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Operators
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Operators
Operators J C Hu Copyright ß 2001 Academic Press doi: 10.1006/rwgn.2001.0935
`Operators' are DNA sites where transcription factors bind and alter the frequency of initiation of transcription. Operators were initially identified as genetic loci that gave a constitutive phenotype when mutated. Operator mutations affect the regulation of genes that are in cis i.e., physically coupled to the operator by being encoded by a contiguous sequence of DNA. Operators control genes that are in an operon, i.e., cotranscribed into the same mRNA from a site in the DNA called the promoter. The existence of operators was postulated by Jacob and Monod as part of the operon model of gene control in the lactose utilization system of Escherichia coli (the lac operon). Pardee, Jacob, and Monod had found that a regulatory molecule, the repressor, controlled the inducible synthesis of lac operon proteins. Jacob and Monod predicted that the repressor should act by recognizing a specific `receiver' physically associated with the regulated genes, which they named the operator. This model predicted that operator mutations would lead to a constitutive phenotype and that they would be dominant, because the presence of a second copy of the operator on another chromosome would not affect the ability of the repressor to bind the mutant operator. In addition, the effects of operator mutations would be `cis-acting'; i.e., they would only affect the genes that were on the same chromosome. By contrast, mutations that inactivated the repressor would either be complemented by a wild-type copy of the repressor or would be dominant in either the cis or trans configuration. The model was confirmed by the isolation of lac constitutive mutants in an E. coli strain that was merodiploid for the lac operon. By genetic crosses to place the operator mutations in cis and in trans to mutations affecting lac operon proteins, Jacob and Monod (1961) showed that the mutations, called `Oc,' were indeed cis-dominant. For the paradigm systems studied by Jacob and Monod, the lac operon and the control of lysogeny in phage l, the repressors are oligomeric proteins, and the operators are DNA sequences that engage the repressors. Mutations in the operators usually act by reducing the binding affinity of the repressor. While it was originally thought that operators were exclusively short DNA sequences that overlapped promoters, it is now clear that many operators involve sequences that can be either far upstream or downstream from the
promoter. Many operators, including lac and l, turn out to function as multipartite elements. Binding to two or more operators is often required to achieve normal transcriptional regulation; transcription factors often bind to multiple operators cooperatively. When the individual operator sites are separated by significant distances, cooperative binding often involves the bending of the intervening DNA into a loop. The molecular mechanisms by which repressors and operators control the initiation of transcription are now known in great detail for many bacterial regulatory systems. Using purified proteins and DNA, it is possible to determine how repressors affect the rates of different steps in the process of transcription initiation, and to examine complexes trapped when an operator is bound by its cognate repressor. Both the lac and l repressors appear to act by preventing the initial binding of RNA polymerase to the promoter. Other repressors act at later steps in the initiation process. Purified proteins and DNA have also allowed the elucidation of the structures of repressor±operator complexes. These structures, which give a molecular form at atomic resolution to the systems defined by genetics and biochemistry, resolve many questions about how the repressor is able to recognize the specific DNA sequence of the operator. In particular, the structures address two classes of models: sequence versus structural reading of the DNA sequence. In the sequence readout model, the repressor recognizes features of the base sequence of the operator by making direct contact with the base pairs, in either the major or minor groove of B-form DNA. In structural readout models, the operator DNA has a propensity to form a non-B structure that is recognized by the repressor. The structures of these repressor±operator complexes revealed that the repressors interacted with operators that were close in structure to B-form DNA by interacting with both the sugar±phosphate backbone and with functional groups in the major groove. However, other DNA±protein complexes involve different mixes of sequence and structural readout. For example, the center of the phage 434 operator is important for repressor recognition, but does not make direct contact with the protein. Instead, it promotes a bend in the DNA that allows the flanking sequences to make favorable contacts with the repressor. In different complexes, the DNA can be found in a variety of bent, twisted, kinked, and unwound structures. Nature does not use a universal protein±DNA recognition code. The operon model was originally formulated on the basis of genetic models and is formally independent of the molecular nature of the repressor or the operator or the mechanism of regulation. However, many
Organelles 1377 genetic elements that would satisfy the original operational definition for an operator are no longer considered to be instances of operators. For example, the attenuators of many bacterial operons are cis-acting elements that are required for the negative regulation of gene expression. Some attenuator mutations lead to a cis-dominant constitutive phenotype. Nevertheless, the differences between the mechanisms of regulation at operators and attenuators has led molecular geneticists to classify them as different kinds of cis-acting genetic elements. Similarly, regulatory sites that affect translation are also cis-acting and are sometimes referred to as operators. Notable examples occur in the autoregulation of translation by the phage MS2 coat protein, and the phage T4 gene 32 and gene 43 products. In the latter case, a short stem±loop RNA structure binds to the gene 43 product, which is the phage DNA polymerase.
References
Jacob F and Monod J (1961) On the regulation of gene activity. Cold Spring Harbor Symposia on Quantitative Biology 26: 193±211.
