Chapter 14-Regulation of bacterial cellular processes
positive control of an inducible gene
*Activator + inducer the activator protein is only able to bind DNA and activates transcription when it interacts with inducer if the activator protein does not interact with the inducer, transcription will not happen
positive control of a repressible gene
*Activator + inhibitor the activator binds DNA and promotes transcription unless the inhibitor is present. when the inhibitor is present the activator undergoes a conformational change that prevents it from binding DNA; this inhibits transcription
Which two of the following are encoded by the lac operon?
3 structural genes, lacI
Which two of the following are characteristics of the lac repressor protein?
4 identical subunits (tetramer) -Each monomer has a helix-turn-helix domain
LuxR
A DNA binding transcriptional activator on luxCDABE operon that encodes bioluminescence proteins - needs high concentrations of autoinducer
Two-component signal transduction system
A message relay system composed of a sensor kinase protein and a response regulator protein that regulates gene expression in response to external stimuli -ex: EnvZ/OmpR system
If transcription and translation were not coupled in bacteria, what type of regulation would be affected?
Attenuation
positive transcriptional control
Control of transcription by an activator protein. When the activator is bound to the activator-binding site, the level of transcription increases.
restriction modification system (innate)
DNA destruction system; only effective against double-stranded DNA viruses -microbes produce methylase enzymes that modify nitrogenous bases in short DNA strands -restriction endonucleases (REs): hydrolyze phosphodiester bonds of DNA that has not been methylated ---which allows the microbe to protect it's own DNA by adding methyl groups ---if unmethylated DNA enters the cytoplasm, they are destroyed by restriction endonucleases
Which three of the following are characteristics of the attenuator terminator loop?
Immediately followed by a poly-U region Formed by the pairing of regions 3 and 4 Similar to factor-independent transcription terminators
negative transcriptional control
Inhibition of transcription by a repressor protein. When bound to the repressor-binding site, transcription is inhibited.
In the sporulation initiation pathway of Bacillus subtilis, ____ acts as a sensor kinase Senses nutrient starvation Autophosphorylates a specific histidine residue
KinA
Transcription of the trp operon is controlled by which two of the following mechanisms?
Premature termination through attenuation Repressor protein inhibits initiation
Which four of the following are characteristics of the attenuator antiterminator loop?
Prevents the generation of the pause loop Formed by the pairing of regions 2 and 3 Prevents the generation of the terminator loop Located in the leader region
Which two of the following are mechanisms that can control transcription of the trp operon by way of the attenuator region?
Ribosome stalls in region 1 due to low tryptophan levels - antiterminator loop forms Ribosome translates at normal rate due to adequate tryptophan levels - pause and terminator loops are formed
Which two of the following are characteristics of the attenuator pause loop?
Slows down RNA polymerase; Formed by the pairing of regions 1 and 2
attenutation
Termination of transcription elongation before RNA polymerase enters the first structural gene of an operon -transcription is terminated in the leader
HAI-1
V. harveyi autoinducer -homoserine lactone -synthesized by LuxM gene
structural gene
a gene that codes for nonregulatory polypeptides ( such as an enzyme, protein, or RNA) rather than serving as a regulator
repressible genes
a gene that is regulated by a corepressor or inhibitor, which are small effector molecules that cause transcription to decrease -in anabolic/biosynthetic pathways -makes repressible enzymes that are not present if the end product of the pathway is available
___ protein is a DNA-binding protein that promotes transcription initiation.
activator
inducible genes
express inducible enzyme; gene expression is turned on by the presence of some substance. Regulate catabolic pathways. -enzyme levels rise in the presence of an inducer (small effector molecule)
constitutive genes
expressed continuously by the cell
DNA-bound activator proteins promote transcription initiation by
facilitating RNA polymerase binding
sensor kinase
protein that spans the plasma membrane and internal part of the cytoplasm so that it can detect outside changes and communicate them inside
response regulator
receives a signal from the sensor kinase and undergoes a conformational change so it can interact with other molecules by: -forming homodimers that bind to DNA and activate or repress transcription initiation -interact with enzymes and proteins in the global network
The trp operon of E. coli is regulated by attenuation. If tryptophan levels are high in the cell, ___
regions 3 & 4 of the mRNA will base pair and transcription terminates
methyleterase CheB
removes methyl groups from MCP
CRISPR/Cas system (adaptive immunity)
used to recognize future viral attacks -found in 50% of bacterial and 90% of archaeal genomes stage 1 function- adaptation: after viral infection, viral genome pieces are added at the end of the genome close to the cas genes stage 2: expression: CRISPR region is transcribed to make a large RNA with all repeats and spacers and cas proteins mature it into crRNAs (each consisting of 1 repeat and 1 spacer) ---crRNA associate with viral DNA or mRNA which leads to destruction stage 3: interference: crRNA prevents viral multiplication -constitutively transcribed at lower levels quorum sensing signals CRISPR/cas expression
Following the partitioning of the mother cell and the forespore, the first sigma factor to be found in the forespore is ____.
