TNBGGA: The No Bullshit Guide to Genetic Analysis

So far, we have been considering simple regulatory systems with either a single repressorplugin-autotooltip__default plugin-autotooltip_bigRepressor: a DNA binding protein that binds to negatively acting cis-acting elements such as operators in bacteria to inhibit transcription. Compare to negative regulator. (Lac) or a single activatorplugin-autotooltip__default plugin-autotooltip_bigTransactivator (activator): a DNA binding protein that binds to promoter sequences to activate the transcription of nearby genes. In the context of gene expression, “activator” is usually a synonym for transactivator. Compare with positive regulator. (Mal). Often genesplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) are regulated by a more complicated set of regulatory steps, which together can be thought of as a regulatory pathwayplugin-autotooltip__default plugin-autotooltip_bigPathway: a series of reactions or events that occur in sequence with some common goal or purpose.. Although there are good methods that can be used to determine the order of steps in a regulatory pathwayplugin-autotooltip__default plugin-autotooltip_bigPathway: a series of reactions or events that occur in sequence with some common goal or purpose. (as will be discussed shortly), it is usually difficult at first to tell whether a given component identified by mutationplugin-autotooltip__default plugin-autotooltip_bigMutation: a change in the DNA of a gene that results in a change of phenotype compared to a reference wildtype allele. See also: mutant. is acting directly on the DNAplugin-autotooltip__default plugin-autotooltip_bigDNA: deoxyribonucleic acid. The genetic material for nearly all life on Earth. of the regulated geneplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) or whether it is acting at a step upstreamplugin-autotooltip__default plugin-autotooltip_bigUpstream/downstream: These descriptors have different meanings depending on context:

* In genetics, these are terms used to describe directions on DNA, usually relative to the transcription start site of a gene. DNA sequences that are located in the same direction as the direction of in a regulatory pathwayplugin-autotooltip__default plugin-autotooltip_bigPathway: a series of reactions or events that occur in sequence with some common goal or purpose..

For example, it will often be the case that a recessiveplugin-autotooltip__default plugin-autotooltip_bigRecessive: used to describe an allele, usually in comparison to wildtype. Recessive alleles do not exhibit their phenotype when combined with a wildtype allele. transplugin-autotooltip__default plugin-autotooltip_bigCis and trans: In genetics, cis and trans are terms used to describe the relative physical locations of genes or genetic elements. If two genes are in cis, this means that they are physically located on the same DNA molecule. If two genes are in trans, this means that they are physically located on two different-acting mutationplugin-autotooltip__default plugin-autotooltip_bigMutation: a change in the DNA of a gene that results in a change of phenotype compared to a reference wildtype allele. See also: mutant. that causes constitutiveplugin-autotooltip__default plugin-autotooltip_bigConstitutive: a term describing a pattern of gene expression, wherein the gene is always expressed no matter what. For some genes, constitutive expression is normal (see housekeeping gene). For inducible genes or operons, constitutive is a mutant state. expressionplugin-autotooltip__default plugin-autotooltip_bigExpression: a term used to describe the idea that the function of a gene is apparent and can be observed. Genes may not always be expressed all the time in all places. is not an actual repressorplugin-autotooltip__default plugin-autotooltip_bigRepressor: a DNA binding protein that binds to negatively acting cis-acting elements such as operators in bacteria to inhibit transcription. Compare to negative regulator. proteinplugin-autotooltip__default plugin-autotooltip_bigProtein: a molecule that is formed by the translation of messenger RNAs (mRNAs). Functions that proteins provide are what usually give organisms their phenotypes., but a proteinplugin-autotooltip__default plugin-autotooltip_bigProtein: a molecule that is formed by the translation of messenger RNAs (mRNAs). Functions that proteins provide are what usually give organisms their phenotypes. acting upstreamplugin-autotooltip__default plugin-autotooltip_bigUpstream/downstream: These descriptors have different meanings depending on context:

