Regulation of Gene Expression
the SteadyState Concentration of a Protein 
Gene Regulation
relies on precise protein-DNA and
protein-protein contacts
Housekeeping gene
constitutive expression
expressed in approximately all cells
Regulated gene
gene product rise and fall
inducible
repressible
Major Target of Regulation
RNA Polymerase Binding to Promoters
near the starting point of transcription initiation
RNA pol-promoter
influences the rate of transcription initiation.
Regulatory proteins enhance or inhibit this interaction between RNA pol and the promoter DNA.
E. Coli Promoters 
Substitutions in this –10 to –35 region usually reduce the
affinity of RNA Pol for the promoter.
interact with the σ factor
upstream element
interacts with the α subunit
Regulate Transcription
in Bacteria
Use of σ factors
recognize different classes of promoters
coordinated expression of different sets of genes
Binding other proteins (transcription factors) to promoters
recognize promoters of specific genes
bind small signaling molecules
posttranslational modifications
protein’s affinity toward DNA is altered by ligand binding or
posttranslational modifications
expression of specific genes in response to signals in the
environment
Most E. coli promoters recognized by σ70
.
Heat shock will replace σ70 with σ32 and direct
RNA Pol to different promoters
transcription of new products including chaperones that
keep proteins in correct conformation
Small-Molecule Effectors Can
Regulate Activators and Repressors
Repressors
reduce RNA Pol-promoter interactions
block the polymerase
bind to operator sequences on DNA
near a promoter in bacteria but further away in many eukaryotes
Effectors
bind to repressor
induce a conformational change
change may increase or decrease repressor’s affinity for the operator and thus may increase or decrease transcription
Activators
enhancers
Binding sites in DNA
In bacteria
adjacent to the promoter
bind RNA polymerase weakly
In eukaryotes
very distant
from the promoter
Regulation
Negative
involves repressors 
Positive
involves activators 
DNA Looping 
facilitated by architectural regulator proteins
Co-activators may mediate binding by binding to both activator and RNA polymerase
Many Bacterial Genes Are Transcribed
And Regulated Together in an Operon
operon is a cluster of genes sharing a promoter
and regulatory sequences
lac operon 
three genes for metabolism of lactose are
regulated together as an operon
Β-galactosidase (lacZ)
actose permease (galactoside permease; lacY)
thiogalactoside transacetylase (lacA)
They rely on negative regulation via a repressor
Lactose Metabolism in E. Coli 
glucose is abundant and lactose is lacking
Transcription is repressed
glucose is scarce and cells are fed lactose
Transcription is no longer repressed.
Inhibiting the Transcription via a Repressor Protein
a gene lacI encodes a repressor called the Lac repressor 
The repressor can bind to three operator sites (O1–O3)
binds primarily to the operator O1
prevent RNA polymerase from binding to the promoter
also binds to one of two secondary operators, with the DNA
looped between this secondary operator and O1
It reduces transcription, but transcription occurs at a low, basal rate, evenwith the repressor bound.
Induced by
Allolactose
binds to the repressor and
causes it to dissociate from the operator
[Allolactose] 上升 when[Lactose] 上升
The lac Operon Is Governed by More
Than Repressor Binding
The availability of glucose governs expression of
lactose-digesting genes via catabolite repression
mediated by cAMP and cAMP receptor protein
cAMP is made when [glucose] is low.
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
Binding of Proteins to DNA Often Involves Hydrogen Bonding
Protein-DNA Binding Motifs
helix-turn-helix
zinc finger
leucine zipper
Common in DNA-Binding Proteins
one helix for recognition for DNA , then Β
turn, then another α helix
Common in
Eukaryotic Transcription Factors
Zn2+ usually coordinated by 4 Cys, or 2 Cys, 2 His
Interact with DNA or RNA
Binding is weak so it need several zinc fingers often act in tandem
Each helix is hydrophobic on one side and hydrophilic on the other.
Approximately every seventh residue in helices is Leu (L).
Helices form a coiled coil.
The DNA-binding domain has basic residues (Lys (K), Arg (R)) to
interact with polyanionic DNA.