See also: Attenuation; Attenuation, Transcriptional; lac Operon; Repressor
3. The operator (O), comprising a short segment of DNA found adjacent to the promoter is a control element which binds a regulator protein that can either repress or activate transcription. Usually the regulatory gene is located in a different region of the chromosome. If the specific repressor binds to the operator, transcription of the structural genes is blocked. In some operons a small molecule may act as an inducer, binding to the repressor, inactivating it and thereby derepressing the operon. In others, a repressor may be unable to bind to the operator unless it is bound to a small molecule, the corepressor. Some operons are under attenuator control, in which transcription is initiated but is arrested before the mRNA is transcribed. The resultant introductory mRNA sequence (the leader sequence) includes the attenuator, which by folding back on itself to produce a loop, blocks the progress of RNA polymerase along the DNA strand. The operon theory was first proposed by Jacob and Monod in the early 1960s, who described the regulatory mechanism of the lac operon in Escherichia coli. See also: Histidine Operon; Jacob, FrancËois; lac Operon; Tryptophan Operon
Operon
Organelles
T M Picknett and S Brenner
M W Gray
Copyright ß 2001 Academic Press doi: 10.1006/rwgn.2001.0936
Copyright ß 2001 Academic Press doi: 10.1006/rwgn.2001.0937
An operon is a genetic regulatory system found in bacteria and their viruses in which genes coding for functionally related proteins are clustered together and transcribed from one promoter into a single RNA. This is a functional unit and allows protein synthesis to be controlled in a coordinated and regulated fashion in response to the cell's needs. Proteins can thus be produced only when they are required. A typical operon comprises of several types of genes:
Definition
1. Structural genes (S1±Sn) which code for the primary structures of enzyme proteins involved in a metabolic pathway, such as the biosynthesis of an amino acid. 2. The promoter (P), a short sequence of DNA acting as the start point, and to which RNA polymerase binds. The promoter is controlled by various regulatory elements that respond to environmental stimuli.
A characteristic feature of eukaryotic (nucleuscontaining) cells is the variety of `organelles' they contain. One or more lipid membranes form the outer boundary of these distinct subcellular structures, defining discrete compartments within which the biochemical reactions typical of each kind of organelle type occur. By this definition, macromolecular complexes that lack a bounding membrane (e.g., ribosomes, nucleoli) are not considered to be organelles, even though they may have a readily recognizable structure and a specialized function within the cell. Organelles may be thought of as analogs of bodily organs (e.g., heart, liver, kidney), each of which has a characteristic size and shape and serves a distinct physiological role that is essential to the life of the organism. Just as organ systems communicate with one another, subcellular organelles interact through
Operators
Operators J C Hu Copyright ß 2001 Academic Press doi: 10.1006/rwgn.2001.0935
`Operators' are DNA sites where transcription factors bind and alter the frequency of initiation of transcription. Operators were initially identified as genetic loci that gave a constitutive phenotype when mutated. Operator mutations affect the regulation of genes that are in cis i.e., physically coupled to the operator by being encoded by a contiguous sequence of DNA. Operators control genes that are in an operon, i.e., cotranscribed into the same mRNA from a site in the DNA called the promoter. The existence of operators was postulated by Jacob and Monod as part of the operon model of gene control in the lactose utilization system of Escherichia coli (the lac operon). Pardee, Jacob, and Monod had found that a regulatory molecule, the repressor, controlled the inducible synthesis of lac operon proteins. Jacob and Monod predicted that the repressor should act by recognizing a specific `receiver' physically associated with the regulated genes, which they named the operator. This model predicted that operator mutations would lead to a constitutive phenotype and that they would be dominant, because the presence of a second copy of the operator on another chromosome would not affect the ability of the repressor to bind the mutant operator. In addition, the effects of operator mutations would be `cis-acting'; i.e., they would only affect the genes that were on the same chromosome. By contrast, mutations that inactivated the repressor would either be complemented by a wild-type copy of the repressor or would be dominant in either the cis or trans configuration. The model was confirmed by the isolation of lac constitutive mutants in an E. coli strain that was merodiploid for the lac operon. By genetic crosses to place the operator mutations in cis and in trans to mutations affecting lac operon proteins, Jacob and Monod (1961) showed that the mutations, called `Oc,' were indeed cis-dominant. For the paradigm systems studied by Jacob and Monod, the lac operon and the control of lysogeny in phage l, the repressors are oligomeric proteins, and the operators are DNA sequences that engage the repressors. Mutations in the operators usually act by reducing the binding affinity of the repressor. While it was originally thought that operators were exclusively short DNA sequences that overlapped promoters, it is now clear that many operators involve sequences that can be either far upstream or downstream from the
