Bacteria Viruses Flashcards
Phage genetics
• Genetic characteristics may be either DNA or RNA,
single or double stranded, circular or linear, and usually
present as a single copy
Phage morphology
Morphology diversity in phages differs from simple,
icosahedral and filamentous phages to more complex
phages with a tail and an icosahedral head.
• Most phages are have tails
Phage environments
• Phages are more common in environments where their
bacteria host are more abundan
Classification of phages
• Phages can be classified into two broad categories:
- Virulent phages:
- Temperate phages
Virulent phages
Virulent phages convert the cell replication machinery of
their bacteria host for viral gene replication resulting in
cell lysis, especially in obligately lytic phages, and release
of progeny virions. Most members undergo the phage
lytic lifecycle as opposed to the lysogenic lifecycle.
In exceptional cases, the filamentous ssDNA phage M13
releases progeny virions continously from cells without
lysis and is commonly known as a ‘’chronically infecting’’
phage.
Temperate phages
. Temperate phages exhibit alternating
replication cycles involving:
i. Productive (lytic) infection
ii. Reductive (lysogenic) infection: occurs when
the phage lies latent or dormant in the
bacterial host usually due to unfavourable
conditions. The phage at the latent stage is known as a
lysogen.
the lysogeny cycle
• In lysogeny, the phage genome is repressed for lytic
functions and most time integrates into the chromosome of
the bacteria.
• An example is the phage lambda (λ) capable of existing
extrachromosomally.
• In phage P1, the prophage replicates together with the host
and remain dormant until the lytic cycle is initiated usually
under conditions that result in the disruption of host DNA.
• Inactivation of the repressor gene follows the damage of
host DNA, initiating a lytic cycle.
last superinfection immunity?
Superinfection immunity
• Superinfection immunity: prophages in bacterial host
(resident phages) can prevent superinfection by the same
or other phages by repressing the incoming phage genome
resulting in protection of the host.
- RNA phages genotypes
ssRNA phages
• dsRNA phages
- DNA phages genotypes and examples
ssDNA phages
• icosahedral ssDNA phages
• Filamentous ssDNA phages
dsDNA phages
• Phage T4
• Phage T7
• Phage lambda
Single-stranded RNA phages
taxonomy
• They are grouped into the family Leviviridae
• They belong to one of the smallest group of
viruses and possess a high rate of mutation.
• Members are small phages with icosahedral
shape.
Single-stranded RNA phages
Genome/ infection
• ssRNA phages have (+) strand RNA, hence
there genome function as a mRNA.
• They possess only a few genes, capable of
infecting gram-negative bacteria such as,
Pseudomonas spp, E. coli and Caulibacter spp.
• ssRNA phages infect enterobacteria via the sex
pilus during conjugation.
The virion of ssRNA phages
- The virion of RNA phages is composed of the following:
- 180 molecules of major capsid protein (CP) or coat per virion.
• One molecule of maturation (A) protein (minor virion protein),
acquired for infectivity by reconition of sex pilus and maturation.
• Typically, ssRNA phages possess
linear ssRNA genome of
approximately 3500-4200
nucleotides.
• The genome exhibits significant amount of secondary structures (around 80%), which affects access of the ribosome binding sites (RBCs) to host ribosome during translation.
The genome of a representative phage (MS2) is composed
of 3569 nucleotides.
4 orfs
MS2 was the first RNA virus identified by genome
MS2 genome has four open reading frames (ORFs) which
codes for the following proteins, characterized by intergenic
spaces:
1. Major coat/capsid protein (coats each virus particle)
2. Maturation (A) protein (maturase)
3. Replicase (RNA-dependent RNA replication)
4. Lysis protein (overlapping the coat and replicase genes)
Figure 3: The genetic map
• The solid blue boxes represent intergenic regions involved with ribosome binding and regulation of translation.
• The MS2 genome is composed of: genes for maturase (maturation protein); coat (capsid) protein; replicase protein for
RNA-dependent RNA replication; and lysis protein (from overlapping coat and replicase genes).
