Transcriptional regulation in Bacteria Thanks to the relative ease of doing genetics with bacteria transcriptional regulation in bacteria is better understood than that in other organisms and has served as a framework for understanding transcriptional regulation in eukaryotic organisms There are important differences between the mechanisms of transcriptional regulation in bacteria and higher organisms, many of which relate to the presence of a nuclear membrane Nevertheless, many of the strategies used are similar throughout the biological world, and many general principles have been uncovered through studies of bacterial transcriptional regulation
• Transcriptional Regulation in Bacteria • Thanks to the relative ease of doing genetics with bacteria, transcriptional regulation in bacteria is better understood than that in other organisms and has served as a framework for understanding transcriptional regulation in eukaryotic organisms. There are important differences between the mechanisms of transcriptional regulation in bacteria and higher organisms, many of which relate to the presence of a nuclear membrane. Nevertheless, many of the strategies used are similar throughout the biological world, and many general principles have been uncovered through studies of bacterial transcriptional regulation
(A)The two general types of transcriptional regulation. In negative regulation, a repressor binds OFF to an operator and turns the operon off. In positive regulation,an activator protein binds upstream of the promoter and turns the operon on B)Graph showing the usual locations of activator sites relative to operators. Activator sites are usually farther upstream Each datum point Act valor sites indicates the middle of the known vo2a region on the dna where a regulatory protein binds LI 80-60-40-20 Base pairs coordinate
(A) The two general types of transcriptional regulation. In negative regulation, a repressor binds to an operator and turns the operon off. In positive regulation, an activator protein binds upstream of the promoter and turns the operon on. (B) Graph showing the usual locations of activator sites relative to operators. Activator sites are usually farther upstream. Each datum point indicates the middle of the known region on the DNA where a regulatory protein binds
The Bacterial Operon The concept of an operon is central to hypotheses about bacterial transcriptional regulation. Bacterial genes are often arranged so that more than one gene can be transcribed into the same polycistronic mRNA. In such cases. the genes are said to be cotranscribed. Cotranscription of more than one gene into a polycistronic mRNA Seems to be unique to bacteria and their phages and affects the types of translational initiation regions TIR)used on the mRNA. In eukaryotes, generally the first AUg codon in an mrNa is used to initiate translation so that only one polypeptide can be encoded by each mRNA However, bacterial TIRs are much more complex. Shine Dalgarno and other sequences help define the tir because of its distinct structure. a bacterial TIR will be recognized wherever it appears in the mRNA, and more than one tir can be recognized in the same mRNA
• The Bacterial Operon • The concept of an operon is central to hypotheses about bacterial transcriptional regulation. Bacterial genes are often arranged so that more than one gene can be transcribed into the same polycistronic mRNA. In such cases, the genes are said to be cotranscribed. Cotranscription of more than one gene into a polycistronic mRNA seems to be unique to bacteria and their phages and affects the types of translational initiation regions (TIR) used on the mRNA. In eukaryotes, generally the first AUG codon in an mRNA is used to initiate translation so that only one polypeptide can be encoded by each mRNA. However, bacterial TIRs are much more complex. ShineDalgarno and other sequences help define the TIR. Because of its distinct structure, a bacterial TIR will be recognized wherever it appears in the mRNA, and more than one TIR can be recognized in the same mRNA
a bacterial operon is the region on the dna that includes genes cotranscribed into the same mRNa plus all of the adjacent cis-acting sequences required for transcription of these genes, including the genes' promoter as well as operators and other sequences involved in regulating the transcription of the genes. Because the genes of an operon are all transcribed from the same promoter and use the same regulatory sequences, all the genes of an operon can be transcriptionally regulated simultaneously
• A bacterial operon is the region on the DNA that includes genes cotranscribed into the same mRNA plus all of the adjacent cis-acting sequences required for transcription of these genes, including the genes' promoter as well as operators and other sequences involved in regulating the transcription of the genes. Because the genes of an operon are all transcribed from the same promoter and use the same regulatory sequences, all the genes of an operon can be transcriptionally regulated simultaneously
Repressors and Activators Before discussing our examples of transcriptional regulation in bacteria, we give a brief overview of the types of regulation known to occur and define some of the terms that describe the factors involved. The transcription of bacterial operons is regulated by the products of regulatory genes, which are often proteins called repressors or activators. These regulatory proteins bind close to the operon,s promoter and regulate transcription from the promoter. Sometimes, a regulatory protein can play dual roles and can also perform an enzymatic reaction in the pathway encoded by the operon Because they bind to DNA. repressors and activators often have the helix-turn-helix motif shared by many dna binding proteins Repressors bind to sites called operators and turn off the promoter, thereby preventing transcription of the genes of the operon. Activators, in contrast, bind to activator sites and turn on the promoter, thereby facilitating transcription of the operon genes
• Repressors and Activators • Before discussing our examples of transcriptional regulation in bacteria, we give a brief overview of the types of regulation known to occur and define some of the terms that describe the factors involved. The transcription of bacterial operons is regulated by the products of regulatory genes, which are often proteins called repressors or activators. These regulatory proteins bind close to the operon's promoter and regulate transcription from the promoter. Sometimes, a regulatory protein can play dual roles and can also perform an enzymatic reaction in the pathway encoded by the operon. Because they bind to DNA, repressors and activators often have the helix-turn-helix motif shared by many DNA binding proteins . • Repressors bind to sites called operators and turn off the promoter, thereby preventing transcription of the genes of the operon. Activators, in contrast, bind to activator sites and turn on the promoter, thereby facilitating transcription of the operon genes
Negative and Positive regulation Another important concept is the distinction between negative and positive regulation by regulatory proteins. If a regulatory protein in its active state turns off the expression of the operon, the operon is said to be negatively regulated by the regulatory protein. If the regulatory protein in its active state turns on the operon, the operon is positively regulated by the regulatory protein. An operon regulated by a repressor is therefore negatively regulated, because the presence of the active repressor prevents transcription of that operon. In contrast an operon regulated by an activator is positively regulated because in its active state the activator protein turns on transcription of the operon under its control Activator and repressor proteins usually bind to different regions of the dna
