15.1 - Regulatory Transcription Factors
Functions of regulatory transcription factor proteins controlled in three common ways
1. Binding of small effector molecule 2. Protein-to-protein interactions 3. Covalent modifications
What are two things TF regulate?
1. Binding of transcriptional complex to to core promoter 2. Switch from initiation to elongation
Examples of domain functions
1. DNA-binding function 2. Binding site for small effector molecule
Two types of TFs
1. General 2. Regulatory
How do activator proteins enhance the ability of TFIID to initiate transcription?
1. Help TFIID bind to the TATA box 2. Helps it recruit RNA polymerase II 3. Interacting with coactivators
What are two way that TFs bind to DNA sequences with the involvement of alpha helices?
1. Hydrogen bonding between the amino acid side chains in an alpha helix and the nucleotide bases in DNA 2. Positively charged amino acids of the recognition helix positively interact with the negatively charged DNA backbone
5 factors that may contribute to combinatorial control
1. One or more activators 2. One or more inhibitors 3. Various modulations of activators and repressors 4. Reg proteins alter nucleosomes hear promoter 5. DNA methylation inhibits transcription
How do repressors inhibit the function of TFIID?
1. Prevent binding of TFIID to TATA box 2. Prevent recruitment of RNA polymerase II to core promoter
3 types of regulation by transcription factors
1. ViaTFIID 2. Via mediator 3. Via changes in chromatin structure
Where are regulatory elements most commonly found?
200 bps upstream from the core promoter (can be up to 100,000 bps away and exert force on RNA polymerase)
Mediator
A protein complex that mediates the interaction between RNA polymerase II and regulatory transcription factors Controls ability of RNA polyermase II to progress
What does the binding of the glucocorticoid receptor homodimer to the GRE cause?
Activation of transcription of the nearby gener, leading to synthesis of encoded gene
Interaction between activator protein and mediator
Activator stimulates mediator to cause phosphorylation of carboxyl-terminal domain, causing switch to elongation
What occurs in helix-loop-helix motifs and helix-turn-helix motifs?
Alpha heliz called recognition helix makes contact with and recognizes a base sequence along the major groove of the DNA
How does protein dimerization occur in leuicne zipper?
Alternating leucines in both proteins zip up resulting in protein dimerization resulting in homodimer or heterodimer
Positively charged amino acids in alpha helices
Arginine and lysine
What is an example of a covalent modification modification?
Attachment of phosphate group
What do regulatory TFs recognize?
Cis-acting elements in the vicinity of the core promoter (control elements)
Where does the glucocorticoid receptor homodimer bind on DNA?
Consensus sequence 5'-AGRACA-3' 3'-TCYTGT-5'
What does the CREB protein recognize?
Consensus sequence: 5'-TGACGTCA-3' 3'-ACTGCAGT-5'
Control elements
DNA sequences where regulatory TF binds, analogous to operator sites near promoter in bacteria
What can the zinc finger recognize?
DNA sequences within the major groove
Besides upstream of the core promoter, where else can regulatory elements be found?
Downstream from the core promoter or in introns
What sequence does the activator bind to?
Enhancer
Glucocorticoid Response Element (GRE)
Enhancer next to many genes with two consensus sequences running in opposite directions
Gonadocorticoids
Estrogen and testosterone that influence growth and function of gonads
How are the mediator and activator protein brought together?
Formation of loop within the intervening DNA
What accounts for the phenotypic difference among cells?
Gene expression
TFIID
General TF that binds to the TATA box and is needed to recruit RNA polymerase II to the core promoter
How is every cell in a eukaryote similar?
Genotypically
HSP
Heat shock protein (i.e. HSP90)
Down Regulation
Inhibition of transcription by regulatory elements called silencers
Why is the alpha structure common in TFs?
It is the proper width to bind into the major groove of the DNA double helix
Who discovered the mediator?
Kornberg in 1990
What motifs mediate protein dimerization?
Leucine zipper and helix-loop-helix motif
What types of cells have a large number of glucocorticoid receptors in the cytoplasm?
Mammalian cells
Do most regulatory TFs bind directly to RNA polymerase?
No
What do glucocorticoid hormones influence?
Nutrient metabolism in most body cells
Combinatorial control
Phenomenon that most eukaryotic genes are regulated by multiple TF
How do cells in a eukaryote differ?
Phenotypically
How does the mediator control the ability of RNA polymerase II to progress to elongation stage?
Phosphorylation of carboxyl-terminal domain
Interaction between repressor and mediator
Prevent mediator from allowing RNA polymerase to proceed to elongation phase of transcription
Coactivators
Proteins that increase the rate of transcription but do not bind to DNA itself
Transcription factor
Proteins that influence the ability of RNA polymerase to transcribe a particular gene
What does the R stand for in in the consensus sequence?
Purine
What does the Y stand for in the consensus sequence?
Pyrimidine
How do regulatory TFs regulate transcription via changes in chromatin structure?
Recruit proteins which affect nucleosome position and composition to the promoter region altering chromatin region
Domain
Region of TF with specific function
Transactivation domain
Region of coactivator that promotes the activation of RNA polymerase, often by interacting with general TFs
Major groove
Region of the DNA double helix where the nucleotide bases are in contact with the water in cellular fluid
Regulatory TF
Regulate rate of transcription at target genes by influencing ability of RNA polymerase to begin transcription at a particular gene
Repressor
Regulatory TF that decrease rate of transcription
Activator
Regulatory TF that increases rate of transcription
Steroid Receptor
Regulatory TF that steroid protein binds directly to
What are other names for control elements?
Regulatory elements or regulatory sequences
CREB Protein
Regulatory transcription factor , composed of two identical subunits, that becomes activated in response to cell-signaling molecules that cause an increase in cytoplasmic concentration of cAMP
General TF
Required for binding for RNA polymerase to core promote and progression to elongation stage (required for any transcription to occur
cAMP response element (CRE)
Response element found near many different genes
What structure occurs frequently in TF?
Secondary structure alpha helix
Nuclear Localization Signal (NLS)
Sequence of amino acids within protein that direct it into the nucleus
Helix-loop-helix motif
Short alpha helix connected to long alpha helix by a loop
What sequence does the repressor bind to?
Silencer
Why discovered regulatory elements?
Susumu Tonegawa in 1980s
What are the processes of proteins of the genes stimulated by glucocorticoid hormones?
Synthesis of glucose Breakdown of proteins Mobilization of fats
Why do plants require greater level of gene regulation?
They are multicellular and have a complex cell structure
What does it mean that the regulatory elements are bidirectional?
They function in forward or reverse direction
What does the binding of CBP lead to?
Transcription activation of RNA polymerase
What occurs when the regulatory TF binds to the regulatory element?
Transcription of an associated gene is affected
Helix-turn-helix motif
Two alpha helices connected by a turn
Motif
When domain or portion of domain has similar structure in many different proteins
Up Regulation
When enhancer stimulate transcription 10-fold to 100-fold
Glucocorticoid receptor
Where glucocorticoid binds
What do these modulating mechanisms determine?
Whether transcription factors bind to DNA Influence on transcription by RNA polymerase
Orientation-independent synonym
bidirectional
What is the second messenger involved in pathway with CREB protein?
cAMP
What does CREB stand for?
cAMP response element binding protein
What does cAMP stand for?
cyclic adenosine monophosphate
Gene regulation
level of gene expression controlled so gene can be expressed as high or low levels
What is a zinc finger motif composed of?
one alpha helix and two beta sheets held together by zinc metal ion (Zn2+)
Heterodimer
when two different transcription factors come together
Homodimer
when two identical TF come together