- The Qβ genome is composed of: genes for maturase (A); coat protein; replicase protein; and read-through protein.
- Note that the MS2 genome is smaller than that of Qβ,
• The maturation protein in the Qβ genome perform additional role of mediating lysis, as the genome lacks a separate
lysis protein
The Qβ genome of ssRNA phages
• The Qβ genome is composed of four genes encoding
proteins namely: genes for maturase (A); coat protein;
replicase protein; and read-through protein. It lacks a
lysis gene.
• The genome for ssRNA phages code efficiently for
some of its needed proteins and determines specific
secondary and tertiary structures that control
functions such as, translation and replication. • ssRNA phages manipulate host proteins for activation
of its proteins; some of which perform multiple
functions.
attachment of ssRNA phages
• Attachment: Infection of a susceptible phage in coliphage
M2 involves attachment to pilin (pilus singular), along the
length of the sex pilus through the maturase (A protein). In
E. coli, binding between phages can prevent conjugation.
gene expression and translation of ssRNA phages
• Gene expression and Translation: Proceeds immediately
after infection of a new phage.
• The (+) strand RNA phage genome directs protein synthesis
using the host (bacterial) ribosomes.
• This results in the translation of phage virion proteins such
as replicase, coat (capsid) protein, A protein (maturase) and
lysis protein.
genome replication in ssRNA phages
• Genome replication: Immediately the replicase is
translated, the ssRNA genome of phages switches from
protein synthesis to template for gene replication.
• Replicase is associated with several host proteins to
form a phage RNA specific polymerase.
• Genome replication occurs in two phases (replication
intermediates [RI]); the (+) strand RNA serves as a
template for synthesis of the (-) RNA strand, while the
(-) RNA strand in turn serves as template for the
synthesize of the (+) strand RNA.
Figure 4: Replication in ssRNA phages
Replication of the single-stranded phage
genome occurs through production of two
replicative intermediates, RI-1 and RI-2.
• First, the (–) strand RNA is synthesized 5′ to 3′ antiparallel and complementary to the (+)
sense template strand by replicase, in a multi- branched structure.
• The (–) strand RNA then serves as template for
formation of new (+) strand genomic RNA. This
is the only role for the (–) strands. Newly
replicated (+) strands can be recycled in
replication, translated to yield the capsid
proteins, or encapsidated in the formation of
progeny phages.
• The inset shows the activation of the replicase
protein (REP) by associating with host proteins:
for MS2 two elongation factors (EFTs and EFTu)
and the ribosomal S1 protein.
• Replicase is an RNA-templated RNA polymerase, synthesizing both plus (+) and minus (–) strands
of phage RNA 5′ to 3′ through specificity of the
replicase for the 3′ end of both template
strands.
Assembly and exit in ssRNA phages
• Assembly and exit: ssRNA phages assembly
occurs by spontaneous accumulation,
whereby protein ‘A’ (maturase) forms
association with (+) strand RNA.
• The association is surrounded by coat (capsid)
proteins forming an icosahedral-shaped shell.
• Exit: Progeny virions exit cells by lysis,
following accumulation of about 10,000
progeny virions.
Figure 5: Replication cycle in ssRNA phages
.
- Attachment along length of sex
(F) pilus - Entry of RNA genome
- Translation: Host ribosomes attach to phage RNA (+) strand for synthesis of some coat protein and replicase.
4/5. Replication of RNA: Replicase binds to (+) strand and synthesises (-) strands. (Replicase switches off coat protein (CP) gene early to allow replication). (-) strand acts as template for (+) strand synthesis. A gene translated during nascent (+) strand synthesis. Translation of coat protein gene continues from (+) strands.
- Assembly of Progeny virions:
‘A’ protein associates with RNA (+) strand and coat protein assembles around it to form an icosahedral shell. 7. Exit: Lysis occurs after ab
dsRNA Phages taxonomy
• Members belong to the family Cystoviridae, derived
from the Greek word Kystic meaning ‘’bladder sac’’
dsRNA phages RNA
• They contain a dsRNA which is segmented and
packaged in a polyhedral linear core with a lipid
containing envelope.