promoter. Many operators, including lac and l, turn out to function as multipartite elements. Binding to two or more operators is often required to achieve normal transcriptional regulation; transcription factors often bind to multiple operators cooperatively. When the individual operator sites are separated by significant distances, cooperative binding often involves the bending of the intervening DNA into a loop. The molecular mechanisms by which repressors and operators control the initiation of transcription are now known in great detail for many bacterial regulatory systems. Using purified proteins and DNA, it is possible to determine how repressors affect the rates of different steps in the process of transcription initiation, and to examine complexes trapped when an operator is bound by its cognate repressor. Both the lac and l repressors appear to act by preventing the initial binding of RNA polymerase to the promoter. Other repressors act at later steps in the initiation process. Purified proteins and DNA have also allowed the elucidation of the structures of repressor±operator complexes. These structures, which give a molecular form at atomic resolution to the systems defined by genetics and biochemistry, resolve many questions about how the repressor is able to recognize the specific DNA sequence of the operator. In particular, the structures address two classes of models: sequence versus structural reading of the DNA sequence. In the sequence readout model, the repressor recognizes features of the base sequence of the operator by making direct contact with the base pairs, in either the major or minor groove of B-form DNA. In structural readout models, the operator DNA has a propensity to form a non-B structure that is recognized by the repressor. The structures of these repressor±operator complexes revealed that the repressors interacted with operators that were close in structure to B-form DNA by interacting with both the sugar±phosphate backbone and with functional groups in the major groove. However, other DNA±protein complexes involve different mixes of sequence and structural readout. For example, the center of the phage 434 operator is important for repressor recognition, but does not make direct contact with the protein. Instead, it promotes a bend in the DNA that allows the flanking sequences to make favorable contacts with the repressor. In different complexes, the DNA can be found in a variety of bent, twisted, kinked, and unwound structures. Nature does not use a universal protein±DNA recognition code. The operon model was originally formulated on the basis of genetic models and is formally independent of the molecular nature of the repressor or the operator or the mechanism of regulation. However, many
Organelles 1377 genetic elements that would satisfy the original operational definition for an operator are no longer considered to be instances of operators. For example, the attenuators of many bacterial operons are cis-acting elements that are required for the negative regulation of gene expression. Some attenuator mutations lead to a cis-dominant constitutive phenotype. Nevertheless, the differences between the mechanisms of regulation at operators and attenuators has led molecular geneticists to classify them as different kinds of cis-acting genetic elements. Similarly, regulatory sites that affect translation are also cis-acting and are sometimes referred to as operators. Notable examples occur in the autoregulation of translation by the phage MS2 coat protein, and the phage T4 gene 32 and gene 43 products. In the latter case, a short stem±loop RNA structure binds to the gene 43 product, which is the phage DNA polymerase.
References
Jacob F and Monod J (1961) On the regulation of gene activity. Cold Spring Harbor Symposia on Quantitative Biology 26: 193±211.
See also: Attenuation; Attenuation, Transcriptional; lac Operon; Repressor
3. The operator (O), comprising a short segment of DNA found adjacent to the promoter is a control element which binds a regulator protein that can either repress or activate transcription. Usually the regulatory gene is located in a different region of the chromosome. If the specific repressor binds to the operator, transcription of the structural genes is blocked. In some operons a small molecule may act as an inducer, binding to the repressor, inactivating it and thereby derepressing the operon. In others, a repressor may be unable to bind to the operator unless it is bound to a small molecule, the corepressor. Some operons are under attenuator control, in which transcription is initiated but is arrested before the mRNA is transcribed. The resultant introductory mRNA sequence (the leader sequence) includes the attenuator, which by folding back on itself to produce a loop, blocks the progress of RNA polymerase along the DNA strand. The operon theory was first proposed by Jacob and Monod in the early 1960s, who described the regulatory mechanism of the lac operon in Escherichia coli. See also: Histidine Operon; Jacob, FrancËois; lac Operon; Tryptophan Operon
Operon
Organelles
T M Picknett and S Brenner
M W Gray
Copyright ß 2001 Academic Press doi: 10.1006/rwgn.2001.0936
Copyright ß 2001 Academic Press doi: 10.1006/rwgn.2001.0937
An operon is a genetic regulatory system found in bacteria and their viruses in which genes coding for functionally related proteins are clustered together and transcribed from one promoter into a single RNA. This is a functional unit and allows protein synthesis to be controlled in a coordinated and regulated fashion in response to the cell's needs. Proteins can thus be produced only when they are required. A typical operon comprises of several types of genes:
Definition
1. Structural genes (S1±Sn) which code for the primary structures of enzyme proteins involved in a metabolic pathway, such as the biosynthesis of an amino acid. 2. The promoter (P), a short sequence of DNA acting as the start point, and to which RNA polymerase binds. The promoter is controlled by various regulatory elements that respond to environmental stimuli.
A characteristic feature of eukaryotic (nucleuscontaining) cells is the variety of `organelles' they contain. One or more lipid membranes form the outer boundary of these distinct subcellular structures, defining discrete compartments within which the biochemical reactions typical of each kind of organelle type occur. By this definition, macromolecular complexes that lack a bounding membrane (e.g., ribosomes, nucleoli) are not considered to be organelles, even though they may have a readily recognizable structure and a specialized function within the cell. Organelles may be thought of as analogs of bodily organs (e.g., heart, liver, kidney), each of which has a characteristic size and shape and serves a distinct physiological role that is essential to the life of the organism. Just as organ systems communicate with one another, subcellular organelles interact through