Regulation Of Gene Expression (Lecture 4)

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levels of gene control

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1. gene structure: packaging/accessibility to RNA polymerase (mostly in eukaryotes)

2. transcription: binding of transcriptional activators ("transcriptional control")

3. mRNA processing: rate of exon splicing; alternative splicing

4. translation: rate of translation ("translational control")

5. protein modification after translation: post-translational processing/chemical modification; protein turnover ("post-translational control")

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genes and regulatory elements

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1. structural genes: gene that is going to produce pdt with clear phenotype; encode proteins used in metabolism or biosynthesis or have a structural role

2. regulatory genes: RNA molecules or proteins that interact with other DNA sequences and affect transcription; affect whether gene gets expressed or not

3. regulatory elements: DNA sequences (NOT transcribed) that regulate gene expression (e.g. enhancers)

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enhancers

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-required for fullest level of transcription

-time and tissue-specific gene expression: have a lot of variability in the genes they interact with

-chickens & globins *****************

-are not located near the transcription start site like core/regulatory promoters (e.g. TATA box)

-can interact with promoters upstream or downstream!

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insulators

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-limit enhancer-promoter activity

-block effects of enhancer

-position-dependent

1. insulator between enhancer and promoter: enhancer activity is blocked by insulator

2. insulator outside of enhancer/promoter region: enhancer can still activate promoter

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DNA binding proteins*****************

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-regulatory proteins that bind to DNA sequences and affect expression; transcriptional activator proteins (don't always have a positive influence on gene expression)

-domains: discrete functional parts; make contact with DNA at regulatory promoter or enhancer; interact with other transcriptional components to alter chromatin structure

-grouped into distinct types based on characteristic motifs: motifs distinguish and serve to fit into the major groove of DNA

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repressors

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-some regulatory proteins act as repressors: inhibit transcription

-bind to regulatory promoter or silencers (distant sequences)

1. compete with activators for DNA binding sites

2. may bind NEAR an activator site and prevent activator from contacting the basal transcription apparatus

3. may interfere with assembly of basal transcription apparatus

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operons

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-prokaryotic genes with related functions are clustered together; single promoter; transcribed together

-organization:

1. set of structural genes: transcribed into a single mRNA --> translated into individual enzymes

2. promoter: control expression control expression of structural genes

3. regulator gene: encodes regulatory protein, which binds to operator and influences transcription

4. operator: DNA sequence between the promoter and structural genes that regulator protein binds to

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types of transcriptional control

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1. negative: regulator protein = repressor

-negative inducible: normally off, so repressor needs to be deactivated by inducer (precursor) to unbind and turn on

-negative repressible: normally on, so repressor needs to be activated by corepressor (end pdt) to bind and turn off

2. positive: regulator protein = activator

-positive inducible: normally off, so activator needs to be activated by inducer (precursor) to bind and turn on

-positive repressible: normally on, so activator needs to be deactivated by product to unbind and turn off

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negative inducible operons

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-normally regulator protein (repressor) is active and bound to the operator --> prevents transcription

-an inducer (precursor) must be present for transcription to occur: binds to repressor and causes a conformational change that deactivates and makes it unable to bind to operator

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negative repressible operons

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-normally regulator protein (repressor) is inactive and can't bind to operator --> transcription occurs

-a corepressor (end pdt) much be present to stop transcription: binds to the repressor and allows to bind to operator

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positive inducible

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-normally regulator protein (activator) is inactive and can't bind to operator --> no transcription

-an inducer (precursor) must be present for transcription to occur: binds to activator and allows to bind to operator

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positive repressible

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-normally regulator protein (activator) is active and bound to operator --> transcription occurs

-product must be present for transcription to stop: binds to activator and deactivates

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lac operon structure

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-gene activity is induced when lactose is present and repressed when lactose is absent: negative inducible

-three structural genes:

1. lacZ: B-galactosidase (lactose --> glucose + galactose)

2. lacY: permease (allows lactose to enter cell)

3. lacA: transacetylase (removes toxins from lactose digestion)

-promoter: lacP

-regulator gene: lacI: has its own promoter, product = regulator protein (repressor)

-operator: lacO

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lac operon mechanism

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lac operon positive control

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-positive control: catabolite repression

-B-galactosidase expression: lactose --> glucose + galactose

-galactose --> glucose

-when cell has both lactose and glucose...

-lactose induces lacZ expression

-glucose is preferred by cell: lac operon is not induced by lactose when present

-more efficient energy control

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CAP mechanism

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-CAP = Catabolite Activating Protein: must bind to promoter for RNA polymerase to bind and transcribe

-low glucose = high cAMP; cAMP binds to CAP; cAMP-CAP complex binds to promoter

-high glucose = low cAMP; cAMP-CAP complex is not formed; promoter binding doesn't occur; RNA polymerase can't bind to transcribe lac operon

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trp operon

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-negative repressible

-5 structural genes: produce enzymes that synthesize tryptophan

-regulator gene: trpR (product = regulator protein = repressor)

-low tryptophan levels: repressor can't bind to DNA operator, RNA polymerase binds, transcription occurs --> tryptophan is formed

