Download The Structure and Genetic Map of Lambda phage

NPTEL – Biotechnology - Systems Biology
The Structure and Genetic Map of
Lambda phage
Dr. M. Vijayalakshmi
School of Chemical and Biotechnology
SASTRA University
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Table of Contents
1 FLUCTUATIONS IN GENE EXPRESSION ............. ERROR! BOOKMARK NOT
DEFINED.
1.1IS NOISE AN ADVANTAGE TO BIOLOGICAL SYSTEMS? ....... ERROR! BOOKMARK NOT
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1.2 MEASUREMENT OF EXPRESSION NOISE...........ERROR! BOOKMARK NOT DEFINED.
2 REFERENCE ......................................... ERROR! BOOKMARK NOT DEFINED.
2.1 LITERATURE REFERENCES .............................ERROR! BOOKMARK NOT DEFINED.
1.2 VIDEO LINK ...................................................ERROR! BOOKMARK NOT DEFINED.
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1 Introduction
Viruses are obligate intracellular parasites. Bacteriophages are viruses infecting
bacteria. They multiply inside the host system through partial or complete utilization of
the host biosynthetic machinery.
Bacteriophages may be

RNA phages such as Q-beta

Filamentous with single stranded DNA such as M13

T- even phages including T2,T4,T6 infecting E.coli

Temperate phages like lambda and mu

Spherical phages with single stranded DNA like PhiX174
The genetic material in bacteriophage may either be RNA or DNA but not both. The
nucleic acids of phages contain unusual or modified bases which enable to circumvent
the degradation of the host nuclease. Further, the number of genes in bacteriophage
varies with the complexity of the genome. Complex phages have more than 100 genes
while simple phages have only 3-5 genes.
1.1 Structure of the Lambda Phage
Lambda phage is a temperate phage. The genes of the lambda phage make a single
DNA molecule-the chromosome wrapped within a protein coat, composed of 12-15
different proteins all of which are encoded by the lambda chromosome. The coat is
structurally composed of an icosahedral head with a diameter of 64nm and a tail, 150
nm in length as shown in Fig 1. The head is composed of double stranded linear DNA
surrounded by a capsid made up of protein capsomers. At the 5’ end of each strand are
12 nucleotide long sequences complementary to each other. Thus on circularization, the
bacteriophage DNA has 48,514 base pairs. The 5’ends are called cos sites and the
opposite of cos site is att site meant for attachment. The lambda phage attaches to the
cell surface of E.coli through its tail, making a hole in the cell wall. It thus pushes its
chromosome into the bacterium E.coli, leaving behind the protein coat.
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Fig 1 (a) Structure of a Lambda phage , (b) measurement of different parts of a Lambda phage
First stage of infection involves a process called adsorption. Adsorption involves
landing and attachment. Tail fibres play a critical role in this stage . Tail less phages use
analogous structures for adsorption. Specific receptors on the bacterial cell like proteins,
lipopolysaccharides, pili apart from lipoproteins are exploited by phages for attachment.
This is reversible condition. Base plate components mediate permanent binding.
Second stage in infection process is penetration.
The sheath of phages contracts
resulting in insertion of hollow tail fiber through bacterial envelope. Some phages utilize
their enzymes to digest components of bacterial envelope. Nucleic acid is inserted
inside bacterial cell via hollow tail. Remaining part of the phage outside bacteria is
called ghost. Thus in nutshell penetration involves contraction of sheath till DNA
insertion.
Some phages upon infecting bacteria lyse the bacterial cell after forming their progeny.
Such phages are called virulent. Some phages integrate their genome into bacterial
genome and can remain inside host without harming them but under drastic conditions
can become virulent and can causes host cell lysis. Such phages which normally follow
lysogeny but under drastic conditions become lytic are called temperate phages.
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1.2 Receptor targeting λ- phage
The λ - phage uses the maltose pore LamB for delivering its genetic material into the
host cell. The phage binds to the cells of the target E.coli and the J-protein in the tip of
its tail interacts with the LamB, gene product of E.coli (LamB is a porin molecule and is
a part of the maltose operon). Most of the E.coli K-12 mutations resistant to λ phage are
located in two genetic regions malA and malB. LamB is composed of three identical
