A promoter is the DNA sequence that tells RNA polymerase where to start transcribing. Promoter elements are conserved near the transcription start site, and transcription factors recognize them and recruit the polymerase.
Bacterial Promoters
Bacterial (E. coli) promoters have two main elements upstream of the start site:
Pribnow box (-10): TATAAT consensus, about 10 bp upstream.
-35 box: TTGACA consensus, about 35 bp upstream.
The sigma factor of RNA polymerase recognizes these two boxes and positions the polymerase for initiation. Different sigma factors can recognize different promoters, allowing bacteria to activate different gene programs.
Eukaryotic Promoters (Pol II)
Eukaryotic promoters are more varied. The most common element is the TATA box, about 25 bp upstream, recognized by TATA-binding protein (TBP, part of TFIID). Additional upstream elements (CAAT box, GC box) bind other factors that help recruit the polymerase. Farther upstream, enhancers can activate transcription from thousands of bp away through DNA looping.
Three Eukaryotic RNA Polymerases
Eukaryotes divide the work among three polymerases:
Polymerase
Transcribes
Location
Sensitivity to alpha-amanitin
Pol I
rRNA (except 5S)
Nucleolus
Insensitive
Pol II
mRNA, most snRNAs
Nucleus
Very sensitive
Pol III
tRNA, 5S rRNA
Nucleus
Moderately sensitive
Alpha-amanitin is a toxin from death cap mushrooms that strongly inhibits Pol II. This property is used in the lab to distinguish which polymerase made a given RNA.
Which eukaryotic RNA polymerase makes mRNA, and what toxin strongly inhibits it?
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RNA polymerase II transcribes mRNA. Alpha-amanitin, a toxin from the death cap mushroom (Amanita phalloides), strongly inhibits Pol II. This is why death cap poisoning causes broad cellular dysfunction - protein synthesis stops throughout the body.
What is the function of a sigma factor in bacterial transcription?
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Sigma factors help RNA polymerase recognize promoter sequences (-10 and -35 boxes). Different sigma factors recognize different classes of promoters, allowing the cell to switch between gene expression programs (e.g., under heat shock, sporulation). After initiation, sigma dissociates and the core polymerase continues elongation on its own.
Why can bacteria couple transcription and translation while eukaryotes cannot?
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Bacteria have no nucleus, so ribosomes can attach to nascent mRNA as it is still being transcribed. Eukaryotic transcription happens inside the nucleus, and the mRNA must be processed (cap, poly-A tail, splicing) and exported before it can be translated. The physical compartmentalization and required processing decouple the two steps in eukaryotes.
