{"id":3274,"date":"2016-11-02T20:43:13","date_gmt":"2016-11-02T20:43:13","guid":{"rendered":"https:\/\/courses.lumenlearning.com\/wm-biology1\/?post_type=chapter&p=3274"},"modified":"2017-04-18T22:33:09","modified_gmt":"2017-04-18T22:33:09","slug":"outcome-prokaryotic-gene-regulation","status":"publish","type":"chapter","link":"https:\/\/courses.lumenlearning.com\/suny-wmopen-biology1\/chapter\/outcome-prokaryotic-gene-regulation\/","title":{"raw":"Prokaryotic Gene Regulation","rendered":"Prokaryotic Gene Regulation"},"content":{"raw":"

Discuss different components of prokaryotic gene regulation<\/h2>\r\nThe DNA of prokaryotes is organized into a circular chromosome supercoiled in the nucleoid region of the cell cytoplasm. Proteins that are needed for a specific function are encoded together in blocks called operons<\/strong>. For example, all of the genes needed to use lactose as an energy source are coded next to each other in the lactose (or lac) operon.\r\n\r\nIn prokaryotic cells, there are three types of regulatory molecules that can affect the expression of operons: repressors, activators, and inducers. Repressors<\/strong> are proteins that suppress transcription of a gene in response to an external stimulus, whereas activators<\/strong> are proteins that increase the transcription of a gene in response to an external stimulus. Finally, inducers<\/strong> are small molecules that either activate or repress transcription depending on the needs of the cell and the availability of substrate.\r\n
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Learning Objectives<\/h3>\r\n
    \r\n \t
  • Understand the basic steps in gene regulation in prokaryotic cells<\/li>\r\n \t
  • Explain the roles of repressors in negative gene regulation<\/li>\r\n \t
  • Explain the role of activators and inducers in positive gene regulation<\/li>\r\n<\/ul>\r\n<\/div>\r\n

    Gene Regulation in Prokaryotes<\/h2>\r\nIn bacteria and archaea, structural proteins with related functions\u2014such as the genes that encode the enzymes that catalyze the many steps in a single biochemical pathway\u2014are usually encoded together within the genome in a block called an operon<\/strong> and are transcribed together under the control of a single promoter. <\/strong>This forms\u00a0a polycistronic transcript (Figure 1).\u00a0The promoter then has simultaneous control over the regulation of the transcription of these structural genes because they will either all be needed at the same time, or none will be needed.\r\n\r\n[caption id=\"attachment_4032\" align=\"aligncenter\" width=\"1024\"]\"Diagram Figure 1. In prokaryotes, structural genes of related function are often organized together on the genome and transcribed together under the control of a single promoter. The operon\u2019s regulatory region includes both the promoter and the operator. If a repressor binds to the operator, then the structural genes will not be transcribed. Alternatively, activators may bind to the regulatory region, enhancing transcription.[\/caption]\r\n\r\nFrench scientists Fran\u00e7ois Jacob\u00a0<\/strong>(1920\u20132013) and Jacques Monod<\/strong> at the Pasteur Institute were the first to show the organization of bacterial genes into operons, through their studies on the lac<\/em> operon<\/strong> of E. coli<\/em>. They found that in E. coli<\/em>, all of the structural genes that encode enzymes needed to use lactose as an energy source lie next to each other in the lactose (or lac<\/em>) operon under the control of a single promoter, the lac<\/em> promoter. For this work, they won the Nobel Prize in Physiology or Medicine in 1965.\r\n\r\nAlthough eukaryotic genes are not organized into operons, prokaryotic operons are excellent models for learning about gene regulation generally. There are some gene clusters in eukaryotes that function similar to operons. Many of the principles can be applied to eukaryotic systems and contribute to our understanding of changes in gene expression in eukaryotes that can result pathological changes such as cancer.\r\n\r\nEach operon includes DNA sequences that influence its own transcription; these are located in a region called the regulatory region. The regulatory region includes the promoter and the region surrounding the promoter, to which transcription factors<\/strong>, proteins encoded by regulatory genes, can bind. Transcription factors influence the binding of RNA polymerase<\/strong> to the promoter and allow its progression to transcribe structural genes. A repressor<\/strong> is a transcription factor that suppresses transcription of a gene in response to an external stimulus by binding to a DNA sequence within the regulatory region called the operator<\/strong>, which is located between the RNA polymerase binding site of the promoter and the transcriptional start site of the first structural gene. Repressor binding physically blocks RNA polymerase from transcribing structural genes. Conversely, an activator<\/strong> is a transcription factor that increases the transcription of a gene in response to an external stimulus by facilitating RNA polymerase binding to the promoter. An inducer<\/strong>, a third type of regulatory molecule, is a small molecule that either activates or represses transcription by interacting with a repressor or an activator.\r\n\r\nIn prokaryotes, there are examples of operons whose gene products are required rather consistently and whose expression, therefore, is unregulated. Such operons are constitutively expressed<\/strong>, meaning they are transcribed and translated continuously to provide the cell with constant intermediate levels of the protein products. Such genes encode enzymes involved in housekeeping functions required for cellular maintenance, including DNA replication, repair, and expression, as well as enzymes involved in core metabolism. In contrast, there are other prokaryotic operons that are expressed only when needed and are regulated by repressors, activators, and inducers.\r\n
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    Practice Questions<\/h3>\r\nWhat are the parts in the DNA sequence of an operon?\r\n\r\n[practice-area rows=\"2\"][\/practice-area]\r\n[reveal-answer q=\"665976\"]Show Answer[\/reveal-answer]\r\n[hidden-answer a=\"665976\"]An operon is composed of\u00a0a promoter, an operator, and the structural genes. They must occur in that order.\r\n\r\n[\/hidden-answer]\r\n\r\nWhat types of regulatory molecules are there?\r\n\r\n[practice-area rows=\"2\"][\/practice-area]\r\n[reveal-answer q=\"665979\"]Show Answer[\/reveal-answer]\r\n[hidden-answer a=\"665979\"]There are three types of regulatory molecules: repressors, activators, and inducers.[\/hidden-answer]\r\n\r\n<\/div>\r\n

