Lambda phage
Lambda genome
lambda phage gene transcription
Above a siphovirus, e.g. lambda bacteriophage. Phage lambda is a parasite of enteric bacteria such
as
Escherichia coli. Unlike T4 it only has a single tail fibre and it has a tapering tail tube. Like T4,
however, it still injects its DNA into the host cell, although the tail is non-contractile. The lambda
phage has a remarkable developmental sequence which is quite well understood, and an excellent
model of how genetic systems regulate living processes. Lambda is a siphovirus, characterised by
their long, thin and non-contractile tails, which are often flexible, as in lambda. The lambda genome is
48.5 kb (compared to that of T4 which is 172 kb). This virus is about 150 nm by 50 nm.
Adsorption

The life-cycle of lambda phage begins when it absorbs to the surface of the host bacterial cell. The J
protein is a protein in the tip of the lambda tail which binds specifically to its target receptor - the
LamB outer membrane protein of the host (which functions normally to import the sugars maltose and
maltodextrin). As for T4, initial adhesion is reversible but it triggers a change in the phage that results
in permanent binding.

DNA Injection and Circularisation

Like T4, lambda injects its single linear dsDNA (double-stranded DNA) chromosome into the host
bacterial cell, however, unlike T4 the tail of lambda does not contract, instead the pressure of the
DNA inside the head seems sufficient for its injection. Once inside the cell, the DNA, which has
single-stranded sticky ends which bind to and stick to one-another (by hydrogen-bonding between the
complementary bases) circularises as the two ends stick together. The host enzyme
DNA ligase
seals this join (by covalently bonding the DNA sugar-phosphate backbone together) to make the join
permanent. In this state the DNA cannot be attacked and destroyed by host defence enzymes called
exonucleases which breaks-up foreign DNA by attacking the free ends.

Gene Transcription

The region of the chromosome involved in early and middle gene transcription is shown below:
Recall that promoters are regions where the enzyme RNA polymerase (RNA-dependent RNA polymerase)
binds and begins transcribing the DNA message into mRNA (messenger RNA). In this instance, the RNA
polymerase used is that belonging to the host cell. Transcription proceeds until a
terminator is reached,
at which point the polymerase stops and detached. The host cell ribosomes then translate this viral mRNA
into viral proteins. The polymerase initially transcribes the early genes:
lambda phage gene transcription 2
The mRNA transcript produced from the PR promoter does not go beyond PR' at this stage.

For the rest of the cycle, lambda phage has two choices:

1. It can follow the
lytic cycle, where, like T4, it will replicate and assemble virus particles, then
lyses (burst open) the host cell to allow the viral progeny to escape and attack new hosts.

2. It can instead undergo
lysogeny, in which the phage becomes quiescent and incorporates its
DNA into the host's chromosome, quietly allowing itself to be replicated when the host chromosome
replicates and so get passed to the daughter cells and down the generations of bacteria. The virus
can then switch to the lytic cycle at a later time.

There exists a remarkable genetic mechanism or switch that determines which cycle is followed and
this was the first developmental switch to be described at the molecular level. We now describe this
switch.
Bacteriophage lambda
Lambda phage gene transcription 3
Lambda phage gene transcription 4
Integration

If the phage decides to undergo lysogeny, then its DNA inserts at a specific site on the host
chromosome (called
attB) which is inbetween two genes and so viral DNA insertion does not
disrupt the functioning of the host. The lambda DNA inserts via its
att region (attP) with the help of
the viral protein
integrase (Int) and a host protein called IHF (integration host factor). The
circular molecule opens up at the
att region, and the host chromosome opens up at the attB
region and the lambda DNA inserts. The viral DNA is quiescent, except that it produces  C
I
continuosuly, ensuring lysogeny is maintained. C
I keeps the PR promoter blocked, preventing the
production of Q protein. Q protein switches the phage into lytic mode.

The reverse process may occur later on, that is the viral DNA may excise itself, again using Int and
IHF but also the viral protein
Xis (excision or 'excise'). Like many viruses, lambda will abandon its
host cell if the host cell becomes badly damaged. One such trigger is UV light (which also triggers,
amongst other things, dormant chicken-pox virus in neurones in humans to activate and cause
shingles). UV damages host DNA, triggering the so-called
SOS response. One of the key
bacterial proteins produced which switches on the SOS response also interacts with C
I, cleaving it
and switching on the lytic phase. Thus, C
I senses the SOS response. Within about 35 minutes the
virus will have replicated, assembled virions and burst out of the damaged host cell. Other factors
are likely to also cause the switch from lysogeny to lysis.

