Bacteriophage lambda repressor mediates the formation of a complex enhancer-like structure

Transcription

Volumn 4, Issue 5, 2013, Pages 201-205

  Cui, Lun ^a   Murchland, Iain ^a   Dodd, Ian B ^a   Shearwin, Keith E ^a  

^a UNIVERSITY OF ADELAIDE   (Australia)

Author keywords

Bacteriophage; CAP; CI repressor; DNA looping; Enhancer; Lambda

Indexed keywords

CYCLIC AMP BINDING PROTEIN; RNA POLYMERASE; PHAGE REPRESSOR PROTEINS; REPRESSOR PROTEIN; VIRUS PROTEIN;

AMINO TERMINAL SEQUENCE; ARTICLE; BACTERIOPHAGE LAMBDA; CARBOXY TERMINAL SEQUENCE; COMPLEX FORMATION; DNA SEQUENCE; ENHANCER REGION; FEEDBACK SYSTEM; MOLECULAR INTERACTION; MOLECULAR MODEL; NONHUMAN; PROMOTER REGION; PROTEIN DNA BINDING; PROTEIN PROTEIN INTERACTION; THERMODYNAMICS; TRANSCRIPTION REGULATION; BIOLOGICAL MODEL; CONFORMATION; ENTEROBACTERIA PHAGE LAMBDA; GENETICS; METABOLISM;

ENTEROBACTERIA PHAGE LAMBDA;

BACTERIOPHAGE LAMBDA; ENHANCER ELEMENTS, GENETIC; MODELS, BIOLOGICAL; NUCLEIC ACID CONFORMATION; REPRESSOR PROTEINS; VIRAL REGULATORY AND ACCESSORY PROTEINS;

EID: 84884616952     PISSN: 21541264     EISSN: 21541272     Source Type: Journal    
DOI: 10.4161/trns.26101     Document Type: Article

References (30)

