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