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regulation of gene expression - Coggle Diagram
regulation of gene expression
volcobulary
Housekeeping gene
under constitutive expression
expressed in approximately all cells
Regulated gene
gene product rise and fall with the
needs of the organism.
promoter
DNA sequence
RNA polymerase bind to
RNA pol-promoter interaction greatly influences
the rate of transcription initiation
A Consensus Sequence Is Found in
Many E. Coli Promoters
conserved –10
and –35 regions
reduce the
affinity of RNA Pol for the promoter
Some promoters also include the upstream element
other protein bind to promoter
recognize promoters of specific genes
undergo posttranslational modifications
protein’s affinity toward DNA is altered by ligand binding or
posttranslational modifications
allows expression of specific genes in response to signals in the
environment
σ factors
recognize different classes of promoters
allows coordinated expression of different sets of genes
Repressors
bind to operator sequences on DNA
usually near a promoter in bacteria but further away in many
eukaryotes
Effectors
bind to repressor
induce a
conformational change
increase or decrease repressor’s affinity for
the operator(induce or inhibit transcription)
enhancers
"Binding sites" in DNA for activators
In bacteria, enhancers are usually adjacent to the
"promoter"
activator
often adjacent to promoters that are “weak” (bind
RNA polymerase weakly), so the activator is necessary
operon
a cluster of genes
sharing a promoter
and regulatory sequences
Negative Regulation
repressors
Positive Regulation
activators
others
Heat Shock Induces Transcription of
New Products to Protect Cell
Occurs when bacteria are subject to heat stress
Causes RNA Pol to bind to different set of promoters
RNA Pol replaces σ70 with σ32
DNA Looping Allows Eukaryotic
Enhancers to Be Far from Promoters
involve:
architectural regulator proteins
Co-activators
activator & RNA poiymerase
Activators
從鹼基對上看很遠，但可以透過architectural regulator proteins轉彎
The lac Operon
three genes for metabolism of lactose are
regulated together
beta-galactosidase (lacZ)
isomerize lactose into allolactose
[Allolactose] 上升 when[Lactose] 上升
hydrolyzes lactose
lactose permease
thiogalactoside transacetylase
glucose
cAMP、CRP
cAMP binds near the promoter
bend DNA
cAMP is made when [glucose] is
low
abundent - Transcription is repressed
mechanism
catabolite repression
The availability of glucose governs expression of
lactose-digesting genes via
When glucose is present, lactose genes are turned off
lactose
repressor
Lac repressor binds primarily to the operator O1
The repressor also binds to one of two secondary operators, with the DNA
looped between this secondary operator and O1
prevent RNA polymerase from binding to
the promoter
abundent - permitting transcription
The lac Operon Is Induced by
Allolactose
allolactose異乳糖
an inducer
bind to repressor
negative regulation
Binding of Proteins to DNA
Often
Involves Hydrogen Bonding
Gln/Asn & A(base pair)
Arg & C-G(base pair)
Motifs
Helix-Turn-Helix
composed of
one α helix for recognition for DNA
one β turn
one α helix
binding due to specific contacts between the recognition helix and the major groove
Zinc Finger Motif
Interact with DNA or RNA
Binding is weak, several 串聯
Each Zn2+
coordinates with two His and two Cys residues.
Leucine Zipper
composed of
two amphipathic α helices
DNA-binding domain
The DNA-binding domain has basic residues (Lys (K), Arg (R)) to
interact with polyanionic DNA
Each helix is hydrophobic on one side and hydrophilic on the
other
Eukaryotic Gene Regulation
relies on protein-protein interactions
Eukaryotic RNA-Binding Domain
RNA recognition motifs – (RRMs)
composed of
four strand antiparallel β sheet
two α helices
Binding to lncRNAs, decreasing gene
transcription
role
DNA-binding regulatory proteins
proteins binding only RNA
bind to DNA&RNA with Hydrogen bonding interactions
usage
transcription factors that regulate cell growth and apoptosis
amino acid regulation
transcriptional attenuation
trp operon
leader
sequence(chane in gene conformation)
trp levels are high
transcription of trp mRNA is attenuated
3 and 4 base-pair/attenuation signal
formation
Abundance of tRNATrp
2 and 3 base-pair/transcription proceed
formation
Low Availability of tRNATrp Signals
rules are suitale for other amino acids
repressor
Trp is abundant, it binds to repressor, slow down Trp synthesis
helix-turn-helix motifs interact wih DNA
SOS Response
response to extensive DNA damage
Damaged DNA produces a lot of single strands
alter
cell cycle arrest
activation of DNA repair systems
protein RecA(in E.coil)=Rad51( in eukaryotes)
binds to single-stranded DNA
LexA repressor(co-protease)
binds to LexA
self-cleave
dissociate from DNA
Link Between the SOS Response
and Virus Propagation
in bacterial
Some repressors keep viruses in a dormant
state
in eukaryotes
allows virus to replicate, lyse cell, and release new
virus particles
translation feedback & ribosomal protein
major rules
When bacteria need more protein, they make more ribosomes
Ribosmal protein (r-protein) operons are regulated
via translational feedback
translation feedback
translational repressor
only works when r-protein too much
rRNA synthesis
Amino Acid Availability
The stringent response
ppGpp
Binding of ppGpp to RNA polymerase
reduce rRNA synthesis
lack of uncharged tRNA
Some RNAs Participate in Regulation
“Cis” regulation
affects its own
function
Riboswitches
domain of an
mRNA that can bind a smallmolecule ligand
“Trans” regulation
affected by
another separate molecule
DsrA RNA promotes translation
opens up the stem-loop and
allows mRNA binding to the ribosome
OxyS RNA inhibits translation
blocks the ribosome binding site
in mRNA
sRNA-mRNA interactions are facilitated by a
chaperone protein called Hfq
