Deep sequencing-based identification of small non-coding RNAs in Streptomyces coelicolor

RNA Biology

Volumn 8, Issue 3, 2011, Pages 468-477

  Vockenhuber, Michael Paul ^a   Sharma, Cynthia M ^b   Statt, Michaela G ^a   Schmidt, Denis ^a   Xu, Zhenjiang ^c   Dietrich, Sascha ^d   Liesegang, Heiko ^d   Mathews, David H ^c   Suess, Beatrix ^a  

^a GOETHE UNIVERSITY   (Germany)

^b UNIVERSITY OF WÜRZBURG   (Germany)

^c UNIVERSITY OF ROCHESTER MEDICAL CENTER   (United States)

^d UNIVERSITY OF GÖTTINGEN   (Germany)

Author keywords

Bioinformatic prediction; Deep sequencing; Small non coding RNA; Streptomyces coelicolor; Transcriptome

Indexed keywords

CIS ACTING ELEMENT; COMPLEMENTARY RNA; MESSENGER RNA; SMALL UNTRANSLATED RNA; TRANSCRIPTOME; TRANSFER RNA;

ARTICLE; BIOINFORMATICS; GROWTH; METABOLISM; NONHUMAN; PREDICTION; PROTEIN ANALYSIS; PROTEIN EXPRESSION; RNA PROCESSING; RNA SEQUENCE; STREPTOMYCES COELICOLOR;

POSIBACTERIA; STREPTOMYCES COELICOLOR;

EID: 79956086810     PISSN: 15476286     EISSN: 15558584     Source Type: Journal    
DOI: 10.4161/rna.8.3.14421     Document Type: Article

References (55)

