Transcription 5----3 direction RNA polymerase consensus sequence Initiation Elongation Termination a2

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Transcription5----3 directionRNA
polymeraseconsensus sequenceInitiationElongatio
nTerminationa2ßßs s Initiation
factorPromotor-35 TTGACA-10 TATAAT
(Pribnow box) ? dependent, independentStem
Loop? Factor
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Structural similarity between a bacterial RNA
polymerase and a eucaryotic RNA polymerase II.
Regions of the two RNA polymerases that have
similar structures are indicated in green. The
eucaryotic polymerase is larger than the
bacterial enzyme (12 subunits instead of 5), and
some of the additional regions are shown in gray.
The blue spheres represent Zn atoms that serve as
structural components of the polymerases, and the
red sphere represents the Mg atom present at the
active site, where polymerization takes place.
The RNA polymerases in all modern-day cells
(bacteria, archaea, and eucaryotes) are closely
related, indicating that the basic features of
the enzyme were in place before the divergence of
the three major branches of life
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Transcription Bubble. A schematic representation
of a transcription bubble in the elongation of an
RNA transcript. Duplex DNA is unwound at the
forward end of RNA polymerase and rewound at its
rear end. The RNA-DNA hybrid rotates during
elongation.
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The structure of a bacterial RNA polymerase. Two
depictions of the three-dimensional structure of
a bacterial RNA polymerase, with the DNA and RNA
modeled in. This RNA polymerase is formed from
four different subunits, indicated by different
colors (right). The DNA strand used as a template
is red, and the non-template strand is yellow.
The rudder wedges apart the DNA-RNA hybrid as the
polymerase moves. For simplicity only the
polypeptide backbone of the rudder is shown in
the right-hand figure, and the DNA exiting from
the polymerase has been omitted. Because the RNA
polymerase is depicted in the elongation mode,
the s factor is absent
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Schematic representation of the major form of E.
coli RNA polymerase bound to DNA. By convention,
the transcription-initiation site is generally
numbered 1. Base pairs extending in the
direction of transcription are said to be
downstream of the start site those extending in
the opposite direction are upstream. The s70
subunit binds to specific sequences near the -10
and -35 positions in the promoter. The a subunits
lie close to the DNA in the upstream direction.
The ß and ß' subunits associate with the start
site
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Alternative Promoter Sequences. A comparison of
the consensus sequences of standard promoters,
heat-shock promoters, and nitrogen-starvation
promoters of E. coli. These promoters are
recognized by s70, s32, and s54, respectively.
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Members of the s70 family of sigma
factors have 4 conserved regions
Region 1 masks the DNA binding activities that
are present in regions 2 and 4, which become
unmasked when the sigma factor binds to the core
RNA polymerase Region 2 Subregion 2.3 and 2.4
form a DNA binding activity that recognizes the
-10 promoter motif, region 2 also interacts with
core enzyme components Region 4 a DNA binding
activity that recognizes the -35 promoter motif
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subunit sizeaa size(Kd) gene function
alpha (?) 329 36511 rpoA required for assembly of the enzyme interacts with some regulatory proteins also involved in catalysis
beta (b) 1342 150616 rpoB involved in catalysis chain initiation and elongation
beta' (b') 1407 155159 rpoC binds to the DNA template
sigma (s) 613 70263 rpoD directs enzyme to the promoter
omega (w) 91 10237 rpoZ required to restore denatured RNA polymerase in vitro to its fully functional form
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sigma factor gene function
s70 rpoD principal sigma factor
s54 rpoN (ntrA, glnF) nitrogen-regulated gene transcription
s32 rpoH heat-shock gene transcription
sS  rpoS gene expression in stationary phase cells
sF  rpoF expression of flagellar operons
sE  rpoE involved in heat shock and oxidative stress responses regulates expression of extracytoplasmic proteins
sFecI  fecI regulates the fec genes for iron dicitrate transport
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Sigma Factor Sigma Factor Promoters Recognized Promoter Consensus



-35 Region -10 Region
s70 Most genes Most genes TTGACAT TATAAT
s32 Genes induced by heat shock Genes induced by heat shock TCTCNCCCTTGAA CCCCATNTA
s28 Genes for motility and chemotaxis Genes for motility and chemotaxis CTAAA CCGATAT
s38 Genes for stationary phase and stress response Genes for stationary phase and stress response ? ?
-24 Region -12 Region
s54 Genes for nitrogen metabolism and other functions Genes for nitrogen metabolism and other functions CTGGNA TTGCA
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Structure of the s Subunit. The structure of a
fragment from the E. coli subunit s70 reveals the
position of an a helix on the protein surface
this helix plays an important role in binding to
the -10 TATAAT sequence.
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RNA-DNA Hybrid Separation.      A structure
within RNA polymerase forces the separation of
the RNA-DNA hybrid, allowing the DNA strand to
exit in one direction and the RNA product to exit
in another
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Mechanism For the Termination of Transcription by
? Protein. This protein is an ATP-dependent
helicase that binds the nascent RNA chain and
pulls it away from RNA polymerase and the DNA
template.
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Rho factor
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Rho-dependent termination. Rho is a helicase that
follows the RNA polymerase along the transcript.
When the polymerase stalls at a hairpin, Rho
catches up and breaks the RNA-DNA base pairs,
releasing the transcript. Note that the diagram
is schematic and does not reflect the relative
sizes of Rho and the RNA polymerase.
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Termination at an intrinsic terminator. The
presence of an inverted palindrome in the DNA
sequence results in formation of a hairpin loop
in the transcript
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Termination Signal. A termination signal found at
the 3' end of an mRNA transcript consists of a
series of bases that form a stable stem-loop
structure and a series of U residues
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Rho Dependent Transcription Termination
Rho Independent Transcription Termination
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