Lecture 6 bacterial Genome and Replication expression, and regulation 2 Flashcards
Transcription regulation
- nucleoid-associated proteins can either increase or decrease transcription
- genetic regulatory proteins can bind to the DNA and control whether or not transcription begins
- Attenuation: transcription can terminate very early after it has begun due to the formation of a transcriptional terminator
- binding of a metabolite to a riboswitch in mRNA can cause premature termination of transcription
Regulation of Translation
- Secondary structure in 3’ end of mRNA prevents degradation of mRNA
- Translational repressor proteins can the mRNA and prevent translation from starting
- Antisense RNA can bind to mRNA and control whether or not translation begins
- Binding of a metabolite to a riboswitch in mRNA can block translation
Posttranslational regulation
- small molecules can bind (noncovalently) to a protein and affect its function. An example is feedback inhibition, in which the product of a metabolic pathway inhibits the first enzyme in the pathway
- The structure and function of a protein can be altered by covalent changes to the protein. These can be reversible (phosphorylation/dephosphorylation) or irreversible (removal of amino acid residues) these are called post translational modifications
Constitutive genes
housekeeping genes that are expressed continuously
inducible enzymes
levels of the enzymes rise in presence of a small effector molecule called an inducer (ex. Beta-galactosidase)
Repressible enzymes
- enzymes that are responsible for repressing formation
- usually present in biosynthetic pathways
what kind of regulation is Trp operon
negative transcriptional control of repressor genes
Characteristics of regulatory proteins
- have DNA binding domains
- either inhibit transcription (negative control) or promote transcription (negative control)
- Can also have allosteric regulatory site
The lac repressor binds to the ___ and inhibits transcription
lac repressor (LacO)
The binding of ____ to the lac repressor prevents it from binding to the operator (LacO) site
Allolactose
what is the positive control of the lac operon
Regulated by catabolite activator protein (CAP)
Catabolite activator protein regulates in response to
presence or absence of glucose
thus allows for preferential use of glucose
what is the negative control of the lac operon
Lac repressor
What are the 3 structural genes of the lac operon
Lac Z: encodes for beta-galactosidase, lacY: endcodes for lactose permease, LacA encodes galactoside transacetylase
The catabolite activator protein (CAP) is also called
cyclic AMP receptor protein (CRP)
CAP exists in what to forms
- active form when 3’,5’- cycle adenosine monophosphate (cAMP) is bound
- inactive form when free of cAMP
what happens to the lac operon in the presence of lactose and glucose
transcription is inhibited by lack of CAP
What happens to lac operon in presence of lactose but absence of glucose
binding of RNA polymerase to promotor is enhanced by CAP and repressor is inactive
what happens to lac operon in absence of both lactose and glucose
CAP is activated but transcription is blocked due to activated repressor
What happens to the lac operon when glucose is present but there is no lactose
transcription is inhibited by lack of CAP and presence of repressor
CAP activity is modulated by ____
cAMP
Levels of cAMP are controlled by
- adenyl cyclase (converts ATP to cAMP and PPi) by PEP
- adenyl cyclase is active only when little or no glucose is present
- in absence of glucose, CAP is active and promotes transcription of operons used for catabolism of other sugars
Explain the regulation of cAMP
when glucose is available, the phosphate of PEP is transferred to EIIA by way of EI and HPr. EIIA then transfers the phosphate to EIIB, which in turn transfers it to the incoming glucose. When glucose is not available, the phosphate cannot be transferred to EIIB and instead remains on EIIA. EIIA-P activates adenyl cyclase and cAMP is made.
What kind of regulation is the tryptophan operon
negative control of repressible genes
what kind of regulation is the Arabinose (ara) Operon
Transcriptional Control by a protein that acts both positively and negatively
- when arabinose is absent then the operon is closed
- when arabinose is present it can bind to the AraC protein and actually open up the operon increasing transcription
what is the difference between riboswitches in gram positive and gram negative bacteria
in gram positive bacteria they function by transcriptional termination, whereas the riboswitches discovered in Gram-negative bacteria regulate the translation of mRNA (note that effector biding elements at 5’ end alters mRNA leader folding pattern)
Translation is usually regulated by
blocking its initiation
functions of sRNAs and noncoding (ncRNAs)
some have been implicated in the regulation of DNA replication and transcription, while many others regulate at the level of translation (may inhibit or enhance)
What are antisense RNAs
RNAs that are complementary to mRNA and function by base pairing (these are ncRNAs or sRNAs that can inhibit or enhance translation)
regulatory systems that affect many genes and pathways simultaneously
global regulatory systems
Genes or operons controlled by a common regulatory protein
Regulon
Operon network under control of a common global regulatory protein but individual operons are controlled separately by their own regulators
Modulon
what is an example of a Modulon
Catabolite repression
Global regulatory systems often use many types of regulation such as
- two component signal transduction systems
- Phosphorelay system
- regulatory proteins
- alternative sigma factors
Many genes and operons are turned on or off in response to enviromental conditions. What are the two types of regulatory system that function this way
Two-component regulatory systems, and phosphorelay systems
The _____ proteins involved are part of a two-component signal system which links external events to regulation of gene expression
Regulatory proteins
Is the two component regulatory system in all three domains
