lecture 5-How transcription factors are activated Flashcards
Learning Objectives
➢Explain the principles governing interactions between DNA and protein that take place at the promoter or enhancer.
➢Describe the differences between DNA binding domains, using an example protein of each to help you explain their functional differences.
➢Explain the effect of multicomponent complexes on DNA binding, including those recruited to the mediator complex
DNA binding proteins can move to the nucleus after “activation”
1.Movement to the nucleus may require a shape change or dissociation from another protein.
2.The change reveals the nuclear localisation signal (NLS).
3.This then allows the protein to bind to importins to allow it to move through the nuclear pore complex and into the nucleus.
4.Once in the nucleus it can dimerise with other proteins and DNA.
5.(…and therefore affect gene expression by controlling initiation of transcription)
DNA binding proteins are not always in the nucleus- So how do they get there?
DNA binding proteins are not always in the nucleusSo how do they get there? Part 2
DNA binding proteins can move to the nucleus after “activation
Revealing the NLS can be achieved by:
*Ligand binding
*Post translational modification (covalent modification)
*Addition of subunits (also known as dimerization)
*Dissociation from an inhibitor through covalent modification (unmasking) or naturally separating (stimulation of nuclear entry)
*Proteins being released from the plasma membrane
Homeobox (HOX) genes contain homeodomains
Homeobox (HOX) proteins control body patterning during development. e.g. HOX9 is involved in limb development
Homeodomains contain 3 α helices which are packed closely together by hydrophobic interactions, one (red) touches the major grove of the DNA (left)
p53: A β-sheet recognition protein
*Typical tumour suppressor gene.
*Contains a DNA binding domain made of two β-sheets which “sandwich” the DNA.
*Forms multimers through its oligomerisation domain (OD) which can modify its DNA sequence specificity
Functions of p53
Zinc fingered nuclear hormone receptors
*Strangely they do not always bind to zinc, some bind other metals, others nothing.
*They all have the finger like domains that interact with the DNA.
*Many different types.
*Regulate processes like bile acid detoxification.
*Contents of the dimer are key to sequence specificity and effect
Nuclear Receptors (which include steroid hormone receptors)
➢Contain two Zn-binding domains, one interacts with DNA, the other enables dimerisation.
➢Where the first “finger” determines sequence specificity
Fos: A Leucine Zipper that regulates bone
*Always bind to DNA as dimers.
*Dimer formation is enabled by hydrophobic interactions between alpha helices (mainly by leucine residues).
*Sometimes have a globular domain with basic properties, called a basic leucine zipper (bZIP).
*Activated by phosphorylation (by Mitogen Activated [MAP] Kinase)
Fos Activation
Mycand its role in cancer
*Mycis often upregulated in cancer
*Components of the heterodimer control the outcome of the signalling pathways.
*Mycis associated with
-cell cycle progression
-apoptosis
-proliferation
-metabolism
Effects of multi-protein complexes
-Two are always better than one!
➢Some DNA binding domains only fold completely in the presence of DNA.
➢Usually this is because the DNA binding domain is partially unstructured and dimerisation enables better folding and support.
➢The composition of the dimer affects sequence recognition and therefore range of targets affected
How dimer make up affects transcription
Greater DNA binding by monomers can reduce transcription rates.
Dimerization—the process where two molecules (often proteins) bind together to form a dimer—plays a crucial role in regulating transcription. Many transcription factors (TFs) function as dimers, and the formation of these dimers directly impacts their ability to regulate gene expression.
Here’s how dimer formation can affect transcription:
- Stability and DNA Binding Affinity
Increased Stability: When transcription factors dimerize, the dimer often becomes more stable than the monomer form. This stability enhances the ability of the TFs to stay bound to DNA, allowing them to regulate gene expression more effectively.
Increased DNA Binding Affinity: Many TFs bind more strongly to DNA when in dimer form. Dimerization allows for greater surface area interaction between the TFs and the DNA, increasing the strength and specificity of binding to target sequences in the genome.