1. Bulger M, Groudine M. Functional and mechanistic diversity of distal transcription enhancers. Cell 2011; 144:327-39; PMID:21295696; http://dx.doi.org/10.1016/j.cell.2011.01.024
2. Browning DF, Busby SJ. The regulation of bacterial transcription initiation. Nat Rev Microbiol 2004; 2:57-65; PMID:15035009; http://dx.doi.org/10.1038/nrmicro787
3. Gama-Castro S, Salgado H, Peralta-Gil M, Santos-Zavaleta A, Muñiz-Rascado L, Solano-Lira H, Jiménez-Jacinto V, Weiss V, García-Sotelo JS, López-Fuentes A, et al. RegulonDB version 7.0: tran-scriptional regulation of Escherichia coli K-12 integrated within genetic sensory response units (Gensor Units). Nucleic Acids Res 2011; 39:D98-105; PMID:21051347; http://dx.doi.org/10.1093/nar/gkqlll0
4. Ptashne M, Gann A. Genes & Signals. Cold Spring Harbor, New York: Cold Spring Harbor Laboratory Press, 2002.
5. Ushida C, Aiba H. Helical phase dependent action of CRP: effect of the distance between the CRP site and the -35 region on promoter activity. Nucleic Acids Res 1990; 18:6325-30; PMID:2173826; http://dx.doi.org/10.1093/nar/18.21.6325
6. Estrem ST, Ross W, Gaal T, Chen ZW, Niu W, Ebright RH, Gourse RL. Bacterial promoter architecture: subsite structure of UP elements and interactions with the carboxy-terminal domain of the RNA polymerase alpha subunit. Genes Dev 1999; 13:2134-47; PMID:10465790; http://dx.doi.org/10.1101/gad.l3.16.2134
7. Meng W, Belyaeva T, Savery NJ, Busby SJ, Ross WE, Gaal T, Gourse RL, Thomas MS. UP element-dependent transcription at the Escherichia coli rrnB PI promoter: positional requirements and role of the RNA polymerase alpha subunit linker. Nucleic Acids Res 2001; 29:4166-78; PMID:11600705; http://dx.doi.org/10.1093/nar/29.20.4l66
8. Rappas M, Bose D, Zhang X. Bacterial enhancer-binding proteins: unlocking sigma54-dependent gene transcription. Curr Opin Struct Biol 2007; 17:110-6; PMID:17157497; http://dx.doi.org/10.1016/).sbi.2006.11.002
9. Révet B, von Wilcken-Bergmann B, Bessert H, Barker A, Müller-Hill B. Four dimers of lambda repressor bound to two suitably spaced pairs of lambda operators form octamers and DNA loops over large distances. Curr Biol 1999; 9:151-4; PMIDT0021390; http://dx.doi.org/10.1016/S0960-9822(99)80069-4
10. Bell CE, Lewis M. Crystal structure of the lambda repressor C-terminal domain octamer. J Mol Biol 2001; 314:1127-36; PMIDT1743728; http://dx.doi.org/10.1006/jmbi.2000.5196
11. Dodd IB, Shearwin KE, Perkins AJ, Burr T, Hochschild A, Egan JB. Cooperativity in long-range gene regulation by the lambda CI repressor. Genes Dev 2004; 18:344-54; PMID:14871931; http://dx.doi.org/10.1101/gad.1167904
12. Svenningsen SL, Costantino N, Court DL, Adhya S. On the role of Cro in lambda prophage induction. Proc Nati Acad Sci U S A 2005; 102:4465-9; PMID:15728734; http://dx.doi.org/10.1073/pnas.0409839102
13. Dodd IB, Perkins AJ, Tsemitsidis D, Egan JB. Octamerization of lambda CI repressor is needed for effective repression of P(RM) and efficient switching from lysogeny. Genes Dev 2001; 15:3013-22; PMID:11711436; http://dx.doi.org/10.1101/gad.937301
14. Zurla C, Manzo C, Dunlap D, Lewis DE, Adhya S, Finzi L. Direct demonstration and quantification of long-range DNA looping by the lambda bacterio-phage repressor. Nucleic Acids Res 2009; 37:2789-95; PMID:19276206; http://dx.doi.org/10.1093/nar/gkpl34
15. Lewis D, Le P, Zurla C, Finzi L, Adhya S. Multilevel autoregulation of λ. repressor protein CI by DNA looping in vitro. Proc Nati Acad Sci USA 2011; 108:14807-12; PMID:21873207; http://dx.doi.org/10.1073/pnas.H11221108
16. Cui L, Murchland I, Shearwin KE, Dodd IB. Enhancer-like long-range transcriptional activation by λ Cl-mediated DNA looping. Proc Nati Acad Sci USA 2013; 110:2922-7; PMID:23382214; http://dx.doi.org/10.1073/pnas.1221322110
17. Michalowski CB, Little JW. Role of cis-Acting Sites in Stimulation of the Phage λ. PRM Promoter by CI-Mediated Looping. J Bacteriol 2013; 195:3401-11; PMID:23708136; http://dx.doi.org/10.1128/JB.02148-12
18. Li M, McClure WR, Susskind MM. Changing the mechanism of transcriptional activation by phage lambda repressor. Proc Nati Acad Sci USA 1997; 94:3691-6; PMID:9108039; http://dx.doi.org/10.1073/pnas.94.8.3691
19. Jain D, Nickels BE, Sun L, Hochschild A, Darst SA. Structure of a ternary transcription activation complex. Mol Cell 2004; 13:45-53; PMID:14731393; http://dx.doi.org/10.1016/S1097-2765(03)00483-0
20. Kedzierska B, Szambowska A, Herman-Antosiewicz A, Lee DJ, Busby SJ, Wegrzyn G, Thomas MS. The C-terminal domain of the Escherichia coli RNA polymerase alpha subunit plays a role in the Cl-dependent activation of the bacteriophage lambda PM promoter. Nucleic Acids Res 2007; 35:2311-20; PMID:17389649; http://dx.doi.org/10.1093/nar/gkml23
21. Anderson LM, Yang H. DNA looping can enhance lysogenic CI transcription in phage lambda. Proc Nati AcadSciUSA2008; 105:5827-32; PMIDT8391225; http://dx.doi.org/10.1073/pnas.0705570105
22. Little JW, Michalowski CB. Stability and instability in the lysogenic state of phage lambda. J Bacteriol 2010; 192:6064-76; PMID:20870769; http://dx.doi.org/10.1128/JB.00726-10
23. Ackers GK, Johnson AD, Shea MA. Quantitative model for gene regulation by lambda phage repressor. Proc Nati Acad Sci U S A 1982; 79:1129-33; PMID:6461856; http://dx.doi.org/10.1073/pnas.79-4.1129
24. Shea MA, Ackers GK. The OR control system of bacteriophage lambda. A physical-chemical model for gene regulation. J Mol Biol 1985; 181:211-30; PMID:3157005; http://dx.doi.org/10.1016/0022-2836(85)90086-5
25. Dodd IB, Shearwin KE, Perkins AJ, Burr T, Hochschild A, Egan JB. Cooperativity in long-range gene regulation by the lambda CI repressor. Genes Dev 2004; 18:344-54; PMID:14871931; http://dx.doi.org/10.1101/gad.1167904
26. Johnson AD, Meyer BJ, Ptashne M. Interactions between DNA-bound repressors govern regulation by the lambda phage repressor. Proc Nati Acad Sci U S A 1979; 76:5061-5; PMID:159452; http://dx.doi.org/10.1073/pnas.76.10.5061
27. Ptashne M. A Genetic Switch. Phage Lambda rev-isted. New York: Cold Spring Harbor Laboratory Press, 2004.
28. Hensel Z, Weng X, Lagda AC, Xiao J. Transcription-Factor-Mediated DNA Looping Probed by High-Resolution, Single-Molecule Imaging in Live E. coli Cells. PLoS Biol 2013; 11:el001591; PMID:23853547; http://dx.doi.org/10.1371/journal.pbio.1001591
29. Giladi H, Gottesman M, Oppenheim AB. Integration host factor stimulates the phage lambda pL promoter. J Mol Biol 1990; 213:109-21; PMID:2140136; http://dx.doi.org/10.1016/S0022-2836(05)80124-X
30. Lawson CL, Swigon D, Murakami KS, Darst SA, Berman HM, Ebright RH. Catabolite activator protein: DNA binding and transcription activation. Curr Opin Struct Biol 2004; 14:10-20; PMID:15102444; http://dx.doi.Org/10.1016/j.sbi.2004.01.012