Transcript Chapter 12 Expression and Regulation

Chapter 12
Expression and Regulation
Comparative Genomics
NCBI
CMR
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GC content – low of 29% for B. burdorferi to a high
of 68% for M. tubercuolosis
The difference in GC content affects the codon
usage and amino acid composition for a species
Glycine, alanine, proline, and arginine are represented
by GC rich genomes.
Isoleucine, phenylalnine, tyrosine, and methionine are
represented by AT rich codons
Shared genes
½ of all genes are similar or homologous
in bacterial species
 The number of genes involved in
processes like transcription and
translation are similar even when there
is a vast difference in the size of
genomes
 Suggestive of a basic number for all
processes in the cell
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Transport Genes
A high number of transport genes
required to move molecules across a
membrane
 Genome size and the different
transport mechanisms are related
 Many transport systems are based on
the life style, for instance heterotrophy
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Unique genes
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¼ of all genes are unique to a particular
organism
Evolution
Vertical transmission
 Duplication of genes after vertical
transmission
 Horizontal or lateral transmission of unique
genes
Conjugation, transformation, and transduction(
phages)
Pathogenicity islands – blocks of pathogenic
genes transferred with selective advantage
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Molecular evidence
BLAST – similarity in genes by homology
and alignment
 COG – Clusters of orthologous groups,
classifies genes on the basis of similar
function
 Ribosomal genes and small RNA’s
 Whole genome analysis
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Gene expression
Transcription
 Translation
 Protein folding
 Genes and gene regulation
 Operons
 Small RNAs
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Prokaryote mRNA
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Ss RNA( 5’ ---------3’)
Directions for one or more polypeptides
Non translated leader sequence of 24 to 150 bases at
the 5’ end
Polygenic RNAs that code for more than one
polypeptide have spacers
At the 3’ end following the termination codon there is
a non translated trailer .
RNA Polymerase
RNA is synthesized under the direction of RNA
polymerase
 The synthesis is similar to that of DNA
Nucleotide tri-phosphates
n[ ATP,GTP,CTP,UTP]
RNA+ nPPi
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Pyrophosphate( PPi )
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Pyrophosphate is produced in both DNA and RNA
Polymerase reactions
Pyrophosphate is then removed by hydrolysis to
orthophosphate in a reaction catalyzed by the
phosphatase enzyme
The reaction is irreversible
RNA polymerase
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The RNA polymerase of E. coli is an extremely large enzyme
It contains four polypeptide chains
The RNA polymerase opens or unwinds the double helix to form
a transcription bubble about 12 – 20 base pairs in length
It transcribes the mRNA from 5’ to 3’
It produces mRNA at about 40 nucleotides/second at 37oC.
Core enzyme component
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Catalytic activity
Composed of four chains
The Sigma factor has no catalytic activity but assists in the
recognition of genes. Once transcription begins this factor
dissociates from the core enzyme complex
The Beta and Beta prime polypeptides are involved with the
ginding of DNA and regulation. Rifampin which is a polymerase
inhibitor binds to the B’
The function of the Alpha subunit is involved in the recognition
of the promoters
RNA Polymerase
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These are the different
views of the core RNA
polymerase molecules as they
observed on the surface of a
lipid bilayer tube.
Each picture shows three
molecules which appear
linked. It happens because
negative stain does not
penetrate between the
molecules due to their tight
packing within a helical
crystal.
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The most striking feature of
the core structure is a
thumb-like projection
surrounding a channel. The
channel is 25 Å in diameter
and can easily accommodate
double stranded DNA. For
more information on this
Core Enzyme
Holoenzyme
Sigma Factors
Sigma70
 Primary sigma factor, or
housekeeping sigma factor.
 Encoded by rpoD .
 When bound to RNAP Core
allows recognition of -35 and
-10 promoters.
 No other factors required
for RNAP binding and
transcription initiation.
Sigma54
 alternative sigma factor
involved in transcribing
nitrogen-regulated genes
(among others).
 Encoded by rpoN (ntrA ).
 When bound to RNAP Core
allows recognition of
different -26 and -12
promoters.
 Requires an additional
activator to allow open
complex formation for
transcription.
Sigma factors
Sigma32
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heat shock factor involved in
