Φ6 (

Phi Phi ( ; uppercase Φ, lowercase φ or ϕ; ''pheî'' ; Modern Greek: ''fi'' ) is the twenty-first letter of the Greek alphabet. In Archaic and Classical Greek (c. 9th to 4th century BC), it represented an aspirated voiceless bilabial plos ...

6) is the best-studied

bacteriophage A bacteriophage (), also known informally as a phage (), is a virus that infects and replicates within bacteria. The term is derived . Bacteriophages are composed of proteins that Capsid, encapsulate a DNA or RNA genome, and may have structu ...

of the

virus A virus is a submicroscopic infectious agent that replicates only inside the living Cell (biology), cells of an organism. Viruses infect all life forms, from animals and plants to microorganisms, including bacteria and archaea. Viruses are ...

family Family (from ) is a Social group, group of people related either by consanguinity (by recognized birth) or Affinity (law), affinity (by marriage or other relationship). It forms the basis for social order. Ideally, families offer predictabili ...

'' Cystoviridae''. It infects ''

Pseudomonas ''Pseudomonas'' is a genus of Gram-negative bacteria belonging to the family Pseudomonadaceae in the class Gammaproteobacteria. The 348 members of the genus demonstrate a great deal of metabolic diversity and consequently are able to colonize a ...

'' bacteria (typically plant-pathogenic '' P. syringae''). It has a three-part, segmented, double-stranded

RNA Ribonucleic acid (RNA) is a polymeric molecule that is essential for most biological functions, either by performing the function itself (non-coding RNA) or by forming a template for the production of proteins (messenger RNA). RNA and deoxyrib ...

genome A genome is all the genetic information of an organism. It consists of nucleotide sequences of DNA (or RNA in RNA viruses). The nuclear genome includes protein-coding genes and non-coding genes, other functional regions of the genome such as ...

, totalling ~13.5 kb in length. Φ6 and its relatives have a

lipid membrane The lipid bilayer (or phospholipid bilayer) is a thin polar membrane made of two layers of lipid molecules. These membranes form a continuous barrier around all cells. The cell membranes of almost all organisms and many viruses are made of a l ...

around their nucleo

capsid A capsid is the protein shell of a virus, enclosing its genetic material. It consists of several oligomeric (repeating) structural subunits made of protein called protomers. The observable 3-dimensional morphological subunits, which may or m ...

, a rare trait among bacteriophages. It is a

lytic The lytic cycle ( ) is one of the two cycles of viral reproduction (referring to bacterial viruses or bacteriophages), the other being the lysogenic cycle. The lytic cycle results in the destruction of the infected cell and its membrane. Bact ...

phage A bacteriophage (), also known informally as a phage (), is a virus that infects and replicates within bacteria. The term is derived . Bacteriophages are composed of proteins that encapsulate a DNA or RNA genome, and may have structures tha ...

, though under certain circumstances has been observed to display a delay in lysis which may be described as a "carrier state".

Proteins

The genome of Φ6 codes for 12

proteins Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, re ...

. P1 is a major

protein which is responsible of forming the skeleton of the

polymerase In biochemistry, a polymerase is an enzyme (Enzyme Commission number, EC 2.7.7.6/7/19/48/49) that synthesizes long chains of polymers or nucleic acids. DNA polymerase and RNA polymerase are used to assemble DNA and RNA molecules, respectively, by ...

complex. In the interior of the shell formed by P1 is the P2 viral replicase and transcriptase protein. The spikes binding to receptors on the Φ6 virion are formed by the protein P3. P4 is a nucleoside-triphosphatase which is required for the genome packaging and transcription. P5 is a lytic enzyme. The spike protein P3 is anchored to a fusogenic

envelope An envelope is a common packaging item, usually made of thin, flat material. It is designed to contain a flat object, such as a letter (message), letter or Greeting card, card. Traditional envelopes are made from sheets of paper cut to one o ...

protein in P6. P7 is a minor capsid protein, P8 is responsible of forming the nucleocapsid surface shell and P9 is a major envelope protein. P12 is a non-structural morphogenic protein shown to be a part of the envelope assembly. P10 and P13 are proteins coding genes that are associated with the viral envelope and P14 is a non-structural protein.

Life cycle

Φ6 typically attaches to the Type IV

pilus A pilus (Latin for 'hair'; : pili) is a hair-like cell-surface appendage found on many bacteria and archaea. The terms ''pilus'' and '' fimbria'' (Latin for 'fringe'; plural: ''fimbriae'') can be used interchangeably, although some researchers ...

of '' P. syringae'' with its attachment protein, P3. It is thought that the cell then retracts its pilus, pulling the phage toward the bacterium. Fusion of the

viral envelope A viral envelope is the outermost layer of many types of viruses. It protects the genetic material in their life cycle when traveling between host cells. Not all viruses have envelopes. A viral envelope protein or E protein is a protein in the en ...

with the

bacteria Bacteria (; : bacterium) are ubiquitous, mostly free-living organisms often consisting of one Cell (biology), biological cell. They constitute a large domain (biology), domain of Prokaryote, prokaryotic microorganisms. Typically a few micr ...

l outer membrane is facilitated by the phage protein, P6. The muralytic (

peptidoglycan Peptidoglycan or murein is a unique large macromolecule, a polysaccharide, consisting of sugars and amino acids that forms a mesh-like layer (sacculus) that surrounds the bacterial cytoplasmic membrane. The sugar component consists of alternating ...

