Promoters

A commonly quoted statistic is that the human genome contains roughly 23,000 protein coding genes. Such a massive number of proteins working together seems like it would be utter chaos. How could their activities be coordinated with enough precision to make a sentient being such as ourselves? Clearly, how genes are regulated is of crucial importance to overall function. For instance, genes responsible for contorting the tissues of a growing embryo into their proper forms are useless, or perhaps harmful, to the adult. Life has evolved an impressive array of mechanisms for regulating genes. Promoters are one of these mechanisms, and they are of such importance that they have been conserved across evolutionary history. They are a key player in the organization of bacterial genomes as well as our own, though some of the details differ. I will be focusing on promoters in bacteria because the details are simpler and more familiar to me.

The information contained in genes is, in a sense, locked in the DNA. DNA contains the instructions for a protein, but the DNA itself neither exhibits the protein's function nor has the ability to generate a protein directly. Protein synthesis begins with transcription, in which the enzyme RNA polymerase makes a mRNA molecule carrying the same instructions as the DNA. This messenger RNA is chemically very similar to DNA, but a mRNA molecule carries only the instruction of one or several genes whereas DNA contains every gene. However, RNA polymerase does not bind just anywhere on the DNA. It only binds where the shape of the DNA bases closely fits the shape of a particular surface of the protein. This particular DNA shape is found in promoters. By looking at every promoter in E. coli, one can generate a consensus sequence of the most common DNA bases in each position.

When studying promoters, it is useful to number the DNA bases such that +1 is the first nucleotide transcribed into mRNA. Thus, the second transcribed base is +2, and the untranscribed base immediately upstream of +1 is -1. In E. coli, regions around -10 and -35 are critical for recruiting free RNA polymerase in the cell. The E. coli consensus sequence of the -10 region contains the sequence TATAAT, and the -35 region the sequence TTGACA. The consensus is a basis for comparison between two different promoters. The sequence of a promoter's -35 and -10 regions, as well as the intervening space, determines how efficiently RNA polymerase binds, and thus the promoter's strength. Genes regulated by strong promoters yield more mRNA and therefore more product protein than genes regulated by weak promoters. This is useful because some proteins are required in abundance while others are required only in low quantities.

Economy is a significant driving force in evolution. Cells that are wasting resources will be selected against in favor of those that are more efficient. Part of this economy is maintained by promoters. Proteins that are always required in the cell tend to be regulated by constitutive promoters, or promoters that are always "on," recruiting RNA polymerase to transcribe the gene or genes under their control. However in many cases, a particular protein is required only at a specific time. The most common example of this scenario is the lac operon in E. coli. An operon is a set of genes all regulated by the same promoter. In the case of the lac operon, the genes lacZ, lacY, and lacA are all regulated by the lac promoter. All three genes code for proteins used in the uptake and metabolism of the sugar lactose. Clearly it is wasteful to expend energy producing these proteins if there is no lactose available. Evolution has produced a wide array of promoters that solve this problem. The lac promoter is known as an inducible promoter because it is switched off by default but switched on (induced) by lactose.

The details of how the lac promoter works are fascinating and I think worth a brief exploration. A protein called LacI (pronounced "lack eye") binds strongly to a region of DNA called the operator, which overlaps the promoter. When LacI is bound to the operator, RNA polymerase is unable to transcribe the three genes regulated by the lac promoter. However, if the E. coli cell encounters a food source with abundant lactose, some of the lactose seeps into the cell and binds to the LacI protein. When lactose is bound to LacI, the LacI changes shape and is unable to bind to the operator on the DNA. This allows RNA polymerase to freely transcribe the genes for lactose metabolism. When the source of lactose is exhausted, LacI again binds to the operator and the proteins of the lac operon cease to be produced. Such operons are common in bacteria, each with a unique strategy for efficiently regulating the production of their protein products.

Image Credit: DBGthekafu (via Wikimedia)

References and Further Reading:

Brown, T. A. Genetics: A Molecular Approach. 2nd ed. London: Chapman & Hall, 1992.

Dale, J. W. Molecular Genetics of Bacteria. Chichester: John Wiley & Sons, 1989.