activation of genes after
heat shock.
Encoded by rpoH (htpR ).
Turned on by heat shock
(either at the transcription
or protein level).
Activates multiple genes
involved in the heat shock
response.
SigmaS (sigma38)
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Stationary phase sigma
factor.
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Encoded by rpoS .
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Turned on in stationary
phase.
Activates genes involved in
long term survival,
peroxidase.
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RNA Binding
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Binding occurs with the aid of the Sigma factor
Recognition site is TTGACA about 35 bases upstream of the
gene
The TATAAT sequence or Pribnow box lies within the promoter
about 10 base pairs before the starting point of transcription.
RNA polymerase recognizes these sequences
The DNA begins to unwind near the Pribnow box
Transcription begins about 6 or 7 base pairs from the 3’ end of
the promoter
Thermus aquaticus – RNA polymerase
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The enzyme is composed of four subunits and is
complexed with the sigma factor
The structure is claw shaped. Has an internal channel
that contains Mg++
This may provide an entry point for DNA
The sigma unit binds to the -10 and -35 elements of
the promoter
Termination
There should be a stop codon
 And there must also be signals for termination
 Terminator often contain a sequence coding for an
RNA stretch that can form a hair pin with
complementary base pairing
 This works as a signal for RNA polymerase to stop
transcription
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Prokaryote Transcription
Eukaryote Transcription
Protein Synthesis
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The mRNA is translated into the amino acid sequence
of a protein
In E. coli protein synthesis is rapid and accurate.
It occurs at a rate of 900 residues per minute
The synthesis of a polypeptide chain begins at he
free amino group end( N- terminus) and concludes
with the carboxyl group at the end( the C- terminus )
Bacterial translation
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To account for the rapid growth of bacteria, m RNAs
must be used efficiently
They can complex with several ribosomes at a time
There may be a ribosome every 80 nucleotides on the
mRNA and as many as 20 ribosomes reading the
mRNA transcript
These complexes are called polyribosomes
Polysomes or polyribosomes
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While RNA polymerase is synthesizing mRNA, the
mRNA can already be attached to a ribosome
Protein synthesis can be initiated
tRNA – Clover leaf – loops and
stem
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CCA terminus( 3’ ) attachment for amino acid
Anticodon at the base 3’-----5’ Three letters
complementary to mRNA sequence
There are two large arms : the D arm has a
substitution of a pyrimidine nucleotide –
dihydrouridine
tRNA is folded into an L-shaped structure. The
amino acid is held on one end of the L
Attachment of an amino acid
to a tRNA
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This is called Amino Acid activation
The tRNAs are approximately 73-93 nucleotides in
length
The acceptor end of the tRNA ends in C-C- A. ( 3’
end)
The amino acid attaches to the terminal adenylic acid
Attachment of an amino acid
to a tRNA
The attachment of an amino acid to a
tRNA is catalyzed by an enzyme called
aino-acyl-tRNA synthetase
 The association of the amino acid and
the tRNA requires the use of ATP in
the presence of a Mg++
 There are at least 20 amino acyl tRNA
synthetases
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Site for attachment of the
amino acid to the t- RNA
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3’ CCA – attaches to
the terminal A
Amino acyl tRNA synthetase
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Amino acyl tRNA
synthetase has two
sites – one for the
binding of the amino
acid and a tRNA
Prokaryote ribosome
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Prokaryote ribosomes consist of a 30 s and a 50 s
subunit
Each subunit is composed of one or two rRNA
molecules and many proteins
The total complex is 70s
Prokaryote Ribosomes
Ribosomal RNA has three
roles
 The 16 s rRNA of the
30 s portion of the
ribosomes may aid in the
initiation of protein
synthesis
 It can bind to the
initiation factors
 It may also have a
catalytic function
16s rRNA
E. coli ribosome
Figure 12.13
Ribosomal binding sites
P site or Donor site
 A site or Acceptor site
 E site or Exit site
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Initiation
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Initiation in prokaryotes(
Domain Bacteria) begins with
a specially modified Nformylmeththionyl-tRNA
This molecule binds to the
30s sub unit of the ribosome
and is possitioned with both
the 3’ end and the 16srRNA
and the anticodon of the
fMet-tRNA
Messengers have a special
initiator codon 5’ AUG or
