Regulation of Gene Expression

General

bacteria regulate their metabolism through gene expression much more so than eukaryotes

possible due to high growth rate; rapid degradation of mRNA (2-3 min)

most gene expression is accomplished at initiation of transcription

operon model: genes related to a single process are often adjacent and transcribed as a single mRNA

repressor: regulator that binds to DNA and blocks initiation (in combination with allosteric effectors)

corepressor: acts with regulator to promote DNA binding

i.e. presence of histadine stops transcription of histidine synthesis Þ repressed by his

inducer: binds to regulator and prevents repression

i.e. presence of lactose promotes transcription of lactose utilization enzymes Þ induced by lac

diauxie (biphasic growth): i.e. if two nutrients i.e. glu and lac are present, enzymes for lac metabolism are not induced until glucose is depleted

Lac Operon Regulation

genes and regulatory elements of the lac operon:

p: promotor (site of RNA polymerase binding)
o: operator (site of repressor binding)
lacZ: gene for beta-galactosidase
lacY: gene for lactose permease
lacA: unimportant
lacI: not part of operon; but codes for the repressor protein

if no inducer present Þ repressor binds to operator Þ little or no transcription

if inducer present Þ inducer/repressor complex does not bind DNA Þ transciption

mutants: lacI^- Þ no repressor; lacO^cÞ operator constitutive

preferential utilization of glucose:

assume lac promotor region is weak

CAP (catabolic gene activating protein) makes it a better promotor by binding upstream

CAP is cAMP dependant

if glucose present, cAMP levels are low Þ no promotion of lac operon

if no glucose, cAMP levels rise Þ promotion of lac operon enhanced by CAP

lac operon is actually controlled by three operator regions (repressor binding sites)

01: primary repressor (100% binding); 02 (10% binding); 03 (0.3% binding)

DNA can loop to bind tetramers of repressor at 01-02 or 03-01 or both loops; each loop Ý repression 30-fold

looping can provide repression of 70-fold compared to that in single binding of 17-fold

Pap Operon

ability to turn pili formation on/off since pili help adhesion to walls but also lead to phagocytosis

signals – increased temperature or lousy nutrition Þ on

regulation – protein binding to specific sites on DNA, looping, methylation of GATC sites on the DNA proper

Attenuation

relies on simultaneous transcription and translation

involves speed of ribosome movement down the mRNA molecule and alternative base pairing

proportional to levels of tRNA for the amino acid synthesized by the transcribed genes

trp similar to his (see figure below):

attenuator stops transcription
attenuator can be modified by changes in the secondary structure of the mRNA

Schematic representation of the control of transcription by the process of attenuation. The example chosen is the his operon of Escherichia coli. How attenuation works is fascinating. The leader region is always transcribed and translated into a small oligopeptide. The peptide near the attenuator site has a string of seven his codons. Movement of the first ribosome coming behind the polymerase is drastically affected by the supply of charged his tRNA. If there is an adequate supply, the ribosome is not delayed, and an attenuator loop forms in the mRNA, causingranscription to terminate. With a shortage of histidine, the first ribosome gets hung up over the his codons, and the attenuator loop is not formed, because alternate loops form. As a result, transcription proceeds, the complete his mRNA is made, and the biosynthetic enzymes can be made in large quantities. the upper portion of the figure illustrates the difference in transcription of the his operon in histidine sufficiency and insufficiency; the lower two diagrams depict the molecular mechanism of attenuation.