Infection begins when G protein binds to
lipopolysaccharides on the bacterial host cell surface. H protein (or the DNA Pilot Protein) pilots the viral genome through the bacterial membrane of
E. coli bacteria most likely via a predicted N-terminal
transmembrane domain helix. However, it has become apparent that H protein is a multifunctional protein. This is the only viral
capsid protein of ΦX174 to lack a crystal structure for a couple of reasons. It has low aromatic content and high
glycine content, making the protein structure very flexible and in addition, individual hydrogen atoms (the R group for glycines) are difficult to detect in protein crystallography. Additionally, H protein induces
lysis of the bacterial host at high concentrations as the predicted N-terminal transmembrane helix easily pokes holes through the bacterial wall. By
bioinformatics, this protein contains four predicted
coiled-coil domains which has a significant homology to known transcription factors. Additionally, it was determined that
de novo H protein was required for optimal synthesis of other viral proteins. Mutations in H protein that prevent viral incorporation, can be overcome when excess amounts of protein B, the internal scaffolding protein, are supplied. The DNA is ejected through a hydrophilic channel at the 5-fold vertex. It is understood that H protein resides in this area but experimental evidence has not verified its exact location. Once inside the host bacterium, replication of the [+] ssDNA genome proceeds via
negative sense DNA intermediate. This is done as the phage genome supercoils and the secondary structure formed by such supercoiling attracts a
primosome protein complex. This translocates once around the genome and synthesizes a [−]ssDNA from the positive original genome. [+]ssDNA genomes to package into viruses are created from this by a rolling circle mechanism. This is the mechanism by which the double stranded supercoiled genome is nicked on the positive strand by a virus-encoded A protein, also attracting a bacterial
DNA polymerase (DNAP) to the site of cleavage. DNAP uses the negative strand as a template to make positive sense DNA. As it translocates around the genome it displaces the outer strand of already-synthesised DNA, which is immediately coated by
SSBP proteins. The A protein cleaves the complete genome every time it recognises the origin sequence. As D protein is the most abundant gene transcript, it is the most abundant protein in the viral procapsid. Similarly, gene transcripts for F, J, and G are more abundant than for H as the
stoichiometry for these structural proteins is 5:5:5:1. The primosomes are protein complexes which attach/bind the enzyme
helicase on the template. Primosomes gives RNA primers for DNA synthesis to strands.
Mutation rate The
mutation rate of phiX174 is estimated to be 1.0 × 10−6 substitutions per base per round of copying, a value that is consistent with Drake's rule (0.003 mutations per genome per round of copying in DNA-based microorganisms).
Recombination PhiX174 is able to undergo
genetic recombination. Based on recombination frequencies obtained in genetic crosses, a genetic map was constructed. Recombination in phi X174 is associated with high negative interference, i.e., a positive correlation (negative interference) of recombinational events (see wikipedia
crossover interference). == Phylogenetics and diversity ==