Corrigendum: ScbR- and ScbR2- mediated signal transduction networks coordinate complex physiological responses in Streptomyces coelicolor (Scientific Reports (2016) 5 (14831) DOI: 10.1038/srep14831);ScbR-and ScbR2-mediated signal transduction networks coordinate complex physiological responses in Streptomyces coelicolor

Scientific Reports

Volumn 5, Issue , 2015, Pages

  Li, Xiao ^a   Wang, Juan ^a   Li, Shanshan ^a   Ji, Junjie ^a   Wang, Weishan ^a   Yang, Keqian ^a  

^a INSTITUTE OF MICROBIOLOGY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ANTIINFECTIVE AGENT; BACTERIAL DNA; BACTERIAL PROTEIN; DNA BINDING PROTEIN; GAMMA BUTYROLACTONE; SCBR PROTEIN, STREPTOMYCES COELICOLOR;

CHROMATIN IMMUNOPRECIPITATION; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETICS; METABOLISM; PHYSIOLOGY; PROMOTER REGION; SIGNAL TRANSDUCTION; STREPTOMYCES COELICOLOR; WESTERN BLOTTING;

4-BUTYROLACTONE; ANTI-BACTERIAL AGENTS; BACTERIAL PROTEINS; BLOTTING, WESTERN; CHROMATIN IMMUNOPRECIPITATION; DNA, BACTERIAL; DNA-BINDING PROTEINS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, BACTERIAL; PROMOTER REGIONS, GENETIC; SIGNAL TRANSDUCTION; STREPTOMYCES COELICOLOR;

EID: 84943279502     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep21574     Document Type: Erratum

References (56)

