title: Using synthetic bacterial enhancers to reveal a looping-based mechanism for quenching-like repression.
abstract: We explore a model for 'quenching-like' repression by studying synthetic bacterial enhancers, each characterized by a different binding site architecture. To do so, we take a three-pronged approach: first, we compute the probability that a protein-bound dsDNA molecule will loop. Second, we use hundreds of synthetic enhancers to test the model's predictions in bacteria. Finally, we verify the mechanism bioinformatically in native genomes. Here we show that excluded volume effects generated by DNA-bound proteins can generate substantial quenching. Moreover, the type and extent of the regulatory effect depend strongly on the relative arrangement of the binding sites. The implications of these results are that enhancers should be insensitive to 10-11 bp insertions or deletions (INDELs) and sensitive to 5-6 bp INDELs. We test this prediction on 61 σ(54)-regulated qrr genes from the Vibrio genus and confirm the tolerance of these enhancers' sequences to the DNA's helical repeat.
authors.affiliation: Department of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa 32000, Israel.
authors.forename: Michal
authors.initials: M
authors.lastname: Brunwasser-Meirom
authors.affiliation: Russell Berrie Nanotechnology Institute, Technion-Israel Institute of Technology, Haifa 32000, Israel.
authors.forename: Yaroslav
authors.initials: Y
authors.lastname: Pollak
authors.affiliation: Department of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa 32000, Israel.
authors.forename: Sarah
authors.initials: S
authors.lastname: Goldberg
authors.affiliation: Department of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa 32000, Israel.
authors.forename: Lior
authors.initials: L
authors.lastname: Levy
authors.affiliation: Department of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa 32000, Israel.
authors.forename: Orna
authors.initials: O
authors.lastname: Atar
authors.affiliation: Department of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa 32000, Israel.|Russell Berrie Nanotechnology Institute, Technion-Israel Institute of Technology, Haifa 32000, Israel.
authors.forename: Roee
authors.initials: R
authors.lastname: Amit
mesh_terms: D001419:Bacteria / Q000235:genetics; D004269:DNA, Bacterial / Q000737:chemistry*; D004742:Enhancer Elements, Genetic; D015964:Gene Expression Regulation, Bacterial / Q000502:physiology; D008954:Models, Biological; D011401:Promoter Regions, Genetic; D053038:Quorum Sensing; D058615:Synthetic Biology / Q000379:methods*
chemical_list: D004269:DNA, Bacterial
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