaiQ, PiccirilliJ, et al. (2011) Nascent peptide in the ribosome exit tunnel affects functional properties of the A-site of the peptidyl transferase center. Mol Cell 41 : 321–330.
27. CorcoranCP, PodkaminskiD, PapenfortK, UrbanJH, HintonJC, et al. (2012) Superfolder GFP reporters validate diverse new mRNA targets of the classic porin regulator, MicF RNA. Mol Microbiol 84 : 428–445.
28. UrbanJH, VogelJ (2009) A green fluorescent protein (GFP)-based plasmid system to study post-transcriptional control of gene expression in vivo. Methods Mol Biol 540 : 301–319.
29. PedelacqJD, CabantousS, TranT, TerwilligerTC, WaldoGS (2006) Engineering and characterization of a superfolder green fluorescent protein. Nat Biotechnol 24 : 79–88.
30. WilsonDN, BeckmannR (2011) The ribosomal tunnel as a functional environment for nascent polypeptide folding and translational stalling. Curr Opin Struct Biol 21 : 274–282.
31. TannerDR, CarielloDA, WoolstenhulmeCJ, BroadbentMA, BuskirkAR (2009) Genetic identification of nascent peptides that induce ribosome stalling. J Biol Chem 284 : 34809–34818.
32. NakatogawaH, ItoK (2002) The ribosomal exit tunnel functions as a discriminating gate. Cell 108 : 629–636.
33. BhushanS, HoffmannT, SeideltB, FrauenfeldJ, MielkeT, et al. (2011) SecM-stalled ribosomes adopt an altered geometry at the peptidyl transferase center. PLoS Biol 9: e1000581.
34. DanaA, TullerT (2012) Determinants of translation elongation speed and ribosomal profiling biases in mouse embryonic stem cells. PLoS Comput Biol 8: e1002755.
35. WolinSL, WalterP (1988) Ribosome pausing and stacking during translation of a eukaryotic mRNA. EMBO J 7 : 3559–3569.
36. RychkovaA, MukherjeeS, BoraRP, WarshelA (2013) Simulating the pulling of stalled elongated peptide from the ribosome by the translocon. Proc Natl Acad Sci U S A 110 : 10195–10200.
37. WilsonDN (2011) Peptides in the ribosomal tunnel talk back. Mol Cell 41 : 247–248.
38. CanoVS, JeonGA, JohanssonHE, HendersonCA, ParkJH, et al. (2008) Mutational analyses of human eIF5A-1–identification of amino acid residues critical for eIF5A activity and hypusine modification. FEBS J 275 : 44–58.
39. DiasCA, CanoVS, RangelSM, ApponiLH, FrigieriMC, et al. (2008) Structural modeling and mutational analysis of yeast eukaryotic translation initiation factor 5A reveal new critical residues and reinforce its involvement in protein synthesis. FEBS J 275 : 1874–1888.
40. RossiD, KuroshuR, ZanelliCF, ValentiniSR (2014) eIF5A and EF-P: two unique translation factors are now traveling the same road. Wiley Interdiscip Rev RNA 5 : 209–222.
41. BoëlG, SmithPC, NingW, EnglanderMT, ChenB, et al. (2014) The ABC-F protein EttA gates ribosome entry into the translation elongation cycle. Nat Struct Mol Biol 21 : 143–51 doi: 10.1038/nsmb.2740
42. ChenB, BoelG, HashemY, NingW, FeiJ, et al. (2014) EttA regulates translation by binding the ribosomal E site and restricting ribosome-tRNA dynamics. Nat Struct Mol Biol 21 : 152–159.
43. Vila-SanjurjoA, SchuwirthBS, HauCW, CateJH (2004) Structural basis for the control of translation initiation during stress. Nat Struct Mol Biol 11 : 1054–1059.
44. IzutsuK, WadaC, KomineY, SakoT, UeguchiC, et al. (2001) Escherichia coli ribosome-associated protein SRA, whose copy number increases during stationary phase. J Bacteriol 183 : 2765–2773.
45. ReuvenNB, DeutscherMP (1993) Multiple exoribonucleases are required for the 3′ processing of Escherichia coli tRNA precursors in vivo. FASEB J 7 : 143–148.
46. ElseviersD, PetrulloLA, GallagherPJ (1984) Novel E. coli mutants deficient in biosynthesis of 5-methylaminomethyl-2-thiouridine. Nucleic Acids Res 12 : 3521–3534.
47. WolfeMD, AhmedF, LacourciereGM, LauhonCT, StadtmanTC, et al. (2004) Functional diversity of the rhodanese homology domain: the Escherichia coli ybbB gene encodes a selenophosphate-dependent tRNA 2-selenouridine synthase. J Biol Chem 279 : 1801–1809.
48. IbbaM, SollD (2000) Aminoacyl-tRNA synthesis. Annu Rev Biochem 69 : 617–650.
49. SeongIS, OhJY, LeeJW, TanakaK, ChungCH (2000) The HslU ATPase acts as a molecular chaperone in prevention of aggregation of SulA, an inhibitor of cell division in Escherichia coli. FEBS Lett 477 : 224–229.
50. MalkiA, CaldasT, AbdallahJ, KernR, EckeyV, et al. (2005) Peptidase activity of the Escherichia coli Hsp31 chaperone. J Biol Chem 280 : 14420–14426.
51. BabaT, AraT, HasegawaM, TakaiY, OkumuraY, et al. (2006) Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol Syst Biol 2 : 2006 0008.
52. 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.
53. GuzmanLM, BelinD, CarsonMJ, BeckwithJ (1995) Tight regulation, modulation, and high-level expression by vectors containing the arabinose PBAD promoter. J Bacteriol 177 : 4121–4130.
54. GibsonDG, YoungL, ChuangRY, VenterJC, HutchisonCA3rd, et al. (2009) Enzymatic assembly of DNA molecules up to several hundred kilobases. Nat Methods 6 : 343–345.
55. LiH, DurbinR (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25 : 1754–1760.
56. LetzringDP, DeanKM, GrayhackEJ (2010) Control of translation efficiency in yeast by codon-anticodon interactions. RNA 16 : 2516–2528.
57. CrooksGE, HonG, ChandoniaJM, BrennerSE (2004) WebLogo: a sequence logo generator. Genome Res 14 : 1188–1190.
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