GUG that specifically binds
with the fMet- tRNA
Initiation Factors( associated
with the 30s subunit)
Three initiation factors are required
 IF-3 promotes the binding of the mRNA to
the 30s unit( also stabilizes the binding)
 IF-2 binds GTP and fMet-tRNA and the 30s
unit
 IF-1 is needed for the release of IF-2 and
GDP from the reaction which requires the use
of a phosphate for energy
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IF3
IF3 recognizes the sequence of the ribosome
binding site on the bacterial m RNA.
 This is called the Shine-Dalgarno sequence.
 AGGAGGU) is the signal for initiation of
protein biosynthesis in bacterial mRNA. It is
located 5' of the first coding AUG, and
consists primarily, but not exclusively, of
purines.
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Shine-Dalgarno
The requirement for a Shine-Dalgarno
sequence in addition to AUG for proper
initiation allows the AUG to be chosen from
among multiple AUG trinucleotides in mRNA,
most coding for internal methionines or
representing out of phase codons.
 Binding of mRNA to rRNA via the Shine
Dalgarno sequence may stimulate initiation by
increasing the local concentration of AUG
near the correct site on the ribosome.
 Other sequences, in addition to the AUG and
Shine-Dalgarno sequence, are also important.
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Initiation codon
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AUG
GUG
UUG
In bacteria the initiator tRNA carries a
methionine residue that has been formylated
on its amino group forming a molecule of Nformyl-methionyl-tRNA
The tRNA that matches this is for initiation
only tRNAmet
m
Initiation
The AUG at the start position in mRNA
codes for formyl methionine
 The AUG in other positions codes for
methionine
 The translation of AUG and GUG
depends upon the context
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Translation
In bacteria and mitochondria,the formyl
residue is removed by a specific
deformylase enzyme to generate a
normal NH2 terminus.
 If methionine is to be the NH2 terminal
amino acid this is the only step.
 In about ½ of the proteins
aminopeptidase removes the methionine
creating a new terminus.
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Elongation of the Polypeptide
Chain
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a.
b.
c.
Every amino acid added to the growing
polypeptide chain is the result of
three phases
Amino acyl- tRNA binding
Transpeptidation reaction
Translocation
Elongation factors
GTP and the elongation factor EF-Tu are
required for the insertion of the first t-RNA
into the A site( EF-Tu is associated with the
ribosome.
 This is followed by GTP hydrolysis and the
GDPTu complex leaves the ribosome
 EF-Tu.GDP is converted to EF-Tu.GTP with
the aid of a second elongation factor
EF-Ts.
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GTP – The entry of the amino acyl t- RNA
to the A site is dependent upon a guanine
nucleotide
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When GTP is present, the factor is in its active state
When the GTP is hydrolyzed to GDP, the factor
becomes inactive
Activity is restored when the GDP is replaced by GTP
Elongation cycle
At the beginning of the elongation cycle
the peptidyl site is filld with either Nformylmethionyl-tRNAor peptidyl-tRNA and the A and E sites are empty
 The second amino acyl-tRNA is inserted
into the A site
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Transpeptidation
Occurs between amino acids
 This is catalyzed by peptidly
transferase located on the 50s subunit
 The two amino acids are joined by a
peptide bond
 No extra energy source is required
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Transpeptidation reaction
catalyzed by peptidyl transferase
Figure 12.16
Transpeptidation factors
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Transcription elongation
factors stimulate the
activity of the RNA
polymerase by increasing the
overall elongation rate and
the completion of RNA
chains.
E. coli GreA is one such
factor. It acts by inducing
cleavage of the transcript
within the RNA polymerase,
followed by release of the
RNA 3'-terminal fragment.
Translocation
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The final stage of the elongation process of protein
synthesis
The peptidyl – tRNA moves about 20 Angstroms from
the A to the P site
The ribosome moves one codon along the mRNA so
that a new codon is positioned on the A site
The empty rRNA leaves the ribosome
Ribosomal proteins are involved in this movement
Translocation the final step in
elongation
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The three aspects
of this process
occur simultaneously
Translation and Moving Molecules
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faculty.smu.edu/
svik/5304/molecules.html
Termination of Translation in
Prokaryote
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Protein synthesis stops when
a nonsense codon. UAA, UGA,
UAG reaches the ribosome
Three release factors are
