-Sigma Factor-

(http://www.pingrysmartteam.com/)

 

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• An Overview of Transcription

Definition: the formation of an RNA molecule upon a DNA template by complementary base pairing; mediated by RNA polymerase

 

The process of transcription can be divided into three stages:

1) Initiation of a new RNA chain  (parts 1-4 of the picture below).

2) Elongation of the chain  (parts 5&6 of the picture below).

3) Termination of transcription and release of the brand new RNA molecule  (parts 6&7 of the picture below).

 

 

 

The Sigma Factor is involved in the initiation process of prokaryotic transcritption.

 

The initiation process can be broken down:

     1) Binding of the RNA polymerase holoenzyme to a promoter region in DNA,

     2) The localized unwinding of the two strands of DNA by RNA polymerase, providing a template strand free to base-pair with incoming ribonucleotides, and

     3) The formation of phosphodiester bonds between the first few ribonucleotides in the nascent RNA chain.

The holoenzyme remains bound at the promoter region during the synthesis of the first eight or nine bonds, then the sigma factor is released, and the core enzyme begins the elongation phase of RNA synthesis. During initiation, short chains of two to nine ribonucleotides are synthesized and released. This abortive synthesis stops once chains of ten or more ribonucleotides have been synthesized and RNA polymerase has begun to move downstream from the promoter.

 

Two good videos of Transcription (that sadly do not explain the role of the Sigma Factor)

http://henge.bio.miami.edu/mallery/movies/transcription.mov

http://www.dnai.org/lesson/go/19436/15510

 

 

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• Description of the Sigma Factor

The Sigma Factor is involved in the Initiation step of Trancscription in Prokaryotic life.

It is a polypeptide subunit of the RNA polymerase.  It serves to recognize specific binding sites on DNA molecules for initiation of RNA transcription.

(http://www.bio.miami.edu/~cmallery/)

 

The sigma factor is the subunit of the RNA Polymerase complex that recognizes the specific promoter sequence of DNA that the RNA Polymerase complex should bind to.  This will be the initial site for DNA transcription, or where it initiates.

 

 

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• Structure & Function

Different Sigma Factors are activated in response to different environmental conditions, so that not all genes are being expressed at the same time.  By simply modifying the Sigma Factor used, prokaryotes only have to use one type of RNA Polymerase to regulate gene expression.

 

Sigma Factor	Promoters Recognized	PromoterConsensus
		-35 region	-10 region
σ70	most genes	TTGACAT	TATAAT
σ32	genes induced by heat shock	TCTCNCCCTTGAA	CCCCATNTA
σ38	genes for stationary phase and stress response	?	?
σ28	genes involved in motility and chemotaxis	CTAAA	CCGATAT
		-24 region	-12 region
σ54	genes for nitrogen metabolism	CTGGNA	TTGCA

*The sigma factor designations refer to their approximate molecular weights, in kilodaltons.* 1, 2

 

The Sigma factor recognizes the promoter sequence on the DNA, a special sequence of nucleotides indicating the starting point for RNA synthesis, by having a sequence on it that matches to the promoter sequence.  The likelihood of the bases in the promoter are shown below:

  

 

 

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• Without The Sigma Factor

  Without the sigma factor, RNA polymerase would bind loosely and randomly to DNA, but would not be able to start transcription.  Therefore no proteins would be made and the cell would die.

 

 

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• Anti-Sigma Factors

In the regulation of gene expression in prokaryotes, anti-sigma factors bind to sigma factors and inhibit their transcriptional activity. (wikipedia.org)  They regulate promoter utilization by targetting specific sigma factors.  (Yuan et al, 2009). 

 

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• Current Work Involving Sigma Factors

-The Sigma Factor has been shown to be a useful pathway for the inhibition of transcription using phages that restrict it's use  (Dehbi et al, 2009).

-There has been much work on locating sigma-dependent genes in different bacterial species.  (Ding et al, 2009), (Mehra et al, 2009).  Some studies have examined how the regulation of the different sigma subunits affects gene expression.  (Polari et al, 2009), (Burrows et al, 2009)

-A study of the long-term effects of the induction of sigma(H) on the global transcription in Mycobacterium tuberculosis.  (Mehra et al, 2009)

-A study also suggests that the extracytoplasmic sigma factor, rpoE4, has a relevant function in the cell envelope biogenesis, and that it plays a role as a general regulator in the response to several kinds of stress.  (Matinez-Salazer et al, 2009)

 

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• References

emporia.edu

wikipedia.org/Sigma_factor

ncbi.nlm.nih.gov/books/

http://henge.bio.miami.edu/mallery/movies/transcription.mov

http://www.dnai.org/lesson/go/19436/15510

1http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=mboc4.table.1319

2http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=mcb.table.2520

http://en.wikipedia.org/wiki/Anti-sigma_factors

http://www.ncbi.nlm.nih.gov/pubmed/19376864

http://www.ncbi.nlm.nih.gov/pubmed/19383707

http://www.ncbi.nlm.nih.gov/pubmed/19376862

http://www.ncbi.nlm.nih.gov/pubmed/19376862

http://www.ncbi.nlm.nih.gov/pubmed/19366670

http://www.ncbi.nlm.nih.gov/pubmed/19363110

http://www.ncbi.nlm.nih.gov/pubmed/19356588

http://www.ncbi.nlm.nih.gov/pubmed/19376852