Regulation of Transcription and translation Slide 2 All the cells in your body contain all the genetic information you had at the time of conception. Somehow, some way, your ears ended up on the sides of your head, your hands ended up with five fingers each, and your toes ended up on your feet. All this happened even though the cells in your toes encode the information needed to develop your ears, and the cells in your ears contain the genetic information required to make toes. Pretty amazing. So how does it happen that the cells in your body differentiate to become the various tissues, organs, and other body parts that make you, you? Obviously not all the genes in your body are expressed all the time quite the contrary the expression of all genes must be carefully controlled, otherwise you would be a giant mass of cells that were all the same. Indeed, this careful control of gene expression must occur in all multicellular organisms that have differentiated tissues. Consider the mushrooms that emerge in lawns these are the tissues made by fungi for the production of spores. All the cells of a fungus encode the information needed to make mushrooms, but these genes are only expressed by specific cells, at specific times, and under specific conditions. For this to occur, there must be rather sophisticated means to control the expression of genes, so that the mrna molecules they encode are made at the proper time and in the proper amounts, and so that proteins made from the mrna s are present when they are needed, and absent when they are not. These mechanisms used to control the transcription of genes and the translation of messenger RNA are the topics we will review in this lesson. Slide 3 The transcription of all genes begins with RNA polymerase binding to DNA but binding just anywhere would be useless; instead, it must bind at a location that is just before the sequence of DNA that encodes a messenger RNA. This targeted binding of RNA polymerase occurs by way of specific nucleotide sequences that can be recognized by RNA polymerase these sequences are called promoters because they promote the binding of RNA polymerase. The binding of RNA polymerase to a promoter sequence is made possible because one of the five subunits of RNA polymerase the sigma factor is able to recognize the correct sequence of nucleotides that constitute the promoter, and it mediates the docking of RNA polymerase to the proper locations in the chromosome. Quite cleverly, there are several interchangeable sigma factors made by cells, and each recognizes a somewhat different sequence of nucleotides in DNA. If a particular sigma factor in RNA polymerase is swapped out for a different one, then a completely different kind of promoter will be recognized and a completely different set of genes will be transcribed. These different sets of genes are called regulons because their expression is coordinated through the selective binding of RNA polymerases that have specific sigma factors. This is but one way that cells orchestrate the expression of genes within cells. Since the binding of RNA polymerase to a promoter is an essential first step one that must occur before the synthesis of messenger RNA can begin then one could readily imagine that various mechanisms exist to facilitate or hinder this binding event. Indeed this does occur. There are operator sequences near genes in DNA that can either make it easier or more difficult for RNA polymerase to bind to promoters. The existence of these genetic elements provides a means
to fine-tune the transcription of genes by modulating the binding of RNA polymerase molecules to promoter regions. In prokaryotic organisms, all the genes that encode proteins for a given pathway are often adjacent to one another. Moreover the genes that encode the regulatory proteins are also nearby. This cluster of regulatory protein structural genes, promoter and operator regions, and structural genes for pathway enzymes are called operons. This organization of genetic elements provides a very simple and efficient means to regulate the expression of related genes. In eukaryotic organisms the genes that encode enzymes for a given pathway are typically not adjacent to each other in an operon. Nonetheless, many of the basic mechanisms used to regulate gene expression are conserved in all life forms. Slide 4 Following a binding of RNA polymerase to the promoter region, the two strands of DNA are separated and the synthesis of messenger RNA begins using one strand of DNA as a template. The synthesis of messenger RNA is said to be processive - that is, it begins at the promoter region and continues to the end of the DNA sequence that encodes a gene or set of genes. Anything that prevents or slows the movement of RNA polymerase will reduce the amount of messenger RNA that is made, and this decreases the expression of the corresponding gene. For example, there are different kinds of regulatory proteins that monitor the cellular environment. If the levels of a protein encoded by a gene are adequate, then a regulatory protein may bind to a region near the promoter, and block the binding or movement of RNA polymerase, thereby preventing the synthesis of messenger RNA. In the absence of this regulatory protein the binding of RNA polymerase and the synthesis of messenger RNA can occur. One can easily imagine that these regulatory proteins act as on-off switches. Slide 5 Consider a situation in which the product of a specific gene was generally not needed except under specific conditions. An easy example would be genes that encode enzymes in a pathway used for the metabolism of a carbon source that was usually not available to an organism. In this situation it would not make sense for the organism to produce the enzymes for this pathway unless the carbon source was present. Under these circumstances a regulatory protein binds near the promoter region and prevents transcription of the genes by RNA polymerase. However, when the substrate is present, it acts as an inducer, binds to the regulatory protein, and changes its conformation so it is no longer able to bind to DNA. Through this mechanism the enzymes of the metabolic catabolic pathway would only be made when the substrate is present. This general mechanism for the control of gene expression is called positive regulation. Slide 6 The classic example of this form of gene regulation is the lac operon of the bacterium Escherichia coli that encodes the genes needed for the metabolism of lactose. As you can see in the diagram, the promoter and operator regions of the lac operon are located just ahead