    The trp<\/em> Operon: A Repressor Operon<\/h2>\r\nBacteria such as E. coli<\/em> need amino acids to survive. Tryptophan<\/strong> is one such amino acid that E. coli<\/em> can ingest from the environment. E. coli<\/em> can also synthesize tryptophan using enzymes that are encoded by five genes. These five genes are next to each other in what is called the tryptophan (trp<\/em>) operon<\/strong> (Figure 1). If tryptophan is present in the environment, then E. coli<\/em> does not need to synthesize it and the switch controlling the activation of the genes in the trp<\/em> operon is switched off. However, when tryptophan availability is low, the switch controlling the operon is turned on, transcription is initiated, the genes are expressed, and tryptophan is synthesized.\r\n\r\n[caption id=\"attachment_3555\" align=\"aligncenter\" width=\"800\"]\"The Figure 1. The five genes that are needed to synthesize tryptophan in E. coli<\/em> are located next to each other in the trp<\/em> operon. When tryptophan is plentiful, two tryptophan molecules bind the repressor protein at the operator sequence. This physically blocks the RNA polymerase from transcribing the tryptophan genes. When tryptophan is absent, the repressor protein does not bind to the operator and the genes are transcribed.[\/caption]\r\n\r\nA DNA sequence that codes for proteins is referred to as the coding region. The five coding regions for the tryptophan biosynthesis enzymes are arranged sequentially on the chromosome in the operon. Just before the coding region is the transcriptional start site<\/strong>. This is the region of DNA to which RNA polymerase binds to initiate transcription. The promoter sequence is upstream of the transcriptional start site; each operon has a sequence within or near the promoter to which proteins (activators or repressors) can bind and regulate transcription.\r\n\r\nA DNA sequence called the operator sequence is encoded between the promoter region and the first trp<\/em> coding gene. This operator\u00a0<\/strong>contains the DNA code to which the repressor protein can bind. When tryptophan is present in the cell, two tryptophan molecules bind to the trp<\/em> repressor, which changes shape to bind to the trp<\/em> operator. Binding of the tryptophan\u2013repressor complex at the operator physically prevents the RNA polymerase from binding, and transcribing the downstream genes.\r\n\r\nWhen tryptophan is not present in the cell, the repressor by itself does not bind to the operator; therefore, the operon is active and tryptophan is synthesized. Because the repressor protein actively binds to the operator to keep the genes turned off, the trp<\/em> operon is negatively regulated and the proteins that bind to the operator to silence trp<\/em> expression are negative regulators<\/strong>.\r\n
    \r\n\r\nWatch this video to learn more about the trp<\/em> operon.\r\n\r\nhttps:\/\/youtu.be\/8aAYtMa3GFU\r\n\r\n<\/div>\r\n