required
GTP hydrolysis is required
The ribosomal subunits
dissociate from each other
and the mRNA is released
Antibiotics that affect the
process of translation
Kirromycin inhibits the function of EFTu
 Puromycin mimics amino acyl t RNA
 Erythromycin blocks peptidyl
transferase
 Streptomycin blocks initiation
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Protein folding and chaperones
Molecules called chaperone recognize
only unfolded polypeptides or partially
denatured proteins
 They suppress incorrect folding and
promote correct folding to achieve the
conformation of the tertiary structure
and shape of the protein
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Bacterial Chaperones
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Best studied in E. coli
Four chaperons are invovlved
DnaK, DnaJ,GroEL, and GroES
Also the stress protein GrpE
Protein splicing in prokaryotes
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Some microbial proteins are spliced after translation
In microbial splicing a part of the polypeptide is
removed before it folds into its final shape
Self-splicing proteins are large and have internal
intervening sequences called inteins ( 130-600 bases
in length) flanked by external sequences exteins.
Inteins are removed by an autocatalytic process.
Protein splicing in prokaryotes
Removal of part of
polypeptide before
folding
 Inteins – removed
portion
 Exteins – portions that
remain in protein
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Prokaryote vs. Eukaryote
folding
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Domains
– structurally independent regions of polypeptide
– separated from each other by less structured portions of
polypeptide
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In eucaryotes
– domains fold independently right after being synthesized
– molecular chaperones not as important
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In procaryotes
– polypeptide does not fold until after synthesis of entire
polypeptide
– molecular chaperones play important role
Chaperone Action
DnaJ binds to the unfolded chain
 DnaK is complexed with ATP and attaches to the
polypeptide to prevent improper folding as it is
synthesized
 The ATP is hydrolyzed after binding
 GrpE binds to the chaperone-polypeptide complex and
causes the release of ADP and DnaJ and K are also
released from the polypeptide
 Often GrolEl abd GroEs will be involved in the final
folding
 They receive the protein from DnaJ and DnaK
 This process also requires the hydrolysis of ATP
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Prokaryote folding and splicing
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A part of the protein is removed before folding
Inteins are about 130-600 amino acids in length are
removed in an autocatalytic process
This is a relatively new discovery – examples include
the RecA protein in Mycobacterium tuberculosis (
Bacteria)and the DNA polymerase in Pyrococcus(
Archaea).
The presence of these self splicing proteins in
Bacteria and Archaea suggest that this principle is
wide spread.
Chaperone activity
Regulation of mRNA synthesis
The control of metabolism by the regulation
of enzyme activity is a necessary means of
control in a unicellular entity.
 The need to control gene expression is vital
to their ability to adjust to changing
environmental conditions
 It is also necessary to conserve energy by
only expressing those genes that are
necessary at any moment in time for survival
under a set of conditions.
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Induction and repression
Inducible enzymes are those that are
produced as a result of the presence of a
small molecule called an inducer
 They are used only in the presence of their
substrate
 Repressible enzymes are those that are
regulated by the end product of the reaction.
 Repressible enzymes are regulated by the
formation of their product which acts to slow
their production
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Control
Negative control – A controlling factor can
either inhibit or activate transcription.
 Both induction and repression are forms of
negative control.
 mRNA synthesis proceeds more rapidly in the
absence of the controlling factor.
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Control II
The rate of mRNA synthesis is controlled by special
repressor proteins that are synthesized under the
direction of regulator genes.
 The repressor binds to a special site on the DNA
called the operator.
 The inactivation of the regulatory gene produces a
constitutive mutant – in which mRNA synthesis occurs
whether the repressor is present or absent
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Inducible systems
The regulator gene directs the
synthesis of an active repressor
 The inducer stimulates transcription by
binding to the repressor causing it to
change to an inactive shape.
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Repressible systems