* In genetics, these are terms used to describe directions on DNA, usually relative to the transcription start site of a gene. DNA sequences that are located in the same direction as the direction of in a regulatory pathwayplugin-autotooltip__default plugin-autotooltip_bigPathway: a series of reactions or events that occur in sequence with some common goal or purpose. in such a way that the net effect of this proteinsplugin-autotooltip__default plugin-autotooltip_bigProtein: a molecule that is formed by the translation of messenger RNAs (mRNAs). Functions that proteins provide are what usually give organisms their phenotypes. is to cause repression of geneplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) function. The best way to represent this situation is to call the gene productplugin-autotooltip__default plugin-autotooltip_bigGene product: the molecule that is produced based on information contained within a gene and provides function to the organism. Most of the time, a gene product is a protein. Sometimes gene products can also be an RNA molecule. In forward genetic analysis, we can't formally tell if a gene product is a negative regulatorplugin-autotooltip__default plugin-autotooltip_bigNegative regulator: in the context of gene regulation, a negative regulator is a gene whose activity blocks the expression of another gene. Compare to repressor. and to reserve the term “repressorplugin-autotooltip__default plugin-autotooltip_bigRepressor: a DNA binding protein that binds to negatively acting cis-acting elements such as operators in bacteria to inhibit transcription. Compare to negative regulator.” for cases in which we know that the proteinplugin-autotooltip__default plugin-autotooltip_bigProtein: a molecule that is formed by the translation of messenger RNAs (mRNAs). Functions that proteins provide are what usually give organisms their phenotypes. actually shuts off transcriptionplugin-autotooltip__default plugin-autotooltip_bigRNA transcription: the process of RNA polymerase using the DNA sequence of a gene as a template to form an mRNA (in prokaryotes) or pre-mRNA (in eukaryotes). In most cases, “transcription” implies RNA transcription. directly by binding to an operatorplugin-autotooltip__default plugin-autotooltip_bigOperator: in bacterial genetics, an operator is a cis-acting genetic element that negatively regulates the expression of nearby genes. $lacO$ of the Lac operon is an example of an operator. site. Similarly, the best way to represent a geneplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) defined by a recessiveplugin-autotooltip__default plugin-autotooltip_bigRecessive: used to describe an allele, usually in comparison to wildtype. Recessive alleles do not exhibit their phenotype when combined with a wildtype allele., transplugin-autotooltip__default plugin-autotooltip_bigCis and trans: In genetics, cis and trans are terms used to describe the relative physical locations of genes or genetic elements. If two genes are in cis, this means that they are physically located on the same DNA molecule. If two genes are in trans, this means that they are physically located on two different-acting mutationplugin-autotooltip__default plugin-autotooltip_bigMutation: a change in the DNA of a gene that results in a change of phenotype compared to a reference wildtype allele. See also: mutant. that causes uninducibleplugin-autotooltip__default plugin-autotooltip_bigUninducible: a mutant state wherein normally inducible genes are no longer inducible (and in fact may no longer be expressed at all). expressionplugin-autotooltip__default plugin-autotooltip_bigExpression: a term used to describe the idea that the function of a gene is apparent and can be observed. Genes may not always be expressed all the time in all places. is as a positive regulatorplugin-autotooltip__default plugin-autotooltip_bigPositive regulator: in the context of gene regulation, a positive regulator is a gene whose activity increases the expression of another gene. Compare to transactivator/activator. until more specific information can be obtained about whether or not the gene productplugin-autotooltip__default plugin-autotooltip_bigGene product: the molecule that is produced based on information contained within a gene and provides function to the organism. Most of the time, a gene product is a protein. Sometimes gene products can also be an RNA molecule. In forward genetic analysis, we can't formally tell if a gene product is directly activates transcriptionplugin-autotooltip__default plugin-autotooltip_bigRNA transcription: the process of RNA polymerase using the DNA sequence of a gene as a template to form an mRNA (in prokaryotes) or pre-mRNA (in eukaryotes). In most cases, “transcription” implies RNA transcription. (Fig. 11.2).

An important note about interpreting such diagrams is that the arrow or blocking symbol do not necessarily imply direct physical interaction; they simply mean that the negative regulatorplugin-autotooltip__default plugin-autotooltip_bigNegative regulator: in the context of gene regulation, a negative regulator is a gene whose activity blocks the expression of another gene. Compare to repressor. or positive activatorplugin-autotooltip__default plugin-autotooltip_bigTransactivator (activator): a DNA binding protein that binds to promoter sequences to activate the transcription of nearby genes. In the context of gene expression, “activator” is usually a synonym for transactivator. Compare with positive regulator. have a net negative or positive effect, respectively, on geneplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) expressionplugin-autotooltip__default plugin-autotooltip_bigExpression: a term used to describe the idea that the function of a gene is apparent and can be observed. Genes may not always be expressed all the time in all places.. There may (or may not) be other intermediate factors involved.