1. Zhuang, X. L., Gao, J., Ma, A. Z., Fu, S. L., Zhuang, G. Q. Bioactive Molecules in Soil Ecosystems: Masters of the Underground. International Journal of Molecular Sciences 14, 8841-8868, doi: 10.3390/Ijms14058841 (2013).
2. Rutherford, S. T., Bassler, B. L. Bacterial Quorum Sensing: Its Role in Virulence and Possibilities for Its Control. Cold Spring Harbor Perspectives in Medicine 2, a012427, doi: 10.1101/cshperspect.a012427 (2012).
3. Horinouchi, S. A microbial hormone, A-factor, as a master switch for morphological differentiation and secondary metabolism in Streptomyces griseus. Front Biosci 7, d2045-2057 (2002).
4. Li, Y.-H., Tian, X. Quorum Sensing and Bacterial Social Interactions in Biofilms. Sensors (Basel, Switzerland) 12, 2519-2538, doi: 10.3390/s120302519 (2012).
5. Takano, E., Chakraburtty, R., Nihira, T., Yamada, Y., Calasso, M. A complex role for the gamma-butyrolactone SCB1 in regulating antibiotic production in Streptomyces coelicolor A3(2). Mol Microbiol 41, 1015-1028 (2001).
6. Wang, W. et al. Angucyclines as signals modulate the behaviors of Streptomyces coelicolor. Proceedings of the National Academy of Sciences of the United States of America 111, 5688-5693, doi: 10.1073/pnas.1324253111 (2014).
7. Ohnishi, Y., Yamazaki, H., Kato, J. Y., Tomono, A., Horinouchi, S. AdpA, a central transcriptional regulator in the A-factor regulatory cascade that leads to morphological development and secondary metabolism in Streptomyces griseus. Bioscience, biotechnology, and biochemistry 69, 431-439, doi: 10.1271/bbb.69.431 (2005).
8. Gomez-Escribano, J. P. et al. Structure and biosynthesis of the unusual polyketide alkaloid coelimycin P1, a metabolic product of the cpk gene cluster of Streptomyces coelicolor M145. Chemical Science 3, 2716-2720, doi: 10.1039/C2SC20410J (2012).
9. Takano, E. et al. A bacterial hormone (the SCB1) directly controls the expression of a pathway-specific regulatory gene in the cryptic type I polyketide biosynthetic gene cluster of Streptomyces coelicolor. Mol Microbiol 56, 465-479, doi: 10.1111/j.1365-2958.2005.04543.x (2005).
10. Xu, G. et al. "Pseudo" gamma-butyrolactone receptors respond to antibiotic signals to coordinate antibiotic biosynthesis. J Biol Chem 285, 27440-27448, doi: 10.1074/jbc.M110.143081 (2010).
11. Wang, J. et al. A novel role of 'pseudo'gamma-butyrolactone receptors in controlling gamma-butyrolactone biosynthesis in Streptomyces. Mol Microbiol 82, 236-250, doi: 10.1111/j.1365-2958.2011.07811.x (2011).
12. Bunet, R. et al. Characterization and manipulation of the pathway-specific late regulator AlpW reveals Streptomyces ambofaciens as a new producer of Kinamycins. J Bacteriol 193, 1142-1153, doi: 10.1128/jb.01269-10 (2011).
13. Salehi-Najafabadi, Z. et al. The gamma-butyrolactone receptors BulR1 and BulR2 of Streptomyces tsukubaensis: tacrolimus (FK506) and butyrolactone synthetases production control. Appl Microbiol Biotechnol 98, 4919-4936, doi: 10.1007/s00253-014-5595-9 (2014).
14. Gottelt, M., Kol, S., Gomez-Escribano, J. P., Bibb, M., Takano, E. Deletion of a regulatory gene within the cpk gene cluster reveals novel antibacterial activity in Streptomyces coelicolor A3(2). Microbiology 156, 2343-2353, doi: 10.1099/mic.0.038281-0 (2010).
15. Zhang, Y. et al. Model-based analysis of ChIP-Seq (MACS). Genome biology 9, R137, doi: 10.1186/gb-2008-9-9-r137 (2008).
16. Bailey, T. L. et al. MEME SUITE: tools for motif discovery and searching. Nucleic acids research 37, W202-208, doi: 10.1093/nar/gkp335 (2009).
17. Allenby, N. E., Laing, E., Bucca, G., Kierzek, A. M., Smith, C. P. Diverse control of metabolism and other cellular processes in Streptomyces coelicolor by the PhoP transcription factor: genome-wide identification of in vivo targets. Nucleic acids research 40, 9543-9556, doi: 10.1093/nar/gks766 (2012).
18. Li, M., Zhang, Y., Zhang, L., Yang, X., Jiang, X. Exploring the electron transfer pathway in the oxidation of avermectin by CYP107Z13 in Streptomyces ahygroscopicus ZB01. PLoS One 9, e98916, doi: 10.1371/journal.pone.0098916 (2014).
19. Lee, P. C., Umeyama, T., Horinouchi, S. afsS is a target of AfsR, a transcriptional factor with ATPase activity that globally controls secondary metabolism in Streptomyces coelicolor A3(2). Mol Microbiol 43, 1413-1430 (2002).