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The repressor is initially in an inactive form called
the aporepressor.
The aporepressor becomes active only when a
corepressor binds to it
The corepressor inhibits transcription by activating
the aporepressor
Regulation of biosynthesis
The synthesis of genes for a pathway can be
sequentially arranged in the DNA
 There may be only one repressor to regulate
the action of the structural genes coding for
a polypeptide.
 A single messenger RNA will contain the
genetic code for all the proteins in the
pathway
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Operon
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The sequence of bases coding for one or
more polypeptides together with the
operator that controls its expression is
called an operon
Lac Operon
Works by negative control
 Contains three structural genes
 Controlled by the lac repressor
 Beta galactosidase
 Beta galactoside permease
 Beta galactoside transacetylase
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Beta galactosidase Reaction
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The lac operon is
necessary for
the metabolism
of the sugar,
lactose
Negative control
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The inducer can bond to
the repressor and
inactivate it
When this occurs the
genes are transcribed
promoter
usually substrate of
pathway
operator
negative control of
catabolic pathway
an operon
structural gene =
gene coding for
polypeptide
Lactose repressor
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The lactose
repressor binds to
the DNA and
prevents the
transcription of the
three structural
genes
The lac Operon is also under
postive control
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It is regulated by CAP or
catabolite activator protein
or cyclic AMP receptor
protein and the small cyclic
nucleotide
3’,5’- cyclic adenosine
monophosphate
cAMP or cyclic AMP
CAP
recognize
and bind
regulatory
region of
lactose
operon
Repressor and CAP bound to the
lac operon
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The lac operator is violet
The operators are red
The promoters are green,
CAP is blue
In this conformation there is
no transcription
CAP
Absence of the lac repressor is essential but
not sufficient for effective transcription of
the lac operon.
 The activity of RNA polymerase also depends
on the presence of another DNA-binding
protein called catabolite activator protein or
CAP. Like the lac repressor, CAP has two
types of binding sites:
 One binds the nucleotide cyclic AMP; the
other
 binds a sequence of 16 base pairs upstream of
the promoter
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CAP
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However, CAP can bind to DNA only
when cAMP is bound to CAP. so when
cAMP levels in the cell are low, CAP fails
to bind DNA and thus RNA polymerase
cannot begin its work, even in the
absence of the repressor.
Structure of CAP
Two recognition
sequences
 Recognition
sequences are 34 A
apart
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CAP binding
CAP strategy
They usually contain two subunits.
Therefore, they are dimers.
 They recognize and bind to DNA
sequences with inverted repeats.
 In prokaryotes, recognition and binding
to a particular sequence of DNA is
accomplished by a segment of alpha
helix. Hence these proteins are often
described as helix-turn-helix proteins
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Catabolite repression
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Catabolite repression of lactose and other operons by
glucose
– glucose decreases cAMP levels, thereby blocking
CAP binding and decreasing mRNA synthesis
– When glucose is present, the cAMP level decreases
and the lac operon is inhibited
– The decrease in cAMP may be due to the effect of
the PTS system on the activity of adenyl cylase,
the enzyme that sytnesizes cAMP
Attenuation
Bacteria can regulated transcription in
an alternative manner
 An example of this is the tryptophan
operon in E. coli.
 The operon which contains the code for
five structural genes is under the
control of a repressor protein
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TrpR gene
The trp gene codes for the repressor
protein
 Excess tryptophan inhibits transcription
of the operon genes by acting as a
corepressor and activating the
repressor protein.
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Attenuation
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A leader region lies between the operator and the
first structural gene in the operon
The trp gene is responsible for controlling the
continuation of transcription after the RNA
polymerase has bound to the promoter
The leader region contains an attenuator and a
sequence that codes for the leader peptide
The attenuator is a rho independent termination site
– It is GC rich followed by eight uridine residues
The residues can pair with each other to form hairpin
loops.
In the absence of a ribosome, the loops are formed
and transcription will terminate