Imagine that we are studying the regulation of an enzymeplugin-autotooltip__default plugin-autotooltip_bigEnzyme: a macromolecule, usually a protein (but sometimes an RNA), that functions as a catalyst of some kind of biochemical reaction.-coding geneplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) and we find a recessiveplugin-autotooltip__default plugin-autotooltip_bigRecessive: used to describe an allele, usually in comparison to wildtype. Recessive alleles do not exhibit their phenotype when combined with a wildtype allele. transplugin-autotooltip__default plugin-autotooltip_bigCis and trans: In genetics, cis and trans are terms used to describe the relative physical locations of genes or genetic elements. If two genes are in cis, this means that they are physically located on the same DNA molecule. If two genes are in trans, this means that they are physically located on two different-acting mutationplugin-autotooltip__default plugin-autotooltip_bigMutation: a change in the DNA of a gene that results in a change of phenotype compared to a reference wildtype allele. See also: mutant. in geneplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) $A$ that gives uninducibleplugin-autotooltip__default plugin-autotooltip_bigUninducible: a mutant state wherein normally inducible genes are no longer inducible (and in fact may no longer be expressed at all). enzymeplugin-autotooltip__default plugin-autotooltip_bigEnzyme: a macromolecule, usually a protein (but sometimes an RNA), that functions as a catalyst of some kind of biochemical reaction. expressionplugin-autotooltip__default plugin-autotooltip_bigExpression: a term used to describe the idea that the function of a gene is apparent and can be observed. Genes may not always be expressed all the time in all places.. The simplest interpretation is that geneplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) $A$ is a positive activatorplugin-autotooltip__default plugin-autotooltip_bigTransactivator (activator): a DNA binding protein that binds to promoter sequences to activate the transcription of nearby genes. In the context of gene expression, “activator” is usually a synonym for transactivator. Compare with positive regulator. of the enzymeplugin-autotooltip__default plugin-autotooltip_bigEnzyme: a macromolecule, usually a protein (but sometimes an RNA), that functions as a catalyst of some kind of biochemical reaction. (Fig. 3):

Next, say that we find a recessiveplugin-autotooltip__default plugin-autotooltip_bigRecessive: used to describe an allele, usually in comparison to wildtype. Recessive alleles do not exhibit their phenotype when combined with a wildtype allele. transplugin-autotooltip__default plugin-autotooltip_bigCis and trans: In genetics, cis and trans are terms used to describe the relative physical locations of genes or genetic elements. If two genes are in cis, this means that they are physically located on the same DNA molecule. If two genes are in trans, this means that they are physically located on two different-acting mutationplugin-autotooltip__default plugin-autotooltip_bigMutation: a change in the DNA of a gene that results in a change of phenotype compared to a reference wildtype allele. See also: mutant. in geneplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) $B$ that gives constitutiveplugin-autotooltip__default plugin-autotooltip_bigConstitutive: a term describing a pattern of gene expression, wherein the gene is always expressed no matter what. For some genes, constitutive expression is normal (see housekeeping gene). For inducible genes or operons, constitutive is a mutant state. enzymeplugin-autotooltip__default plugin-autotooltip_bigEnzyme: a macromolecule, usually a protein (but sometimes an RNA), that functions as a catalyst of some kind of biochemical reaction. expressionplugin-autotooltip__default plugin-autotooltip_bigExpression: a term used to describe the idea that the function of a gene is apparent and can be observed. Genes may not always be expressed all the time in all places.. The following model takes into account the behavior of mutationsplugin-autotooltip__default plugin-autotooltip_bigMutation: a change in the DNA of a gene that results in a change of phenotype compared to a reference wildtype allele. See also: mutant. in both $A$ and $B$ (Fig. 4):

The idea is that the geneplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) for the enzymeplugin-autotooltip__default plugin-autotooltip_bigEnzyme: a macromolecule, usually a protein (but sometimes an RNA), that functions as a catalyst of some kind of biochemical reaction. is negatively regulated by geneplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) $B$, which in turn is negatively regulated by geneplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) $A$. The net outcome is still a positive effect of geneplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) $A$ on enzymeplugin-autotooltip__default plugin-autotooltip_bigEnzyme: a macromolecule, usually a protein (but sometimes an RNA), that functions as a catalyst of some kind of biochemical reaction. expressionplugin-autotooltip__default plugin-autotooltip_bigExpression: a term used to describe the idea that the function of a gene is apparent and can be observed. Genes may not always be expressed all the time in all places.. To distinguish between the two models, we will need more mutantsplugin-autotooltip__default plugin-autotooltip_bigMutant: an individual that has a different phenotype than wildtype and likely contains one more mutations that cause this difference. to analyze. However, we can also revise Model 1 to fit the new data (Fig. 5).