    Catabolite Activator Protein (CAP): An Activator Regulator<\/h2>\r\n

    Just as the trp<\/em> operon is negatively regulated by tryptophan molecules, there are proteins that bind to the operator sequences that act as a positive regulator<\/strong> to turn genes on and activate them. For example, when glucose is scarce, E. coli<\/em> bacteria can turn to other sugar sources for fuel. To do this, new genes to process these alternate genes must be transcribed. When glucose levels drop, cyclic AMP (cAMP) begins to accumulate in the cell. The cAMP molecule is a signaling molecule that is involved in glucose and energy metabolism in E. coli<\/em>. When glucose levels decline in the cell, accumulating cAMP binds to the positive regulator catabolite activator protein (CAP)<\/strong>, a protein that binds to the promoters of operons that control the processing of alternative sugars. When cAMP binds to CAP, the complex binds to the promoter region of the genes that are needed to use the alternate sugar sources (Figure 1). In these operons, a CAP binding site is located upstream of the RNA polymerase binding site in the promoter. This increases the binding ability of RNA polymerase to the promoter region and the transcription of the genes.<\/p>\r\n\r\n\r\n[caption id=\"attachment_3558\" align=\"aligncenter\" width=\"800\"]\"The Figure 1. When glucose levels fall, E. coli<\/em> may use other sugars for fuel but must transcribe new genes to do so. As glucose supplies become limited, cAMP levels increase. This cAMP binds to the CAP protein, a positive regulator that binds to an operator region upstream of the genes required to use other sugar sources.[\/caption]\r\n