20. Liu, G., Chater, K. F., Chandra, G., Niu, G., Tan, H. Molecular regulation of antibiotic biosynthesis in streptomyces. Microbiology and molecular biology reviews: MMBR 77, 112-143, doi: 10.1128/MMBR.00054-12 (2013).
21. Hempel, A. M. et al. The Ser/Thr protein kinase AfsK regulates polar growth and hyphal branching in the filamentous bacteria Streptomyces. Proceedings of the National Academy of Sciences of the United States of America 109, E2371-E2379, doi: 10.1073/pnas.1207409109 (2012).
22. Onaka, H., Nakagawa, T., Horinouchi, S. Involvement of two A-factor receptor homologues in Streptomyces coelicolor A3(2) in the regulation of secondary metabolism and morphogenesis. Mol Microbiol 28, 743-753 (1998).
23. Swiatek-Polatynska, M. A. et al. Genome-Wide Analysis of In Vivo Binding of the Master Regulator DasR in Streptomyces coelicolor Identifies Novel Non-Canonical Targets. PLoS One 10, e0122479, doi: 10.1371/journal.pone.0122479 (2015).
24. Cerdeno, A. M., Bibb, M. J., Challis, G. L. Analysis of the prodiginine biosynthesis gene cluster of Streptomyces coelicolor A3(2): new mechanisms for chain initiation and termination in modular multienzymes. Chem Biol 8, 817-829 (2001).
25. Uguru, G. C. et al. Transcriptional activation of the pathway-specific regulator of the actinorhodin biosynthetic genes in Streptomyces coelicolor. Mol Microbiol 58, 131-150, doi: 10.1111/j.1365-2958.2005.04817.x (2005).
26. McKenzie, N. L., Nodwell, J. R. Phosphorylated AbsA2 negatively regulates antibiotic production in Streptomyces coelicolor through interactions with pathway-specific regulatory gene promoters. J Bacteriol 189, 5284-5292, doi: 10.1128/jb.00305-07 (2007).
27. Fischer, M., Alderson, J., van Keulen, G., White, J., Sawers, R. G. The obligate aerobe Streptomyces coelicolor A3(2) synthesizes three active respiratory nitrate reductases. Microbiology 156, 3166-3179, doi: 10.1099/mic.0.042572-0 (2010).
28. Rigali, S. et al. Feast or famine: the global regulator DasR links nutrient stress to antibiotic production by Streptomyces. EMBO Reports 9, 670-675, doi: 10.1038/embor.2008.83 (2008).
29. Chater, K. F., Biro, S., Lee, K. J., Palmer, T., Schrempf, H. The complex extracellular biology of Streptomyces. FEMS microbiology reviews 34, 171-198, doi: 10.1111/j.1574-6976.2009.00206.x (2010).
30. Santos-Beneit, F., Rodriguez-Garcia, A., Martin, J. F. Overlapping binding of PhoP and AfsR to the promoter region of glnR in Streptomyces coelicolor. Microbiological Research 167, 532-535, http://dx.doi.org/10.1016/j.micres.2012.02.010 (2012).
31. Santos-Beneit, F., Rodriguez-Garcia, A., Sola-Landa, A., Martin, J. F. Cross-talk between two global regulators in Streptomyces: PhoP and AfsR interact in the control of afsS, pstS and phoRP transcription. Mol Microbiol 72, 53-68, doi: 10.1111/j.1365-2958.2009.06624.x (2009).
32. Rodriguez-Garcia, A., Sola-Landa, A., Apel, K., Santos-Beneit, F., Martin, J. F. Phosphate control over nitrogen metabolism in Streptomyces coelicolor: direct and indirect negative control of glnR, glnA, glnII and amtB expression by the response regulator PhoP. Nucleic Acids Research 37, 3230-3242, doi: 10.1093/nar/gkp162 (2009).
33. Davies, J., Spiegelman, G. B., Yim, G. The world of subinhibitory antibiotic concentrations. Curr Opin Microbiol 9, 445-453, doi: 10.1016/j.mib.2006.08.006 (2006).
34. Hosaka, T., Xu, J., Ochi, K. Increased expression of ribosome recycling factor is responsible for the enhanced protein synthesis during the late growth phase in an antibiotic-overproducing Streptomyces coelicolor ribosomal rpsL mutant. Mol Microbiol 61, 883-897, doi: 10.1111/j.1365-2958.2006.05285.x (2006).
35. Lian, W. et al. Genome-wide transcriptome analysis reveals that a pleiotropic antibiotic regulator, AfsS, modulates nutritional stress response in Streptomyces coelicolor A3(2). BMC genomics 9, 56, doi: 10.1186/1471-2164-9-56 (2008).
36. Paget, M. S., Kang, J. G., Roe, J. H., Buttner, M. J. Sigma, R an RNA polymerase sigma factor that modulates expression of the thioredoxin system in response to oxidative stress in Streptomyces coelicolor A3(2). The EMBO journal 17, 5776-5782, doi: 10.1093/emboj/17.19.5776 (1998).
