Bacteriophages

Viruses

• can persist by themselves
• but can replicate only by infecting a host cell and redirecting this cell to produce virus progeny.
• Viruses do not have a cellular structure!!
• Many viruses consist only of:
• genomic nucleic acid (DNA or RNA) and
• a protective protein coat or capsid
• The most common  phage genomes are double-stranded linear DNA, but you also find ss DNA, ds RNA and ss RNA.
• Genome size varies a lot between different types of phage- but in general- the more complex the genome, the more complex the phage.

Three basic phage structures observed are:

• tailless icosahedral phage - which consist of an icosahedral capsid but no tail
• icosahedral phage with tail
• filamentous phage

The life cycles of phages fit into 2 categories:

• lytic cycle - phage converts the metabolism of the infected cell to produce phage progeny. Phage that can only undergo lytic cycle is called virulent.
• lysogenic cycle - In lysogenic cycle phage DNA is usually inserted into the host chromosome where it is silent (no phage progeny produced) and but is passed on from cell generation to cell generation.  A phage that is integrated into the bacterial chromosome is called a prophage.

 

Lytic Cycle
The LYTIC cycle is somewhat variable but the general features are as follows:

• Adsorption
  In this step, the phage attaches to the cell wall of the bacterial cell. This is a highly specific interaction dependent upon the binding of the phage to specific receptors on the cell surface.
• Penetration
  In this step, the phage genome passes through the bacterial cell wall and enters the cytoplasm. This occurs within seconds of adsorption and in the vast majority of cases, the capsid and additional structural elements remain outside of the bacterial cell. Often and enzyme such as lysozyme, is used to weaken the cell wall so that the genome can pass through.
•   Conversion of bacterium into a phage-producing cell
  This step involves the shutdown of bacterial DNA and RNA synthesis which may even extend to DNA fragmentation and degradation. Nucleotides can then be used during viral DNA replication!.
•  Biosynthesis
  In this step, phage nucleic acids and proteins are synthesized.
• Phage DNA is replicated
• Phage DNA is transcribed into phage mRNA
• Phage mRNA is translated into phage proteins
• Transciption is regulated, i.e. not all bacteriophage DNA is transcribed at the same time. Phage mRNA and phage proteins are synthesized as needed.
• Early mRNAs:
• mRNAs which encode the enzymes required for the take over of a bacterium
• mRNAs which encode the proteins required for DNA replication
• mRNAs which encode proteins that are required for the transcription of Late mRNAs.
•  Late mRNAs
• mRNAs which encode phage structural proteins (capsid proteins, tail sheath proteins, etc.)
• mRNAs which encode proteins needed for packaging phage nucleic acid into newly formed capsids.
• mRNAs which encode proteins required for lysis of the bacterial cell.
• Morphogenesis
  In this step, the progeny phage are assembled. Structural proteins are assembled to form capsid, tail sheath, tail fibers, etc. In addition, the phage genome is packaged inside the newly-formed capsids.
•  Lysis
  In this step, the progeny phage are released then the bacterial cell undergoes lysis. Lysis is stimulated by the release of enzymes such as lysozyme or endolysin. Obviously these two enzymes are synthesized very late in the cycle of infection.

 The sequential events of the lytic cycle occur over a 20-60 second period depending upon the individual type of phage involved. This time period is termed: Burst Time

 Certain bacteriophage also have an optional lysogenic cycle. If environmental conditions are poor, the phage genome can survive by integrating into the bacterial chromosome.

What decides? Seems to be the concentration of an activator protein transcribed from lambda DNA this activator is designated cII:

• high concentration of cII ---- lysogenic cycle favored
• low concentration of cII ---- lytic cycle favored

But: concentration of activator not dependent on lambda but on host cell: concentration determined by amount of proteases present in the host cell which in turn depends on growth conditions:

•  favorable growth conditions ---- high amount of proteases ---- high degree of activator degradation ---- low levels of cII ----- lytic cycle
•  poor growth conditions ---- low amount of proteases ---- low degree of activator degradation ---- high levels of activator ----- lysogenic cycle

 Therefore, phage progeny only produced when cell has many resources.
When infecting resource-depleted bacterium, lambda can "hide" in cell
 
 

Lysogenic Cycle:

• 1. lambda integrase and lambda repressor cI synthesized due to activation of the transcription of their genes by cII.
• 2. cI repressor turns off phage transcription
• 3. integrase catalyzes integration of lambda DNA into bacterial chromosome via short sites of homology (site-specific recombination) ---- prophage

But prophage can be excised, because lambda cleverly uses host response system to potentially lethal situations:

• if host DNA damaged
• one reaction by host cell is to activate a protease
• protease also cleaves lambda repressor
• lambda DNA now transcibed including a gene for an enzyme that cuts prophage DNA from bacterial chromosome
• circularization of lambda DNA
• lytic cycle can start

 

 
 
 

 Term transduction refers to the packaging of bacterial DNA (chromosomal DNA) into the phage capsid. This occurs with only a small % of phage.
 

Specialized transduction
During induction, a prophage is excised from the bacterial chromosome and carries along with it some of the chromosomal DNA. In other words, there is an imprecise excision of the prophage DNA. The chromosomal DNA probably does not represent entire genes, but when this phage infects a bacterial cell, homologous recombination is a likely possibility. [very similar to formation of F' bacterium]
 

Generalized transduction
Bacterial DNA fragments are randomly (and accidentally) packaged into the capsid along with the phage genome. This occurs during the lytic cycle and is especially common in situations in which the host cell DNA is fragmented during conversion phase.
 

More on bacteriophages.

Activity

Quiz

Lodish, H., Berk, A., Zipursky, S.L., Matsudaira, P., Baltimore, D., Darnell, J., 2000, Molecular Cell Biology, 4th Ed., W.H. Freeman and Company, NY, New York.  ISBN 0-7167-3136-3.