yes
what are the two proteins that govern the two component regulatory system
- Sensory Kinase
- Response-regulator protein
What is the sensor kinase
- one of the proteins that govern the two component regulatory system
- extracellular receptor for metabolite
- intracellular communication pathway
what is the response-regulator protein
- one of the two proteins that govern the two component regulatory system
- Activated by sensor kinase
- DNA binding protein
- activator- enhances transcription needed
- repressor- inhibits transcription unless needed
what is an example of sensor kinase in E. coli
EnvZ
What is an example of a response regulator in E. coli
OmpR
What is the function of EnvZ (sensor kinase) in E. coli
Autophosphorylates in high osmolarity
What is the function of OmpR (response regulator) in E. coli
phosphorylated and regulates transcription
The EnvZ and OmpR is a soluble, cytoplasmic protein that controls the expression of porin proteins ___ and ____ depending on ___-
ompF, ompC, osmolarity
Which is the smaller porin protein OmpC or OmpF
OmpC
When is porin protein ompC dominant
When E. coli is in high osmolarity intestinal tract
What is the function of OmpC
lower levels of diffusion
When is the porin protein OmpF dominant
dominant when E. coli is in dilute environment
What is the function of porin protein OmpF
allows more diffusion of solutes
Regulatory enzymes control chemotaxis proteins by
-phosphorelay system and covalent modification
what is irreversible covalent modification
proteolysis
What is reversible covalent modification
- methylation/demethylation
- phosphorylation/dephosphorylation
methyl-accepting chemotaxis proteins (MCPs) are chemoreceptors in membrane that bind _______ and initiates
binds environmental chemicals and initiates a series of interactions with cytoplasmic proteins that affects flagellar rotation
MCPs acitvates ______ (with help of ___) which autophosphorylates
sensor kinase CheA (with help of CheW) which autophosphorylates
CheA phosphorylates the response regulator ___
CheY
CheY governs ____
roation of the flagella
what is the default (unphosphorylated) state of MCPs
CCW rotation (run)
when attractant concentration is high MCP is ____ and what occurs
methylated (CheR) then CheA autphosphorylates with the help of CheW an passes this phosphorylation onto CheY. CheY diffuses to flagellar motor and switches to clockwise (CW) rotation thus causing a tumble. Concentration of attractant is measured every few seconds (receptors reset)
When attractant concentration decreases MCP is ______ and what occurs
not methylated (CheB) this means that CheA is inactive (not phosphorylated) thus it can not activate CheY and flagellar rotation continues in its default CCW rotation thus a run occurs
cell-to-cell communication mediated by small signaling molecules such as N-acyl-homoserine lactone (AHL)
Quorum sensing
quorum sensing couples cells ____ and ______ to transcription regulation
density and intercellular communication
Quorum sensing in V. fischeri and many other Gram-negative bacteria uses an _____________ signal
N-acylhomoserine lactone (AHL)
Explain Quorum sensing in V. fischeri
- High concentrations of AHL produced by increased density of cells diffuse back into the cell, bind to the transcriptional regulator LuxR and activate transcription.
- LuxR stimulates transcription of the genes for AHL synthase (Luxl) and proteins needed for light production
V. harveyi responds to how many autoinducers and for what purpose
- 3
- maximizes expression of bioluminescence
What happens when the three autoinducers of V. harveyi are in low cell density
LuxR is not made and there is no bioluminescence
What happens when any combination of the V. harvey autoinducers are in high cell density
LuxR is made, bioluminescence occurs
The ____ response occurs when bacterial cells are starved for amino acids and is regulated by the second messenger guanosine tetraphosphate (ppGpp)
Stringent response
What does cyclic dimeric GMP (c-di-GMP) regulate
- virulence genes
- regulates transition from motile to nonmotile lifestly in biofilm formation
What is the stringent response
- when cells are starved for amino acids
- protein synthesis cannot proceed
- Cell decreases production of tRNA and rRNA to conserve energy (protein RelA downregulates synthesis through production of ppGpp, ppGpp and DksA destabilizes transition initiation open complexes)
- cell increases biosynthesis of needed amino acids
in sporulation of bacillus subtilis starvation signal induces produciton fo
alternative sigma factors
Explain sporulation
KinA and Kin B autophosphorylate due to starvation signals and phosphorylate Spo0F-P this passes the phosphate to Spo0B and then to Spo0A, which activates sigma F for early sporulation gene transcription, sigma f activates sigma g for late sporulation gene transcription
Mutations can be _____ or ____
spontaneous or induced
Spontaneous mutations arise without
exposure to external agents
Spontaneous mutations may result from
errors in DNA replication and action of mobile genetic elements such as transposons
What is the most prevalent form of a gene
the wild type
What is a forward mutation
wild type to mutant form
what is a reversion mutation
mutant phenotype to wild type phenotype
what is a suppressor mutation
is a type of reversion mutation in which the second mutation is at a different site than the original mutation
what are conditional mutations
mutations expressed only under certain environmental conditions
What are auxotrophic mutant
unable to make an essential macromolecule such an amino acid or nucleotide (has a conditional phenotype, wild-type strain from which it arose is called a prototroph)
conditional lac operon mutants
- many of these mutations map in the operator site and produce altered operator sequences not recognized by repressor
- Operon is always transcribed and beta-galactosidase is always synthesized
Is protein synthesis disrupted when their are mutations in tRNA and rRNA genes
yes
mutations are generally rare about 1 per ____ cells
1 per 10^7 to 10^11 cells
