Download Viral particles

Bacteriophages
(Phages or Bacterial Viruses)
• Obligate intracellular parasites, using eubacteria or
archaea as hosts
• Many generalities of phage lifecycle hold true for
plant/animal viruses
• Different representatives known with variety of
genomes: ssRNA, dsRNA (rare in phage), ssDNA,
and dsDNA, with either linear or circular molecules
packaged into viral particles (see Table 10.1)
• Phage genomes vary in size from 3000 bases to
650kb in size
• Phage morphology varies from simple icosahedra or
helical filaments to complex tailed structures
Viral particles
• Typically, genomic material of phage is 25-50% of
virus mass
• Usually the viral genomes tightly packed with “useful"
info (e.g., 90% of M13 genome represents protein
coding region)
• Phage particles are metabolically inactive, but they
may contain enzymes involved in virus proliferation
(e.g., lysozyme or RNA/DNA polymerase)
Viral particle structure
Enveloped viruses typical for euks
Fig. 10.3
Phages typically with simple protein capsid around genome
Replication cycle of
bacterial virus
Will see temporal
regulation for
expression and
(or viral RNA)
activity of
different
viral proteins. Early viral proteins often
Fig. 10.8
to specific surface
receptor
inhibit host functions.
Different phages
will exploit
Late viral proteins often act in
different host capsid assembly and genome
packaging.
proteins during
their replication.
Cells usually lyse.
Variations in genetic material and
examples of different classes of viruses
Herpes virus;
Phages T4, "
Parvoviruses;
Phages M13, !X174
See Fig 10.11 &
Table 10.2
HIV
Polio virus; Phage MS2
Fig. 19.2
ssRNA
phage MS2
•
•
•
•
Icosahedral capsid surrounds +
strand linear genome, copied 5!
#3! by viral RNA polymerase
(replicase); no DNA intermed.
Template for viral genome is –
strand, which is also made by
viral replicase
Replicase composed of viral
protein + 3 host proteins
normally involved in translation.
No proofreading activity for the
viral RNA polymerase
Influenza;
Rabies
Reovirus
Terminology for ssRNA/ssDNA viral genomes
If mRNA is:
5!…GAC UCG AGC …3!
+ strand DNA:
– strand DNA:
5!…GAC TCG AGC …3! (sense)
3!…CTG AGC TCG …5!
(template)
+ strand RNA:
– strand RNA:
5!…GAC UCG AGC …3!
3!…CUG AGC UCG …5!
mRNA is always considered to be + strand
Translational control in MS2
Step I: RBS for coat is always
open. Translation of this
gene opens up RBS for
replicase.
Step II: Translation of replicase
gene can occur when RNA
structure blocking that RBS
is disrupted.
Translation of replicase allows
+/- RNA strand synthesis
Step III: maturation RBS usually
blocked by RNA folding but
open during transcription of
viral + strand
*
*
*
*
i/t = translation initiation/termination site
* = open RBS
Binding of MS2 and M13 to E. coli
• Filamentous ssDNA
phage M13 binds to
tip of pilus on F+
cells
• Icosahedral MS2
binds to side of pilus
• F plasmid-deficient
E. coli strains are
resistant to both
M13 and MS2
(Also see Fig. 19.1)
Budding without cell lysis
Bacteriophage M13
• + strand circular
ssDNA, 6500 bases
and 9-10 genes
• DNA does not form
significant 2° struct.
inside cell
• Assymetric capsid:
2700 coat proteins,
with distinct binding
protein at one end
• Virus buds from host
without lysis/killing
Fig. 19.5
Complex phage assembly (or export) apparatus
assembles capsid proteins and DNA and allows
transit through CM and OM of cell
xxxxx
XXXXX ssb
Fig. 19.3
$X174
• + strand ssDNA
genome, 5386 nt
with 10 genes
• Icosahedral capsid,
attaches to LPS
• Genome contains
overlapping genes:
some regions of
polycistronic mRNA
can be translated in
>1 reading frame
$X174 rolling circle replication
Infection by T4 (T even phages)
•
Many phages use this
strategy to produce
lots of progeny
genomes
$X174 CisA nicks +
strand of Replicative
Form dsDNA; 3!OH of
nicked strand primes
synthesis (but no
“lagging strand
synthesis” for this
phage)
•
!
•
•
!
•
!
Fig. 19.4
Program of T4 lytic cycle
Fig. 10.10
Fig. 10.15
Early phage proteins subvert host RNA synthesis (modifying host
%) and degrade host DNA, allowing phage to take over host
cell; Specific phage DNA synthesis proteins.
Late proteins: capsids assembled in 3 different paths.
T4 binds to LPS in
OM (recognition by
tail fibers)
169 kd linear dsDNA
is injected into cell
from head by tail
Capsid remains
outside cell
200 phage in 25! lytic
cycle
Genomes of T2, T4,
and T6 are 85%
identical, with
differences
accounting for binding
different host
receptors
Replication of T4 DNA, part I
Viral DNA pol carries out bidirectional replication on linear DNA
molecules. Viral recombination proteins produce complex
intermediates (includes concatemers), that subsequently are
processed into progeny genomes.
Processing T4
genomic DNA
Phage "
• Recombination yields
long concatemers
• Phage nuclease
processes DNA into
linear molecules of
specific length =105%
of genome (no cutting
at specific sequence)
• Terminal redundancy
of varying sequence
called circular
permutation
• Linear dsDNA
genome, 48.5Kb
• Simpler tail structure
than T even phages
• Binds to maltoporin
in OM of E. coli
• Temperate phage,
capable of 2 distinct
fates upon infection
Fig. 10.13
": lysis or lysogeny
Temperate phages
can proceed with
lytic infection or
can integrate into
genome and
maintain prolonged
association with
host.
Fig. 10.16
Forming a " lysogen
• "-encoded Integrase
catalyzes site-specific
recombination with
E. coli chromosome
between gal-bio
• Maintenance of
lysogeny requires
continued expression
of cI repressor
• Reversible process…
Fig. 10.18