    The lac<\/em> Operon: An Inducer Operon<\/h2>\r\nThe third type of gene regulation in prokaryotic cells occurs through inducible operons<\/strong>, which have proteins that bind to activate or repress transcription depending on the local environment and the needs of the cell. The lac<\/em> operon is a typical inducible operon. As mentioned previously, E. coli<\/em> is able to use other sugars as energy sources when glucose concentrations are low. To do so, the cAMP\u2013CAP protein complex serves as a positive regulator to induce transcription. One such sugar source is lactose. The lac<\/em> operon\u00a0<\/strong>encodes the genes necessary to acquire and process the lactose from the local environment. CAP binds to the operator sequence upstream of the promoter that initiates transcription of the lac<\/em> operon. However, for the lac<\/em> operon to be activated, two conditions must be met. First, the level of glucose must be very low or non-existent. Second, lactose must be present. Only when glucose is absent and lactose is present will the lac<\/em> operon be transcribed. This makes sense for the cell, because it would be energetically wasteful to create the proteins to process lactose if glucose was plentiful or lactose was not available.\r\n
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    Practice Question<\/h3>\r\nTranscription of the lac<\/em> operon is carefully regulated so that its expression only occurs when glucose is limited and lactose is present to serve as an alternative fuel source.\r\n\r\n\"The\r\n\r\nIn E. coli<\/em>, the trp<\/em> operon is on by default, while the lac<\/em> operon is off. Why do you think this is the case?\r\n\r\n[practice-area rows=\"2\"][\/practice-area]\r\n[reveal-answer q=\"703127\"]Show Answer[\/reveal-answer]\r\n[hidden-answer a=\"703127\"]Tryptophan is an amino acid essential for making proteins, so the cell always needs to have some on hand. However, if plenty of tryptophan is present, it is wasteful to make more, and the expression of the trp<\/em> receptor is repressed. Lactose, a sugar found in milk, is not always available. It makes no sense to make the enzymes necessary to digest an energy source that is not available, so the lac operon is only turned on when lactose is present.[\/hidden-answer]\r\n\r\n<\/div>\r\nIf glucose is absent, then CAP can bind to the operator sequence to activate transcription. If lactose is absent, then the repressor binds to the operator to prevent transcription. If either of these requirements is met, then transcription remains off. Only when both conditions are satisfied is the lac<\/em> operon transcribed (Table 1).\r\n\r\n\r\n\r\n\r\n\r\n\r\n\r\n\r\n\r\n
    Table 1. Signals that Induce or Repress Transcription of the lac<\/em> Operon<\/th>\r\n<\/tr>\r\n
    Glucose<\/th>\r\nCAP binds<\/th>\r\nLactose<\/th>\r\nRepressor binds<\/th>\r\nTranscription<\/th>\r\n<\/tr>\r\n<\/thead>\r\n
    +<\/td>\r\n\u2212<\/td>\r\n\u2212<\/td>\r\n+<\/td>\r\nNo<\/td>\r\n<\/tr>\r\n
    +<\/td>\r\n\u2212<\/td>\r\n+<\/td>\r\n\u2212<\/td>\r\nSome<\/td>\r\n<\/tr>\r\n
    \u2212<\/td>\r\n+<\/td>\r\n\u2212<\/td>\r\n+<\/td>\r\nNo<\/td>\r\n<\/tr>\r\n
    \u2212<\/td>\r\n+<\/td>\r\n+<\/td>\r\n\u2212<\/td>\r\nYes<\/td>\r\n<\/tr>\r\n<\/tbody>\r\n<\/table>\r\n
    \r\n\r\nWatch an animated tutorial about the workings of lac<\/em> operon here.\r\n\r\nhttps:\/\/youtu.be\/iPQZXMKZEfw\r\n\r\n<\/div>\r\n
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    Practice Questions<\/h3>\r\nIf glucose is absent, but so is lactose, the lac operon will be ________.\r\n
      \r\n \t
    1. activated<\/li>\r\n \t
    2. repressed<\/li>\r\n \t
    3. activated, but only partially<\/li>\r\n \t
    4. mutated<\/li>\r\n<\/ol>\r\n[reveal-answer q=\"88859\"]Show Answer[\/reveal-answer]\r\n[hidden-answer a=\"88859\"]Answer b. If glucose is absent, but so is lactose, the lac operon will be repressed.\r\n\r\n[\/hidden-answer]\r\n\r\nDescribe how transcription in prokaryotic cells can be altered by external stimulation such as excess lactose in the environment.\r\n\r\n[practice-area rows=\"2\"][\/practice-area]\r\n[reveal-answer q=\"742266\"]Show Answer[\/reveal-answer]\r\n[hidden-answer a=\"742266\"]Environmental stimuli can increase or induce transcription in prokaryotic cells. In this example, lactose in the environment will induce the transcription of the lac<\/em> operon, but only if glucose is not available in the environment.\r\n\r\n[\/hidden-answer]\r\n\r\nWhat is the difference between a repressible and an inducible operon?\r\n\r\n[practice-area rows=\"2\"][\/practice-area]\r\n[reveal-answer q=\"353005\"]Show Answer[\/reveal-answer]\r\n[hidden-answer a=\"353005\"]A repressible operon uses a protein bound to the promoter region of a gene to keep the gene repressed or silent. This repressor must be actively removed in order to transcribe the gene. An inducible operon is either activated or repressed depending on the needs of the cell and what is available in the local environment.[\/hidden-answer]\r\n\r\n<\/div>\r\n

      Prokaryotic Gene Regulation at Work<\/h2>\r\nAs we've just learned, there are three types of regulatory molecules that can affect the expression of operons: repressors, activators, and inducers.\r\n
        \r\n \t
      • Repressors<\/strong> are proteins that suppress transcription of a gene in response to an external stimulus. In other words, a repressor keeps a gene \"off.\"<\/li>\r\n \t
      • Activators<\/strong> are proteins that increase the transcription of a gene in response to an external stimulus. In other words, an activator turns a gene \"on.\"<\/li>\r\n \t
      • Inducers<\/strong> are small molecules that either activate or repress transcription depending on the needs of the cell and the availability of substrate. Inducers basically help speed up or slow down \"on\" or \"off\" by binding to a repressor or activator. In other words: they don't work alone.<\/li>\r\n<\/ul>\r\nIn the interactive below, we will focus on the differences between activators and repressors:\r\n\r\n