subunits, each of which is formed by an 18-stranded antiparallel β-barrel, which forms a
wide channel with a diameter of about 2.5 nm. The phage consists of a hollow tube
composed of 32 –stacked discs, each of which has a 3nm central hole to eject its
genetic material into the host. Lambda phage uses this channel for ejecting its genetic
material. After injecting the DNA into bacteria, the double stranded linear DNA
circularizes due to the presence of cos sites and site specific nucleases cut DNA at the
att site of the phage DNA.
Fig 2. Genetic mapping of lambda phage
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Table 1
The genes involved in the switching mechanism of the lambda phage
Name of gene/promotor/operator
Att
Function
Provides site of attachment for phage to
host chromosome
cI
Repressor protein
cII
Coding
for
promotor
establishment
activator protein
cIII
Codes for stabilizing protein
OR
Operator right
PR
Promotor right
OL
Operator left
PL
Promotor left
Cro
Gene for second repressor
N
Positive
regulator
counteracting
rho
dependent termination
J through U
Genes encoding tail proteins
Z through A
Genes encoding head proteins
Int
Gene encoding integrase
Xis
Encodes excisionase
O and P
Encode proteins involved in replication of
Lambda DNA
Q
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Encodes anti terminator protein
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Bacteriophage lambda is episomic and consequently its genome exists in at least two
states within which genetic recombination is possible. This allows the construction of
two genetic maps termed vegetative and prophage after these states. In the vegetative
state, the replication of the lambda genome is independent of the replication of the host
genome. Such replica are finally packaged into the head of the mature phage as single
duplex DNA molecules, 15 to 17 microns in length. These molecules contain ~ 47,000
base pairs, to accommodate 40 to 45 structural genes. In the prophage state the viral
genome integrates into the host genome replicating in synchrony with the host genome.
Lambda genes are organized into operons. The Left operon genes are meant for
recombination and integration resulting in lysogeny, while right operon and the late
operon genes are meant for lysis. The genetic map of the lambda phage is shown in
Fig2.
The lambda phage infects the bacterium directing it to two different fates. In some of the
cells, as the infection happens the different set of phage genes are turned ON and OFF
in a precisely regulated manner. The lambda chromosome is replicated, newer head
and tail proteins are synthesized, forming new phage particles within the bacterium. As
the phage chromosome begins to replicate, the phage gene cI, is expressed. The
product of cI is the bacteriophage lambda repressor which keeps the other phage genes
in the OFF state. When exposed to ultraviolet light, the inert phage genes (lytic genes)
are switched ON and the repressor gene is switched OFF. Nearly 45 minutes after the
infection the bacterial cell ‘lyses’ releasing around 100 new progeny phage.
In the other population of cells, the injected phage chromosome turns OFF all the phage
genes except one. The single phage chromosome called the prophage now becomes a
part of the host chromosome. The bacterium carrying the dormant phage chromosome
is called the lysogen. As the lysogen grows, the prophage is passively replicated with
the host genome and distributed to the progeny bacteria. Thus, we understand that the
phage genes upon exposure of a lysogen to a signal such as UV, switch from their
stable lysogenic state to a lytic growth state. The switch from the lysogeny to the lytic
growth is termed induction. We shall discuss the classic switch of a lambda phage in the
next class.
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2 References
2.1 Text Book
1. A Genetic switch: Phage lambda revisited, 3/e, CSHL Press, New York, (2004).
2.2 Literature References
1. DAVID S. HOGNESS et al., The Structure and Function of the DNA from
Bacteriophage Lambda. The Journal of General Physiology,(1966), 49, 29-57
2. Oppenheim A B, Oren Kobiler, Joel Stavans, Donald L. Court, and Sankar
Adhya. Switches in bacteriophage Lambda development, Annu. Rev. Genet.,
(2005), 39, 409-429
3. Fogg P C M, Allison H E eta al, Bacteriophage lambda: A paradigm revisited,
J.Virol, (2010), 84, 6876-6879.
2.3 Video Link
http://www.blackwellpublishing.com/trun/artwork/Animations/Lambda/lambda.html
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