16 Control of Gene Expression Concept Outline 16.1 Gene expression is controlled by regulating transcription. An Overview of Transcriptional Control. In bacteria transcription is regulated by controlling access of RNA polymerase to the promoter in a flexible and reversible way; eukaryotes by contrast regulate many of their genes by turning them on and off in a more permanent fashion. 16.2 Regulatory proteins read DNA without unwinding it. How to Read a Helix without Unwinding It. Regulatory proteins slide special segments called DNA- binding motifs along the major groove of the DNA helix, reading the sides of the bases. Four Important DNA-Binding Motifs. DNA-binding proteins contain structural motifs such as the helix-turn- helix which fit into the major groove of the DNA helix. 16.3 Bacteria limit transcription by blocking RNA FIGURE 16.1 polymerase. Chromosome puffs. In this chromosome of the fly Drosophila Controlling Transcription Initiation. Repressor melanogaster, individual active genes can be visualized as “puffs” proteins inhibit RNA polymerase’s access to the promoter, on the chromosomes. The RNA being transcribed from the DNA while activators facilitate its binding. template has been radioactively labeled, and the dark specks indicate its position on the chromosome. 16.4 Transcriptional control in eukaryotes operates at a distance. Designing a Complex Gene Control System. n an orchestra, all of the instruments do not play all the Eukaryotic genes use a complex collection of transcription Itime; if they did, all they would produce is noise. In- factors and enhancers to aid the polymerase in stead, a musical score determines which instruments in the transcription. orchestra play when. Similarly, all of the genes in an organ- The Effect of Chromosome Structure on Gene ism are not expressed at the same time, each gene produc- Regulation. The tight packaging of eukaryotic DNA into ing the protein it encodes full tilt. Instead, different genes nucleosomes does not interfere with gene expression. are expressed at different times, with a genetic score writ- Posttranscriptional Control in Eukaryotes. Gene ten in regulatory regions of the DNA determining which expression can be controlled at a variety of levels after genes are active when (figure 16.1). transcription. 313 16.1 Gene expression is controlled by regulating transcription. An Overview of the maintenance of a constant internal environment—is considered by many to be the hallmark of multicellular or- Transcriptional Control ganisms. Although cells in such organisms still respond to Control of gene expression is essential to all organisms. signals in their immediate environment (such as growth In bacteria, it allows the cell to take advantage of chang- factors and hormones) by altering gene expression, in ing environmental conditions. In multicellular organisms, doing so they participate in regulating the body as a it is critical for directing development and maintaining whole. In multicellular organisms with relatively constant homeostasis. internal environments, the primary function of gene con- trol in a cell is not to respond to that cell’s immediate en- vironment, but rather to participate in regulating the body Regulating Promoter Access as a whole. One way to control transcription is to regulate the initia- Some of these changes in gene expression compensate tion of transcription. In order for a gene to be tran- for changes in the physiological condition of the body. scribed, RNA polymerase must have access to the DNA Others mediate the decisions that produce the body, en- helix and must be capable of binding to the gene’s pro- suring that the right genes are expressed in the right cells moter, a specific sequence of nucleotides at one end of at the right time during development. The growth and the gene that tells the polymerase where to begin tran- development of multicellular organisms entail a long se- scribing. How is the initiation of transcription regulated? ries of biochemical reactions, each catalyzed by a specific Protein-binding nucleotide sequences on the DNA regu- enzyme. Once a particular developmental change has oc- late the initiation of transcription by modulating the abil- curred, these enzymes cease to be active, lest they disrupt ity of RNA polymerase to bind to the promoter. These the events that must follow. To produce these enzymes, protein-binding sites are usually only 10 to 15 nucleotides genes are transcribed in a carefully prescribed order, each in length (even a large regulatory protein has a “foot- for a specified period of time. In fact, many genes are ac- print,” or binding area, of only about 20 nucleotides). tivated only once, producing irreversible effects. In many Hundreds of these regulatory sequences have been char- animals, for example, stem cells develop into differenti- acterized, and each provides a binding site for a specific ated tissues like skin cells or red blood cells, following a protein able to recognize the sequence. Binding the