1. Bentley SD, Chater KF, Cerdeño-Tárraga AM, Challis GL, Thomson NR, James KD, et al. Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2). Nature 2002; 417:141-7.
2. Binnie C, Jenish D, Cossar D, Szabo A, Trudeau D, Krygsman P, et al. Expression and characterization of soluble human erythropoietin receptor made in Streptomyces lividans 66. Protein Expr Purif 1997; 11:271-8. (Pubitemid 28014100)
3. Watve MG, Tickoo R, Jog MM, Bhole BD. How many antibiotics are produced by the genus Streptomyces? Archives of Microbiology 2001; 176:386-90.
4. Chater KF. Regulation of sporulation in Streptomyces coelicolor A3(2): a checkpoint multiplex? Curr Opin Microbiol 2001; 4:667-73.
5. Reuther J, Wohlleben W. Nitrogen metabolism in Streptomyces coelicolor: transcriptional and post-translational regulation. J Mol Microbiol Biotechnol 2007; 12:139-46. (Pubitemid 46011135)
6. Sharma CM, Vogel J. Experimental approaches for the discovery and characterization of regulatory small RNA. Curr Opin Microbiol 2009; 12:536-46.
7. Storz G, Altuvia S, Wassarman KM. An abundance of RNA regulators. Annu Rev Biochem 2005; 74:199-217. (Pubitemid 40995506)
8. Gottesman S. The small RNA regulators of Escherichia coli: Roles and Mechanisms. Annu Rev Microbiol 2004; 58:303-28. (Pubitemid 39551989)
9. Waters LS, Storz G. Regulatory RNAs in bacteria. Cell 2009; 136:615-28.
10. Jäger D, Sharma CM, Thomsen J, Ehlers C, Vogel J, Schmitz RA. Deep sequencing analysis of the Methanosarcina mazei Go1 transcriptome in response to nitrogen availability. Proc Natl Acad Sci USA 2009.
11. Sharma CM, Hoffmann S, Darfeuille F, Reignier J, Findeiß S, Sittka A, et al. The primary transcriptome of the major human pathogen Helicobacter pylori. Nature 2010.
12. Albrecht M, Sharma CM, Reinhardt R, Vogel J, Rudel T. Deep sequencing-based discovery of the Chlamydia trachomatis transcriptome. Nucleic Acids Research 2009.
13. van Vliet AH. Next generation sequencing of microbial transcriptomes: challenges and opportunities. FEMS Microbiol Lett 2010; 302:1-7.
14. Sorek R, Cossart P. Prokaryotic transcriptomics: a new view on regulation, physiology and pathogenicity. Nat Rev Genet 11:9-16.
15. Pánek J, Bobek J, Mikulik K, Basler M, Vohradsky J. Biocomputational prediction of small non-coding RNAs in Streptomyces. BMC Genomics 2008; 9:217.
16. Swiercz J, Hindra, Bobek J, Haiser H, Di Berardo C, Tjaden B, et al. Small non-coding RNAs in Streptomyces coelicolor. Nucleic Acids Research 2008.
17. D'alia D, Nieselt K, Steigele S, Müller J, Verburg I, Takano E. Non-coding RNA of glutamine synthetase I modulates antibiotic production in Streptomyces coelicolor A3(2). Journal of Bacteriology 2009.
18. Tezuka T, Hara H, Ohnishi Y, Horinouchi S. Identification and Gene Disruption of Small Non-coding RNAs in Streptomyces griseus. Journal of Bacteriology 2009.
19. Tobias Kieser MJB, Buttner MJ, Chater KF, Hopwood DA. Practical Streptomyces Genetics. Colney, Norwich NR4 7UH, England: John Innes Foundation.
20. Caballero JL, Malpartida F, Hopwood DA. Transcriptional organization and regulation of an antibiotic export complex in the producing Streptomyces culture. Mol Gen Genet 1991; 228:372-80.
21. Viollier PH, Nguyen KT, Minas W, Folcher M, Dale G, Thompson CJ. Roles of aconitase in growth, metabolism and morphological differentiation of Streptomyces coelicolor. Journal of Bacteriology 2001; 183:3193-203. (Pubitemid 32433538)
22. Van Etten WJ, Janssen GR. An AUG initiation codon, not codon-anticodon complementarity, is required for the translation of unleadered mRNA in Escherichia coli. Mol Microbiol 1998; 27:987-1001. (Pubitemid 28254948)
23. Hering O, Brenneis M, Beer J, Suess B, Soppa J. A novel mechanism for translation initiation operates in haloarchaea. Mol Microbiol 2009; 71:1451-63.
24. Janssen GR. Eubacterial, Archaebacterial and Eucaryotic Genes That Encode Leaderless mRNA. In: Balz RH, Ed. Industrial Microorganisms: Basic and Applied Molecular Genetics. Washington DC: American Society for Microbiology 1993.
25. Bibb MJ, White J, Ward JM, Janssen GR. The mRNA for the 23S rRNA methylase encoded by the ermE gene of Saccharopolyspora erythraea is translated in the absence of a conventional ribosome-binding site. Mol Microbiol 1994; 14:533-45. (Pubitemid 24337333)
26. Janssen GR, Ward JM, Bibb MJ. Unusual transcriptional and translational features of the aminoglycoside phosphotransferase gene (aph) from Streptomyces fradiae. Genes & Development 1989; 3:415-29.
27. Jones RL, Jaskula JC, Janssen GR. In vivo translational start site selection on leaderless mRNA transcribed from the Streptomyces fradiae aph gene. Journal of Bacteriology 1992; 174:4753-60.
