Control Of Gene Expression I-Iii

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Ways of Controlling What Proteins Get Expressed When: 7 Categories/Levels

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1) Chromosomal placement: genomic location of gene in either heterochromatin (inactive) or euchromatin (active)

2) Transcriptional control - <b> dominant control mechanism </b>

3) RNA Processing Control: regulates levels of RNA species, also dictates which mature (spliced) RNAs are produced

4) RNA transport and localization control: determines which mRNAs leave nucleus and where they go in the cell

5) Translational control: Fine-tuning mechanism at ribosomal level

6) Turnover of mRNA - how long the mRNA stays around, some mRNAs have longer half lives than others

7) Protein Activity Control: Includes post-translational processing that affects activity, folding, turnover, addition of cofactors, etc.

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How can one measure the amount of mRNA in a sample?

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Northern Blotting

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How to measure amount of protein in the sample?

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Western Blotting

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What is the main level of control?

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Initiation of transcription

Ex., cell differentiation and tissue development are controlled here. Type of mRNAs will be very different depending on tissue type

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<i> lac </i> operon: main purpose/overview

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Example of bacterial transcriptional control.

Bacteria prefer to use glucose, but in presence of hi lactose and low glucose, they can use lactose with a different set of genes/proteins that must be activated.

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operon: defn

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In bacteria

An expression unit made of a gene collection producing proteins with complementary functions (multiple proteins from a single mRNA/polycistronic)

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lac repressor protein

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a protein that is constitutively expressed and bound to lac operator, preventing transcription of lac operon (lactose catabolizing genes) It's not perfect, so some lac operon genes manage to get transcribed.

When lactose is around, B galactosidase converts it to allolactose, which binds to the lac repressor protein, which then is removed from the operator, making it free to be transcribed.

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In presence of low glucose (and high lactose,) what happens?

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When glucose levels are low, adenylate cyclase makes cAMP. cAMP binds to CAP, which binds to the activator, which increases affinity of RNA pol to the lac operon.

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trp operon: briefly, what are the two mechanisms of control?

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A) Repression by trp repressor

B) Transcriptional attenuation

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How does repression of trp operon work?

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Trp operon is constitutively expressed to synthesize tryptophan.

When there's plenty of tryptophan, a repressor protein (that's also constitutively expressed) binds to the tryptophan molecules, and then binds to the operator, preventing transcription.

The repressor protein cannot bind the operator unless it is bound to tryptophan!

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How does attenuation of trp operon work?

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At the beginning of the trp operon is a short sequence designed 1, 2, 3, and 4. Each can partially H bond to each other in the mRNA (e.g., 2-3, 3-4).

When this gene is started to get translated, and it comes to a trp codon, the ribosome adds trp to the growing polypeptide chain. The 3-4 region pairs up, forming a hairpin loop that terminates translation.

When there is no trp, when the ribosome comes to a trp codon, it pauses. During this time, the 2-3 hairpin forms, preventing 3-4 hairpin from forming and stopping transcription/translation (taking place simultaneously in bacteria!)

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What are the 4 most common amino acids that bind to DNA in a protein?

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Histidine
Arginine
Asparagine
Glutamine

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Helix-turn-helix

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A common motif in DNA-binding proteins.

About 20 amino acids long with two alpha helices separated by a Beta turn. One of the helices is for <b> recognition </b> that binds in major groove of DNA.

Ex., lac repressor protein binding operator. The binding site for allolactose is nearby, and when it binds, it prevents helix-turn-helix from binding.

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Zinc finger

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Biggest group of DNA binding transcription factors

About 30 a.a. long, contains either 4 Cys or 2 Cys/2 His that coordinately bind zinc atom.

Zn stabilizes the orientation of the finger helices that bind dna.

<b> Zn itself does <i> NOT </i> bind DNA </b>

Most proteins have >1 zinc finger regions.

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Homeodomain

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DNA binding domain, common in development-related transcription factors.

Homeotic genes dictate body segment changes, and DNA binding domain is encoded by "homeo box" sequence.

consists of a 60-amino acid helix-turn-helix structure in which three alpha helices are connected by short loop regions

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Leucine zipper

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Protein-binding (NOT DNA BINDING) motif.

Significant in that it allows proteins to form dimers

Is an amphipathic helix with leucines every 7th position, leading to coiled coils helping to hold the Lys/Arg rich DNA binding region of the subunits in appropriate juxtaposition.

