Local Absence of Secondary Structure Permits Translation of mRNAs that Lack Ribosome-Binding Sites

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The initiation of translation is a fundamental and highly regulated process in gene expression. Translation initiation in prokaryotic systems usually requires interaction between the ribosome and an mRNA sequence upstream of the initiation codon, the so-called ribosome-binding site (Shine-Dalgarno sequence). However, a large number of genes do not possess Shine-Dalgarno sequences, and it is unknown how start codon recognition occurs in these mRNAs. We have performed genome-wide searches in various groups of prokaryotes in order to identify sequence elements and/or RNA secondary structural motifs that could mediate translation initiation in mRNAs lacking Shine-Dalgarno sequences. We find that mRNAs without a Shine-Dalgarno sequence are generally less structured in their translation initiation region and show a minimum of mRNA folding at the start codon. Using reporter gene constructs in bacteria, we also provide experimental support for local RNA unfoldedness determining start codon recognition in Shine-Dalgarno–independent translation. Consistent with this, we show that AUG start codons reside in single-stranded regions, whereas internal AUG codons are usually in structured regions of the mRNA. Taken together, our bioinformatics analyses and experimental data suggest that local absence of RNA secondary structure is necessary and sufficient to initiate Shine-Dalgarno–independent translation. Thus, our results provide a plausible mechanism for how the correct translation initiation site is recognized in the absence of a ribosome-binding site.

Vyšlo v časopise: Local Absence of Secondary Structure Permits Translation of mRNAs that Lack Ribosome-Binding Sites. PLoS Genet 7(6): e32767. doi:10.1371/journal.pgen.1002155
Kategorie: Research Article
prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.pgen.1002155

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Zdroje

1. McCarthyJEGBrimacombeR 1994 Prokaryotic translation initiation: the interactive pathway leading to initiation. Trends Genet 10 402 407

2. KozakM 1999 Initiation of translation in prokaryotes and eukaryotes. Gene 234 187 208

3. ApelWSchulzeWXBockR 2010 Identification of protein stability determinants in chloroplasts. Plant J 63 636 650

4. DrechselOBockR 2010 Selection of Shine-Dalgarno sequences in plastids. Nucleic Acids Res 39 1427 1438

5. FargoDCZhangMGillhamNWBoyntonJE 1998 Shine-Dalgarno-like sequences are not required for translation of chloroplast mRNAs in Chlamydomonas reinhardtii chloroplasts or in Escherichia coli. Mol Gen Genet 257 271 282

6. SkorskiPLeroyPFayetODreyfusMHermann-Le DenmatS 2006 The highly efficient translation initiation region from the Escherichia coli rpsA gene lacks a Shine-Dalgarno element. J Bacteriol 188 6277 6285

7. NakagawaSNiimuraYMiuraK-IGojoboriT 2010 Dynamic evolution of translation initiation mechanisms in prokaryotes. Proc Natl Acad Sci USA 107 6382 6387

8. HazleTBonenL 2007 Comparative analysis of sequences preceding protein-coding mitochondrial genes in flowering plants. Mol Biol Evol 24 1101 1112

9. BoniIVIsaevaDMMusychenkoMLTzarevaNV 1991 Ribosome-messenger recognition: mRNA target sites for ribosomal protein S1. Nucleic Acids Res 19 155 162

10. KomarovaAVTchufistovaLSDreyfusMBoniIV 2005 AU-rich sequences within 5′ untranslated leaders enhance translation and stabilize mRNA in Escherichia coli. J Bacteriol 187 1344 1349

11. KomarovaAVTchufistovaLSSupinaEVBoniIV 2002 Protein S1 counteracts the inhibitory effect of the extended Shine-Dalgarno sequence on translation. RNA 8 1137 1147

12. BaileyTLElkanC 1994 Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology 28 36

13. LinhartCHalperinYShamirR 2008 Transcription factor and microRNA motif discovery: The Amadeus platform and a compendium of metazoan target sets. Genome Res 18 1180 1189

14. ReederJGiegerichR 2005 Consensus shapes: an alternative to the Sankoff algorithm for RNA consensus structure prediction. Bioinformatics 21 3516 3523

15. NakamotoT 2006 A unified view of the initiation of protein synthesis. Biochem Biophys Res Commun 341 675 678

16. RicardBSalserW 1975 Secondary structures formed by random RNA sequences. Biochem Biophys Res Commun 63 548 554

17. RicardBSalserW 1976 Optical measurements reveal base-pairing in T4-specific mRNAs. Biochim Biophys Acta 425 196 201

18. GrallaJDeLisiC 1974 mRNA is expected to form stable secondary structures. Nature 248 330 332

19. KudlaGMurrayAWTollerveyDPlotkinJB 2009 Coding-sequence determinants of gene expression in Escherichia coli. Science 324 255 258

20. HofackerILFontanaWStadlerPFBonhoefferLSTackerM 1994 Fast folding and comparison of RNA secondary structures. Monatshefte f Chemie 125 167 188

21. HüttenhoferANollerHF 1994 Footprinting mRNA-ribosome complexes with chemical probes. EMBO J 13 3892 3901

22. WikströmPMLindLKBergDE 1992 Importance of mRNA folding and start codon accessibility in the expression of genes in a ribosomal protein operon of Escherichia coli. J Mol Biol 224 949 966

23. KerteszMWanYMazorERinnJLNutterRC 2010 Genome-wide measurement of RNA secondary structure in yeast. Nature 467 103 107

24. StuderSMJosephS 2006 Unfolding of mRNA secondary structure by the bacterial translation initiation complex. Mol Cell 22 105 115

25. JonesCNWilkinsonKAHungKTWeeksKMSpremulliLL 2008 Lack of secondary structure characterizes the 5′ ends of mammalian mitochondrial mRNAs. RNA 14 862 871

26. ChristianBESpremulliLL 2010 Preferential selection of the 5′-terminal start codon on leaderless mRNAs by mammalian mitochondrial ribosomes. J Biol Chem 285 28379 28386

27. KaberdinaACSzaflarskiWNierhausKHMollI 2009 An unexpected type of ribosomes induced by kasugamycin: a look into ancestral times of protein synthesis. Mol Cell 33 227 236

28. PruittKDHarrowJHarteRAWallinCDiekhansM 2009 The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes. Genome Res 19 1316 1323

29. BaileyTLGribskovM 1998 Combining evidence using p-values: application to sequence homology searches. Bioinformatics 14 48 54

30. StarmerJStompAVoukMBitzerD 2006 Predicting Shine-Dalgarno sequence locations exposes genome annotation errors. PLoS Comput Biol 2 e57 doi:10.1371/journal.pcbi.0020057

31. NeupertJKarcherDBockR 2008 Design of simple synthetic RNA thermometers for temperature-controlled gene expression in Escherichia coli. Nucleic Acids Res 36 e124

32. HayashiKMorookaNYamamotoYFujitaKIsonoK 2006 Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110. Mol Syst Biol 2 e0007

33. NeupertJBockR 2009 Designing and using synthetic RNA thermometers for temperature-controlled gene expression in bacteria. Nature Protoc 4 1262 1273

34. BernhartSHHofackerILStadlerPF 2006 Local base pairing probabilities in large RNAs. Bioinformatics 22 614 615

35. SharpPMLiW-H 1987 The codon adaptation index -⁠ a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Res 15 1281 1295

36. DongHNilssonLKurlandCG 1996 Co-variation of tRNA abundance and codon usage in Escherichia coli at different growth rates. J Mol Biol 260 649 663