The best way to distinguish between the two possible models is to test the phenotypeplugin-autotooltip__default plugin-autotooltip_bigPhenotype: an observable feature or property of an organism. of a double mutantplugin-autotooltip__default plugin-autotooltip_bigMutant: an individual that has a different phenotype than wildtype and likely contains one more mutations that cause this difference.. In revised Model 1 (Fig. 5), the $A^–; B^–$ double mutantplugin-autotooltip__default plugin-autotooltip_bigMutant: an individual that has a different phenotype than wildtype and likely contains one more mutations that cause this difference. is predicted to be uninducibleplugin-autotooltip__default plugin-autotooltip_bigUninducible: a mutant state wherein normally inducible genes are no longer inducible (and in fact may no longer be expressed at all). and in Model 2 (Fig. 4) it is predicted to be constitutiveplugin-autotooltip__default plugin-autotooltip_bigConstitutive: a term describing a pattern of gene expression, wherein the gene is always expressed no matter what. For some genes, constitutive expression is normal (see housekeeping gene). For inducible genes or operons, constitutive is a mutant state.. This experiment represents a powerful form of genetic analysis known as an epistasisplugin-autotooltip__default plugin-autotooltip_bigEpistasis: describes a relationship between two mutant alleles $a$ and $b$. If the phenotype of a double mutant $a \cdot b$ is the same as the single mutant $a$ we say that $a$ is epistatic to $b$, and that $a$ likely functions after $b$ in a pathway. test. In the example above, if the double mutantplugin-autotooltip__default plugin-autotooltip_bigMutant: an individual that has a different phenotype than wildtype and likely contains one more mutations that cause this difference. were constitutiveplugin-autotooltip__default plugin-autotooltip_bigConstitutive: a term describing a pattern of gene expression, wherein the gene is always expressed no matter what. For some genes, constitutive expression is normal (see housekeeping gene). For inducible genes or operons, constitutive is a mutant state., we would say that the mutationplugin-autotooltip__default plugin-autotooltip_bigMutation: a change in the DNA of a gene that results in a change of phenotype compared to a reference wildtype allele. See also: mutant. $B^–$ is epistaticplugin-autotooltip__default plugin-autotooltip_bigEpistasis: describes a relationship between two mutant alleles $a$ and $b$. If the phenotype of a double mutant $a \cdot b$ is the same as the single mutant $a$ we say that $a$ is epistatic to $b$, and that $a$ likely functions after $b$ in a pathway. to $A^–$. Such a test allows us to determine the order in which different functions in a regulatory pathwayplugin-autotooltip__default plugin-autotooltip_bigPathway: a series of reactions or events that occur in sequence with some common goal or purpose. act. If the double mutantplugin-autotooltip__default plugin-autotooltip_bigMutant: an individual that has a different phenotype than wildtype and likely contains one more mutations that cause this difference. in the example were constitutiveplugin-autotooltip__default plugin-autotooltip_bigConstitutive: a term describing a pattern of gene expression, wherein the gene is always expressed no matter what. For some genes, constitutive expression is normal (see housekeeping gene). For inducible genes or operons, constitutive is a mutant state., we would deduce that geneplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) $B$ functions after geneplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) $A$ in the regulatory pathwayplugin-autotooltip__default plugin-autotooltip_bigPathway: a series of reactions or events that occur in sequence with some common goal or purpose..

