Sigma factor: Difference between revisions

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== Specific Function and Structure ==

The '''σ-factor''' performs two chief functions: to direct the catalytic core of RNAP to the promotoer upstream of the +1 start site of transcription, and finally to assist in the initiation of strand seperation of double-helical DNA, forming the transcription "bubble." Each gene promoter utilizes a specific promoter region about 40 bp upstream of the transcription start site, and therefore different σ-factors play a role in the regulation of different genes. This process, which includes association of the σ-factor with RNAP to recognize and open DNA at the promoter site, followed by dissociation of the σ to allow elongation, is referred to as the '''σ cycle'''.

The '''σ-factor''' performs two chief functions: to direct the catalytic core of RNAP to the promotoer upstream of the +1 start site of transcription, and finally to assist in the initiation of strand seperation of double-helical DNA, forming the transcription "bubble." Each gene promoter utilizes a specific promoter region about 40 bp upstream of the transcription start site, and therefore different σ-factors play a role in the regulation of different genes. This process, which includes association of the σ-factor with RNAP to recognize and open DNA at the promoter site, followed by dissociation of the σ to allow elongation, which can then activate additional RNAP enzymes, is referred to as the '''σ-cycle'''.

===Domains===

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===Transcription Bubble===

The <scene name='59/591940/Transcription_bubble/1'>transcription bubble</scene>, also referred to as the '''open complex''' is formed through the common '''housekeeping σ factors''' which unwind about 13 bp of duplex DNA in an ATP independent process. ~~As such,~~ σ factors require invariant basic and aromatic residues (Phe, Tyr, Trp) critical for this formation. The process of bubble formation begins at the -11 formation (usually A) and propogates to +1 site, through <scene name='59/591940/Transcription_bubble_flipped/1'>Base Flipping</scene> which interrupts the stacking interactions stabilizing the double helix conformation. As ~~a result~~, the processes of -35 and -10 motif sequence recognition and helix strand separation are coupled by the σ factor.

The <scene name='59/591940/Transcription_bubble/1'>transcription bubble</scene>, also referred to as the '''open complex''' is formed through the common '''housekeeping σ factors''' which unwind about 13 bp of duplex DNA in an ATP independent process. Research has shown that σ factors require invariant basic and aromatic residues (Phe, Tyr, Trp) critical for this formation. The process of bubble formation begins at the -11 formation (usually A) and propogates to +1 site, through a phenomenon called <scene name='59/591940/Transcription_bubble_flipped/1'>Base Flipping</scene>, which interrupts the stacking interactions stabilizing the double helix conformation. As this process occurs and the DNA transitions into the open promoter complex, certain RNAP-σ contacts are lost, initiating the dissociation of σ. In summary, the processes of -35 and -10 motif sequence recognition and helix strand separation are coupled by the σ factor.

== Gene Regulation and Differentiation ==

Sigma factor: Difference between revisions

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@@ Line 7: / Line 7: @@
 == Specific Function and Structure ==
-The '''σ-factor''' performs two chief functions: to direct the catalytic core of RNAP to the  promotoer upstream of the +1 start site of transcription, and finally to assist in the initiation of strand seperation of double-helical DNA, forming the transcription "bubble."  Each gene promoter utilizes a specific promoter region about 40 bp upstream of the transcription start site,  and therefore different σ-factors play a role in the regulation of different genes.  This process, which includes association of the σ-factor with RNAP to recognize and open DNA at the promoter site, followed by dissociation of the σ to allow elongation, is referred to as the '''σ cycle'''.
+The '''σ-factor''' performs two chief functions: to direct the catalytic core of RNAP to the  promotoer upstream of the +1 start site of transcription, and finally to assist in the initiation of strand seperation of double-helical DNA, forming the transcription "bubble."  Each gene promoter utilizes a specific promoter region about 40 bp upstream of the transcription start site,  and therefore different σ-factors play a role in the regulation of different genes.  This process, which includes association of the σ-factor with RNAP to recognize and open DNA at the promoter site, followed by dissociation of the σ to allow elongation, which can then activate additional RNAP enzymes, is referred to as the '''σ-cycle'''.
 ===Domains===
@@ Line 21: / Line 21: @@
 ===Transcription Bubble===
-The <scene name='59/591940/Transcription_bubble/1'>transcription bubble</scene>, also referred to as the '''open complex''' is formed through the common '''housekeeping σ factors''' which unwind about 13 bp of duplex DNA in an ATP independent process.  As such, σ factors require invariant basic and aromatic residues (Phe, Tyr, Trp) critical for this formation.  The process of bubble formation begins at the -11 formation (usually A) and propogates to +1 site, through <scene name='59/591940/Transcription_bubble_flipped/1'>Base Flipping</scene> which interrupts the stacking interactions stabilizing the double helix conformation.  As a result, the processes of -35 and -10 motif sequence recognition and helix strand separation are coupled by the σ factor.
+The <scene name='59/591940/Transcription_bubble/1'>transcription bubble</scene>, also referred to as the '''open complex''' is formed through the common '''housekeeping σ factors''' which unwind about 13 bp of duplex DNA in an ATP independent process.  Research has shown that σ factors require invariant basic and aromatic residues (Phe, Tyr, Trp) critical for this formation.  The process of bubble formation begins at the -11 formation (usually A) and propogates to +1 site, through a phenomenon called <scene name='59/591940/Transcription_bubble_flipped/1'>Base Flipping</scene>, which interrupts the stacking interactions stabilizing the double helix conformation.  As this process occurs and the DNA transitions into the open promoter complex, certain RNAP-σ contacts are lost, initiating the dissociation of σ.  In summary, the processes of -35 and -10 motif sequence recognition and helix strand separation are coupled by the σ factor.
 == Gene Regulation and Differentiation ==