pro- fixed genetic program that often leads to programmed tein to the regulatory sequence either blocks transcription cell death. The one-time expression of the genes that by getting in the way of RNA polymerase, or stimulates guide this program is fundamentally different from the transcription by facilitating the binding of RNA poly- reversible metabolic adjustments bacterial cells make to merase to the promoter. the environment. In all multicellular organisms, changes in gene expression within particular cells serve the needs of the whole organism, rather than the survival of indi- Transcriptional Control in Prokaryotes vidual cells. Control of gene expression is accomplished very differently in bacteria than in the cells of complex multicellular organ- Posttranscriptional Control isms. Bacterial cells have been shaped by evolution to grow and divide as rapidly as possible, enabling them to exploit Gene expression can be regulated at many levels. By far transient resources. In bacteria, the primary function of the most common form of regulation in both bacteria and gene control is to adjust the cell’s activities to its immediate eukaryotes is transcriptional control, that is, control of environment. Changes in gene expression alter which en- the transcription of particular genes by RNA polymerase. zymes are present in the cell in response to the quantity Other less common forms of control occur after transcrip- and type of available nutrients and the amount of oxygen tion, influencing the mRNA that is produced from the present. Almost all of these changes are fully reversible, al- genes or the activity of the proteins encoded by the lowing the cell to adjust its enzyme levels up or down as the mRNA. These controls, collectively referred to as post- environment changes. transcriptional controls, will be discussed briefly later in this chapter. Transcriptional Control in Eukaryotes The cells of multicellular organisms, on the other hand, have Gene expression is controlled at the transcriptional and been shaped by evolution to be protected from transient posttranscriptional levels. Transcriptional control, more common, is effected by the binding of proteins to changes in their immediate environment. Most of them ex- regulatory sequences within the DNA. perience fairly constant conditions. Indeed, homeostasis— 314 Part V Molecular Genetics 16.2 Regulatory proteins read DNA without unwinding it. How to Read a Helix without groove, the nucleotides’ hydrophobic methyl groups, hy- drogen atoms, and hydrogen bond donors and acceptors Unwinding It protrude. The pattern created by these chemical groups is It is the ability of certain proteins to bind to specific DNA unique for each of the four possible base-pair arrange- regulatory sequences that provides the basic tool of gene ments, providing a ready way for a protein nestled in the regulation, the key ability that makes transcriptional con- groove to read the sequence of bases (figure 16.2). trol possible. To understand how cells control gene expres- sion, it is first necessary to gain a clear picture of this mole- DNA-Binding Motifs cular recognition process. Protein-DNA recognition is an area of active research; so far, the structures of over 30 regulatory proteins have been Looking into the Major Groove analyzed. Although each protein is unique in its fine details, Molecular biologists used to think that the DNA helix had the part of the protein that actually binds to the DNA is to unwind before proteins could distinguish one DNA se- much less variable. Almost all of these proteins employ one quence from another; only in this way, they reasoned, of a small set of structural, or DNA-binding, motifs, par- could regulatory proteins gain access to the hydrogen ticular bends of the protein chain that permit it to interlock bonds between base-pairs. We now know it is unnecessary with the major groove of the DNA helix. for the helix to unwind because proteins can bind to its outside surface, where the edges of the base-pairs are ex- Regulatory proteins identify specific sequences on the posed. Careful inspection of a DNA molecule reveals two DNA double helix, without unwinding it, by inserting helical grooves winding round the molecule, one deeper DNA-binding motifs into the major groove of the double helix where the edges of the bases protrude. than the other. Within the deeper groove, called the major Major groove Major groove H H H N O HN H H N N H O CH3 N G NH N C H N A NHN T H N N N N Sugar N H O H O H Phosphate Minor groove Minor groove Key: = Hydrogen bond donors = Hydrogen bond acceptors = Hydrophobic methyl group = Hydrogen atoms unable to form hydrogen bonds FIGURE 16.2 Reading the major groove of DNA. Looking down into the major groove of a DNA helix, we can see the edges of the bases protruding into the groove. Each of the four possible base-pair arrangements (two are shown here) extends a unique set of chemical groups into the groove, indicated in this diagram by differently colored balls.