To perform an epistasisplugin-autotooltip__default plugin-autotooltip_bigEpistasis: describes a relationship between two mutant alleles $a$ and $b$. If the phenotype of a double mutant $a \cdot b$ is the same as the single mutant $a$ we say that $a$ is epistatic to $b$, and that $a$ likely functions after $b$ in a pathway. test, it is necessary that the different mutationsplugin-autotooltip__default plugin-autotooltip_bigMutation: a change in the DNA of a gene that results in a change of phenotype compared to a reference wildtype allele. See also: mutant. under examination produce opposite (or at least different) phenotypicplugin-autotooltip__default plugin-autotooltip_bigPhenotype: an observable feature or property of an organism. consequences. It doesn't matter if mutationsplugin-autotooltip__default plugin-autotooltip_bigMutation: a change in the DNA of a gene that results in a change of phenotype compared to a reference wildtype allele. See also: mutant. are dominantplugin-autotooltip__default plugin-autotooltip_bigDominant: used to describe an allele, usually in comparison to wildtype. Dominant alleles will express their phenotype when combined with a wildtype allele. or recessiveplugin-autotooltip__default plugin-autotooltip_bigRecessive: used to describe an allele, usually in comparison to wildtype. Recessive alleles do not exhibit their phenotype when combined with a wildtype allele.; either will work in the epistasisplugin-autotooltip__default plugin-autotooltip_bigEpistasis: describes a relationship between two mutant alleles $a$ and $b$. If the phenotype of a double mutant $a \cdot b$ is the same as the single mutant $a$ we say that $a$ is epistatic to $b$, and that $a$ likely functions after $b$ in a pathway. test. When the double mutantplugin-autotooltip__default plugin-autotooltip_bigMutant: an individual that has a different phenotype than wildtype and likely contains one more mutations that cause this difference. is constructed, its phenotypeplugin-autotooltip__default plugin-autotooltip_bigPhenotype: an observable feature or property of an organism. will be that of the function that acts later in the pathwayplugin-autotooltip__default plugin-autotooltip_bigPathway: a series of reactions or events that occur in sequence with some common goal or purpose.. Constructing double mutantsplugin-autotooltip__default plugin-autotooltip_bigMutant: an individual that has a different phenotype than wildtype and likely contains one more mutations that cause this difference. in E. coliplugin-autotooltip__default plugin-autotooltip_bigEscherichia coli: an enteric bacterium used both as a model organism and as a utility organism in genetics research. E. coli is commonly used to host various cloning vectors, such as plasmids, cosmids, F factors, and bacterial artificiak chromosomes (BACs). uses techniques that are somewhat esoteric and probably not of general interest to most students unless they plan to become molecular microbiologists. For the purposes of this book, we can just assume that “we made the E. coliplugin-autotooltip__default plugin-autotooltip_bigEscherichia coli: an enteric bacterium used both as a model organism and as a utility organism in genetics research. E. coli is commonly used to host various cloning vectors, such as plasmids, cosmids, F factors, and bacterial artificiak chromosomes (BACs). double mutantplugin-autotooltip__default plugin-autotooltip_bigMutant: an individual that has a different phenotype than wildtype and likely contains one more mutations that cause this difference.” without worrying about the technical details. If you are interested in those details, a good reference to look up would be a textbook on molecular microbiology. We will, however, be examining how to make double mutantsplugin-autotooltip__default plugin-autotooltip_bigMutant: an individual that has a different phenotype than wildtype and likely contains one more mutations that cause this difference. in yeastplugin-autotooltip__default plugin-autotooltip_bigYeast: in this book, refers to Saccharomyces cerevisiae, a single-celled eukaryotic microbe used as a model genetic organism. See Chapter 02 using tetrad analysisplugin-autotooltip__default plugin-autotooltip_bigTetrad analysis: an experimental method to analysis meiosis in yeasts and other fungi. See Appendix A. in Chap. 14.

