Regulation and Signaling Flashcards
What are the two main categories of protein regulation?
-Protein activity: Activate or inactivate a protein that’s already made
-protein amount: control the synthesis or degradation of a protein
Examples of protein Activity regulation
-allosteric inhibition
-covalent modification
(phosphorylation/methylation, cleavage)
Examples of protein amount regulation
-transcriptional regulation and attenuation (lac and trp operons)
-mRNA degradation
-repression of translation
-proteolysis
-any step along gene expression
What is a Kinase?
an enzyme that transfers a phosphate to an acceptor molecule
What is a phospatase?
An enzyme that removes phosphates
An example of
transcriptional
repression,
a type of regulation
of protein amounts
-The lac operon
-encodes enzymes for lactose utilization (LacZ, Y, A)
- amounts of these enzymes is regulated because lactose is not a common nutrient for E.coli
Methods of regulating protein amounts
-every step from the gene to the functional protein could be regulated
- the type of regulation involved varies from gene to gene
-often multiple types of regulations are involved
What is attenuation?
-Premature termination of transcription
-attenuation regulates other amino acid biosynthesis operons in addition to the trp operon
What do sRNAs do?
Inhibition of translation
-have a hair loop structure
What happens when trp is scarce?
-There is no attenuation
- The ribosome stalls but doesn’t stop bc Trp is scarce
-anti terminator on tRNA forms
-RNA polymerase will continue transcribing
-trpE-A is expressed
What happens when trp is abundant?
-attenuation occurs
-tRNA charged with trp are abundant so ribosome doesn’t stall
-terminator forms
- RNA polymerase stops transcribing
-trpE-A is not expressed
What are the two important properties of the transcript of trpL?
- can form different stem loop structures; terminator or anti terminator
- has 2 adjacent tryptophan codons (UGG-UGG)
Where is the trpL located?
Upstream of trpE-A in genome
When does attenuation occur?
occurs when excess tryptophan is present
What is a regulon?
a set of operons controlled by a common regulator
What is a modulon?
-A set of regulons controlled by a common regulator such as (CAP-cAMP for glucose mediated catabolite repression)
Globular Regulation
-catabolite repression
- a common regulator controls transcription of many different catabolic
enzymes, so bacteria selectively use their preferred energy source first
CAP-cAMP
-binding of CAP-cAMP to regulatory region helps RNAP to bind, activating
transcription of catabolic enzymes (CAP = catabolite activator protein)
-high cAMP levels needed for CAP-cAMP binding
-enhances transcription of operons already induced, e.g. lac
operon by lactose
-CAP binding is sensitive to
cellular cAMP levels
-low glucose levels result in high
cAMP levels
-basis for “glucose effect” in many
bacteria = repression of
catabolism of other carbon
sources when glucose is present
Signaling
Bacteria sense and respond to their environment
Stress
=change
- to ability to cope with stress is critical to a microbes survival
Two component Regulatory Systems
–highly conserved and
ubiquitous in bacteria
(also in fungi, plants)
-sensor kinases and
response regulators have
conserved amino acid
sequence motifs – easy
to annotate in the
genome
-absent from animals and
humans and important
for bacterial survival;
thus a great potential
drug target
Two-component regulatory systems - examples from rhizobia
Rhizobia are root-associated bacteria that “fix” nitrogen in a symbiosis
with plants. Rhizobia convert dinitrogen gas into a form usable by plants.
Fixed nitrogen is critical for agricultural productivity.
Nitrogen-fixing bacteria and legumes
- establishment of the symbiosis involves infection of plant cells in the root
by the bacteria (which act as endosymbionts in the nodule).
*the plant receives fixed nitrogen from the bacteria while the bacteria receive
carbon sources from the plant
Two-component regulatory systems - examples from rhizobia
low [O2 ]
FixL
FixJ
Genes encoding enzymes for nitrogen fixation
FixL/J in Sinorhizobium
meliloti is a two-
component system that
controls transcription in
response to O 2
concentration.
*FixL/J activates
transcription of the gene
for nitrogenase, which
catalyzes nitrogen fixation
when [O 2 ] is low.
*Nitrogenase enzyme is
inactive when [O 2 ] is high,
so it would be a waste to
make it then.
Two-component regulatory systems - examples from rhizobia
?
ExoS
ChvI
Genes encoding enzymes for polysaccharide production
*ExoS/ChvI is a two-
component system in
Sinorhizobium meliloti
that controls transcription
in response to an
unknown signal.
*ExoS/ChvI activates
transcription of genes for
polysaccharide
production.
*The right amount of
polysaccharide is needed
to form the nitrogen-fixing
symbiosis with plants.
Main points of lac operon
⇰ Glucose is present, Lactose is absent:
No transcription of the lac operon occurs. that’s b/c the lac repressor remains bound to the operator and prevents transcription by RNA pol. Also, cAMP levels are low b/c glucose levels are high, so CAP is inactive and cannot bind DNA.
⇰ Glucose is present, Lactose is present:
Low-level transcription of the lac operon occurs. the lac repressor is released from the operator b/c the inducer (allolactose) is present. cAMP levels, however, are low b/c glucose is present. Thus, CAP remains inactive and cannot bind to DNA, so transcription only occurs at a low, entry level.
⇰ Glucose is absent, Lactose is absent:
No transcription of the lac operon occurs. cAMP levels are high b/c glucose levels are low, so CAP is active and will bind to the DNA. However, the lac repressor will also be bound to the operator due to the absence of allolactose. This acts as a roadblock to RNA pol, preventing transcription.
⇰ Glucose is absent, Lactose is present:
Strong transcription of the lac operon occurs. the lac repressor is released from the operator b/c the inducer, allolactose, is present. cAMP levels are high b/c glucose is absent, so CAP is active and bound to the DNA. CAP helps RNA pol bind to the promoter, permitting high levels of transcription.
Takeaway:
The lac operon will be expressed at high levels if 2 conditions are met:
⇰ Glucose must be unavailable: when glucose is absent, cAMP binds to CAP, making CAP able to bind to DNA. Bound CAP helps RNA Pol attach to the lac operon promoter.
⇰Lactose must be available: if lactose is available, the lac repressor will released from the operator via binding of allolactose. this allows RNA pol to move forward on the DNA and transcribe the operon.