Tryptophan operon
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http://science.nhmccd.edu/biol/operon/
toff.html
Attenuation continued
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If When tryptophan is present, there is sufficient
tryptophanyl-tRNA for protein synthesis – therefore
the leader peptide will continue moving along the
mRNA until it reaches a UGA stop codon, at which
time will form hairpin loops with complementary base
pairing
Ribosome behavior influences translation of the
mRNA as it regulates the RNA polymerase activity.
Five other amino acid pathways have similar means of
regulation
Please refer to diagram in booklet
Attenuation I
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A leader region lies between the operator and the first
structural gene in the operon the trpE. It is responsible for
controlling the continuation of transcription after the RNA
polymerase has bound to the promoter
the tryptophan operon
leader of
operon
High and Low Tryptophan levels
Tryptophan Operon
Arabinose operon
Arabinose products
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The ara operon codes for three enzymes that are required to
catalyze the metabolism of arabinose.
Arabinose isomerase - encoded by araA - coverts arabinose to
ribulose
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Ribulokinase - encoded by araB -- phosphorylates ribulose
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Ribulose-5-phosphate epimerase - encoded by araD -- converts
ribulose-5-phosphate to xylulose-5-phosphate which can then be
metabolized via the pentose phosphate pathway.
Arabinose operon
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araO1 is an operator site. AraC binds to this site and represses
its own transcription from the PC promoter. In the presence of
arabinose, however, AraC bound at this site helps to activate
expression of the PBAD promoter.
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araO2 is also an operator site. AraC bound at this site can
simultaneously bind to the araI site to repress transcription
from the PBAD promoter
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araI is also the inducer site. AraC bound at this site can
simultaneously bind to the araO2 site to repress transcription
from the PBAD promoter. In the presence of arabinose,
however, AraC bound at this site helps to activate expression of
the PBAD promoter.
CRP binding site
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CRP binds to the CRP binding site. It does not
directly assist RNA polymerase to bind to the
promoter in this case. Instead, in the
presence of arabinose, it promotes the
rearrangement of AraC when arabinose is
present from a state in which it represses
transcription of the PBAD promoter to one in
which it activates transcription of the PBAD
promoter.
Arabinose absent
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When arabinose is absent, there is no need to
express the structural genes. AraC does this by
binding simultaneously to araI and araO2. As a result
the intervening DNA is looped. These two events
block access to the PBAD promoter which is, in any
case, a very weak promoter (unlike the lac promoter):
Arabinose present
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When arabinose is present, it binds to AraC and
allosterically induces it to bind to araI instead
araO2. If glucose is also absent, then the presence
of CRP bound to its site between araO1 and araI
helps to break the DNA loop and also helps AraC to
bind to araI:
Global Regulatory Systems
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Affect many genes and pathways simultaneously
Regulon
– collection of genes or operons controlled by a
common regulatory protein
– This enhances the cells ability to coordinate
cellular processes
Asn C transcriptional regulator
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ATGGAAAATT ATCTGATCGA CAATCTGGAC CGTGGCATCC TGGAAGCATT AATGGGCAAT
GCGCGCACCG CTTACGCCGA ACTGGCGAAA CAATTTGGCG TCAGTCCGGG GACGATTCAC
GTTCGAGTAG AGAAAATGAA GCAGGCGGGG ATCATTACCG GGGCGCGTAT TGATGTCAGC
CCGAAGCAGC TCGGTTATGA CGTAGGCTGC TTTATCGGCA TTATATTAAA GAGCGCCAAA
GACTACCCTT CCGCGCTGGC AAAGCTGGAA AGCCTTGATG AAGTCACTGA AGCCTATTAC
ACAACCGGCC ACTACAGCAT CTTTATAAAA GTGATGTGCC GTTCGATCGA CGCTCTCCAG
CATGTACTTA TCAACAAGAT CCAAACAATT GATGAAATTC AGTCCACCGA GACATTGATC
GTCCTGCAAA ACCCGATCAT GCGTACCATC AAGCCCTGA
Global regulatory
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Heat shock – chaperones that respond to elevations in
temperature – If the cell temperature is too highthe amount of heat shock proteins increases
SOS repair system – in which the damage to DNA is
so extreme that it utilizes ( Rec system)
Catabolite Repression
Occurs when operon is under control of
catabolite other than initial substrate of
pathway
 Allows preferential use of one carbon
source over another when both are
available in environment
 E. coli preferentialloy uses glucose – when
the glucose supply is exhausted, the
bacterium can switch to lactose