28. Kaberdin VR, Bläsi U. Translation initiation and the fate of bacterial mRNAs. FEMS Microbiol Rev 2006; 30:967-79. (Pubitemid 44583798)
29. Moll I, Grill S, Gualerzi CO, Blasi U. Leaderless mRNAs in bacteria: surprises in ribosomal recruitment and translational control. Mol Microbiol 2002; 43:239-46. (Pubitemid 34212205)
30. Grill S, Gualerzi CO, Londei P, Blasi U. Selective stimulation of translation of leaderless mRNA by initiation factor 2: evolutionary implications for translation. EMBO J 2000; 19:4101-10. (Pubitemid 30608548)
31. Kaberdina AC, Szaflarski W, Nierhaus KH, Moll I. An unexpected type of ribosomes induced by kasugamycin: a look into ancestral times of protein synthesis? Molecular Cell 2009; 33:227-36.
32. Sorokin A, Serror P, Pujic P, Azevedo V, Ehrlich SD. The Bacillus subtilis chromosome region encoding homologues of the Escherichia coli mssA and rpsA gene products. Microbiology 1995; 141:311-9.
33. Weinberg Z, Barrick JE, Yao Z, Roth A, Kim JN, Gore J, et al. Identification of 22 candidate structured RNAs in bacteria using the CMfinder comparative genomics pipeline. Nucleic Acids Research 2007; 35:4809-19. (Pubitemid 47250352)
34. Wassarman KM. 6S RNA: a small RNA regulator of transcription. Curr Opin Microbiol 2007; 10:164-8. (Pubitemid 46590048)
35. Gruber A, Lorenz R, Bernhart S, Neubock R, Hofacker IL. The Vienna RNA Websuite. Nucleic Acids Research 2008; 188.
36. Kormanec J, Farkasovsky M, Potuckova L. Four genes in Streptomyces aureofaciens containing a domain characteristic of principal sigma factors. Gene 1992; 122:63-70.
37. Xiao B, Li W, Guo G, Li B, Liu Z, Jia K, et al. Identification of small noncoding RNAs in Helicobacter pylori by a bioinformatics-based approach. Curr Microbiol 2009; 58:258-63.
38. Boisset S, Geissmann T, Huntzinger E, Fechter P, Bendridi N, Possedko M, et al. Staphylococcus aureus RNAIII coordinately represses the synthesis of virulence factors and the transcription regulator Rot by an antisense mechanism. Genes Dev 2007; 21:1353-66. (Pubitemid 46871039)
39. Tjaden B, Goodwin SS, Opdyke JA, Guillier M, Fu DX, Gottesman S, et al. Target prediction for small, noncoding RNAs in bacteria. Nucleic Acids Research 2006; 34:2791-802. (Pubitemid 43985640)
40. Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet 2000; 16:276-7.
41. Tjaden B. Prediction of small, noncoding RNAs in bacteria using heterogeneous data. J Math Biol 2008; 56:183-200. (Pubitemid 350172190)
42. Kingsford CL, Ayanbule K, Salzberg SL. Rapid, accurate, computational discovery of Rho-independent transcription terminators illuminates their relationship to DNA uptake. Genome Biol 2007; 8:22.
43. Washietl S, Hofacker IL, Stadler PF. Fast and reliable prediction of noncoding RNAs. Proc Natl Acad Sci USA 2005; 102:2454-9. (Pubitemid 40279397)
44. Uzilov AV, Keegan JM, Mathews DH. Detection of non-coding RNAs on the basis of predicted secondary structure formation free energy change. BMC Bioinformatics 2006; 7:173.
45. Thompson J, Higgins D, Gibson T. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994; 22:4673-80. (Pubitemid 24354800)
46. Altschul S, Gish W, Miller W, Myers E, Lipman D. Basic local alignment search tool. J Mol Biol 1990; 215:403-10.
47. Axmann I, Kensche P, Vogel J, Kohl S, Herzel H, Hess WR. Identification of cyanobacterial non-coding RNAs by comparative genome analysis. Genome Biol 2005; 6:73.
48. Gorodkin J, Hofacker IL, Torarinsson E, Yao Z, Havgaard JH, Ruzzo WL. De novo prediction of structured RNAs from genomic sequences. Trends Biotechnol 28:9-19.
49. Mattatall NR, Sanderson KE. Salmonella typhimurium LT2 possesses three distinct 23S rRNA intervening sequences. J Bacteriol 1996; 178:2272-8. (Pubitemid 26123492)
50. Sittka A, Lucchini S, Papenfort K, Sharma CM, Rolle K, Binnewies TT, et al. Deep sequencing analysis of small noncoding RNA and mRNA targets of the global post-transcriptional regulator, Hfq. PLoS Genetics 2008; 4:1000163.
51. Kurtz S, Phillippy A, Delcher AL, Smoot M, Shumway M, Antonescu C, et al. Versatile and open software for comparing large genomes. Genome Biol 2004; 5:12.
52. Mathews DH, Turner DH. Dynalign: an algorithm for finding the secondary structure common to two RNA sequences. J Mol Biol 2002; 317:191-203. (Pubitemid 34722187)
53. Chang C, Lin C. LIBSVM: a library for support vector machines. http://www.csie.ntu.edu.tw/~cjlin/libsvm.
54. Lu Z. Secondary Structure Prediction of Non-coding RNA. Rochester: University of Rochester 2008.
55. Tjaden B. Prediction of small, noncoding RNAs in bacteria using heterogeneous data. J Math Biol 2008; 56:183-200. (Pubitemid 350172190)