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Regulation of Gene Expression - Coggle Diagram
Regulation of Gene Expression
Heat Shock Induces Transcription of New Products to Protect Cell
RNA POI replaces σ70 with σ32
Causes RNA POI to bind to different set of promoters (chaperones)
Binding of Proteins to DNA Often Involves Hydrogen Bonding
Arg can form specific H-bonds with the cytosine-guanine base pair.
The maior groove is the right size for the a helix and has exposed H-bonding groups.
Gln/Asn can form a specific H-bond with adenine's N-6 and H-7 H's.
DNA Looping Allows Eukaryotic Enhancers to Be Far from Promoters
DNA Looping can be facilitated by architectural regulator proteins.
Co-activators may mediate binding by binding to both activator and RNA polymerase.
Affect the Steady- State Concentration of a Protein
Transcription initiation
Post transcriptional processing
RNA stability
Translational regulation
Protein modification
Protein degradation
Protein transport
RNA Polymerase Binding to Promoters Is a Major Target of Regulation
RNA polymerases bind to promoter sequences near the starting point of transcription initiation.
Regulatory proteins (transcription factors) work to enhance or inhibit this interaction between RNA pol and the promoter DNA.
Mechanisms to Regulate Transcription in Bacteria
Use of σ factors
Binding other proteins to promoters
Small-Molecule Effectors
Repressors reduce RNA Pol-promoter interactions or block the polymerase.
Effectors can bind to repressor and induce a conformational change.
change may increase or decrease repressor's affinity for the operator
Binding sites in DNA for activators are called enhancers.
Negative Regulation involves repressors.
Alternative: Signal causes repressor to dissociate from DNA; transcription induced
Positive Regulation involves activators.
Alternatively, the activator may only bind when signaled.
the Iac operon
An operon is a cluster of genes sharing a promoter and regulatory sequences.
three genes for metabolism of lactose are regulated together as an operon:
β galactosidase (lacZ)
transports lactose into cell
thiogalactoside transacetylase (lacA)
lactose permease (galactoside permease;lacY)
cleaves lactose to yield glucose and galactose
When glucose is abundant and lactose is lacking, cells make only very low levels of enzymes for lactose metabolism.
If glucose is scarce and cells are fed lactose, the cells suddenly express the genes for the enzymes for lactose metabolism.
galactoside (lactose) permease and ß-galactosidase.
A gene called lacl encodes a repressor called the Lac repressor.
has its own promoter Pl.
binds primarily to the operator O1. binds to one of two secondary operators with DNA looped (O2 or O3)
It reduces transcription. but transcription occurs at a low. basal rate, even with the repressor bound.
Allolactose (an inducer) binds to the repressor and causes it to dissociate from the operator.
β galactosidase not only hydrolyzes lactose, but it can also isomerize lactose into allolactose.
The availability of glucose governs expression of lactose-digesting genes via “catabolite repression”
It is mediated by cAMP and cAMP receptor protein
CRP-cAMP only has this effect when the Lac repressor has dissociated.
cAMP is made when [glucose] is low.
When Lactose Is Absent Little to No Transcription Occurs
Whether [glucose] is high or low, if lactose is absent -> repressor stays bound -> no transcription even when CRP-cAMP bind.
When Lactose Is Present, Transcription Depends On Glucose Level
Repressor dissociates, but transcription is only stimulated significantly if cAMP rises.
Two Requirements for Strongest Induction of the lac Operon
reducing repression (lactose)
causing activation ([Glucose] must be low)
Combined Effects of Glucose and Lactose on the lac Operon
When lactose is low, repressor is bound: inhibition
When lactose is high, repressor dissociates: permitting transcription
When glucose is high, CRP is not bound: transcription is dampened
When glucose is low, cAMP is high and CRP is bound: activation
The Vocabulary of Gene Regulation
Housekeeping gene
constantly expressed in approximately all cells
Regulated gene
Levels of the gene product rise and fall with the needs of the organism.
