Prokaryotic transcription factors Flashcards
What is a transcription factor?
Protein that plays a critical role in the regulation of transcription. Typically at the initiation stage
What are the 2 functions of transcription factors?
- Direct sequence specific binding to DNA, often close to core promoter
- Regulate transcription
What is the typical mechanism for how transcriptional activators increase the rate of transcription?
Stabilize the interactions between RNAP and the promoter by forming direct physical contact
Why are transcription factors modular?
They have distinct domains with distinct functions, and they all function relatively independently. We can mix and match domains in the lab
What are the 2 main domains of transcription factors?
- DNA binding domain
2. Activation domain that makes the physical contact with the basal transcription machinery
What are two other domains that transcription factors may have?
Ligand/protein binding domains that can sense environmental changes, and dimerization domains
How conserved are the DNA binding domains of transcription factors?
Highly conserved between transcription factors
What is one common protein motif found in the DNA binding domains of transcription factors?
Helix-turn-helix
What is the helix-turn-helix motif?
Two alpha helices connected by a short amino acid turn
How do transcription factors acting as dimers help with increasing the strength of the protein’s interaction with the target DNA?
Each subunit has a DNA binding domain, so they’ll use them to interact with adjacent major grooves in the DNA. The interaction is stronger when two cooperating proteins are binding to DNA
How do helix-turn-helix motifs bind to DNA?
The second helix will recognize and bind to the major groove in the target DNA. That helix will lie inside the major groove
What sequences in the DNA are recognized by the DNA binding domains of transcription factors?
Palindromic sequences, even imperfect ones
How are transcription factors sequence specific when the overall structure of the DNA binding domains are conserved?
Hydrogen bonds between the DNA and a small number of amino acids just outside the recognition helix
What are hydrogen bonds formed between the DNA backbone and amino acids from outside the recognition helix doing?
Stabilizing the interaction. Not sequence specificity
What are two ways to control the expression of transcription factors at the level of transcription?
- Control if they’re expressed at all
2. Control how much they’re expressed
What are 5 ways to control the expression of transcription factors at the post-translation level?
- Concentration of the protein (targeting for degradation when there’s too much)
- Phosphorylation and other modifications that cause reversible conformation changes
- Small ligand binding
- Interactions with other proteins
- Localizing a transcription factor away from the DNA
What are 5 mechanisms of transcription activation through transcription factors?
- Form direct physical contact with RNAP and DNA to stabilize their interaction
- Alter the conformation of promoter DNA
- Anti-repression
- Pre-recruitment activation
- DNA looping with enhancers
How can transcription factors activate transcription by forming direct physical contact with RNAP?
Stabilize the interactions between RNAP and the promoter, which makes transcription more likely to proceed
How can transcription factors activate transcription by altering the conformation of promoter DNA?
Changes the spacing of the core promoter elements, so the consensus sequences make better contact with the sigma subunit
How can transcription factors activate transcription by anti-repression?
Blocks the activity of a repressor so that RNAP can do its thing
How can transcription factors activate transcription by pre-recruitment activation?
Enhances the assembly of the RNAP holoenzyme
How can transcription factors activate transcription by DNA looping through enhancers?
Only happens with the sigma 54 subunit. Activators bind to enhancers and loop the DNA, then the sigma can form the open complex
What are 3 mechanisms by which transcription factors can repress transcription?
- Steric hindrance and blocking RNAP from binding
- Altering promoter conformation
- Interfering with activators
What is a complex promoter? How common are they?
A promoter regulated by more than one transcription factor. Most promoters are complex
