Phage strategies

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Chapter 11

• Phage strategies

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11.1 Introduction 11.2 Lytic development is
divided into two periods 11.3 Lytic development
is controlled by a cascade 11.4 Functional
clustering in phages T7 and T4 11.5 Lambda
immediate early and delayed genes are needed for
both lysogeny and the lytic cycle 11.6
The lytic cycle depends on antitermination 11.7
Lysogeny is maintained by repressor protein 11.8
Repressor maintains an autogenous circuit 11.9
The repressor and its operators define the
immunity region 11.10 The DNA-binding form of
repressor is a dimer 11.11 Repressor uses a
helix-turn-helix motif to bind DNA 11.12
Repressor dimers bind cooperatively to the
operator 11.13 Repressor at OR2 interacts with
RNA polymerase at PRM 11.14 The cII and cIII
genes are needed to establish lysogeny 11.15 PRE
is a poor promoter that requires cII
protein 11.16 Lysogeny requires several
events 11.17 The cro repressor is needed for
lytic infection 11.18 What determines the
balance between lysogenic and the lytic cycle?
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Episome is a plasmid able to integrate into
bacterial DNA. EpistasisImmunity in phages
refers to the ability of a prophage to prevent
another phage of the same type from infecting a
cell. It results from the synthesis of phage
repressor by the prophage genome.Induction
refers to the ability of bacteria (or yeast) to
synthesize certain enzymes only when their
substrates are present applied to gene
expression, refers to switching on transcription
as a result of interaction of the inducer with
the regulator protein.Lysogeny describes the
ability of a phage to survive in a bacterium as a
stable prophage component of the bacterial
genome.Lytic infection of bacteria by a phage
ends in destruction of bacteria and release of
progeny phage.Plasmid is an autonomous
self-replicating extrachromosomal circular
DNA.Prophage is a phage genome covalently
integrated as a linear part of the bacterial
chromosome.
11.1 Introduction
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Figure 11.1 Lytic development involves the
reproduction of phage particles with destruction
of the host bacterium, but lysogenic existence
allows the phage genome to be carried as part of
the bacterial genetic information.
11.1 Introduction
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Figure 11.2 Several types of independent genetic
units exist in bacteria.
11.1 Introduction
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Figure 11.3 Lytic development takes place by
producing phage genomes and protein particles
that are assembled into progeny phages.
11.2 Lytic development is controlled by a cascade
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Figure 11.4 Phage lytic development proceeds by
a regulatory cascade, in which a gene product at
each stage is needed for expression of the genes
at the next stage.
11.2 Lytic development is controlled by a cascade
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Figure 9.31 Switches in transcriptional
specificity can be controlled at initiation or
termination.
11.2 Lytic development is controlled by a cascade
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Figure 11.5 Phage T7 contains three classes of
genes that are expressed sequentially. The genome
is 38 kb.
11.3 Functional clustering in phages T7 and T4
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Essential genes are indicated by numbers.
Nonessential genes are identified by letters.
Only some representative T4 genes are shown on
the map.
11.3 Functional clustering in phages T7 and T4
Figure 11.6 The map of T4 is circular. There is
extensive clustering of genes coding for
components of the phage and processes such as DNA
replication, but there is also dispersion of
genes coding for a variety of enzymatic and other
functions.
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Figure 11.7 The phage T4 lytic cascade falls into
two parts early and quasi-late functions are
concerned with DNA synthesis and gene expression
late functions are concerned with particle
assembly.
11.3 Functional clustering in phages T7 and T4
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Figure 11.24 RNA polymerase binds to PRE only in
the presence of CII, which contacts the region
around -35.
11.3 Functional clustering in phages T7 and T4
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Figure 11.8 The lambda lytic cascade is
interlocked with the circuitry for lysogeny.
11.4 The lambda lytic cascade relies on
antitermination
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Figure 11.9 The lambda map shows clustering of
related functions. The genome is 48,514 bp.
11.4 The lambda lytic cascade relies on
antitermination
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Figure 11.10 Phage lambda has two early
transcription units in the "leftward" unit, the
"upper" strand is transcribed toward the left in
the "rightward" unit, the "lower" strand is
transcribed toward the right. Promoters are
indicated by the shaded red or blue arrowheads.
Terminators are indicated by the shaded green
boxes. Genes N and cro are the immediate early
functions, and are separated from the delayed
early genes by the terminators. Synthesis of N
protein allows RNA polymerase to pass the
terminators tL1 to the left and tR1 to the right.
11.4 The lambda lytic cascade relies on
antitermination
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Figure 11.11 Lambda DNA circularizes during
infection, so that the late gene cluster is
intact in one transcription unit.
11.4 The lambda lytic cascade relies on
antitermination
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Immunity in phages refers to the ability of a
prophage to prevent another phage of the same
type from infecting a cell. It results from the
synthesis of phage repressor by the prophage
genome.Virulent phage mutants are unable to
establish lysogeny.
11.5 Lysogeny is maintained by an autogenous
circuit
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Figure 11.12 The lambda regulatory region
contains a cluster of trans-acting functions and
cis-acting elements.
11.5 Lysogeny is maintained by an autogenous
circuit
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Figure 11.13 Wild-type and virulent lambda
mutants can be distinguished by their plaque
types. Photograph kindly provided by Dale Kaiser.
11.5 Lysogeny is maintained by an autogenous
circuit
