Transcription activation in bacteria: ancient and modern

References

1. Woods DD. Marjory Stephenson, 1885-1948. Biochem J 1950; 46:562–577[PubMed]
   [Google Scholar]
2. Ullmann A. Origins of Molecular Biology: A Tribute to Jacques Monod Herndon, VA, USA: ASM Press; 2004
   [Google Scholar]
3. Santos-Zavaleta A, Sánchez-Pérez M, Salgado H, Velázquez-Ramírez DA, Gama-Castro S et al. A unified resource for transcriptional regulation in Escherichia coli K-12 incorporating high-throughput-generated binding data into RegulonDB version 10.0. BMC Biol 2018; 16:91 [View Article][PubMed]
   [Google Scholar]
4. Muller-Hill B. The Lac Operon Berlin: Walter de Gruyter & Co; 1996
   [Google Scholar]
5. Kolb A, Busby S, Buc H, Garges S, Adhya S. Transcriptional regulation by cAMP and its receptor protein. Annu Rev Biochem 1993; 62:749–797 [View Article][PubMed]
   [Google Scholar]
6. Feklístov A, Sharon BD, Darst SA, Gross CA. Bacterial sigma factors: a historical, structural, and genomic perspective. Annu Rev Microbiol 2014; 68:357–376 [View Article][PubMed]
   [Google Scholar]
7. Feklistov A, Darst SA. Structural basis for promoter-10 element recognition by the bacterial RNA polymerase σ subunit. Cell 2011; 147:1257–1269 [View Article][PubMed]
   [Google Scholar]
8. Zhang Y, Feng Y, Chatterjee S, Tuske S, Ho MX et al. Structural basis of transcription initiation. Science 2012; 338:1076–1080 [View Article][PubMed]
   [Google Scholar]
9. Zuo Y, Steitz TA. Crystal structures of the E. coli transcription initiation complexes with a complete bubble. Mol Cell 2015; 58:534–540 [View Article][PubMed]
   [Google Scholar]
10. Rhodius VA, Busby SJ. Positive activation of gene expression. Curr Opin Microbiol 1998; 1:152–159 [View Article][PubMed]
    [Google Scholar]
11. de Crombrugghe B, Busby S, Buc H. Cyclic AMP receptor protein: role in transcription activation. Science 1984; 224:831–838 [View Article][PubMed]
    [Google Scholar]
12. Schultz SC, Shields GC, Steitz TA. Crystal structure of a CAP-DNA complex: the DNA is bent by 90 degrees. Science 1991; 253:1001–1007 [View Article][PubMed]
    [Google Scholar]
13. Busby S, Ebright RH. Transcription activation by catabolite activator protein (CAP). J Mol Biol 1999; 293:199–213 [View Article][PubMed]
    [Google Scholar]
14. Benoff B, Yang H, Lawson CL, Parkinson G, Liu J et al. Structural basis of transcription activation: the CAP-alpha CTD-DNA complex. Science 2002; 297:1562–1566 [View Article][PubMed]
    [Google Scholar]
15. Lawson CL, Swigon D, Murakami KS, Darst SA, Berman HM et al. Catabolite activator protein: DNA binding and transcription activation. Curr Opin Struct Biol 2004; 14:10–20 [View Article][PubMed]
    [Google Scholar]
16. Liu B, Hong C, Huang RK, Yu Z, Steitz TA. Structural basis of bacterial transcription activation. Science 2017; 358:947–951 [View Article][PubMed]
    [Google Scholar]
17. Hudson BP, Quispe J, Lara-González S, Kim Y, Berman HM et al. Three-dimensional EM structure of an intact activator-dependent transcription initiation complex. Proc Natl Acad Sci USA 2009; 106:19830–19835 [View Article][PubMed]
    [Google Scholar]
18. Feng Y, Zhang Y, Ebright RH. Structural basis of transcription activation. Science 2016; 352:1330–1333 [View Article][PubMed]
    [Google Scholar]
19. Lee DJ, Minchin SD, Busby SJ. Activating transcription in bacteria. Annu Rev Microbiol 2012; 66:125–152 [View Article][PubMed]
    [Google Scholar]
20. Browning D, Lee D, Green J, Busby S. Secrets of bacterial transcription initiation taught by the Escherichia coli FNR protein. Signals, Switches, Regulons & Cascades: Control of Bacterial Gene Expression vol. 61 SGM Symposium; 2002 pp. 127–142
    [Google Scholar]