Epistasisplugin-autotooltip__default plugin-autotooltip_bigEpistasis: describes a relationship between two mutant alleles $a$ and $b$. If the phenotype of a double mutant $a \cdot b$ is the same as the single mutant $a$ we say that $a$ is epistatic to $b$, and that $a$ likely functions after $b$ in a pathway. tests are of very general utility. If the requirement that two mutationsplugin-autotooltip__default plugin-autotooltip_bigMutation: a change in the DNA of a gene that results in a change of phenotype compared to a reference wildtype allele. See also: mutant. have opposite phenotypesplugin-autotooltip__default plugin-autotooltip_bigPhenotype: an observable feature or property of an organism. is met, almost any type of hierarchical relationship between elements in a regulatory pathwayplugin-autotooltip__default plugin-autotooltip_bigPathway: a series of reactions or events that occur in sequence with some common goal or purpose. can be worked out. For example, the $lacO^c$ mutationplugin-autotooltip__default plugin-autotooltip_bigMutation: a change in the DNA of a gene that results in a change of phenotype compared to a reference wildtype allele. See also: mutant. is in a regulatory site, not a coding sequenceplugin-autotooltip__default plugin-autotooltip_bigCoding sequence: refers to the portion of DNA or mRNA in a gene that contains direct information on the gene product. In most cases, this means a portion of DNA or mRNA that correlates to codons. Note that not all parts of a gene will necessarily be coding sequence (e.g., intron sequences)., but it is still possible to perform an epistasisplugin-autotooltip__default plugin-autotooltip_bigEpistasis: describes a relationship between two mutant alleles $a$ and $b$. If the phenotype of a double mutant $a \cdot b$ is the same as the single mutant $a$ we say that $a$ is epistatic to $b$, and that $a$ likely functions after $b$ in a pathway. between $lacO^c$ and $lacI^s$ since these mutationsplugin-autotooltip__default plugin-autotooltip_bigMutation: a change in the DNA of a gene that results in a change of phenotype compared to a reference wildtype allele. See also: mutant. satisfy the basic requirement for an epistasisplugin-autotooltip__default plugin-autotooltip_bigEpistasis: describes a relationship between two mutant alleles $a$ and $b$. If the phenotype of a double mutant $a \cdot b$ is the same as the single mutant $a$ we say that $a$ is epistatic to $b$, and that $a$ likely functions after $b$ in a pathway. test. One mutationplugin-autotooltip__default plugin-autotooltip_bigMutation: a change in the DNA of a gene that results in a change of phenotype compared to a reference wildtype allele. See also: mutant. is uninducibleplugin-autotooltip__default plugin-autotooltip_bigUninducible: a mutant state wherein normally inducible genes are no longer inducible (and in fact may no longer be expressed at all). while the other is constitutiveplugin-autotooltip__default plugin-autotooltip_bigConstitutive: a term describing a pattern of gene expression, wherein the gene is always expressed no matter what. For some genes, constitutive expression is normal (see housekeeping gene). For inducible genes or operons, constitutive is a mutant state. for Lac geneplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) expressionplugin-autotooltip__default plugin-autotooltip_bigExpression: a term used to describe the idea that the function of a gene is apparent and can be observed. Genes may not always be expressed all the time in all places.. When the actual double mutantplugin-autotooltip__default plugin-autotooltip_bigMutant: an individual that has a different phenotype than wildtype and likely contains one more mutations that cause this difference., $lacO^c; lacI^s$, is evaluated it is constitutiveplugin-autotooltip__default plugin-autotooltip_bigConstitutive: a term describing a pattern of gene expression, wherein the gene is always expressed no matter what. For some genes, constitutive expression is normal (see housekeeping gene). For inducible genes or operons, constitutive is a mutant state.. This makes sense given what we know about the Lac operonplugin-autotooltip__default plugin-autotooltip_bigLac operon: an operon in E. coli that contains the cis-acting regulatory elements $lacP$ and $lacO$, and the protein coding genes $lacZ$, $lacY$, and $lacA$. The Lac operon is an example of a negatively-regulated operon., since a defective operatorplugin-autotooltip__default plugin-autotooltip_bigOperator: in bacterial genetics, an operator is a cis-acting genetic element that negatively regulates the expression of nearby genes. $lacO$ of the Lac operon is an example of an operator. site that prevents repressorplugin-autotooltip__default plugin-autotooltip_bigRepressor: a DNA binding protein that binds to negatively acting cis-acting elements such as operators in bacteria to inhibit transcription. Compare to negative regulator. binding should allow constitutiveplugin-autotooltip__default plugin-autotooltip_bigConstitutive: a term describing a pattern of gene expression, wherein the gene is always expressed no matter what. For some genes, constitutive expression is normal (see housekeeping gene). For inducible genes or operons, constitutive is a mutant state. expressionplugin-autotooltip__default plugin-autotooltip_bigExpression: a term used to describe the idea that the function of a gene is apparent and can be observed. Genes may not always be expressed all the time in all places. regardless of the form of the repressorplugin-autotooltip__default plugin-autotooltip_bigRepressor: a DNA binding protein that binds to negatively acting cis-acting elements such as operators in bacteria to inhibit transcription. Compare to negative regulator. proteinplugin-autotooltip__default plugin-autotooltip_bigProtein: a molecule that is formed by the translation of messenger RNAs (mRNAs). Functions that proteins provide are what usually give organisms their phenotypes.. Formally, this result shows that a mutationplugin-autotooltip__default plugin-autotooltip_bigMutation: a change in the DNA of a gene that results in a change of phenotype compared to a reference wildtype allele. See also: mutant. in $lacO$ is epistaticplugin-autotooltip__default plugin-autotooltip_bigEpistasis: describes a relationship between two mutant alleles $a$ and $b$. If the phenotype of a double mutant $a \cdot b$ is the same as the single mutant $a$ we say that $a$ is epistatic to $b$, and that $a$ likely functions after $b$ in a pathway. to a mutationplugin-autotooltip__default plugin-autotooltip_bigMutation: a change in the DNA of a gene that results in a change of phenotype compared to a reference wildtype allele. See also: mutant. in $lacI$. Even if we did not know the details of Lac operonplugin-autotooltip__default plugin-autotooltip_bigLac operon: an operon in E. coli that contains the cis-acting regulatory elements $lacP$ and $lacO$, and the protein coding genes $lacZ$, $lacY$, and $lacA$. The Lac operon is an example of a negatively-regulated operon. regulation beforehand, this epistasisplugin-autotooltip__default plugin-autotooltip_bigEpistasis: describes a relationship between two mutant alleles $a$ and $b$. If the phenotype of a double mutant $a \cdot b$ is the same as the single mutant $a$ we say that $a$ is epistatic to $b$, and that $a$ likely functions after $b$ in a pathway. test would allow us to deduce that the operatorplugin-autotooltip__default plugin-autotooltip_bigOperator: in bacterial genetics, an operator is a cis-acting genetic element that negatively regulates the expression of nearby genes. $lacO$ of the Lac operon is an example of an operator. functions at a later step than the repressorplugin-autotooltip__default plugin-autotooltip_bigRepressor: a DNA binding protein that binds to negatively acting cis-acting elements such as operators in bacteria to inhibit transcription. Compare to negative regulator..