σF
In E.coli regulatory pathways, which molecule functions to ensure that glucose is used as the preferred carbon and energy source?
CAP
Which statement best describes the result of CAP binding to the CAP recognition site?
CAP bends the DNA within two helical turns
when glucose is present but not lactose
CAP is inactive because cAMP does not bind, lac repressor binds to the operator and inhibits transcription
cells run (counterclockwise) when attractants bind MCPs and ___ is inactive
CheA
Which type of motion results from the interaction of activated CheY with flagellar motor protein?
Clockwise rotation (tumble)
The two types of response regulators in two-component signal transduction systems are
DNA-binding proteins Proteins that control enzymes
housekeeping genes
a gene that is transcribed continually because housekeeping enzymes are needed at all times and in all cells
In the absence of lactose, the lac repressor is __________.
active and can bind to the operator
Which of the following is the inducer of the lac operon?
allacotose
A repressor protein synthesized in its inactive form is referred to as a(n)
aporepressor; activated by a corepressor
Transcription of the trp operon is regulated at the level of initiation by the trp repressor, and at the level of elongation by a process called
attenutation
for the lac operon, transcription levels are highest when lactose is _____ and glucose is ____
available, NOT
The lac repressor protein inhibits transcription by ____.
bending DNA in the promoter region
activator proteins
bind to the activator binding site (upstream from the promoter) and makes the promoter a better target for RNA polymerase or interacts with RNA polymerase's alpha and beta subunits to facilitate binding
repressor proteins
bind to the operator (downstream of promoter) and block RNA polymerase from binding
An active repressor protein _________.
binds to the DNA molecule and prevents transcription
when neither lactose nor glucose are present
cAMP binds to CAP and activates it, activated CAP binds to the CAP operon binding site, the lac repressor binds to the operator site and transcription is blocked
Types of second messengers
cAMP, ppGpp, pppGpp, GMP, c-di-AMP, cGMP, ATP, ppTpp
When in a complex with ________, the CAP protein binds to the CAP site and ________ the expression of the lac operon.
cAMP; switches on
The global control of operons encoding enzymes for the catabolism of carbohydrates that must be modified prior to entering glycolysis is referred to as
catabolite repression
The positive regulatory system called ____ prevents the expression of genes encoding proteins necessary for the utilization of sugars other than glucose when adequate supplies of glucose are present.
catabolite repression
MCP (methyl-accepting chemotaxis proteins)
chemoreceptors that bind to 2 component signal transduction system that control flagellar rotation; in the plasma membrane, with parts exposed on each side
CAI-2
cholerae autoinducer -product of CqsA enzyme (made by vibrios genus)
lac repressor protein
inhibits transcription when lactose is absent (negative control) -binds to O1 operator site and either 03 or 02 to make a DNA loop transcription happens when an inducer (allolactose) binds to the lac repressor
Negative transcriptional control of inducible genes (i.e., turned "off" until turned "on")
lac operon
AHL is synthesized by the enzyme AHL synthase, encoded by the gene
luxI
CheR and CheB
measure methylation of MCPs at different times to remember attractant concentration
Cellular DNA is _____; viral DNA is not.
methylated
The "modification" component of a restriction-modification system involves _____ in DNA.
methylation of nitrogenous bases
The lac operon is considered a _____ control system because it is considered to be turned off until lactose is present.
negative
The trp operon is a ____ control system because it is turned off by a repressor protein when not needed.