Complete proteins exhibiting leucine domains and basic DNA-binding domains are referred to as <b> basic zippers </b>

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Helix-loop-helix

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Motif in protein-to-protein binding domain has two helices tethered by a variable length loop region (unlike Beta turn).

Protein binding motifs lie adjacent to basic DNA binding domain. Helices are amphipathic.

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TATA binding protein (TBP)

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transcription factor that binds specifically to a DNA sequence called the TATA box.

As one of the few proteins in the preinitiation complex that binds DNA in a sequence-specific manner, it helps position RNA polymerase II over the transcription start site of the gene.

TBP is involved in DNA melting (double strand separation) by bending the DNA by 80° (the AT-rich sequence to which it binds facilitates easy melting). The TBP is an unusual protein in that it <b>binds the minor groove using a β sheet </b>.

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Epigenetic information

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information passed to daughter cells, but is not a sequence of DNA

Examples include histone code, DNA methylation

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Chromatin remodeling: defn

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Reversible loosening of chromatin structure

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Two systems remodeling chromatin

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1) Histone tail modifications: e.g., acetylation, ubiquitination, phosphorylation, methylation

2) ATP-dept chromatin remodeling complexes

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Histone acetyl transferases (HATs)

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Hyperacetylate lysines of histone amino-terminal tails at surface of nucleosome.

Process reduces the positive character of the nucleosome and thus its affinity for DNA --> loosening of structure and greater exposure of promoter regions to transcription factors.

"coactivators"

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HDACs: deacetylases

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Remove histone acetyl groups, deactivating DNA to silence gene expression

"corepressors"

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Methylation of histones: what are the effects?

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It depends on what amino acid residue gets methylated.

Can either activate or deactivate regions of DNA

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Histone Code

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Pattern of modifications (addition of different chemical groups) to histones determines what proteins recognize them, proteins that bind and either condense or de-condense chromatin in those regions.

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ATP-dependent remodeling complexes

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Non-covalently modify chromatin, making it more or less accessible

Use ATP-derived energy to slide or transfer histones or make nucleosome structure looser.

Eg. Orange peel for nucleosome "loosening," Spooling model for nucleosome repositioning

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promoter

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DNA sequence that binds RNA polymerase.
<b> position and orientation dependent </b>

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enhancer

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DNA sequence that binds varied transcription factors (repressors or activators)

Can be located far or close to promoter or gene (even within the gene) - work through looping

<b> position and orientation independent </b>

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initiator

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normally located within transcription start site

There is a general consensus for it

Very often together with TATA box

Strong promoters will have both TATA box and initiator (adds strength to promoter)

Initiator also binds TFIID - Tatabinding protein associated factor TAFII250

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TATA Box

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Bound by protein complex TFIID
core is TATA binding protein (TBP)


Most common core promoter element
5-10% of genes

Every single promoter has TBP even if no TATA box

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TFIID

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Transcription Factor for Polymerase II D

Part of TFIID is Tata binding protein

Has additional components

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Housekeeping genes

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expressed at high levels

not regulated too much

need all the time

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Homeotic genes

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Embryonic development

Encode transcription factors containing homeodomains

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Upstream element

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Protein binding sequences (cis-elements) that increase initiation

Bound by <i>gene-specific factors</i>
(not an enhancer - you can't move it)

Contains:

“GC” box: GC-rich elements that bind factor Sp1; this interacts with TFIID

BRE: TFIIB recognition element :

• located immediately upstream of some TATA boxes

• binds general transcription factor TFIIB

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Downstream promoter element

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Recently discovered--best characterized in Drosophila

Cooperates functionally with Inr to bind TFIID:
efficient and accurate initiation from TATA-less promoters

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RBP1 C terminal domain:

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impt for initiation of transcription because it needs to be phosphorylated

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pre-initiation complex

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rate limiting step in transcription

RNAP II, plus Six general transcription factor complexes:
TFII-A, -B, -D, -E, -F, -H
Form closed complex: DNA melted, RNAP II ready to go!

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TBIIF

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TBP + TBP Associated Factors (TAFs)

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Enhanceosome

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Enhancers become activated by the binding of often large numbers of protein factors (the enhancesome) that bend the DNA to maximize cooperative protein-protein and protein-DNA interactions

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Nuclear receptor superfamily proteins

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Act as transcription activators in response to binding of some incoming ligand (e.g., estrogen, thyroxine).

Exhibit common features:

A) Variable transcription activation region
B) DNA binding domain
C) Ligand binding domain