We have been considering enzymeplugin-autotooltip__default plugin-autotooltip_bigEnzyme: a macromolecule, usually a protein (but sometimes an RNA), that functions as a catalyst of some kind of biochemical reaction.-coding genesplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) that are regulated in response to the availability of nutrients. There is another general type of regulation whereby genesplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) can be held in stable on or off states. During the development of multicellular organisms, all cells (except for the germ cellsplugin-autotooltip__default plugin-autotooltip_bigGamete: a specialized (usually haploid) cell used for sexual reproduction. Eggs (oocytes) and sperm are gametes. and some cells of the immune system) have the same genotypeplugin-autotooltip__default plugin-autotooltip_bigGenotype: the combination of alleles within an organism or strain. When used as a verb, it means to determine the genotype experimentally.; yet cells in different tissues express different sets of genesplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-). Cell-type specification is in part a program of geneplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) transcriptionplugin-autotooltip__default plugin-autotooltip_bigRNA transcription: the process of RNA polymerase using the DNA sequence of a gene as a template to form an mRNA (in prokaryotes) or pre-mRNA (in eukaryotes). In most cases, “transcription” implies RNA transcription. that is established by extracellular signals. In most cases, after the cell type has been specified the cells do not readily change back when the signals are removed. This general behavior of cells in development implies the existence of stable regulatory states for geneplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) control.

The best understood case of a stable switch is the lysis vs. lysogeny decision made by bacteriophageplugin-autotooltip__default plugin-autotooltip_bigBacteriophage: viruses that infect bacteria. λ. When λ infects cells there are two different developmental fates of the phageplugin-autotooltip__default plugin-autotooltip_bigBacteriophage: viruses that infect bacteria..

1. In the lyticplugin-autotooltip__default plugin-autotooltip_bigLytic: a stage in the bacteriophage life cycle where the phage lyse their host cells and are released into the environment. program the phageplugin-autotooltip__default plugin-autotooltip_bigBacteriophage: viruses that infect bacteria. replicates DNAplugin-autotooltip__default plugin-autotooltip_bigDNA: deoxyribonucleic acid. The genetic material for nearly all life on Earth., make heads, tails, packages DNAplugin-autotooltip__default plugin-autotooltip_bigDNA: deoxyribonucleic acid. The genetic material for nearly all life on Earth., and lyses host cells.
2. In the lysogenicplugin-autotooltip__default plugin-autotooltip_bigLysogenic: a stage in the bacteriophage life cycle wherein the phage DNA integrates into the host cell genome and lays dormant. program the phageplugin-autotooltip__default plugin-autotooltip_bigBacteriophage: viruses that infect bacteria. integrates into the host DNAplugin-autotooltip__default plugin-autotooltip_bigDNA: deoxyribonucleic acid. The genetic material for nearly all life on Earth. and shuts down phageplugin-autotooltip__default plugin-autotooltip_bigBacteriophage: viruses that infect bacteria. genesplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-). The resulting quiescent phageplugin-autotooltip__default plugin-autotooltip_bigBacteriophage: viruses that infect bacteria. integrated into the genomeplugin-autotooltip__default plugin-autotooltip_bigGenome: a dataset that contains all DNA information of an organism. Most of the time, this also includes annotation and curation of that information, e.g., the names, locations, and functions of genes within the genome. As an adjective (“genomic”), this usually is used in the context of is known as a lysogen.

The decision between these two options must be made in a committed way so the proper functions act in concert. The switch in the case of phageplugin-autotooltip__default plugin-autotooltip_bigBacteriophage: viruses that infect bacteria. λ hinges on the activity of two repressorplugin-autotooltip__default plugin-autotooltip_bigRepressor: a DNA binding protein that binds to negatively acting cis-acting elements such as operators in bacteria to inhibit transcription. Compare to negative regulator. genesplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) $cI$ and $cro$. The $cI$ and $cro$ genesplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) have mutually antagonistic regulatory interactions (Fig. 6):

After an initial unstable period immediately after infection, either $cro$ expressionplugin-autotooltip__default plugin-autotooltip_bigExpression: a term used to describe the idea that the function of a gene is apparent and can be observed. Genes may not always be expressed all the time in all places. or $cI$ expressionplugin-autotooltip__default plugin-autotooltip_bigExpression: a term used to describe the idea that the function of a gene is apparent and can be observed. Genes may not always be expressed all the time in all places. will dominate.

