Bacteriophage P1 – Structure and Life Cycle.

P1 is a temperate bacteriophage (phage) that infects Escherichia coli and a some other bacteria. When undergoing a lysogenic cycle the phage genome exists as a autonomous plasmid, that is maintained at low copy number, in the bacterium. It is not integrated in to host genome.

Structure and Genome:

P1 has an icosahedral “head” containing the phage DNA attached to a 220nm long tube, contractile tail or shealth, and base plate with six tail fibers.

In a same virion population, 80% of virions have a head diameter of 85nm, while the other 20% have a diameter of 65nm.

Genome :

The genome of P1 Phage is linear double stranded DNA Which is moderately large, about 94 Kbp. The genome is longer, about 120Kbs, than the actual length when in viral particle as it is created by cutting an appropriately sized fragment from a concatemeric DNA chain having multiple copies of the genome. Due to this the ends of the DNA molecule are identical and are referred to as being “terminally redundant”. It has large, about 15 kbp, terminal redundancy. 

Population of phages exhibit Circular Permutation. Means that a given linear molecule can start at any location on the circular genome.  It is another consequence of DNA being cut out of a concatemer.

Though, in the viral particle it is in the form of a linear double stranded DNA molecule, once inserted into the host it circularizes because of the its large terminal redundancy mentioned before and replicates as a plasmid.

The genome contains two origins of replication, oriR which replicates it during the lysogenic cycle and oriL which replicates it during the lytic stage. The genome of P1 has 112 protein coding and 5 untranslated genes. It even encodes 3 of its own tRNAs which are expressed in the lytic stage.

 

The Life Cycle of P1 Phage

Temperate phage, such as P1, have the ability to exist within the bacterial cell they infect in two different ways. In lysogeny, P1 can exist within a bacterial cell as a circular DNA in that it exists by replicating as if it were a plasmid and does not cause cell death. Alternatively, in its lytic phase, P1 can promote cell lysis during growth resulting in host cell death.

During lysogeny new phage particles are not produced. In contrast, during lytic growth many new phage particles are assembled and released from the cell. By alternating between these two modes of infection, P1 can survive during extreme nutritional conditions that may be imposed upon the bacterial host in which it exists.

1. Absorption, Injection and protection of the genome.

P1 absorbs to the receptors on the host cells – terminal glucose on the lipopolysaccharide present on the outer surface of the outer membrane of the host cell. P1 can contract its tail and inject its DNA into a wide range of species but cannot replicate in these species. 

Once inside the cell, P1 DNA circularizes by homologous recombination because these DNA when packed it is packed by Head full Mechanism. This can be done either by host or phage recombination system. In head full mechanism it requires a certain amount or length of genes in the sequence to get packed. So when phage DNA is packed, Some extra genes about 107% to 112% of the phage genome is incorporated in to the capsid. This ensures that the minimum Kb of gene required to get packed is available by ensuring between 7% to 12% homology at the end; a property called Terminal Redundancy. The terminal redundancy is used to circularize the genome.

 Sequence repeated in the both terminal of the genome sequence is called Terminal Redundancy.

 

 2. P1 DNA Replication and Phage Assembly. (Lytic Cycle)

The P1 plasmid has a separate origin of replication (oriL) that is activated during the lytic cycle. Like Lambda, early P1 replication takes place by the theta mode of replication. Later in infection, P1 switch to rolling circle replication. Rolling circle replication produces concatemers for packaging into phage heads. 

Polymeric Structure of complete genome (Multiple repeats of a nucleotide sequence) end to end is known as concatemer.

At approx 45 minutes after the infection, the cells are filled with concatemers of phage DNA, assembled phage heads, and assembled phage tails. Now complete phage must take place. A protein made from phage genome recognizes a site on the concatomers of phage DNA called the pac site. The protein cuts the DNA, making a double-stranded end. This end is inserted into a phage head. The DNA continues to be pushed inside the head until the head is full, a process called head-full packaging.

Once the first phage head is full, another empty phage starts packaging. Experiments shows five head-full of DNA can be packaged sequentially from a single pac site at 100% efficiency. An additional five head-fulls of DNA can be packed although the efficiency gradually decreases to only 5%. While each phage head contains the same genes, the gene order changes. This is known as circular permutation of the genome. 

Circularly permuted means that the order of the genes on each DNA molecule is different but the every DNA molecule contains the same genes.

P1 genome are both circularly permuted and terminally redundant. 

Terminal redundancy means that the same sequences are present on the both end of one DNA molecule.

A- Complete genome, B- Concatemer, C- Shows how concatemer is cut and packed in the head. Each shows circularly permutation and terminally redundancy. 

 

After the head is full of DNA, a double stranded cut is made and a tail is attached. This part of phage development is very much an assembly line. Once the complete virions are assembled, the host cell is lysed, releasing the viral particles.

3.The Location of the P1 Prophage in a lysogen (Lysogenic Cycle)

Prophages can be physically located in one or two places in a lysogen. In case of Lambda, the phage genome is recombined into the bacterial chromosome. P1 contains an origin for DNA replication and once the phage genome is converted to circular, double-stranded DNA, and is maintained in the cytoplasm as a stably inherited extra-chromosomal piece of DNA or plasmid. 

In P1, no integration of DNA, no int/xis System for recombination, So coordinated DNA replication along with the host DNA occurs. Coordinated DNA replication occurs, in order to maintain its population in all daughter cells. If not, when multiplied by binary fission only one daughter cell will posses the phage DNA and another daughter cell does not. 

4. P1 Transducing Particles

One unusual aspect of P1 development is the formation of transducing particles or phage particles that contain chromosomal DNA instead of phage DNA. 

E-Coli chromosomes contains many pseudopac sites or sites that can be used ti initiate packaging of host chromosomal DNA into maturing phage. Theses pseudopac sites are used much less frequently than the phage pac sites but they are used; The resulting phage carry random pieces of the chromosome in place of phage genomes.

The ability to package any piece of chromosomal DNA instead of phage DNA makes P1 a generalized transducing gene. 

More about Transduction click Here

 

 

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