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Published by: Shraddha Bhatt Chavan on Jul 02, 2012
Copyright:Attribution Non-commercial


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 Assignment on Regulation of Transcription, Lytic Lysogeny cascade and SOS regulatory system
When isolated from bacteria, prokaryotic RNA polymerase has twoforms: The
and the
. The core enzyme is atetramer whose composition is given as
(two alpha subunits, one beta
 subunit, and one beta-prime subunit). Core RNA polymerase is capable of faithfully copying DNA into RNA but does not initiate at the correct site in agene. That is, it does not recognize the promoter specifically. Correct promoterrecognition is the function of the holoenzyme form of RNApolymerase.
 The RNA polymerase holoenzyme contains another subunit, s(
), inaddition to the subunits found in the core enzyme. Holoenzyme,
, is
 capable of correct initiation at the promoter region of a gene. Sigma thus mustbe involved in promoter recognition. Sigma subunits are related but distinct indifferent forms of RNA polymerase holoenzyme. These specialized subunits
 direct RNA polymerase to promoter sequences for different classes of genes.For example, bacteria exposed to high temperatures synthesize a set of protective proteins called
heat-shock proteins
. The genes for the heat-shockproteins have special promoter sequences that are recognized by an RNApolymerase holoenzyme with a specific subunit. The discussed here is the
δ δ
 major of the common bacterium
E. coli
, about which most is known.
Promoter recognition
RNA polymerase holoenzyme starts by recognizing the promoter of a gene. The promoter isn't copied into RNA, but it is, nonetheless, an important piece
Submitted by: Shraddha Bhatt.Page
 Assignment on Regulation of Transcription, Lytic Lysogeny cascade and SOS regulatory system
of genetic information. The information in a promoter was determined bylining up a large number of promoters and counting how many times aparticular base appeared at a given position in the various promotersequences. The
consensus sequence
is given by the statistically mostprobable base at each point—the bases that appear most often in thepromoter collection. Very few, if any, naturally occurring promoters match theconsensus sequence exactly, but the “strength” of a promoter (how activelyRNA polymerase initiates at it) correlates well with the degree of consensusmatch. For example, the promoters of genes for ribosomal RNA match theconsensus well, while the promoters for the mRNA encoding some regulatoryproteins match the consensus poorly. This correlates with the relative amountsof each gene product that are needed at any one time: many ribosomes, andonly a few regulatory proteins. The consensus sequence for an
E. coli
promoter has two conserved regionsnear positions -35 and -10 relative to the transcription start site. That is, thetemplate-directed synthesis of RNA begins 35 base pairs downstream of thefirst consensus region and ten base pairs downstream of the second. The -35consensus is:
. The -10 consensus is:
.A couple of important points exist about the consensus. First, not all bases inthe consensus are conserved to the same amount. The bases marked withbold type and underlined are more conserved than the others, and the -10region is more conserved overall than is the -35 region. Secondly, thepromoter sequence is asymmetrical; that is, it reads differently in onedirection than in the other. (Compare this to the recognition sequence for therestriction enzyme BamHI, GGATCC.) This asymmetry means that RNApolymerase gets
directional information
from the promoter in addition toinformation about the starting point for transcription.
The transcription process
RNA polymerase only goes one direction from a promoter and only one strandof DNA is used as a template at any one time. To provide this template strand,the initiation of transcription involves a short unwinding of the DNA doublehelix. This is accomplished in a two-step fashion. First, RNA polymerase bindsto the promoter to form the closed complex, which is relatively weak. Then,the double-stranded DNA goes through a conformational change to form themuch stronger open complex through opening of the base pairs at the -10sequence, as shown in Figure2.
Submitted by: Shraddha Bhatt.Page
 Assignment on Regulation of Transcription, Lytic Lysogeny cascade and SOS regulatory system
 The initiator nucleotide binds to the complex and the first phosphodiesterbonds are made, accompanied by release of . The remaining core
 polymerase is now in the elongation mode. Several experimental observationssupport the picture presented in the next figure, namely the fact that less thanone exists in the cell per core enzyme in each cell.
Submitted by: Shraddha Bhatt.Page

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