-tryptophan present: binds to repressor, activates repressor, repressor binds to DNA operator, RNA poly can't bind --> no transcription, no excess tryptophan produced

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trp operon mechanism

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trp operon attenuation

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-severely suppresses the trp operon but does not turn off

-first structural gene (trpE) contains a 5' UTR (attenuator)

-contains 4 regions: 1 complements 2, 2 complements 3, 3 complements 4

-secondary structures result from complementaries: 1 + 2 and 3 + 2 make hairpins

-following 3 + 4 is a string of uracils

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trp operon attenuation mechanism***************

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-excess tryptophan: 3 + 4 form hairpin that stops transcription (terminator structure)

-limited transcription: 2 + 3 form alternative hairpin that promotes transcription (antiterminator structure)

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antisense RNA

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-RNA molecule that is complementary to sequences on mRNA

-binding reduces translation

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riboswitches

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-secondary structures in mRNA where regulatory proteins can bind and affect expression

-also found in archaea, fungi, and plants

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ribozymes

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-self-catalytic activity of some mRNA molecule

-when bound by a regulatory molecule, the ribozyme induces self-cleavage and degradation of the mRNA

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eukaryotic vs prokaryotic gene expression

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-eukaryotic regulation more complex than prokaryotes because:

1. more genetic information

2. packaged as chromatin (DNA with proteins)

-condensed (closed) or decondensed (open) chromatin

-on/off switch for regulation (prokaryotes' operator = on/off switch)

3. site of transcription is separate from translation

4. processing of pre-mRNA into mature mRNA

5. mRNA half-life (prokaryotes = minutes, eukaryotes much longer)

6. differentiated cell types (using different genes)

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chromatin

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-eukaryotic DNA organization

-each chromosome is made of a single DNA molecule and several protein molecules

-chromatin: fibers are a linear array of spherical particles

-"beads" on string = nucleosomes = first level of packaging

-histones: positively charged amino acids (lysine and arginine); bond to negatively charged phosphate groups of DNA

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chromatin remodeling

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-before transcription can occur

-relaxes/opens up via remodeling:

1. dnase I hypersensitivity

2. histone methylation

3. histone acetylation

4. demethylation of cytosine bases

-once chromatin is open, the promoters are exposed, and enhancers and transcription factors can regulate transcription

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flowering in Arabdopsis

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-deacetylase acts on FLC to remove acetyl groups so the chromatin closes up and the gene doesn't get expressed --> flowering

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general transcription factors and transcriptional regulatory proteins

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-GTFs: combine with RNA pol to make basal transcription apparatus (binds to core promoter)

-TFII A, B, D, E, F, J, H

-minimal transcription level

-TRPs: activators and repressors

-activators: bind to regulatory promoter and enhancers (normal transcription)

-repressors: inhibit transcription

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GAL4 in yeast

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-GAL4 = transcriptional activator protein

-galactose metabolism

-several zinc fingers

-binds to enhancer: UASg (upstream sequence)

-GAL4 binding to UASg activates transcription and galactose is metabolized

-GAL80 regulates GAL4:

-if galactose is absent: GAL80 binds to GAL4, GAL4 can't bind to UASg --> no transcription

-if galactose is present: galactose binds to GAL 80, GAL80 can't bind to GAL4, GAL4 binds to to UASg --> transcription

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gene regulation through mRNA processing and turnover

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-alternative splicing: variation in which exons are put together depending on the tissue/developmental stage/sex

-flexibility since one gene can encode different protein variants

-one gene = family of related proteins

-e.g. bovine: alternative splicing of PPT in mRNA

-splicing of the K exon results in a-PPT (nervous system tissue)

-inclusion of P and K exons results in B-PPT (thyroid, intestine, nervous system tissues)

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mRNA stability/degradation

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-5' cap and 3' poly(A) tail protect against degradation, but don't want mRNA to live forever either

-ribonucleases degrade RNA molecules: 3' end degraded gradually until poly(A) binding proteins can't bind anymore, then 5' cap exposed and is removed

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RNA interference

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-involves miRNAs (microRNAs) and siRNAs (small interfering RNAs)

-four mechanisms of interference:

1. RNA cleavage

2. inhibition of translation

3. inhibition of transcription

4. slicer-independent degradation of mRNA

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RNA cleavage

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-mechanism of RNA interference

-enzyme "dicer" produces siRNAs from dsRNA

-siRNAs pair with RNA-induced silencing complex (RISC): binds to mRNA and cleaves mRNA with "slicer", then mRNA degraded

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inhibition of transcription

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-siRNAs bind to complementary DNA sequence

-cause DNA to become methylated --> prevents transcription

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slicer-independent degradation of mRNA

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-miRNA triggers the decay of mRNA

-no "slicer"

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inhibition of translation

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-"dicer" (enzyme that makes siRNAs from dsRNA) produces miRNAs

-miRNAs pair with RISC (RNA-induced silencing complex)

-pairs with mRNA preventing translation

-no actual cleavage takes places

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gene regulation****************

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-ribosomes, tRNAs, initiation factors, and elongation factors all needed for translation

-availability of those components can affect translation and gene expression

-e.g. activation of T lymphocytes as an immune response to viruses