Viruses of Archaea and Bacteria
A virus is a genetic element which can’t replicate independently of a living (host) cell. Virology is the study of viruses. A virus particle/virion is an extracellular form of a virus. Virions exist outside the host and facilitate transmission between host cells. They contain the nucleic acid genome surrounded by a protein coat and in some cases other layers.
Phases of viral replication:
attachment/adsorption of the virus to a susceptible host cell
entry/penetration of the virion or its nucleic acid
viral nucleic acid and protein synthesis by cell metabolism redirected by the virus
capsid assembly and packaging of viral genomes into new virions (maturation)
release of mature virions from host cell
Viral replication is typically characterised by a one-step growth curve. Latent period = eclipse and maturation. Burst size = number of virions released.
Phages are used as model organisms for viral growth. In a lab, a cell-phage mixture is poured onto a solidified nutrient agar plate and the mixture is left to solidify, creating an agar ‘sandwich’. The plate is then left to incubate allowing bacterial growth and phage replication.
Bacteriophages are very diverse, and it’s very difficult to isolate the same phages again. The best-studied phages infect enteric bacteria such as E.coli and Salmonella enterica. It’s thought that phages could be used as an alternative to antibiotics in some cases in the future. Most phages contain dsDNA genomes and most are naked, the latter being due to most bacterial hosts not having an exposed lipid membrane. They are structurally complex with heads, tails and other components. Leg-like structures found in some phages allow binding to receptors. It’s estimated there are around 10^ 31 bacteriophages. The bacteriophage-bacteria relationship is the oldest predator-prey interaction and bacteriophages are a major driving force for bacterial evolution.
Attachment of a virion to a host cell is highly specific due to requiring complementary receptors on the host cell surface and its infecting virus. Host cell receptors carry out normal cell functions eg bacteriophage T4 binds iron transport proteins. Attachment results in changes to both the virus and host cell surface, allowing penetration to occur. A permissive cell is a host cell which allows the complete replication cycle of a virus to occur.
T4 is a virus of E. coli and it has one of the most complex penetration mechanisms. T4 virions attach to cells using tail fibres which interact with polysaccharides on the E. coli cell envelope. The tail fibres retract and the tail core makes contact with the E.coli cell wall. Lysozyme-like enzyme forms a small pore in the peptidoglycan. The tail sheath contracts and viral DNA passes into the cytoplasm.
T4 has a dsDNA genome which is circularly permuted (altered) and terminally redundant. Both of these factors require genome packaging. Many eukaryotes possess mechanisms to diminish viral infection eg immune defence mechanisms and RNAi. Prokaryotes have similar mechanisms such as CRISPR which is similar to RNA interference. It’s a DNA destruction system only effective against double-stranded DNA viruses. Restriction endonucleases cleave DNA at specific sequences. The host’s own DNA is modified at restriction enzyme recognition sites to prevent cleavage of own DNA.
Viral mechanisms to evade bacterial restriction systems include chemical modification of viral DNA by glycosylation or methylation or producing proteins which inhibit host cell restriction system. T4 DNA contains the modified base 5-hydroxymethylcytosine meaning its DNA is resistant to almost all known restriction enzymes.
Early and middle proteins are enzymes required for DNA replication and transcription. Late proteins are head and tail proteins and enzymes needed to liberate mature phage particles. The T4 genome can be divided into three parts: early, middle and late proteins. T4 early proteins include the enzyme for synthesis and glucosylation of T4 base hydroxymethylcytosine, enzymes in the T4 replisome and proteins which modify host RNA polymerase. T4 middle proteins are additional proteins which modify host RNA polymerase and viral proteins. T4 late proteins are typically structural components eg proteins of virus coat, and are synthesised in larger amounts. To package the T4 genome, the precursor of the phage head is assembled as is the packaging motor. Double-stranded DNA is pumped into the head under pressure using ATP. The tail, tail fibres and other components are then added.
Virulent mode = viruses lyse host cells after infection.
Temperate mode = viruses replicate their genomes in tandem with host genome without killing host. Can undergo stable genetic relationship within the host but can also kill cells through lytic cycle.
Lysogeny = state where most viral genes aren’t expressed and virus genome (prophage) is replicated in synchrony with the host chromosome. Lysogenic viruses may revert to the lytic pathway and begin to produce virions under certain conditions.
Lysogen = bacteria containing a prophage.
Bacteriophage lambda has a linear, dsDNA genome. Complementary, single stranded regions 12 nucleotides long are found at the 5’ terminus of each strand. Upon penetration, DNA ends the base pair, forming the cos site, and the DNA ligates forming a double stranded circle. When lambda is lysogenic, its DNA integrates into E. coli chromosome at the lambda attachment site. When lambda enters the lytic pathway it synthesises long linear concatemers of DNA by rolling circle replication.
Regulation of lytic vs lysogenic events in lambda is controlled by a complex genetic switch. Key elements are repressor proteins cl and Cro.
cl protein causes repression of lambda lytic events, activating lysogeny. The Cro repressor controls activation of lytic events by repressing lysogenic genes. Bacterial host physiology is key to the balance of the two repressor proteins in the cell.
Transduction is the transfer of DNA from one cell to another by a bacteriophage due to mispackaging of the bacteriophage genome, driving bacterial evolution. Generalised transduction is where DNA from any portion of the host genome is packaged inside the virion. Specialised transduction is where DNA from a specific region of the host chromosome is integrated directly into the viral genome.
Most viruses which infect archaea resemble those which infect enteric bacteria. Only double stranded DNA viruses of archaea have been identified so far, however this is a very understudied area.