DNA looping in prokaryotes: experimental and theoretical approaches

Abstract

Transcriptional regulation is at the heart of biological functions such as adaptation to a changing environment or to new carbon sources. One of the mechanisms which has been found to modulate transcription, either positively (activation) or negatively (repression), involves the formation of DNA loops. A DNA loop occurs when a protein or a complex of proteins simultaneously binds to two different sites on DNA with looping out of the intervening DNA. This simple mechanism is central to the regulation of several operons in the genome of the bacterium Escherichia coli, like the lac operon, one of the paradigms of genetic regulation. The aim of this review is to gather and discuss concepts and ideas from experimental biology and theoretical physics concerning DNA looping in genetic regulation. We first describe experimental techniques designed to show the formation of a DNA loop. We then present the benefits that can or could be derived from a mechanism involving DNA looping. Some of these are already experimentally proven, but others are theoretical predictions and merit experimental investigation. Then, we try to identify other genetic systems that could be regulated by a DNA looping mechanism in the genome of Escherichia coli. We found many operons that, according to our set of criteria, have a good chance to be regulated with a DNA loop. Finally, we discuss the proposition recently made by both biologists and physicists that this mechanism could also act at the genomic scale and play a crucial role in the spatial organization of genomes.

Fig 1

The two main mechanisms of DNA looping in transcriptional regulation are depicted. (A) A DNA loop can be responsible for transcriptional repression. A bivalent transcription factor binds simultaneously to two binding sites and blocks access to the RNA polymerase (e.g., the regulation of the lac operon, the best studied in E. coli). (B) A DNA loop can be responsible for transcriptional activation. Transcription factors bind away from the site of fixation of RNA polymerase (normally of σ⁵⁴ type) and help the recruitment of RNA polymerase and formation of an open complex (in E. coli, the glnALG operon is regulated by this mechanism).

Fig 2

The mechanism of DNA looping could generate the phenomenon of “bistability.” The nonlinear response associated with the cooperativity of DNA looping, as well as a positive feedback in the regulation of the system, can generate bistability. Bistable systems can be in one state or another depending on their history, which can have consequences for the biology of the system. The pink area indicates the concentrations of inducer where the gene can be either repressed or expressed depending upon its initial condition (with low inducer or high inducer concentration).

Fig 3

The mechanism of DNA looping could apply to the regulatory regions of two different genes so that binding to distant sites becomes cooperative (16, 121). We can imagine that cooperativity can occur between the regulatory regions of two genes that are relatively close on the genome (separation of the order of 1 kb [120]) (A) or between two genes that are far away in a 1-D representation of the genome (separation of the order of 100 kb) but near in a 3-D one (B). If these kinds of interactions exist, inactivation of binding sites adjacent to one gene would also affect the expression of other genes via the mechanism of DNA looping.