title: Enhancer-like long-range transcriptional activation by λ CI-mediated DNA looping.
abstract: How distant enhancer elements regulate the assembly of a transcription complex at a promoter remains poorly understood. Here, we use long-range gene regulation by the bacteriophage λ CI protein as a powerful system to examine this process in vivo. A 2.3-kb DNA loop, formed by CI bridging its binding sites at OR and OL, is known already to enhance repression at the lysogenic promoter PRM, located at OR. Here, we show that CI looping also activates PRM by allowing the C-terminal domain of the α subunit of the RNA polymerase bound at PRM to contact a DNA site adjacent to the distal CI sites at OL. Our results establish OL as a multifaceted enhancer element, able to activate transcription from long distances independently of orientation and position. We develop a physicochemical model of our in vivo data and use it to show that the observed activation is consistent with a simple recruitment mechanism, where the α-C-terminal domain to DNA contact need only provide ∼2.7 kcal/mol of additional binding energy for RNA polymerase. Structural modeling of this complete enhancer-promoter complex reveals how the contact is achieved and regulated, and suggests that distal enhancer elements, once appropriately positioned at the promoter, can function in essentially the same way as proximal promoter elements.
authors: School of Molecular and Biomedical Science (Biochemistry),  University of Adelaide, Adelaide, SA 5005,  Australia.
authors: Lun
authors: L
authors: Cui
authors: Iain
authors: I
authors: Murchland
authors: Keith E
authors: KE
authors: Shearwin
authors: Ian B
authors: IB
authors: Dodd
mesh_terms: D010582:Bacteriophage lambda / Q000235:genetics*; D004279:DNA, Viral / Q000235:genetics*; D004742:Enhancer Elements, Genetic; D008958:Models, Molecular; D015533:Transcriptional Activation
chemical_list: D004279:DNA, Viral
references: Curr Opin Struct Biol. 2007 Feb;17(1):110-6
references: 17157497
references: Annu Rev Cell Biol. 1988;4:127-53
references: 2848550
references: Curr Opin Genet Dev. 2012 Apr;22(2):79-85
references: 22169023
references: J Bacteriol. 2010 Nov;192(22):6064-76
references: 20870769
references: Mol Cell. 2004 Jan 16;13(1):45-53
references: 14731393
references: Proc Natl Acad Sci U S A. 2011 Sep 6;108(36):14807-12
references: 21873207
references: Nucleic Acids Res. 2007;35(7):2311-20
references: 17389649
references: Proc Natl Acad Sci U S A. 1998 Sep 15;95(19):11163-8
references: 9736707
references: Genes Dev. 2004 Feb 1;18(3):344-54
references: 14871931
references: Cell. 2000 Jun 23;101(7):801-11
references: 10892750
references: Nat Rev Microbiol. 2004 Jan;2(1):57-65
references: 15035009
references: Genes Dev. 2001 Nov 15;15(22):3013-22
references: 11711436
references: Acta Crystallogr D Biol Crystallogr. 1998 Sep 1;54(Pt 5):905-21
references: 9757107
references: Nucleic Acids Res. 2001 Oct 15;29(20):4166-78
references: 11600705
references: Mol Microbiol. 1998 Oct;30(2):443-51
references: 9791187
references: Methods Enzymol. 2011;487:545-74
references: 21187238
references: Genetics. 2011 Nov;189(3):705-36
references: 22084422
references: Cell. 2012 Jun 8;149(6):1233-44
references: 22682246
references: Proc Natl Acad Sci U S A. 2008 Apr 15;105(15):5827-32
references: 18391225
references: Science. 2002 May 17;296(5571):1285-90
references: 12016307
references: Nature. 2008 Apr 24;452(7190):1022-5
references: 18432246
references: Nucleic Acids Res. 2009 May;37(9):2789-95
references: 19276206
references: Science. 2002 Aug 30;297(5586):1562-6
references: 12202833
references: Genes Dev. 1999 Aug 15;13(16):2134-47
references: 10465790
references: Nucleic Acids Res. 1990 Nov 11;18(21):6325-30
references: 2173826
references: Curr Biol. 1999 Feb 11;9(3):151-4
references: 10021390
references: Cell. 2004 Jan 23;116(2):247-57
references: 14744435
references: J Mol Biol. 1990 May 5;213(1):109-21
references: 2140136
references: Annu Rev Genomics Hum Genet. 2006;7:29-59
references: 16719718
references: Cell. 1990 Aug 24;62(4):733-43
references: 2167178
references: Proc Natl Acad Sci U S A. 2005 Mar 22;102(12):4465-9
references: 15728734
references: Proc Natl Acad Sci U S A. 1995 Aug 29;92(18):8110-4
references: 7667253
references: Nature. 2012 Sep 6;489(7414):109-13
references: 22955621
references: J Mol Biol. 2001 Dec 14;314(5):1127-36
references: 11743728
references: J Mol Biol. 1996 Jul 26;260(4):484-91
references: 8759315
references: Biochemistry. 1992 Jan 14;31(1):57-65
references: 1531023