The trp Operon
This operon is regulated by two mechanisms: when tryptophan levels are high, (1) the repressor (upper left)binds to its operator and (2) transcription of trp mRNA is attenuated
The Leader Region Can Form Different Stem-Loop Structures
If segments 3 and 4 base-pair, they form a hairpin structure that is the attenuation signal.
segments 2 and 3 base-pair, transcription proceeds and the trp synthetic enzymes are made. no attenuation
The leader is 162 nucleotides long. — includes segments 1-4
Abundance of tRNATrp Leads to Formation of the Attenuator
Segment 1 is transcribed and immediately translated.
If tRNATrp is abundant, translation proceeds so that segment 2 is covered with the ribosome and can't pair with segment 3.
Low Availability of tRNATrP Signals Translation to Continue
If tRNATrp is scarce, the ribosome will stall at the Trp codons in the mRNA.
Other aa synthesis operons also use this regulation mechanism (e.g., Leu, His, Phe). Phenylalanine
Trp Levels
When Trp Levels Are High, Trp Synthesis
(tRNATrp Is High) Is Not Needed
When Trp Levels Are Low, tRNATrp Not Abundant, and Trp Synthesis Is Needed
Repressor Protein
Trp repressor is a homodimer.
When Trp is abundant, it binds to repressor, causes it to bind to the operator, and slows expression of genes for Trp synthesis.
a repressor that binds to DNA in the presence of tryptophan.
It has helix-turn-helix motifs that interact with DNA via the major groove.
rRNA Synthesis Is Also Regulated by Availability
Lack of aa produces uncharged tRNA.
Uncharged tRNA binds to ribosomal A site.
The stringent response occurs when concentrations are low.
rRNA synthesis triggers a cascade that begins with binding stringent factor protein (RelA) to ribosome.
Translation
Synthesis of Ribosomal Proteins and rRNA is Controlled at Translation
When bacteria need more protein (as in cell growth), they make more ribosomes.
Ribosmal protein (r-protein) operons are regulated via translational feedback
Each operon for an r-protein encodes a translational repressor.
Repressor has greater affinity for rRNA than for mRNA.
Protein-DNA Binding Motifs
A few protein arrangements are used in thousands of different regulatory proteins and are hence called motifs.
zinc finger
Interact with DNA or RNA (tandem )
Zn2+ usually coordinated by 4 CYS, or 2 CYS, 2 His
leucine zipper
Dimer of two amphipathic a helices plus a DNA-binding domain
Approximately every seventh residue in helices is Leu (L).
The DNA-binding domain has basic residues (Lys (K), Arg (R)) to interact with polyanionic DNA.
helix-turn-helix • used by Lac repressor
Four DNA-binding helix-turn-helix motifs (gray) in the Lac repressor
Eukaryotic RNA-Binding Domain
RNA recognition motifs— (RRMs)
four strand antiparallel β sheet with two α helices
Found in gene activators and bind to both DNA and RNA
This motif may be part of DNA-binding regulatory proteins or may occur in proteins binding only RNA.
SOS Response = response to extensive DNA damage
Link Between the SOS Response and Virus Propagation
Some repressors keep viruses in a dormant state within the bacterial host.
RecA (Rad51 in eukaryotes) can help cleave and inactivate these other repressors.
Regulation
results in cell cycle arrest and activation of DNA repair systems
Normally, SOS genes are repressed by LexA repressor. (binds to operators at several genes. )
ssDNA(single strands) is bound by the protein RecA (or, in eukaryotes Rad51).
RecA (co-protease)binds to LexA repressor, causing it to self-cleave and dissociate from DNA.
AA Biosynthesis Regulated by Transcriptional Attenuation
The trp operon is regulated by transcription attenuation.
Transcription begins but is then halted by a stop signal (attenuator).
if transcription will be attenuated at the end of the leader or, if transcription will continue into the genes for Trp synthesis
The attenuator sequence is in the 5'-region of a leader sequence, and it can make the ribosome stall.
in bacteria, transcription and translation can proceed simultaneously.
Eukaryotic Gene Regulation Relies Combinatorial Control
Eukaryotic gene regulation relies on protein- protein interactions.
Stringent Factor Catalyzes Formation of Unusual Guanosine-Based Messenger
Stringent factor catalyzes formation of nucleotide guanosine tetraphosphate (ppGpp).
Binding of ppGpp to RNA polymerase reduces rRNA synthesis.