Viruses of Archaea and Bacteria

Virus

A genetic element that can’t replicate independently of a living host cell

Virion

The extracellular form of a virus containing the nucleic acid genome surrounded by a protein coat and sometimes other layers.

Phases of Viral Replication

attachment, entry, synthesis, assembly and release

How is viral replication typically characterised?

One step growth curve

latent period

eclipse and maturation

Burst Size

The number of virions released during viral replication.

Bacteriophages

Viruses which infect bacteria

best studied phages

phages which infect enteric bacteria eg E.coli and Salmonella enterica

Why are most phages naked rather than enveloped?

as most bacterial hosts don’t have an exposed lipid membrane

What happens as a result of viral attachment?

changes to both viral and host cell surface allowing penetration to occur

phage leg-like structures (not found in all)

allow binding to receptor

Permissive Cell

A host cell that allows the complete replication cycle of a virus.

T4 Phage

virus which infects E. coli

T4 attachment

attach to cells using tail fibres which interact with polysaccharides on the E. coli cell envelope.

T4 penetration

tail fibres retract and tail core makes contact with E. coli cell wall. Lysozyme-like enzymes form pores in peptidoglycan. Tail sheath contracts and viral DNA enters cytoplasm

T4 genome

circularly permuted (altered) and terminally redundant dsDNA genome which requires genome packaging

CRISPR

DNA destruction system only effective against dsDNA. Restriction endonucleases cleave DNA at NGG sequences and host DNA modified at recognition sites to prevent cleavage

viral mechanisms to evade bacterial restriction systems

chemical modification of viral DNA by glycosylation/methylation or produce proteins which inhibit host cell restriction system

How does T4 evade bacterial restriction systems?

DNA contains modified base 5-hydroxymethylcytosine - its DNA is resistant to almost all known restriction enzymes

early and middle proteins

enzymes required for DNA replication and transcription

late proteins

head and tail proteins and enzymes needed to liberate mature phage particles

T4 early proteins

eg enzyme for synthesis and glycosylation of 5 HM cytosine, enzymes in replisome and proteins which modify host RNA polymerase

T4 middle proteins

additional proteins which modify host RNA polymerase and viral proteins

T4 late proteins

structural components eg virus coat proteins. Synthesised in larger amounts

How is the T4 genome packaged?

Phage head precursor and packaging motor assembled. dsDNA pumped into the head under pressure using ATP. Tail, tail fibres and other components are added

virulent mode

viruses lyse host cells after infection

temperate mode

viruses replicate their genomes in tandem with host genome without killing host

Lysogeny

Most viral genes aren’t expressed. Viral genome replicated in synchrony with the host chromosome.

lysogen

bacteria containing prophage

Bacteriophage Lambda genome

Linear dsDNA. Complementary, single stranded regions 12 nucleotides long are found at the 5’ terminus of each strand

What happens upon bacteriophage lambda penetration of host cell?

DNA ends undergo base pairing forming cos site. DNA ligates to form double stranded circle

lysogenic bacteriophage lambda

DNA integrates into E. coli chromosome at the lambda attachment site

What happens 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

controlled by a complex genetic switch. Key elements are repressor proteins cl and Cro.

cl protein

causes repression of lambda lytic events, activating lysogeny

Cro repressor protein

controls activation of lytic events by repressing lysogenic genes

Transduction

Transfer of DNA from one cell to another by a bacteriophage, due to mispackaging of the bacteriophage genome → bacterial evolution

generalised transduction

DNA from any portion of the host genome is packaged inside the virion

specialised transduction

DNA from a specific region of the host chromosome is integrated directly into the viral genome

viruses which infect archaea

• resemble phages of enteric bacteria

• only dsDNA viruses of archaea discovered so far