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Chapter: Genetics and Molecular Biology: RNA Polymerase and RNA Initiation

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DNA Looping in Regulating Promoter Activities

DNA looping is a reasonable way enhancers can interact with the transcription apparatus. The available data say that this, indeed, is one of the ways they work.

DNA Looping in Regulating Promoter Activities

DNA looping is a reasonable way enhancers can interact with the transcription apparatus. The available data say that this, indeed, is one of the ways they work. For example, an enhancer can be placed on one DNA circle, and the promoter it stimulates on another DNA circle. When the DNA rings are linked, the enhancer functions. This shows that the enhancer must be close to the promoter in three-dimensional space. The linking experiment also shows that a protein or signal doesn’t move down the DNA from the enhancer to the promoter.

DNA looping solves two physical problems in gene regulation. The first concerns space. Regulatory proteins must do two things. They sense intracellular conditions, for example, the presence of a growth hor-mone. They then must turn on or turn off the expression of only those genes appropriate to the conditions. These responses require that a signal be transmitted from a sensor part of the regulatory protein to the cellular apparatus responsible for transcribing or initiating transcrip-tion from the correct gene. The phrase “correct gene” is the key here. How can the regulatory protein confine its activity to the correct gene?


Figure 4.16 The limited number of sites immediately adjacent to an RNApolymerase molecule.

The easiest, and virtually the only general way for a regulatory protein to recognize the correct gene is for the protein to recognize and bind to a DNA sequence near or within the correct gene.

 

If a regulatory protein is bound adjacent to an RNA polymerase molecule or adjacent to an auxiliary protein required for initiating transcription, we can imagine direct protein-protein contacts for com-munication of the necessary signals. The space problem arises since only a limited number of proteins may bind immediately adjacent to the transcription initiation complex (Fig. 4.16). The limit seems to be two to four proteins. Since the regulatory pattern of many genes is complex and likely to require the combined influence of more than two or three regulatory proteins, we have a problem.

How can more than a couple of proteins directly influence the RNA polymerase? DNA looping is one answer. A regulatory protein can be bound within several hundred or several thousand base pairs of the initiation complex and directly touch the complex by looping the DNA. With DNA looping a sizeable number of proteins can simultaneously affect transcription initiation via multiple loops. Additional possibilities exist. For example, proteins could regulate by helping or hindering loop formation or alternative looping could exist in the regulation scheme of a gene.

A second reason for DNA looping is the cooperativity generated by a system that loops. Consider a system in which a protein can bind to two DNA sites separated by several hundred base pairs and then the proteins can bind each other, thus forming a DNA loop. A different reaction pathway can also be followed. A molecule of the protein could bind to one of the sites and a second molecule of the protein could bind to the first. By virtue of the potential for looping, the concentration of the second protein in the vicinity of the second DNA site has been increased.

 

Such a concentration change increases the occupancy at the second site above the value it would have in the absence of looping. Hence, the presence of one site and looping increases occupancy of the second site. Such a cooperativity can substantially facilitate binding at low concen-trations of regulatory proteins. It also eliminates any time lags upon gene induction associated with diffusion of a protein to its DNA-binding site.


Increasing the local concentration of a regulatory protein near its binding site solves a serious problem for cells. Thousands of regulatory proteins must be present in a bacterial cell and tens of thousands of regulatory proteins may have to be present in the nucleus of some eukaryotic cells. Since the total protein concentration possible in the cell or nucleus is limited to about 200 mg/ml, and since the same space must be shared with the chromosome and housekeeping proteins as well, the concentration possible for any one type of regulatory protein is strictly limited.

How then can the requisite binding of the regulatory protein to its DNA target sequence be achieved? Basically, the effective concentration of the protein must be high relative to the dissociation constant from the site. If the affinity is too high, however, the tightness of binding may make the dissociation rate from the site so slow that the protein’s presence interferes with normal cellular activities like DNA replication, recombination, and repair. A nice solution to these contradictory re-quirements is to build a system in which the affinity of the protein for the site is not too high, the overall concentration of the protein in the cell is not too high, but the local concentration of the protein just in the vicinity of the binding sites is high. DNA looping provides a simple mechanism for increasing the local concentrations of regulatory pro-teins.


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