• Negative and Positive Regulation • Another important concept is the distinction between negative and positive regulation by regulatory proteins. If a regulatory protein in its active state turns off the expression of the operon, the operon is said to be negatively regulated by the regulatory protein. If the regulatory protein in its active state turns on the operon, the operon is positively regulated by the regulatory protein. An operon regulated by a repressor is therefore negatively regulated, because the presence of the active repressor prevents transcription of that operon. In contrast, an operon regulated by an activator is positively regulated, because in its active state the activator protein turns on transcription of the operon under its control. • Activator and repressor proteins usually bind to different regions of the DNA
Activators usually bind upstream of the-35 sequence of the promoter, where they can make contact with the rna polymerase bound to the promoter. repressors often bind to the promoter region itself, or at least very close to it, and thereby block access by rna polymerase to the promoter Some regulatory proteins can be both repressors and activators depending upon the situation. The n repressor is an example. It represses transcription from the the pi and pr promoters but activates the prM promoter. The binding site on the dna for the regulatory protein often changes when the protein shifts from being an activator to a repressor
• Activators usually bind upstream of the -35 sequence of the promoter, where they can make contact with the RNA polymerase bound to the promoter. Repressors often bind to the promoter region itself, or at least very close to it, and thereby block access by RNA polymerase to the promoter. • Some regulatory proteins can be both repressors and activators, depending upon the situation. The λ repressor is an example. It represses transcription from the the pL and pR promoters but activates the pRM promoter. The binding site on the DNA for the regulatory protein often changes when the protein shifts from being an activator to a repressor
Inducers and corepressors Whether a regulatory protein is active sometimes depends on whether it is bound to a small molecule. Small molecules that bind to proteins and change their properties are called effectors An effector that binds to a repressor or activator and thereby initiates transcription of an operon is called the inducer of the operon. In contrast, an effector that binds to a repressor and causes it to block transcription is called a corepressor The activity of regulatory proteins is not necessarily altered only by binding to small molecule effectors. Some repressors and activators are covalently altered under some conditions for example, by methylation or phosphorylation
• Inducers and Corepressors • Whether a regulatory protein is active sometimes depends on whether it is bound to a small molecule. Small molecules that bind to proteins and change their properties are called effectors. An effector that binds to a repressor or activator and thereby initiates transcription of an operon is called the inducer of the operon. In contrast, an effector that binds to a repressor and causes it to block transcription is called a corepressor. • The activity of regulatory proteins is not necessarily altered only by binding to small molecule effectors. Some repressors and activators are covalently altered under some conditions, for example, by methylation or phosphorylation
Genetic Evidence for negative and positive Regulation Negatively and positively regulated operons behave very differently in genetic tests. One difference is in the effect of mutations that inactivate the regulatory gene for the operon. If an operon is negatively regulated a mutation that inactivates the regulatory gene will allow transcription of the operon genes, even in the absence of inducer. If the regulation is positive mutations that inactivate the regulatory gene will prevent transcription of the genes of the operon, even in the presence of the inducer. a mutant in which the genes of an operon are al ways transcribed even in the absence of inducer, is called a constitutive mutant. Constitutive mutations are much more common with negatively than with positively regulated operons because any mutation that inactivates the repressor will result in the constitutive phenotype. With positively regulated operons, a constitutive phenotype can be caused only by changes that do not inactivate the activator protein but alter it so that it can activate transcription without binding to the inducer. Such changes tend to be rare
• Genetic Evidence for Negative and Positive Regulation • Negatively and positively regulated operons behave very differently in genetic tests. One difference is in the effect of mutations that inactivate the regulatory gene for the operon. If an operon is negatively regulated, a mutation that inactivates the regulatory gene will allow transcription of the operon genes, even in the absence of inducer. If the regulation is positive, mutations that inactivate the regulatory gene will prevent transcription of the genes of the operon, even in the presence of the inducer. A mutant in which the genes of an operon are always transcribed, even in the absence of inducer, is called a constitutive mutant. Constitutive mutations are much more common with negatively than with positively regulated operons because any mutation that inactivates the repressor will result in the constitutive phenotype. With positively regulated operons, a constitutive phenotype can be caused only by changes that do not inactivate the activator protein but alter it so that it can activate transcription without binding to the inducer. Such changes tend to be rare
Complementation tests reveal another difference between negatively and postively regulated operons. Constitutive mutations of a negatively regulated operon are often recessive to the wild type This is because any normal repressor protein in the cell encoded by a wild-type copy of the gene will bind to the operator and block transcription, even if the repressor encoded by the mutant copy of the gene in the same cell is inactive. In contrast. constitutive mutations in a solely positively regulated operon should be dominant to the wild type. A mutant activator protein that is active without inducer bound might activate transcription even in the presence of a wild-type activator protein
• Complementation tests reveal another difference between negatively and postively regulated operons. Constitutive mutations of a negatively regulated operon are often recessive to the wild type. This is because any normal repressor protein in the cell encoded by a wild-type copy of the gene will bind to the operator and block transcription, even if the repressor encoded by the mutant copy of the gene in the same cell is inactive. In contrast, constitutive mutations in a solely positively regulated operon should be dominant to the wild type. A mutant activator protein that is active without inducer bound might activate transcription even in the presence of a wild-type activator protein