High-Throughput Identification of Promoters and Screening of Highly Active Promoter-5′-UTR DNA Region with Different Characteristics from Bacillus thuringiensis

PLoS ONE

Volumn 8, Issue 5, 2013, Pages

  Wang, Jieping ^a   Ai, Xulu ^a   Mei, Han ^a   Fu, Yang ^a   Chen, Bo ^a   Yu, Ziniu ^a   He, Jin ^a  

^a HUAZHONG AGRICULTURAL UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA; BACTERIAL PROTEIN; MESSENGER RNA; TRANSCRIPTION FACTOR;

5' UNTRANSLATED REGION; ARTICLE; BACILLUS THURINGIENSIS; BACTERIAL GENE; BACTERIAL GENOME; BACTERIUM IDENTIFICATION; BINDING AFFINITY; BINDING SITE; COMPLEX FORMATION; CONTROLLED STUDY; GENE FUNCTION; GENE IDENTIFICATION; GENETIC ASSOCIATION; GENETIC STABILITY; HIGH THROUGHPUT SCREENING; LIFE CYCLE; NONHUMAN; PREDICTION; PROMOTER REGION; PROTEIN BINDING; PROTEIN EXPRESSION; SEQUENCE ANALYSIS; TRANSCRIPTION INITIATION SITE;

5' UNTRANSLATED REGIONS; BACILLUS THURINGIENSIS; BACTERIAL PROTEINS; BASE SEQUENCE; BINDING SITES; CHROMOSOME MAPPING; GENE EXPRESSION; GENE EXPRESSION REGULATION, BACTERIAL; GENOME-WIDE ASSOCIATION STUDY; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; MOLECULAR SEQUENCE DATA; PROMOTER REGIONS, GENETIC; SIGMA FACTOR; TRANSCRIPTION FACTORS; TRANSCRIPTION INITIATION SITE;

EID: 84877612806     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0062960     Document Type: Article

References (43)