21. Barnard A, Wolfe A, Busby S. Regulation at complex bacterial promoters: how bacteria use different promoter organizations to produce different regulatory outcomes. Curr Opin Microbiol 2004; 7:102–108 [View Article][PubMed]
    [Google Scholar]
22. H-C W, Tyson K, Cole J, Busby S. Regulation of the E. coli nir operon by two transcription factors: a new mechanism to account for co-dependence on two activators. Mol Microbiol 1998; 27:493–505
    [Google Scholar]
23. Browning DF, Cole JA, Busby SJ. Suppression of FNR-dependent transcription activation at the Escherichia coli nir promoter by Fis, IHF and H-NS: modulation of transcription initiation by a complex nucleo-protein assembly. Mol Microbiol 2000; 37:1258–1269 [View Article][PubMed]
    [Google Scholar]
24. Browning DF, Grainger DC, Busby SJ. Effects of nucleoid-associated proteins on bacterial chromosome structure and gene expression. Curr Opin Microbiol 2010; 13:773–780 [View Article][PubMed]
    [Google Scholar]
25. Dillon SC, Dorman CJ. Bacterial nucleoid-associated proteins, nucleoid structure and gene expression. Nat Rev Microbiol 2010; 8:185–195 [View Article][PubMed]
    [Google Scholar]
26. Browning DF, Cole JA, Busby SJ. Transcription activation by remodelling of a nucleoprotein assembly: the role of NarL at the FNR-dependent Escherichia coli nir promoter. Mol Microbiol 2004; 53:203–215 [View Article][PubMed]
    [Google Scholar]
27. Browning DF, Cole JA, Busby SJ. Regulation by nucleoid-associated proteins at the Escherichia coli nir operon promoter. J Bacteriol 2008; 190:7258–7267 [View Article][PubMed]
    [Google Scholar]
28. Browning DF, Busby SJ. Local and global regulation of transcription initiation in bacteria. Nat Rev Microbiol 2016; 14:638–650 [View Article][PubMed]
    [Google Scholar]
29. Buck M, Gallegos MT, Studholme DJ, Guo Y, Gralla JD. The bacterial enhancer-dependent sigma(54) (sigma(N)) transcription factor. J Bacteriol 2000; 182:4129–4136 [View Article][PubMed]
    [Google Scholar]
30. Yang Y, Darbari VC, Zhang N, Lu D, Glyde R et al. Transcription. Structures of the RNA polymerase-σ54 reveal new and conserved regulatory strategies. Science 2015; 349:882–885 [View Article][PubMed]
    [Google Scholar]
31. Campbell EA, Kamath S, Rajashankar KR, Wu M, Darst SA. Crystal structure of Aquifex aeolicus σ(N) bound to promoter DNA and the structure of σ(N)-holoenzyme. Proc Natl Acad Sci USA 2017; 114:1805–1814
    [Google Scholar]
32. Glyde R, Ye F, Darbari VC, Zhang N, Buck M et al. Structures of RNA polymerase closed and intermediate complexes reveal mechanisms of DNA opening and transcription initiation. Mol Cell 2017; 67:106–116 [View Article][PubMed]
    [Google Scholar]
33. Glyde R, Ye F, Jovanovic M, Kotta-Loizou I, Buck M et al. Structures of bacterial RNA polymerase complexes reveal the mechanism of DNA loading and transcription initiation. Mol Cell 2018; 70:1111–1120 [View Article][PubMed]
    [Google Scholar]
34. Visweswariah SS, Busby SJ. Evolution of bacterial transcription factors: how proteins take on new tasks, but do not always stop doing the old ones. Trends Microbiol 2015; 23:463–467 [View Article][PubMed]
    [Google Scholar]
35. Grainger DC, Hurd D, Harrison M, Holdstock J, Busby SJ. Studies of the distribution of Escherichia coli cAMP-receptor protein and RNA polymerase along the E. coli chromosome. Proc Natl Acad Sci USA 2005; 102:17693–17698 [View Article][PubMed]
    [Google Scholar]
36. Shimada T, Ishihama A, Busby SJ, Grainger DC. The Escherichia coli RutR transcription factor binds at targets within genes as well as intergenic regions. Nucleic Acids Res 2008; 36:3950–3955 [View Article][PubMed]
    [Google Scholar]
37. Fouqueau T, Blombach F, Werner F. Evolutionary origins of two-barrel RNA polymerases and site-specific transcription initiation. Annu Rev Microbiol 2017; 71:331–348 [View Article][PubMed]
    [Google Scholar]