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Figure 11.14 Lysogeny is maintained by an
autogenous circuit (upper). If this circuit is
interrupted, the lytic cycle starts (lower).
11.5 Lysogeny is maintained by an autogenous
circuit
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Figure 11.14 Lysogeny is maintained by an
autogenous circuit (upper). If this circuit is
interrupted, the lytic cycle starts (lower).
11.5 Lysogeny is maintained by an autogenous
circuit
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Figure 11.15 The N-terminal and C-terminal
regions of repressor form separate domains. The
C-terminal domains associate to form dimers the
N-terminal domains bind DNA.
11.6 The DNA-binding form of repressor is a dimer
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Figure 11.16 Repressor dimers bind to the
operator. The affinity of the N-terminal domains
for DNA is controlled by the dimerization of the
C-terminal domains.
11.6 The DNA-binding form of repressor is a dimer
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Figure 11.16-2 Lambda repressor binds to
operators with second-order kinetics.
11.6 The DNA-binding form of repressor is a dimer
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Figure 11.17 Lambda repressor's N-terminal domain
contains five stretches of a-helix helices 2 and
3 are involved in binding DNA.
11.7 Repressor binds cooperatively at each
operator using a helix-turn-helix motif
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Figure 11.18 In the two-helix model for DNA
binding, helix-3 of each monomer lies in the wide
groove on the same face of DNA, and helix-2 lies
across the groove.
11.7 Repressor binds cooperatively at each
operator using a helix-turn-helix motif
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Figure 11.19 Two proteins that use the two-helix
arrangement to contact DNA recognize lambda
operators with affinities determined by the amino
acid sequence of helix-3.
11.7 Repressor binds cooperatively at each
operator using a helix-turn-helix motif
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Figure 11.20 A view from the back shows that the
bulk of the repressor contacts one face of DNA,
but its N-terminal arms reach around to the other
face.
11.7 Repressor binds cooperatively at each
operator using a helix-turn-helix motif
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Figure 11.21 Each operator contains three
repressor-binding sites, and overlaps with the
promoter at which RNA polymerase binds. The
orientation of OL has been reversed from usual to
facilitate comparison with OR.
11.7 Repressor binds cooperatively at each
operator using a helix-turn-helix motif
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Figure 11.21 Each operator contains three
repressor-binding sites, and overlaps with the
promoter at which RNA polymerase binds. The
orientation of OL has been reversed from usual to
facilitate comparison with OR.
11.7 Repressor binds cooperatively at each
operator using a helix-turn-helix motif
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Figure 11.14 Lysogeny is maintained by an
autogenous circuit (upper). If this circuit is
interrupted, the lytic cycle starts (lower).
11.7 Repressor binds cooperatively at each
operator using a helix-turn-helix motif
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Figure 11.22 Positive control mutations identify
a small region at helix-2 that interacts directly
with RNA polymerase.
11.7 Repressor binds cooperatively at each
operator using a helix-turn-helix motif
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Figure 11.12 The lambda regulatory region
contains a cluster of trans-acting functions and
cis-acting elements.
11.8 How is repressor synthesis established?
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Figure 11.23 Repressor synthesis is established
by the action of CII and RNA polymerase at PRE to
initiate transcription that extends from the
antisense strand of cro through the cI gene.
11.8 How is repressor synthesis established?
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Figure 11.24 RNA polymerase binds to PRE only in
the presence of CII, which contacts the region
around -35.
11.8 How is repressor synthesis established?
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Figure 11.25 Positive regulation can influence
RNA polymerase at either stage of initiating
transcription.
11.8 How is repressor synthesis established?
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Figure 11.26 A cascade is needed to establish
lysogeny, but then this circuit is switched off
and replaced by the autogenous repressor-maintenan
ce circuit.
11.8 How is repressor synthesis established?
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Figure 11.19 Two proteins that use the two-helix
arrangement to contact DNA recognize lambda
operators with affinities determined by the amino
acid sequence of helix-3.
11.9 A second repressor is needed for lytic
infection
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Figure 11.27 The lytic cascade requires Cro
protein, which directly prevents repressor
maintenance via PRM, as well as turning off
delayed early gene expression, indirectly
preventing repressor establishment
11.9 A second repressor is needed for lytic
infection
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Figure 11.26 A cascade is needed to establish
lysogeny, but then this circuit is switched off
and replaced by the autogenous repressor-maintenan
ce circuit.
11.9 A second repressor is needed for lytic
infection
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1. Phages have a lytic life cycle, in which
infection of a host bacterium is followed by
production of a large number of phage particles,
lysis of the cell, and release of the viruses.
2. Lytic infection falls typically into three
phases. In the first phase a small number of
phage genes are transcribed by the host RNA
polymerase.3. In phage lambda, the genes are
organized into groups whose expression is
controlled by individual regulatory events.
Summary
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4. Each operator consists of three binding sites
for repressor. 5. The helix-turn-helix motif is
used by other DNA-binding proteins, including
lambda Cro, which binds to the same operators,
but has a different affinity for the individual
operator sites, determined by the sequence of
helix-3.6. Establishment of repressor synthesis
requires use of the promoter PRE, which is
activated by the product of the cII gene.
Summary