The C
I protein also serves to prevent superinfection, that is the infection of a single cell by
multiple lambda phages. If a bacterial cell contains a lysogenic phage and another phage enters,
then the second phage cannot undergo the lytic cycle, because of the abundance of C
I. It can
integrate, but if it does so then it is shut-down as the C
I binds to its OL and OR operators,
preventing transcription.

The Lytic Cycle

If enough Q protein accumulates in the cell (the production of which is suppressed by CI and
stimulated b y N) then the phage will switch to the lytic cycle. Q protein binds a region of the
lambda DNA called
qut, which is situated just downstream of the PR' promoter (just to the right of it
in our diagrams). Now transcripts running from the P
R promoter will continue past PR' onto the late
transcription phase structural genes (the head genes and tail genes) producing the proteins
needed to assemble phage particles.

The circular DNA replicates itself, initially in a bidirectional manner similar to that used in
Escherichia coli (and called theta-replication) and then, when churning out phage genomes rapidly
for packaging into the heads, by
rolling circle replication. This results in several copies of the
DNA joined together into
concatemers. One end is fed into a phage head and packed in until the
head is full, then the viral enzyme
terminase cuts the DNA at the cos site in such a way as to
leave the single-stranded overhangs (sticky-ends). As the DNA is inserted into the head and
packaged, the head enlarges and matures and terminase cuts the next
cos site. The neck
connector assembles and then assembled tails add spontaneously to the connector.

Lysis is brought about by three viral proteins: R and S. S forms a hole in the inner membrane,
exposing the peptidoglycan layer to R, which is an endolysin that degrades the peptidoglycan
layer of the periplasm. About 100 progeny phages are liberated (the
burst size is about 100).
The whole cycle takes about 35 minutes.
Podovirus
Above: podoviruses are another binary phage (about 20 by 8 nanometres in size) but with
a short non-contractile tail. An example is phage phi29. The DNA can be packed in so
tightly that the head bulges, appearing almost spherical when full. Bacteriophages come
in a variety of other morphologies, including icosahedral (tectiviruses, corticoviruses,
microviruses, cystoviruses and leviviruses) helical rod-shaped (inoviruses, rudiviruses and
lipothrixiviruses). The fuselloviruses are lemon-shaped, the SNDV sulfolobus virus is
droplet-shaped while the plasmaviridae are enveloped and pleomorphic. Not all contain
dsDNA genomes, the leviviruses have ssRNA, the cystoviruses dsRNA and the inoviruses
and microviruses.
Bacteriophages use a variety of methods to get their DNA (or RNA) inside the target cell. T4 uses its
tail like a hypodermic needle, forcefully injecting its large 172 kbp genome into the host in about 30
seconds. Bacteriophage T7 has a non-contractile tail and although its genome is much smaller than
T4's, at 40 kbp, it takes about 10 minutes for injection of the DNA to complete. Clearly, the elaborate
mechanism of injection used by T4 is an adaptation that complements its large genome.

The tailspikes of phage P22 bind LPS O-antigens in the bacterial outer membrane (LPS or
lipoplysaccharide is the major lipid of the outer leaflet of the outer membrane in Gram(-) bacteria - see
bacteria envelope structures; the O-antigen is part of the long polysaccharide chains of the LPS
molecule which project from the cell surface). It then enzymically 'chews' its way along the LPS
carbohydrate chain to reach the target and then injects
pilot proteins then DNA. The pilot proteins
assist DNA entry. P1 also adsorbs to the LPS polysaccharide chain (to the terminal glucose residue)
but has a contractile tail.

Bacteriophage M13 is filamentous and carries a viral glycoprotein, gpIII, which binds to the tip of the
F-pilus (which is only present in bacteria carrying a certain plasmid and is used in conjugation). The
F-pilus is contractile and presumably pulls the phage in to the cell surface, where gpIII binds to the
inner membrane protein, TolA. It is then thought that gpIII forms a pore in the target cell mebrane
through which the single-stranded DNA genome enters.
Lysogenic cycle part 1
Lysogenic cycle part 2
Lytic cycle
The lambda phage life-cycle has been compacted into a single diagram below (click to enlarge):
Lambda phage cycle