Topic 6-L3 - Transcriptional regulation Flashcards
How to cells adapt to their environment
Controlling the abundance/activity of gene products
Regulating transcriptional initiation
- transcription factors
control whether or not RNA polymerase binds a promoter and initiates transcription (more accurately, the rate at which that occurs). Largely accomplished by DNA-binding
regulatory proteins called transcription factors
Many regulatory proteins are
DNA-binding proteins
DNA-binding proteins have
DNA-binding domains such as the HTH domain that bind to DNA helix
DNA binding proteins often recognize a
consensus sequence
Often DNA sequences with direct or
inverted repeats are bound by homodimers, which are
one monomer binds each repeat,
dimerization required. Ensures specificity
Transcription factors that promote transcription are called
activators
Transcription factors that inhibit transcription are called
Repressors
Activators often work by binding
DNA at promoter & recruiting RNA polymerase (sigma factor) to begin transcription. Gene under “positive control”
Repressors bind DNA & (often)
prevent
RNAP DNA binding or transcriptional initiation after it binds. Sequence bound by repressor often called operator.
Gene under “negative control”
Some transcription factors are regulated allosterically –
binding of an effector (usually a small molecule such as a metabolite) activates or inactivates protein
Inducers
“turn on” activator proteins (or inactivate repressors)
Corepressors
activate repressor proteins
An inducible system is one
that is
off by default, but can be turned on.
repressible system is one
that is
on by default, but can be turned off (a gene can be controlled by both)
Example of a repressible system:
Arginine biosynthesis
Arginine biosynthesis
ArgR is a repressor protein that controls the expression of an arginine
biosynthesis operon
When arginine is present, acts as a
co-repressor.
When arginine levels are high, it
binds ArgR, enabling ArgR to bind
the Operator & prevent transcription of this operon
When arginine levels are low,
ArgR isn’t bound by arginine, doesn’t
bind DNA – genes are expressed and arginine is synthesized by cell
Lac operon
Code for the breakdown for lactose (E source)
Expressing these genes for lac operon in absence of lactose not useful – to prevent this,
LacI repressor protein binds lac Operator, prevents transcription
When lactose is available, a
lactose isomer called
allolactose binds LacI & inactivates it
allolactose = inducer
E. coli doesn’t want to use lactose if a better energy source is available –
Catabolite repression
Lac operon expression requires both:
lactose AND low glucose levels.
In the presence of glucose,
production of cAMP is _________. Low cAMP levels in cell
For lac operon to be expressed, also requires _____________ to bind cAMP. cAMP- bound CRP binds promoter region
& recruits RNA polymerase
inhibited.
CRP (cAMP receptor protein)
Glucose regulation is
indirect (cAMP is direct inducer)
(cAMP) is an example of a
signaling molecule or second messenger
ppGpp produced in response to
amino acid starvation.
ppGpp shuts down protein synthesis & induces amino acid biosynthesis in a process that is called
stringent response
Quorum sensing also involves signaling molecules called
autoinducers
Quorum sensing involves sensing the
local density of cells through
secreting/detecting specific molecules – regulating based on that info.
Quorum sensing is used to
coordinate group behaviours like biofilm formation, virulence, etc. Only want to carry out these activities make certain genes at high cell densities
Produce autoinducer (small molecule) – secrete – it diffuses away. Doesn’t accumulate in cell except at high density. Detect high density –
know you’re in a group – activate group behaviours
Example of autoinducer
AHL
Quorum sensing is a form of
chemical communication.
used by All 3 domains
Quorum sensing using AHLs involves regulating the expression of numerous
genes in response to the concentration of AHLs sensed by the cell
Different species produce/detect their own specific versions of
AHL (different R groups)
Quorum sensing first discovered in
Vibrio fischeri
A very common form of gene regulation in bacteria is the two-component regulatory system – form of
signal transduction
Two-component regulatory system uses two protiens:
Sensor kinase and response regulator
Sensor kinase:
Usually resides in cytoplasmic membrane. Senses specific signal(s), which activates kinase activity - adds phosphate to response regulator. In absence of signal, will dephosphorylate response regulator.
Response regulator:
When phosphorylated, becomes active. Binds DNA to regulate expression of target genes (activator and/or repressor)
Transcriptional silencing:
very tightly shutting off expression of genes by altering the genome structure at promoter regions
Best known silencer is for transcriptional silencing
H-NS
H-NS prevents
binds & restructures DNA to a rigid structure to prevent RNA polymerase from binding the DNA and/or carrying out transcription process
H-NS binds regions of the genome that have a
high % AT
high % AT in H-NS represent
horizontally-acquired DNA (genomes have a characteristic % AT).
Counter-silencing DNA-binding activators bind
specific silenced loci and reverse effects of H-NS (re-structure DNA and/or remove H-NS) allow specific genes to be expressed
Global regulators regulate large numbers of different genes in response to a
given signal or environmental cue
A regulon is the
complete set of genes controlled by a given regulator
Sigma factors, allosteric regulatory proteins, two-component systems, transcriptional silencers, second messengers, quorum sensing – all can potentially exert
global control
PhoPQ acts as a
global regulator of many virulence- related processes in Salmonella
Despite differences in transcription
mechanisms, transcriptional regulatory systems in Archaea often synonymous with
bacterial systems
Activators/repressors bind
DNA to affect recruitment of RNA
polymerase
Two -component regulatory systems
also present in
Arachaea, less common then in bacteria tho