1. Haugen SP, Ross W, Gourse RL, (2008) Advances in bacterial promoter recognition and its control by factors that do not bind DNA. Nat Rev Microbiol 6: 507-519.
2. Browning DF, Busby SJ, (2004) The regulation of bacterial transcription initiation. Nat Rev Microbiol 2: 57-65.
3. Haugen SP, Berkmen MB, Ross W, Gaal T, Ward C, et al. (2006) rRNA promoter regulation by nonoptimal binding of sigma region 1.2: an additional recognition element for RNA polymerase. Cell 125: 1069-1082.
4. Mathew R, Chatterji D, (2006) The evolving story of the omega subunit of bacterial RNA polymerase. Trends Microbiol 14: 450-455.
5. McGrath PT, Lee H, Zhang L, Iniesta AA, Hottes AK, et al. (2007) High-throughput identification of transcription start sites, conserved promoter motifs and predicted regulons. Nat Biotechnol 25: 584-592.
6. Mendoza-Vargas A, Olvera L, Olvera M, Grande R, Vega-Alvarado L, et al. (2009) Genome-wide identification of transcription start sites, promoters and transcription factor binding sites in E. coli. PLoS One 4: e7526.
7. Sorek R, Cossart P, (2010) Prokaryotic transcriptomics: a new view on regulation, physiology and pathogenicity. Nature Rev Genet 11: 9-16.
8. Sharma CM, Hoffmann S, Darfeuille F, Reignier J, Findeiss S, et al. (2010) The primary transcriptome of the major human pathogen Helicobacter pylori. Nature 464: 250-255.
9. Waters LS, Storz G, (2009) Regulatory RNAs in bacteria. Cell 136: 615-628.
10. Gutiérrez-Preciado A, Henkin TM, Grundy FJ, Yanofsky C, Merino E, (2009) Biochemical features and functional implications of the RNA-based T-box regulatory mechanism. Microbiol Mol Biol Rev 73: 36-61.
11. Garst AD, Batey RT, (2009) A switch in time: detailing the life of a riboswitch. Biochim Biophys Acta 1789: 584-591.
12. Loh E, Memarpour F, Vaitkevicius K, Kallipolitis BH, Johansson J, et al. (2012) An unstructured 5′-coding region of the prfA mRNA is required for efficient translation. Nucleic Acids Res 40: 1818-1827.
13. De Lay N, Gottesman S, (2012) A complex network of small non-coding RNAs regulate motility in Escherichia coli. Mol Microbiol 86: 524-538.
14. Lioliou E, Sharma CM, Caldelari I, Helfer AC, Fechter P, et al. (2012) Global regulatory functions of the Staphylococcus aureus endoribonuclease III in gene expression. PLoS Genet 8: e1002782.
15. Bongrand C, Sansonetti PJ, Parsot C, (2012) Characterization of the promoter, MxiE box and 5′ UTR of genes controlled by the activity of the type III secretion apparatus in Shigella flexneri. PLoS One 7: e32862.
16. Berg L, Kucharova V, Bakke I, Valla S, Brautaset T, (2012) Exploring the 5′-UTR DNA region as a target for optimizing recombinant gene expression from the strong and inducible Pm promoter in Escherichia coli. J Biotechnol 158: 224-230.
17. Lale R, Berg L, Stüttgen F, Netzer R, Stafsnes M, et al. (2011) Continuous control of the flow in biochemical pathways through 5′ untranslated region sequence modifications in mRNA expressed from the broad-host-range promoter Pm. Appl Environ Microbiol 77: 2648-2655.
18. Aronson A, (2002) Sporulation and delta-endotoxin synthesis by Bacillus thuringiensis. Cell Mol Life Sci 59: 417-425.
19. Sanahuja G, Banakar R, Twyman RM, Capell T, Christou P, (2011) Bacillus thuringiensis: a century of research, development and commercial applications. Plant Biotechnol J 9: 283-300.
20. van Frankenhuyzen K, (2009) Insecticidal activity of Bacillus thuringiensis crystal proteins. J Invertebr Pathol 101: 1-16.
21. Higgins D, Dworkin J, (2012) Recent progress in Bacillus subtilis sporulation. FEMS Microbiol Rev 36: 131-148.
22. Abee T, Groot MN, Tempelaars M, Zwietering M, Moezelaar R, et al. (2011) Germination and outgrowth of spores of Bacillus cereus group members: diversity and role of germinant receptors. Food Microbiol 28: 199-208.
23. Paredes-Sabja D, Setlow P, Sarker MR, (2011) Germination of spores of Bacillales and Clostridiales species: mechanisms and proteins involved. Trends Microbiol 19: 85-94.
24. Ibrahim MA, Griko N, Junker M, Lee A, (2010) Bacillus thuringiensis: A genomics and proteomics perspective. Bioengineered Bugs 1: 31-50.
25. He J, Wang J, Yin W, Shao X, Zheng H, et al. (2011) Complete genome sequence of Bacillus thuringiensis subsp. chinensis strain CT-43. J Bacteriol 193: 3407-3408.
26. Nickerson KW, St Julian G, Bulla Jr LA, (1974) Physiology of sporeforming bacteria associated with insects: radiorespirometric survey of carbohydrate metabolism in the 12 serotypes of Bacillus thuringiensis. Appl Microbiol 28: 129-132.
27. Wang JP, Mei H, Zheng C, Qian HL, Cui C, et al. (2013) The metabolic regulation of sporulation and parasporal crystal formation in Bacillus thuringiensis revealed by transcriptomics and proteomics. Mol Cell Proteomics doi: 10.1074/mcp.M112.023986.
28. Yoder-Himes DR, Chain PS, Zhu Y, Wurtzel O, Rubin EM, et al. (2009) Mapping the Burkholderia cenocepacia niche response via high-throughput sequencing. Proc Natl Acad Sci USA 106: 3976-3981.
29. Sierro N, Makita Y, de Hoon MJL, Nakai K, (2008) DBTBS: a database of transcriptional regulation in Bacillus subtilis containing upstream intergenic conservation information. Nucleic Acids Res 36: D93-D96.
30. Kang JN, Kim YS, Wang Y, Choi H, Li MS, et al. (2005) Construction of a high-efficiency shuttle vector containing the minimal replication origin of Bacillus thuringiensis. Int J Indust Entomol 11: 125-127.
31. Agaisse H, Lereclus D, (1994) Expression in Bacillus subtilis of the Bacillus thuringiensis cryIIIA toxin gene is not dependent on a sporulation-specific sigma factor and is increased in a spo0A mutant. J Bacteriol 176: 4734-4741.
32. He J, Shao X, Zheng H, Li M, Wang J, et al. (2010) Complete genome sequence of Bacillus thuringiensis mutant strain BMB171. J Bacteriol 192: 4074-4075.
33. Miller JH (1972) Experiments in molecular genetics. NY: Cold Spring Harbor Laboratory. 352-355.
34. Mitschke J, Georg J, Scholz I, Sharma CM, Dienst D, et al. (2011) An experimentally anchored map of transcriptional start sites in the model cyanobacterium Synechocystis sp. PCC6803. Proc Natl Acad Sci USA 108: 2124-2129.
35. Gardner PP, Daub J, Tate JG, Nawrocki EP, Kolbe DL, et al. (2009) Rfam: updates to the RNA families database. Nucleic acids res 37: D136-D140.
36. Zuker M, (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 31: 3406-3415.
37. Peng DH, Luo Y, Guo S, Zeng H, Ju S, et al. (2009) Elaboration of an electroporation protocol for large plasmids and wild-type strains of Bacillus thuringiensis. J Appl Microbiol 106: 1849-1858.
38. Phadtare S, (2004) Recent developments in bacterial cold-shock response. Curr Issues Mol Biol 6: 125-136.
39. Sachs R, Max KE, Heinemann U, Balbach J, (2012) RNA single strands bind to a conserved surface of the major cold shock protein in crystals and solution. RNA 18: 65-76.
40. Terpe K, (2006) Overview of bacterial expression systems for heterologous protein production: from molecular and biochemical fundamentals to commercial systems. Appl Microbiol Biotechnol 72: 211-222.
41. Bron S, Bolhuis A, Tjalsma H, Holsappel S, Venema G, et al. (1998) Protein secretion and possible roles for multiple signal peptidases for precursor processing in bacilli. J Biotechnol 64: 3-13.
42. Wong SL, (1995) Advances in the use of Bacillus subtilis for the expression and secretion of heterologous proteins. Curr Opin Biotechnol 6: 517-522.
43. Zhong C, Peng D, Ye W, Chai L, Qi J, et al. (2011) Determination of plasmid copy number reveals the total plasmid DNA amount is greater than the chromosomal DNA amount in Bacillus thuringiensis YBT-1520. PLoS One 6: e16025.