• Mode 1: High $cro$ expressionplugin-autotooltip__default plugin-autotooltip_bigExpression: a term used to describe the idea that the function of a gene is apparent and can be observed. Genes may not always be expressed all the time in all places. blocks $cI$ expressionplugin-autotooltip__default plugin-autotooltip_bigExpression: a term used to describe the idea that the function of a gene is apparent and can be observed. Genes may not always be expressed all the time in all places.. In this state, all of the genesplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) for lyticplugin-autotooltip__default plugin-autotooltip_bigLytic: a stage in the bacteriophage life cycle where the phage lyse their host cells and are released into the environment. growth are made and the phageplugin-autotooltip__default plugin-autotooltip_bigBacteriophage: viruses that infect bacteria. enters the lyticplugin-autotooltip__default plugin-autotooltip_bigLytic: a stage in the bacteriophage life cycle where the phage lyse their host cells and are released into the environment. program.
• Mode 2: High $cI$ expressionplugin-autotooltip__default plugin-autotooltip_bigExpression: a term used to describe the idea that the function of a gene is apparent and can be observed. Genes may not always be expressed all the time in all places. blocks $cro$ expressionplugin-autotooltip__default plugin-autotooltip_bigExpression: a term used to describe the idea that the function of a gene is apparent and can be observed. Genes may not always be expressed all the time in all places.. In this state, none of the genesplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) except for $cI$ are expressedplugin-autotooltip__default plugin-autotooltip_bigExpression: a term used to describe the idea that the function of a gene is apparent and can be observed. Genes may not always be expressed all the time in all places.. This produces a stable lysogen.

In geneplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) regulation, as in good circuit design, stability is achieved by feedback. The result is a bi-stable switch that is similar to a “flip-flop”, one of the basic elements of digital electronic circuits. Other genesplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) participate in the initial period to bias the decision to one mode or the other. These genesplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) act so that the lyticplugin-autotooltip__default plugin-autotooltip_bigLytic: a stage in the bacteriophage life cycle where the phage lyse their host cells and are released into the environment. mode is favored when E. coliplugin-autotooltip__default plugin-autotooltip_bigEscherichia coli: an enteric bacterium used both as a model organism and as a utility organism in genetics research. E. coli is commonly used to host various cloning vectors, such as plasmids, cosmids, F factors, and bacterial artificiak chromosomes (BACs). is growing well and there are few phageplugin-autotooltip__default plugin-autotooltip_bigBacteriophage: viruses that infect bacteria. per infected cell, whereas the lysogenicplugin-autotooltip__default plugin-autotooltip_bigLysogenic: a stage in the bacteriophage life cycle wherein the phage DNA integrates into the host cell genome and lays dormant. mode is favored when cells are growing poorly and there are many phageplugin-autotooltip__default plugin-autotooltip_bigBacteriophage: viruses that infect bacteria. per infected cell.

Exercise 1 (challenge question): Revisit Chapter 02 Figure 3. Is it possible to analyze yeastplugin-autotooltip__default plugin-autotooltip_bigYeast: in this book, refers to Saccharomyces cerevisiae, a single-celled eukaryotic microbe used as a model genetic organism. See Chapter 02 $his$ mutantsplugin-autotooltip__default plugin-autotooltip_bigMutant: an individual that has a different phenotype than wildtype and likely contains one more mutations that cause this difference. using epistasisplugin-autotooltip__default plugin-autotooltip_bigEpistasis: describes a relationship between two mutant alleles $a$ and $b$. If the phenotype of a double mutant $a \cdot b$ is the same as the single mutant $a$ we say that $a$ is epistatic to $b$, and that $a$ likely functions after $b$ in a pathway.? Why or why not? What question would you be answering with epistasisplugin-autotooltip__default plugin-autotooltip_bigEpistasis: describes a relationship between two mutant alleles $a$ and $b$. If the phenotype of a double mutant $a \cdot b$ is the same as the single mutant $a$ we say that $a$ is epistatic to $b$, and that $a$ likely functions after $b$ in a pathway.? What additional information might you need to know first? You may want to look up some classic genetic experiments by Beadle and Tatum using the bread mold Neurospora to help with answering this question.