Regulation by Sigma Factors
and Control of Sporulation


Different sigma factors recognize different
promoters
Substitution of sigma factors changes gene
expression of many genes and operons
Bacillus subtilis sporulation
sigma factors


Synthesized only as cell switches from vegetative
growth to sporulation
Lead to transcription of sporulation-related genes
Small RNAs (sRNAs) and
Regulation





Also called noncoding (nc)RNAs
Do not function as mRNA or rRNA
There are between 50 and 200 of these
In E. coli there may be as many as 50-400 nucleotides in
length
. Appear to regulate genes by three different mechanisms
– Pair directly with other RNAs via RNA-protein
interactions (e.g., OxyS RNA)
– Intrinsic activities (e.g., RNase P RNA and tmRNA)
– Antisense RNA has a base sequence complementary to a
segment of another RNA and preferentially binds to this,
inactivating it
OxyS RNA of E. coli



Made in response to hydrogen peroxide exposure
Can act as an antisense RNA
– binds directly to mRNA and blocks translation
Can also block translation by binding a protein required for
translation of a target mRNA
micF RNA of E. coli


Regulates synthesis of OmpF porin protein
– porin proteins are outer membrane proteins
– different porins produced under different
conditions
 OmpC porin made when in intestine
 OmpF porin made when in dilute environment
MicF antisense RNA binds OmpF RNA and blocks
its translation when bacterium in intestines
RNase P RNA
the RNA component of RNase P
 has catalytic activity responsible for
tRNA processing

tmRNA of E. coli
Helps repair problems caused by defective
mRNAs that lack stop codons
 Acts as both alanyl-tRNA and mRNA when
ribosome stalls at end of defective mRNA
 Two functions

– releases ribosome from defective mRNA
– adds carboxy-terminal polypeptide tag to protein,
marking it for degradation
Two-Component Phosphorelay
Systems
Transfer of phosphoryl groups- control gene
transcription and protein activity
 Signal transduction situation
 Consists of a sensor kinase
And
 A response regulator


Two examples sporulation and chemotaxis
Sporulation continued



SpoOF donates the phosphoryl group to a histidine on
SpoOB.
SpoOA is a response regulator
It has a receive domain aspartate and picks up the
phosphoryl group from SpoOB to become an active
transcription regulator.
Sporulation in B. subtilis
Figure 12.33
Chemotaxis in E. coli
Figure 12.34
Control of the Cell Cycle

Cell cycle
– complete sequence of events extending
from formation of a new cell through next
division
– requires that DNA replication and cell
division be tightly coordinated

Precise mechanisms of control are not
known
Cell cycle control in E. coli

two separate control pathways
– sensitive to cell mass
– sensitive to cell length
Figure 12.36
Effect of growth rate

slow growth rate
– DNA replicated then
septation begins

rapid growth rate
– DNA replicated and
new round of DNA
replication begins
before septation
begins
Figure 12.35