Eukaryotic RNA-Binding Domain
RNA recognition motifs – (RRMs)
four strand antiparallel β sheet with two αhelices
Found in gene activators and bind to both DNA and RNA
Binding to lncRNAs (long noncoding RNAs) forces the proteins
to compete with DNA for binding
decreasing gene transcription
Amino Acid Biosynthesis Regulated
by Transcriptional Attenuation
The trp operon is regulated by transcription attenuation
Transcription begins but is then halted by a stop signal
(attenuator).
in bacteria, transcription and
translation can proceed simultaneously
The attenuator sequence is in the 5’-region of a leader
sequence
can make the ribosome stall.
Role of the Attenuator
part of the leader
transcription will be attenuated at the end of the
leader
or transcription will continue into the genes for
Trp synthesis
The trp Operon 
The Leader Region Can Form
Different Stem-Loop Structures
If tRNATrp is abundant
segment 3 pairs with 4
attenuator
If tRNATrp is scarce
allows 2–3 pairs to form
Translation proceeds unhindered.
A Repressor Protein Also Regulates
Trp Transcription
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
Regulation of the SOS Response
SOS Response 
response to extensive DNA damage
SOS genes are repressed by LexA repressor
LexA binds to operators at several genes
ssDNA is bound by the protein RecA (or, in eukaryotes Rad51).
RecA binds to LexA repressor, causing it to self-cleave and
dissociate from DNA
Synthesis of Ribosomal Proteins and
rRNA is Controlled at Translation
Ribosmal protein (r-protein) operons are regulated
via translational feedback (next slide).
Translational Feedback Mechanism
Each operon for an r-protein encodes a
translational repressor.
repressor binds to mRNA and blocks translation
Repressor has greater affinity for rRNA than for
mRNA
rRNA Synthesis Is Regulated by
Amino Acid Availability
The stringent response occurs when aa
concentrations are low.
Lack of aa produces uncharged tRNA.
Uncharged tRNA binds to ribosomal A site
rRNA synthesis triggers a cascade that begins with binding stringent factor protein (RelA) to ribosome.
Stringent factor catalyzes formation of
nucleotide guanosine tetraphosphate (ppGpp).
Binding of ppGpp to RNA polymerase reduces
rRNA synthesis.
Some RNAs Participate in Regulation
“Cis” regulation
a molecule affects its own
function
“Trans” regualtion
a molecule is affected by
another separate molecule
σS mRNA is present a low levels but is not translated due to a hairpin structure that inhibits its binding to ribosomes.
sRNAs (small RNAs) bind to this mRNA and
inhibit formation of the hairpin.
sRNA-mRNA interactions are facilitated by a
chaperone protein called Hfq.
Activation of Bacterial Translation
by Small RNA Molecules
In the presence of protein Hfq, small regulatory RNA
DsrA binds to the mRNA.
The binding of DsrA opens up the stem-loop and
allows mRNA binding to the ribosome.
DsrA RNA promotes translation.
Inhibition of Bacterial Translation
by Small RNA Molecules
In the presence of protein Hfq, small regulatory RNA
OxyS binds to the mRNA
The binding of OxyS blocks the ribosome binding site
in mRNA
OxyS RNA inhibits translation.
Cis Regulation by Riboswitches
Riboswitch = domain of an
mRNA that can bind a smallmolecule ligand
The binding of ligand affects conformation of the mRNA and its activity.
riboswitches allow mRNA to participate in their own regulation and respond to changing concentrations of the ligand.
respond to
many coenzymes, metabolites
in eukaryotic introns and
seem to regulate splicing.
target for antibiotics.
Regulation by Gene Recombination 
remove promoters relative to the coding sequence or can put genes into multiple orientations to alter the expression.
Features of Eukaryotic Gene Regulation
Access of eukaryotic promoters to RNA polymerase is hindered by chromatin structure.
requires remodeling chromatin
Positive regulation mechanisms
Three Features of Transcriptionally Active Chromatin
nucleosomes repositioned
histone variants
covalent modifications to nucleosomes
Nucleosomes Can Be Restructured by
Specific Protein Complexes
SWI/SNF (SWItch/Sucrose NonFermentable)
complex
remodels chromatin
stimulates binding of transcription factors
works with proteins of ISWI (imitation switch)
family
ATP-dependent alteration of spacing between
nucleosomes
Histone Modification Alters Transcription
Methylation of Lys-4 and Lys-36 at histone3 (H3) and
Arg of H3 and H4:
recruits histone acetyltransferases (HATs) that then
acetylate a particular Lys
reversed by histone deacetylases (HDACs) that make
chromatin inacti
Acetylation of Lys results in decreased affinity of histone
for DNA.