3. The Vocabulary of Gene Regulation
• Housekeeping gene
– under constitutive expression
– constantly expressed in approximately all cells
• Regulated gene
– Levels of the gene product rise and fall with the
needs of the organism.
– Such genes are inducible.
• able to be turned on
– Such genes are also repressible.
• able to be turned off
4. RNA Polymerase Binding to Promoters
Is a Major Target of Regulation
• RNA polymerases bind to promoter sequences near
the starting point of transcription initiation.
• The RNA pol-promoter interaction greatly influences
the rate of transcription initiation.
• Regulatory proteins (transcription factors) work to
enhance or inhibit this interaction between RNA pol
and the promoter DNA.
5. Small-Molecule Effectors Can
Regulate Activators and Repressors
• Repressors reduce RNA Pol-promoter interactions or
block the polymerase.
– bind to operator sequences on DNA
• usually near a promoter in bacteria but further away in many
eukaryotes
• Effectors can bind to repressor and induce a
conformational change.
– change may increase or decrease repressor’s affinity for
the operator and thus may increase or decrease
transcription
6. Activators Improve Contacts Between
RNA Polymerase and the Promoter
• Binding sites in DNA for activators are called
enhancers.
• In bacteria, enhancers are usually adjacent to
the promoter.
– often adjacent to promoters that are “weak” (bind
RNA polymerase weakly), so the activator is
necessary
• In eukaryotes, enhancers may be very distant
from the promoter.
7. Negative Regulation
• Negative regulation involves repressors.
– Example: Repressor binds to DNA and shuts down
transcription
– Alternative: Signal causes repressor to dissociate from
DNA; transcription induced
Despite opposite effects
on transcription, both
are negative regulation
8. Positive Regulation
• Positive regulation involves activators.
• Enhance activity of RNA polymerase
• Activator-binding sites
are near promoters that
weakly bind RNA Pol or
do not bind at all.
• It may remain bound
until a molecule signals
dissociation.
• Alternatively, the
activator may only bind
when signaled.
9. Many Bacterial Genes Are Transcribed
And Regulated Together in an Operon
• An operon is a cluster of genes sharing a promoter
and regulatory sequences.
– Genes are transcribed together, so mRNAs are several
genes represented on one mRNA (polycistronic).
• First example: the lac operon
10. The lac Operon Reveals Many
Principles of Gene Regulation
• Work of Jacob and Monod − 1960
• Shows how three genes for metabolism of lactose are
regulated together as an operon:
– -galactosidase (lacZ)
• cleaves lactose to yield glucose and galactose
– lactose permease (galactoside permease; lacY)
• transports lactose into cell
– thiogalactoside transacetylase (lacA)
• Thet rely on negative regulation via a repressor.
11. Lactose Metabolism in E. Coli
• When glucose is abundant and lactose is lacking,
cells make only very low levels of enzymes for
lactose metabolism.
– Transcription is repressed.
• If glucose is scarce and cells are fed lactose, the
cells can use it as their energy source.
• The cells suddenly express the genes for the
enzymes for lactose metabolism.
– Transcription is no longer repressed.
12. The lac Operon Is Governed by More
Than Repressor Binding
• The availability of glucose governs expression
of lactose-digesting genes via catabolite
repression.
– When glucose is present, lactose genes are turned
off.
– It is mediated by cAMP and cAMP receptor
protein (CRP or CAP for catabolite activator
protein).
13. When Lactose Is Present, Transcription
Depends On Glucose Level
• Repressor dissociates, but transcription is only
stimulated significantly if cAMP rises.
14. Two Requirements for Strongest
Induction of the lac Operon
1. Lactose must be present to form
allolactose to bind to the repressor and
cause it to dissociate from the operator.