37. Kallifidas, D., Thomas, D., Doughty, P., Paget, M. S. The sigmaR regulon of Streptomyces coelicolor A32 reveals a key role in protein quality control during disulphide stress. Microbiology 156, 1661-1672, doi: 10.1099/mic.0.037804-0 (2010).
38. Yang, Y. H. et al. NdgR, an IclR-like regulator involved in amino-acid-dependent growth, quorum sensing, and antibiotic production in Streptomyces coelicolor. Appl Microbiol Biotechnol 82, 501-511, doi: 10.1007/s00253-008-1802-x (2009).
39. Wang, W. et al. An engineered strong promoter for streptomycetes. Appl Environ Microbiol 79, 4484-4492, doi: 10.1128/AEM.00985-13 (2013).
40. Paget, M. S. B., Molle, V., Cohen, G., Aharonowitz, Y., Buttner, M. J. Defining the disulphide stress response in Streptomyces coelicolor A3(2): identification of the ? R regulon. Molecular Microbiology 42, 1007-1020, doi: 10.1046/j.1365-2958.2001.02675.x (2001).
41. Homerova, D., Sevcikova, B., Rezuchova, B., Kormanec, J. Regulation of an alternative sigma factor sigmaI by a partner switching mechanism with an anti-sigma factor PrsI and an anti-anti-sigma factor ArsI in Streptomyces coelicolor A3(2). Gene 492, 71-80, doi: 10.1016/j.gene.2011.11.011 (2012).
42. Potuckova, L. et al. A new RNA polymerase sigma factor, sigma F, is required for the late stages of morphological differentiation in Streptomyces spp. Mol Microbiol 17, 37-48 (1995).
43. Kim, E. S., Song, J. Y., Kim, D. W., Chater, K. F., Lee, K. J. A possible extended family of regulators of sigma factor activity in Streptomyces coelicolor. J Bacteriol 190, 7559-7566, doi: 10.1128/jb.00470-08 (2008).
44. Nothaft, H. et al. The permease gene nagE2 is the key to N-acetylglucosamine sensing and utilization in Streptomyces coelicolor and is subject to multi-level control. Mol Microbiol 75, 1133-1144, doi: 10.1111/j.1365-2958.2009.07020.x (2010).
45. Swiatek, M. A. et al. The ROK family regulator Rok7B7 pleiotropically affects xylose utilization, carbon catabolite repression, and antibiotic production in streptomyces coelicolor. J Bacteriol 195, 1236-1248, doi: 10.1128/jb.02191-12 (2013).
46. van Wezel, G. P., McDowall, K. J. The regulation of the secondary metabolism of Streptomyces: new links and experimental advances. Natural product reports 28, 1311-1333, doi: 10.1039/c1np00003a (2011).
47. Shen-Orr, S. S., Milo, R., Mangan, S., Alon, U. Network motifs in the transcriptional regulation network of Escherichia coli. Nature genetics 31, 64-68, doi: 10.1038/ng881 (2002).
48. Park, S. S. et al. Mass spectrometric screening of transcriptional regulators involved in antibiotic biosynthesis in Streptomyces coelicolor A3(2). Journal of industrial microbiology & biotechnology 36, 1073-1083, doi: 10.1007/s10295-009-0591-2 (2009).
49. Mangan, S., Itzkovitz, S., Zaslaver, A., Alon, U. The incoherent feed-forward loop accelerates the response-time of the gal system of Escherichia coli. Journal of molecular biology 356, 1073-1081, doi: 10.1016/j.jmb.2005.12.003 (2006).
50. Mangan, S., Zaslaver, A., Alon, U. The coherent feedforward loop serves as a sign-sensitive delay element in transcription networks. Journal of molecular biology 334, 197-204 (2003).
51. Li, X. et al. Binding of a biosynthetic intermediate to AtrA modulates the production of lidamycin by Streptomyces globisporus. Mol Microbiol, doi: 10.1111/mmi.13004 (2015).
52. Ma, W., Trusina, A., El-Samad, H., Lim, W. A., Tang, C. Defining network topologies that can achieve biochemical adaptation. Cell 138, 760-773, doi: 10.1016/j.cell.2009.06.013 (2009).
53. Roselius, L. et al. Modelling and analysis of a gene-regulatory feed-forward loop with basal expression of the second regulator. Journal of theoretical biology 363, 290-299, doi: 10.1016/j.jtbi.2014.08.043 (2014).
54. Martin, J. F. et al. Cross-talk of global nutritional regulators in the control of primary and secondary metabolism in Streptomyces. Microbial biotechnology 4, 165-174, doi: 10.1111/j.1751-7915.2010.00235.x (2011).
55. Stothard, P., Wishart, D. S. Circular genome visualization and exploration using CGView. Bioinformatics 21, 537-539, doi: 10.1093/bioinformatics/bti054 (2005).
56. Rudolph, M. M., Vockenhuber, M. P., Suess, B. Synthetic riboswitches for the conditional control of gene expression in Streptomyces coelicolor. Microbiology 159, 1416-1422, doi: 10.1099/mic.0.067322-0 (2013).