Enhancer-like long-range transcriptional activation by λ CI-mediated DNA looping

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.

[1]  I. Dodd,et al.  Octamerization of lambda CI repressor is needed for effective repression of P(RM) and efficient switching from lysogeny. , 2001, Genes & development.

[2]  P. Gregory,et al.  Controlling Long-Range Genomic Interactions at a Native Locus by Targeted Tethering of a Looping Factor , 2012, Cell.

[3]  C. Ushida,et al.  Helical phase dependent action of CRP: effect of the distance between the CRP site and the -35 region on promoter activity. , 1990, Nucleic acids research.

[4]  N. Costantino,et al.  On the role of Cro in lambda prophage induction. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[5]  D. Bose,et al.  Bacterial enhancer-binding proteins: unlocking sigma54-dependent gene transcription. , 2007, Current opinion in structural biology.

[6]  M. Lewis,et al.  Crystal structure of the λ repressor and a model for pairwise cooperative operator binding , 2008, Nature.

[7]  Benno Müller-Hill,et al.  Four dimers of λ repressor bound to two suitably spaced pairs of λ operators form octamers and DNA loops over large distances , 1999, Current Biology.

[8]  S. Busby,et al.  The regulation of bacterial transcription initiation , 2004, Nature Reviews Microbiology.

[9]  Mathieu Rappas,et al.  Bacterial enhancer-binding proteins: unlocking σ54-dependent gene transcription , 2007 .

[10]  D. Jain,et al.  Structure of a ternary transcription activation complex. , 2004, Molecular cell.

[11]  M. Atchison,et al.  Enhancers: mechanisms of action and cell specificity. , 1988, Annual Review of Cell Biology.

[12]  R. Ebright,et al.  Structural basis of transcription activation: the CAP-alpha CTD-DNA complex. , 2002, Science.

[13]  Haw Yang,et al.  DNA looping can enhance lysogenic CI transcription in phage lambda , 2008, Proceedings of the National Academy of Sciences.

[14]  V. Zhurkin,et al.  DNA sequence-dependent deformability deduced from protein-DNA crystal complexes. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[15]  James T Kadonaga,et al.  Regulation of RNA Polymerase II Transcription by Sequence-Specific DNA Binding Factors , 2004, Cell.

[16]  M. Lewis,et al.  Crystal structure of the lambda repressor C-terminal domain provides a model for cooperative operator binding. , 2000, Cell.

[17]  Gary Parkinson,et al.  Structural Basis of Transcription Activation: The CAP-αCTD-DNA Complex , 2002, Science.

[18]  R J Read,et al.  Crystallography & NMR system: A new software suite for macromolecular structure determination. , 1998, Acta crystallographica. Section D, Biological crystallography.

[19]  M. Lewis,et al.  Crystal Structure of the λ Repressor C-Terminal Domain Provides a Model for Cooperative Operator Binding , 2000, Cell.

[20]  R. Ebright,et al.  Bacterial promoter architecture: subsite structure of UP elements and interactions with the carboxy-terminal domain of the RNA polymerase alpha subunit. , 1999, Genes & development.

[21]  Jens Meiler,et al.  ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules. , 2011, Methods in enzymology.

[22]  I. Dodd,et al.  Cooperativity in long-range gene regulation by the lambda CI repressor. , 2004, Genes & development.

[23]  Ann Dean,et al.  Enhancer and promoter interactions-long distance calls. , 2012, Current opinion in genetics & development.

[24]  S. Hahn,et al.  Transcriptional Regulation in Saccharomyces cerevisiae: Transcription Factor Regulation and Function, Mechanisms of Initiation, and Roles of Activators and Coactivators , 2011, Genetics.

[25]  Laura Finzi,et al.  Multilevel autoregulation of λ repressor protein CI by DNA looping in vitro , 2011, Proceedings of the National Academy of Sciences.

[26]  J. W. Little,et al.  Stability and Instability in the Lysogenic State of Phage Lambda , 2010, Journal of bacteriology.

[27]  J. Geiselmann,et al.  Participation of IHF and a distant UP element in the stimulation of the phage λ PL promoter , 1998, Molecular microbiology.

[28]  David Dunlap,et al.  Direct demonstration and quantification of long-range DNA looping by the λ bacteriophage repressor , 2009, Nucleic acids research.

[29]  B. Müller-Hill,et al.  Four dimers of lambda repressor bound to two suitably spaced pairs of lambda operators form octamers and DNA loops over large distances. , 1999, Current biology : CB.

[30]  M. Lewis,et al.  Crystal structure of the ? repressor C-terminal domain octamer1 , 2001 .

[31]  Kevin Gaston,et al.  Stringent spacing requirements for transcription activation by CRP , 1990, Cell.

[32]  Mark S. Thomas,et al.  The C-terminal domain of the Escherichia coli RNA polymerase α subunit plays a role in the CI-dependent activation of the bacteriophage λ pM promoter , 2007, Nucleic acids research.

[33]  A. Oppenheim,et al.  Integration host factor stimulates the phage lambda pL promoter. , 1990, Journal of molecular biology.

[34]  K. Murakami,et al.  Identification of an UP element within the IHF binding site at the PL1-PL2 tandem promoter of bacteriophage lambda. , 1996, Journal of molecular biology.

[35]  K. Murakami,et al.  Structural Basis of Transcription Initiation: An RNA Polymerase Holoenzyme-DNA Complex , 2002, Science.

[36]  N. Costantino,et al.  On the role of Cro in λ prophage induction , 2005 .

[37]  G. K. Ackers,et al.  Site-specific enthalpic regulation of DNA transcription at bacteriophage lambda OR. , 1992, Biochemistry.

[38]  J. Dekker,et al.  The long-range interaction landscape of gene promoters , 2012, Nature.

[39]  R. Gourse,et al.  UP element-dependent transcription at the Escherichia coli rrnB P1 promoter: positional requirements and role of the RNA polymerase alpha subunit linker. , 2001, Nucleic acids research.

[40]  Ian B. Dodd,et al.  Cooperativity in long-range gene regulation by the λ CI repressor , 2004 .

[41]  Michael R. Green,et al.  Transcriptional regulatory elements in the human genome. , 2006, Annual review of genomics and human genetics.