• reducing repression
2. [Glucose] must be low so that cAMP can
increase, bind to CRP, and the complex
can bind near the promoter
• causing activation
15. Combined Effects of Glucose and
Lactose on the lac Operon
• When lactose is low, repressor is bound:
inhibition
• When lactose is high, repressor dissociates
permitting transcription
• When glucose is high, CRP is not bound and
transcription is dampened
• When glucose is low, cAMP is high and CRP is bound
activation
16. Binding of Proteins to DNA Often
Involves Hydrogen Bonding
• Gln/Asn can form a specific H-bond with
adenine’s N-6 and H-7 H’s.
• Arg can form specific H-bonds with the
cytosine-guanine base pair.
• See Fiure. 28-10.
• The major groove is the right size for the
helix and has exposed H-bonding groups.
18. Protein-DNA Binding Motifs
• A few protein arrangements are used in
thousands of different regulatory
proteins and are hence called motifs.
– helix-turn-helix
•used by Lac repressor
– zinc finger
– leucine zipper
– and so on
19. The Helix-Turn-Helix Motif Is
Common in DNA-Binding Proteins
• ~ 20 aa
– one helix for recognition for DNA (red in the
next slide), then turn, then another helix
– sequence-specific binding due to specific contacts
between the recognition helix and the major
groove
• Four DNA-binding helix-turn-helix motifs (gray)
in the Lac repressor
20. The Zinc Finger Motif Is Common in
Eukaryotic Transcription Factors
• ~30 aa
• “Finger” portion is a peptide loop cross-linked by
Zn2+
– Zn2+ usually coordinated by 4 Cys, or 2 Cys, 2 His
• Interact with DNA or RNA
– Binding is weak, so several zinc fingers often act in
tandem.
• Binding can range from sequence specific to
random.
21. The Leucine Zipper Motif
• Dimer of two amphipathic helices plus a DNA-binding domain
• Each helix is hydrophobic on one side and hydrophilic on the
other.
– The hydrophobic side is the contact between the two monomers.
• Approximately every seventh residue in helices is Leu.
• Helices form a coiled coil.
• The DNA-binding domain has basic residues (Lys, Arg) to interact
with polyanionic DNA.
22. Role of the Attenuator
• The attenuator (purple, next slide), which is
part of the leader (light blue) determines:
– if transcription will be attenuated at the end of the
leader
– or, if transcription will continue into the genes for
Trp synthesis
24. A Repressor Protein Also Regulates
TRP Transcription
• The Trp operon also has a repressor that
binds to DNA in the presence of tryptophan.
• Trp repressor is a homodimer.
• When Trp is abundant, it binds to repressor,
causes it to bind to the operator, and slows
expression of genes for Trp synthesis.
• It has helix-turn-helix motifs that interact
with DNA via the major groove.
25. Features of Eukaryotic Gene
Regulation
• Access of eukaryotic promoters to RNA
polymerase is hindered by chromatin structure.
– thus requires remodeling chromatin
• Positive regulation mechanisms predominate
and are required for even a basal level of gene
expression.
• Eukaryotic gene expression requires a
complicated set of proteins.
26. Three Features of Transcriptionally
Active Chromatin
• Euchromatin = less-condensed chromatin,
distinguished from transcriptionally inactive
heterochromatin
• Chromatin remodeling of transcriptionally
active genes:
– nucleosomes repositioned
– histone variants
– covalent modifications to nucleosomes
27. Covalent Modification of Histones
• Methylation
• Phosphorylation
• Acetylation
• Ubiquitination
• Sumoylation
• Occur mostly in the N-terminal domain of
the histones found near the exterior of the
nucleosome particle
28. Histone Modification Alters
Transcription
• Covalent modification of histones allows recruitment
of enzymes and transcription factors.
• Methylation of Lys-4 and Lys-36 at histone3 (H3) and
Arg of H3 and H4:
– results in transcriptional activation
– recruits histone acetyltransferases (HATs) that then
acetylate a particular Lys
– reversed by histone deacetylases (HDACs) that make
chromatin inactive
– Acetylation of Lys results in decreased affinity of histone
for DNA.