-digesting) enzyme, P5, then digests a portion of the

cell wall A cell wall is a structural layer that surrounds some Cell type, cell types, found immediately outside the cell membrane. It can be tough, flexible, and sometimes rigid. Primarily, it provides the cell with structural support, shape, protection, ...

, and the nucleocapsid enters the cell coated with the bacterial outer membrane. ODR

A copy of the sense strand of the large genome segment (6374 bases) is then synthesized ( transcription) on the vertices of the

, with the RNA-dependent

RNA polymerase In molecular biology, RNA polymerase (abbreviated RNAP or RNApol), or more specifically DNA-directed/dependent RNA polymerase (DdRP), is an enzyme that catalyzes the chemical reactions that synthesize RNA from a DNA template. Using the e ...

, P2, and released into the host cell

cytosol The cytosol, also known as cytoplasmic matrix or groundplasm, is one of the liquids found inside cells ( intracellular fluid (ICF)). It is separated into compartments by membranes. For example, the mitochondrial matrix separates the mitochondri ...

. The four proteins translated from the large segment spontaneously assemble into procapsids, which then package a large segment sense strand, polymerizing its complement during entry through the P2

-containing vertices. While the large segment is being translated (expressed) and synthesized (replicated), the parental phage releases copies of the sense strands of the medium segment (4061 bases) and small segment (2948 bases) into the

. They are translated, and packaged into the procapsids in order: medium then small. The filled capsids are then coated with the nucleocapsid protein P8, and then outer membrane proteins somehow attract bacterial inner membrane, which then envelopes the nucleocapsid. The lytic protein, P5, is contained between the P8 nucleocapsid shell and the viral envelope. The completed phage progeny remain in the cytosol until sufficient levels of the lytic protein P5 degrade the host cell wall. The cytosol then bursts forth, disrupting the outer membrane, releasing the phage. The bacterium is killed by this

lysis Lysis ( ; from Greek 'loosening') is the breaking down of the membrane of a cell, often by viral, enzymic, or osmotic (that is, "lytic" ) mechanisms that compromise its integrity. A fluid containing the contents of lysed cells is called a ...

RNA-dependent RNA polymerase

RNA-dependent RNA polymerase RNA-dependent RNA polymerase (RdRp) or RNA replicase is an enzyme that catalyzes the self-replication, replication of RNA from an RNA template. Specifically, it catalyzes synthesis of the RNA strand Complementarity (molecular biology), compleme ...

s (RdRPs) are critical components in the life cycle of double-stranded RNA (dsRNA) viruses. However, it is not fully understood how these important

enzyme An enzyme () is a protein that acts as a biological catalyst by accelerating chemical reactions. The molecules upon which enzymes may act are called substrate (chemistry), substrates, and the enzyme converts the substrates into different mol ...

s function during viral replication. Expression and characterization of the purified recombinant RdRP of Φ6 is the first direct demonstration of RdRP activity catalyzed by a single

protein Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residue (biochemistry), residues. Proteins perform a vast array of functions within organisms, including Enzyme catalysis, catalysing metab ...

from a dsRNA virus. The recombinant Φ6 RdRP is highly active ''in vitro'', possesses RNA replication and transcription activities, and is capable of using both homologous and heterologous

molecule A molecule is a group of two or more atoms that are held together by Force, attractive forces known as chemical bonds; depending on context, the term may or may not include ions that satisfy this criterion. In quantum physics, organic chemi ...

s as templates. The crystal structure of the Φ6 polymerase, solved in complex with a number of ligands, provides insights towards understanding the mechanism of primer-independent initiation of RNA-dependent RNA polymerization. This RNA polymerase appears to operate without a

sigma factor A sigma factor (σ factor or specificity factor) is a protein needed for initiation of Transcription (biology), transcription in bacteria. It is a bacterial transcription initiation factor that enables specific binding of RNA polymerase (RNAP) to g ...

/subunit. The purified Φ6 RdRP displays processive elongation ''in vitro'' and self-assembles along with polymerase complex proteins into subviral particles that are fully functional.

Research

Φ6 has been studied as a model to understand how segmented RNA viruses package their genomes, its structure has been studied by scientists interested in

lipid Lipids are a broad group of organic compounds which include fats, waxes, sterols, fat-soluble vitamins (such as vitamins A, D, E and K), monoglycerides, diglycerides, phospholipids, and others. The functions of lipids include storing ...

-containing bacteriophages, and it has been used as a model organism to test

evolutionary Evolution is the change in the heritable characteristics of biological populations over successive generations. It occurs when evolutionary processes such as natural selection and genetic drift act on genetic variation, resulting in certa ...

theory such as

Muller's ratchet In evolutionary genetics, Muller's ratchet (named after Hermann Joseph Muller, by analogy with a ratchet effect) is a process which, in the absence of recombination (especially in an asexual population), results in an accumulation of irreversibl ...

. Phage Φ6 has been used extensively in additional phage experimental evolution studies.

References

External links