of the structural genes. The regulatory protein called the repressor because it represses transcription of the genes is normally bound to the operator region. However, when lactose is present, it binds to the repressor causing it to lose the ability to bind to the operator region. Now the processive transcription of the lac operon genes can occur. Slide 7 Now consider the opposite situation genes that normally are expressed, and turned off only under exceptional, specific conditions. In such cases, no regulatory genes would normally be bound near the promoter region, and the transcription of DNA to form mrna would freely occur. However, regulatory proteins would loiter in the cytoplasm of a cell. They would remain there, monitoring the level of the product of the pathway. When sufficient levels of the product of the pathway were present, it would bind to the regulatory protein, thereby changing its conformation to one that could bind to DNA. By binding to DNA near the promoter region, expression of the genes would be turned off. This general mechanism for the control of gene expression is called negative regulation. The classic example of this form of gene regulation is the trp operon of the bacterium Escherichia coli that encodes the genes needed for the biosynthesis of the amino acid tryptophan. Normally cells of Escherichia coli would need to make tryptophan for use in protein synthesis. However, in some situations, tryptophan can be obtained from the environment, and so there is no need for the cell to expend resources to make its own. Alternatively, if the growth rate of the cell slows, the rate of protein synthesis will slow, and the supply of tryptophan will be sufficient to meet the demands of protein biosynthesis. The trp operon is an example of a set of genes that are normally transcribed and expressed. As you would predict, this means that there is no repressor bound to the operator region. Indeed, in the absence of tryptophan, the repressor is unable to bind to the operator region. However, when tryptophan is present, it binds to the repressor and changes its conformation so that it can now bind to the operator region. For regulation of the trp operon, tryptophan serves as a corepressor. This binding of the repressor to the operator prevents transcription of the genes that comprise the trp operon, and the genes needed for the biosynthesis of tryptophan are no longer expressed. The overall outcome is that tryptophan is not made by the cells when there is enough of the amino acid in the cytoplasm. The lac and trp operons in E. coli illustrate two basic mechanisms used to regulate the expression of genes in cells. There are a host of other increasingly more complex mechanisms that are used alone or in various combinations that you will learn about in more advanced courses. Together they provide cells with extremely efficient ways to fine tune gene expression so that genes are only expressed by specific cells, at specific times, and under specific conditions. Slide 8 So far we have reviewed how cells control the transcription of genes to make messenger RNA. One could think that once messenger RNA is made then POOF the cell has proteins, and that is that. But as you know, it is not that simple.
In eukaryotic cells the messenger RNA has to be transported from the nucleus to the rough endoplasmic reticulum where protein synthesis occurs. This targeted transportation of the mrna transcript must be carefully controlled, and the mrna cannot be degraded in the process. In prokaryotic cells cells that lack a nucleus there is no need to transport the mrna, and the synthesis of proteins can occur immediately and often begins even as the mrna is being made. In order for the mrna in eukaryotic cells to be properly transported from the nucleus to the rough endoplasmic reticulum without being degraded, a couple of things must first happen. One is that a string of adenine nucleotides a so-called poly[a] tail is added to the 3 end, and a modified guanosine residue is added as a cap to the 5 end of the mrna transcript. The poly[a] tail plays a role in targeting the transport of mrna from the nucleus to the rough endoplasmic reticulum. The modified guanosine helps prevent degradation of the mrna once it is in the cytoplasm, and facilitates binding of the mrna to the ribosome. mrna transcripts that lack a modified guanosine are not readily translated. In some cases such as in oocytes and plant seeds, uncapped mrna is stockpiled for use at a later time. Slide 9 that is made? So can you imagine other ways that cells might control the amount of a protein Let s start where we just left off. Messenger RNA molecules do not last forever within a cell they are degraded in the cytoplasm, and the rate at which different transcripts are degraded varies. As a result, less protein can be made from mrna transcripts that are rapidly degraded as compared to those that are degraded more slowly. In order for protein to be made, ribosomes must bind to the mrna so that translation to form polypeptides can occur. It would be sensible to expect that ribosomes don t bind equally well to all mrnas because the sequences of mrnas are not all the same. Thus, the ability of ribosomes to bind to mrna and begin translation might be another way that the amount of protein made could be varied. The translation of mrna begins at the 5 end of the transcript and proceeds to the 3 end, with amino acids being sequentially added to the growing polypeptide chain. If the mrna is linear then this process can occur more readily than if the mrna has secondary structure regions that are double-stranded as a result of base-pairing among nucleotides in the mrna. Since the ability to form these double stranded regions depends on the sequence of nucleotides in the mrna, and because the sequences of mrna transcripts differ from one another, some will have regions that are double-stranded whereas others will not. This will in turn affect how easily the mrna can be used as a template for translation. These are but a few of the means that life forms have evolved to finely tune the expression of genes and the amounts of a particular protein found in a cell. The key point is to realize that there are many ways that the production of proteins is controlled, and that these mechanisms are employed at several steps along the process, beginning with transcriptional control, to modification of the mrna transcripts, to translational control of protein biosynthesis.