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.