negative
sigma F and sigma B
only found in forespore
sigma E and sigma K
only found in mother cell
Bacterial repressor proteins bind to a DNA sequence called the
operator
factors that control sporulation
phosphorelay posttranslational modification of proteins, transcription initiation regulatory proteins, and alternate sigma factors
CheY
response regulator
SpoOA
response regulator protein -controls sporulation initiationf Activates genes required for sporulation Bacillus subtilis Is phosphorylated by SpoOB Alters the expression of about 500 genes-"master regulator"
CheA
sensor kinase
Sigma factor σF is encoded by the gene
sigF
transcriptional regulatory proteins
small DNA binding proteins that form dimers and bind to palindromes (short, inverted sequences of bases in DNA) -DNA binding protein portion (small portion of this protein) interacts with the palindrome -large portion of the protein interacts with effectors
The ___response is observed in many bacteria that are starved for amino acids.
stringent
Environmental signals like oxygen levels or light are detected by sensory domains on diguanylate cyclase enzymes, and these enzymes act to _____.
synthesize c-di-GMP
trans-encoded sRNA
synthesized at other sites that don't encode their mRNA target but they still have complementary regions; accompanied by their Hfq chaperone
cis-encoded sRNA
synthesized from the sense strand of the gene that creates the mRNA target
adenyl cyclase enzyme
synthesizes cAMP from ATP when glucose is unavailable
when lactose and glucose are both present
the inducer allolactose will bind to and inactivate the lac repressor protein, cAMP will not bind to CAP (inactive) so transcription is inhibited because CAP can't bind to the CAP site on the operon
mycotoxins
toxins produced by fungi; contaminate food, crops, water
When is adenyl cyclase active?
Little or no glucose is available
inducers
Small effector molecules whose presence increases the level of specific enzymes
Aporepressors are activated by the binding of a(n)
corepressor
When E. coli is grown on medium containing glucose and lactose, a two phase pattern called ____ growth is seen as the glucose is preferentially metabolized.
diauxic
regulated genes
encodes enzymes that are only needed at certain times -ex: B-galactosidase enzyme (catalyzes the hydrolysis of lactose to glucose and galactose)
In the early steps of sporulation, sigma factors σF and σE are primarily involved in controlling genes necessary for the process of ____.
engulfment
AI-2
fluoroborate: small molecule that contains a boron atom -made by LuxS gene -both gram +/-
Regulatory systems that simultaneously control the expression of multiple operons or pathways are referred to as ________.
global regulatory systems; ex CAP
riboswitches
regulatory sequences in 5' untranslated mRNA leader that act as switches regulating protein synthesis in response to environmental conditions -small effector molecules binds to the mRNA to stop transcription -can fold into different patterns based upon the binding of an effector molecule to the mRNA. -This type of regulation is used by Gram-positive bacteria to regulate amino acid-related genes.
The nucleotide sequence that encodes the leader sequence of the trp operon is ____.
trpL
The stringent response is regulated by the second messenger _____.
guanosine tetraphosphate and pentaphosphate (ppGpp)
The "restriction" component of a restriction-modification system involves _____ in DNA.
hydrolysis of the phosphodiester bond
The mechanism to synthesize cAMP when glucose is absent involves the system for _____.
phosphorylating glucose as it enters the cell
alarmones
ppGpp/pppGpp; respond to nutritional stress
CAP (catabolite activator protein)
regulates the lac operon in response to the presence or absence of glucose; works alongside with the lac repressor
when lactose is present but not glucose
the inducer allolactose will bind to and inactivate the lac repressor protein, then cAMP will bind to CAP to activate it and transcription will procede
As a general rule, Gram-negative bacteria use riboswitches to regulate the ____ of mRNA, and Gram-positive bacteria use riboswitches to regulate ____ termination.
translation, transcription
The intracellular level of cAMP depends on the state of a protein that functions in the phosphoenolpyruvate:sugar phosphotransferase system (PTS).
true
True or false: The ara operon is an example of both a positive and negative control system.
true
as internal AHL concentration increases, AHL activates LuxR which increases LuxI gene transcription whose products help bioluminescence
true
In E. coli, the production of proteins called ___ are controlled by the EnvZ/OmpR two-component signal transduction system.
porins
negative control of a repressible gene
*Repressor + corepressor (usually a product of the biosynthetic pathway like an amino acid) in the absence of a corepressor, the aporepressor (inactive repressor) is unable to bind DNA and transcription will occur. when the corepressor interacts with the repressor, the repressor is able to attach to DNA and transcription is blocked. -ex: trp operon
negative control of an inducible gene
the repressor protein is active/binds to promoter and prevents transcription when the substrate of the pathway is unavailable -inducible genes encode for enzymes in catabolic pathways the repressor protein is inactivated by the inducer and transcription will happen ex: lac operon