Difference between revisions of "Promoters"

Revision as of 04:50, 30 November 2008

The regsitry symbol for a promoter is shown above a typical sequence for a bacterial promoter. The lavender shaded boxes indicate the two most conserved regions of a bacterial promoter and are located at -10 and -35 bases from the transcriptional start site (shaded in green). There are, on average, 17bp between the -10 and -35 sites and 7bp between the -10 site and the transcriptional start site pribnowharleylisser1lisser2.

A promoter is a DNA sequence that tends to recruit transcriptional machinery and lead to transcription of the downstream DNA sequence. The specific sequence of the promoter determines the binding affinity of the transcriptional machinery for the promoter and how likely the transcriptional machinery is to initiate transcription after being recruited to the DNA. A "strong" promoter is one that leads to a high rate of transcription initiation, while a "weak" promoter leads to a low rate of transcription initiation.

In addition to sequences that "promote" transcription, a promoter may include additional sequences known as operators that control the strength of the promoter. For example, a promoter may include a binding site for a protein that either attracts or obstructs the transcriptional machinery from binding to the promoter. The presence or absence of the protein will affect the strength of the promoter. Such a promoter is known as a regulated promoter.

The registry has a large collection of promoters both unregulated and regulated. Most of our promoters are designed to be recognized by E. coli RNA polymerase but we also have several promtoers that are recognized by T7 RNA polymerase and other RNA polymerase holoenzymes.

An input/output description of promoter function

Sometimes, it is appropriate to ignore the mechanistic details of how a promoter works and think of a promoter as a device that converts some set of inputs into some set of outputs. Such an approach may be appropriate when designing a multi-component system that includes promoters whose activity must be regulated by other species in the system. A promoter can be thought of as a device that outputs a certain number of transcribing RNA polymerases per unit time. In that sense, a promoter might be thought of as a "source" or "generator" of transcriptional activity. Promoters can have different numbers of inputs. A constitutive promoter has no inputs. Technically, even a constitutive promoter has inputs, such as the level of free RNA polymerase, but we often assume that levels of free RNA polymerase are either unchanging, or are changing but are never the limiting factor in transcription initiation. The level of a repressor protein than negatively regulates a promoter might be considered an input to a promoter.

	Catalog: Are you looking for a promoter to use? The registry has a collection of bacterial and phage promoters.
	Design: Are you interested in designing a new promoter or promoter family? Here are some guidelines to help you design and document new promoters.
	Help: A glossary, and further reading on promoters.

References

pribnow pmid=1093168
harley pmid=3550697
lisser1 pmid=8479900
lisser2 pmid=8055959

</biblio>

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 ===An input/output description of promoter function===
-A promoter can be conceptualized as a device that outputs a certain number of transcribing RNA polymerases per unit time.  In that sense, a promoter might be thought of as a "source" or "generator" of transcriptional activity.  Promoters can have different numbers of inputs.  A constitutive promoter has no inputs.  Technically, even a constitutive promoter has inputs, such as the level of free RNA polymerase, but we often assume that levels of free RNA polymerase are either unchanging, or are changing but are never the limiting factor in transcription initiation.  The level of a repressor protein than negatively regulates a promoter might be considered an input to a promoter.
+Sometimes, it is appropriate to ignore the mechanistic details of how a promoter works and think of a promoter as a device that converts some set of inputs into some set of outputs.  Such an approach may be appropriate when designing a multi-component system that includes promoters whose activity must be regulated by other species in the system.  A promoter can be thought of as a device that outputs a certain number of transcribing RNA polymerases per unit time.  In that sense, a promoter might be thought of as a "source" or "generator" of transcriptional activity.  Promoters can have different numbers of inputs.  A constitutive promoter has no inputs.  Technically, even a constitutive promoter has inputs, such as the level of free RNA polymerase, but we often assume that levels of free RNA polymerase are either unchanging, or are changing but are never the limiting factor in transcription initiation.  The level of a repressor protein than negatively regulates a promoter might be considered an input to a promoter.
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