bacterial gene expression Flashcards
transcription unit
- a sequence of DNA bases that is transcribed to give a single, discrete complementary RNA
- In bacteria, multiple genes can be in the same transcriptional unit, this is termed an operon
promoter site
-a special region of DNA where RNA pol binds for the purpose of initiating transcription (-35 and -10 regions are two key elements of most promoters)
termination site
-a site within the DNA or RNA product at which RNa synthesis stops
inhibitors of RNA synthesis
- bind to beta subunit of RNA pol
- rifamycin: blocks elongation (rifampicin)
- lipiarmycins: blocks initiation (fidaxomicin)
sigma subunit of RNA pol
-necessary for recognition of the promoter region of a gene
two forms of RNA pol
- holoenzyme and core enzyme
- holoenzyme releases the sigma subunit upon binding the promoter, transcription is initiated, and becomes the core enzyme
the role of the sigma subunit
- causes very stable binding at promoter regions
- reduces binding at non-promoter regions of DNA (specificity)
- removal of gama allows escape from the promoter (translocation) and elongation of the transcript
- only one type of RNa pol, but many types of gama subunit which recognize promoters with different sequences
holoenzyme composition
- 2 alpha
- 2 beta
- 1 sigma
core enzyme composition
- 2 alpha
- 2 beta
how does transcription stop
- factor dependent termination
- factor independent termination
factor independent termination
-site is encoded in the DNA sequence appearing as a region of dyad symmetry
factor dependent termination
-Rho factor binds directly to RNa polymerase and causes the polymerase to stop and release when reaching the factor dependent terminator
regulation of transcription
- positive regulators bind upstream of the promoter
- negative regulators can overlap the promoter or be downstream
organization of toxin genes, pathogenicity locus
tcdR, tcdB, tcdE, tcdA, tcdC
tcdR
positive regulator
tcdB
toxin B
tcdE
holin
tcdA
toxin A
tcdC
negative regulator
operon of toxin genes
toxin B and holin
when is the toxin produced
during stationary phase
CodY
- represses the toxin gene by binding to the promoter of tcdR
- Ile dependent activation
- active during exponential growth phase due to abundant Ile
- inactive during stationary phase
toxin regulation: nutrient excess and nutrient limitation
- excess: cody is active and inhibits the RNA pol from binding, tcdC is synthesized which inhibits tcdR
- limitation: CodY is inactive, bacteria are in the stationary phase, and TcdR is promoting the
what causes high toxin production?
-mutation in tdcC that inactivates the protein
tcdR is inactive when
associated with tcdC
codY active when
associated wiht Ile
- in the active state, CodY represses toxin expression
- this is a negative regulator active in nutrient excess
rifamycin
ex: rifampycin: blocks elongation by the RNa pol
lipiarmycins
ex: fidaxomycin, blocks initiation