Example: The basic leucine zipper (bZIP) transcription factors, such as AP-1, must dimerize to effectively bind DNA and regulate target genes. - Specificity of DNA Binding
Heterodimer vs. Homodimer: Transcription factors can form either homodimers (two identical proteins) or heterodimers (two different proteins). The combination of different proteins in a heterodimer can change the specificity for which DNA sequences are recognized.
Homodimer: Binds to specific consensus sequences that match the binding preferences of the individual protein.
Heterodimer: The DNA-binding specificity may change because the two proteins in the dimer interact differently with the DNA. This allows cells to regulate different sets of genes depending on which transcription factor pair is formed.
Example: In the case of bHLH (basic helix-loop-helix) proteins, different combinations of heterodimers can bind to different DNA sequences, modulating the regulation of various genes. The transcription factors Myc and Max form heterodimers to regulate genes involved in cell growth and division. - Allosteric Regulation
Conformational Changes: Dimerization can induce conformational changes in transcription factors, altering their activity. This can affect whether they can interact with other proteins, such as coactivators or corepressors, and thus influence transcription.
Example: The dimerization of nuclear hormone receptors like the estrogen receptor (which forms homodimers) is critical for binding to hormone response elements on DNA. The binding of the hormone (ligand) triggers dimerization, which then activates the transcription factor and initiates transcription. - Transcriptional Activation or Repression
Cooperative Binding: In many cases, dimerized transcription factors work together more efficiently than monomers to recruit coactivators or corepressors that modify chromatin and help activate or repress transcription. This cooperativity often depends on dimer formation.
Repression: Some transcription factors, when they form dimers, can act as repressors. By dimerizing, they may mask DNA binding domains or recruit corepressors that inhibit gene expression.
Activation: In other cases, dimerization may be required for transcriptional activation. Some transcription factors can only recruit the necessary coactivators to start transcription when they dimerize.
Example: NF-κB, a key transcription factor involved in immune responses, forms dimers (often p50-p65) that can bind DNA and activate or repress target genes depending on which coactivators or corepressors are recruited. - Response to Signaling Pathways
Signal-Dependent Dimerization: Some transcription factors only dimerize in response to specific signaling events, such as phosphorylation or ligand binding. Dimerization acts as a switch that controls whether the transcription factor can activate or repress genes.
Example: In the STAT (Signal Transducer and Activator of Transcription) proteins, phosphorylation induces dimerization. Once dimerized, STAT proteins can enter the nucleus and activate transcription of target genes involved in immune responses and cell growth. - Functional Diversity
Expanded Regulatory Potential: By forming dimers, especially heterodimers, transcription factors gain functional diversity. This means a single transcription factor can participate in regulating multiple genes depending on its dimerization partner.
Example: Fos and Jun proteins, which form the AP-1 transcription factor, create different responses based on whether they form heterodimers or homodimers. This variation affects which genes are turned on or off, impacting processes like cell differentiation and apoptosis. - Inhibition via Dominant-Negative Dimers
Inactive Dimers: Sometimes, dimerization can result in a non-functional complex. A dominant-negative dimer is when one partner in the dimer lacks the ability to bind DNA or activate transcription but still forms a dimer with a functional partner, blocking the activity of the transcription factor.
Example: In the Myc-Max system, the Mad-Max heterodimer competes with Myc-Max to bind DNA but represses transcription rather than activating it. This competition between dimers helps control the balance between cell growth and differentiation.
Conclusion:
Dimerization profoundly affects transcription by regulating the stability, specificity, and activity of transcription factors. Whether through homodimers or heterodimers, the process allows transcription factors to fine-tune gene expression in response to various cellular signals and conditions. Dimerization expands the range of gene regulation, offering more complexity and flexibility in controlling biological processes.
The significance of a mediator complex
Changes to structure outside the DNA binding domain can enhance DNA binding
how can Contents of the mediator complex can influence the rate of transcription
Contents of the mediator complex can influence the rate of transcription by influencing recruitment to the promoter and through changes to shape of the DNA binding proteins.
Nuclear receptors as co-activators and co-repressors
Same response element, same DNA binding protein, different mediator proteins, different outcomes
