Microbiology Daily Newsletter

February 18, 2014 - Transcription Initiation

Hopefully you remember the basic idea of a gene and the mechanism of transcription as it applies to eukaryotic cells.

For bacterial transcription, we will first look at the promoter. You may recall the TATA box with eukaryotic promoters. In bacteria, we find the Pribnow-Schaller box, commonly just referred to as the Pribnow box. The Pribnow-Schaller box is a six nucleotide sequence TATAAT. QUESTION: Why six nucleotides?

With eukaryotic promoters, you may recall that the TATA box is not the only recognition sequence needed. This is also true of prokaryotic promoters. The Pribnow-Schaller box is found at -10 from the start of the gene. The complete promoter also contains a -35 recognition sequence, and is also comprised of six nucleotides. The -35 promoter element usually has a sequence of TTGACA, but note that this can vary among different bacterial taxa (usually at the class or family level taxa). NOTE: The -10/-35 promoter is used for normal house keeping genes. We will see some variation shortly.

The prokaryotic RNA Polymerase catalyzes the reaction of both coding and non-coding RNA, unlike eukaryotes that have job specific RNA polymerases (for example, you may remember that RNA-Pol I forms the 45S pre-rRNA, while RNA-Pol III forms tRNAs). The prokaryote RNA Polymerase Complex is a holoenzyme composed of RNA Polymerase and a Sigma (σ)factor. The eukaryotic RNA Polymerase complex has a specific RNA polymerase and a variety of initiation factors.

Below is an example of the bacterial transcription initiation complex. Note that you are seeing RNA Polymerase with 2 different σ factors, and that the different sigma factors have slightly different promoter recognition sites. When they bind, they move from a closed complex to an open complex; the open complex gaining its name from the opening of the DNA helix.

Add cFrom: Bush M , and Dixon R Microbiol. Mol. Biol. Rev. 2012;76:497-529. Initiation of transcription by the RNAP-σ70 (A) and RNAP-σ54 (B) holoenzymes. The σ70 factor directs the binding of polymerase to the consensus −10 (TATAAT) and −35 (TTGACA) sequences to form an energetically unfavorable closed complex (CC) that is readily converted into an open complex (OC) to initiate transcription. In contrast, the σ54 factor directs the binding of RNAP to conserved −12 (TGC) and −24 (GG) promoter elements that are part of the wider consensus sequence YTGGCACGrNNNTTGCW (where uppercase type indicates highly conserved residues, lowercase type indicates weakly conserved residues, N is nonconserved, Y is pyrimidines, R is purines, and W is A or T) (10). This forms an energetically favorable CC that rarely isomerizes into the OC. In order to form the transcription “bubble,” a specialized activator (a bacterial enhancer binding protein [bEBP]) must bind and use the energy from ATP hydrolysis to remodel the holoenzyme. aption

Once the RNA Polymerase-σ factor Holoenzyme is bound in the open complex form, transcription can proceed to the elongation phase. The next issue specific for prokaryotic transcription will be termination.

Daily Challenge

Sigma factors play a critical role in coordinating bacterial cell physiological states. Below is a list of common sigma factors.

Sigma Factor	Gene	Function
s⁷⁰	RpoD	Primary s factor, Housekeeping
s¹⁹	FecI	Regulates fec gene for iron transport
s²⁴	RpoE	Extreme heat stress
s²⁸	RpoF	Flagellar genes
s³²	RpoH	Heat shock
s³⁸	RpoS	Starvation/Stationary phase

Along with these can be found anti-sigma factors that block the function of expressed sigma factors (a form of regulation). Discuss the role of sigma factors as means of global gene regulation. Why is having a sigma factor system beneficial to bacteria? How does this differ from eukaryotic promoters?