Φ6 (

Phi Phi (; uppercase Φ, lowercase φ or ϕ; grc, ϕεῖ ''pheî'' ; Modern Greek: ''fi'' ) is the 21st letter of the Greek alphabet. In Archaic and Classical Greek (c. 9th century BC to 4th century BC), it represented an aspirated voicele ...

6) is the best-studied

bacteriophage A bacteriophage (), also known informally as a ''phage'' (), is a duplodnaviria virus that infects and replicates within bacteria and archaea. The term was derived from "bacteria" and the Greek φαγεῖν ('), meaning "to devour". Bacteri ...

of the

virus A virus is a submicroscopic infectious agent that replicates only inside the living cells of an organism. Viruses infect all life forms, from animals and plants to microorganisms, including bacteria and archaea. Since Dmitri Ivanovsky's 1 ...

family Family (from la, familia) is a Social group, group of people related either by consanguinity (by recognized birth) or Affinity (law), affinity (by marriage or other relationship). The purpose of the family is to maintain the well-being of its ...

Cystoviridae ''Cystovirus'' is a genus of double-stranded RNA viruses which infects bacteria. It is the only genus in the family ''Cystoviridae.'' The name of the group c''ysto'' derives from Greek ''kystis'' which means bladder or sack. There are seven spec ...

. It infects ''

Pseudomonas ''Pseudomonas'' is a genus of Gram-negative, Gammaproteobacteria, belonging to the family Pseudomonadaceae and containing 191 described species. The members of the genus demonstrate a great deal of metabolic diversity and consequently are able ...

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

double-stranded A base pair (bp) is a fundamental unit of double-stranded nucleic acids consisting of two nucleobases bound to each other by hydrogen bonds. They form the building blocks of the DNA double helix and contribute to the folded structure of both DN ...

RNA Ribonucleic acid (RNA) is a polymeric molecule essential in various biological roles in coding, decoding, regulation and expression of genes. RNA and deoxyribonucleic acid ( DNA) are nucleic acids. Along with lipids, proteins, and carbohydra ...

genome In the fields of molecular biology and genetics, 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 ge ...

, 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 are flat sheets that form a continuous barrier around all cells. The cell membranes of almost all organisms and many vir ...

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 may ...

, 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. Bacteri ...

phage A bacteriophage (), also known informally as a ''phage'' (), is a duplodnaviria virus that infects and replicates within bacteria and archaea. The term was derived from "bacteria" and the Greek φαγεῖν ('), meaning "to devour". Bacterio ...

, 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, respo ...

. P1 is a major

protein which is responsible of forming the skeleton of the

polymerase A polymerase is an enzyme ( 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 copying a DNA template strand using base- ...

complex. In the interior of the shell formed by P1 is the P2 viral replicase and transcriptase protein. The

spikes The SPIKES protocol is a method used in clinical medicine to break bad news to patients and families. As receiving bad news can cause distress and anxiety, clinicians need to deliver the news carefully. By using the SPIKES method for introducing a ...

binding to receptors on the Φ6 virion are formed by the protein P3. P4 is a

nucleoside-triphosphatase In enzymology, a nucleoside-triphosphatase (NTPase) () is an enzyme that catalyzes the chemical reaction :NTP + H2O \rightleftharpoons NDP + phosphate Thus, the two substrates of this enzyme are NTP and H2O, whereas its two products are NDP ...

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 or card. Traditional envelopes are made from sheets of paper cut to one of three shapes: a rhombus, a shor ...

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

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. Numerous human pathogenic viruses in circulation are encase ...

with the

bacteria Bacteria (; singular: bacterium) are ubiquitous, mostly free-living organisms often consisting of one biological cell. They constitute a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria were among ...

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 peptidoglycan layer outside the plasma membrane, the rigid cell wall (murein sacculus) characteristic of most ...

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

cell wall A cell wall is a structural layer surrounding some types of cells, just outside the cell membrane. It can be tough, flexible, and sometimes rigid. It provides the cell with both structural support and protection, and also acts as a filtering mech ...

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

A copy of the

sense strand In genetics, a sense strand, or coding strand, is the segment within double-stranded DNA that carries the translatable code in the 5′ to 3′ direction, and which is complementary to the antisense strand of DNA, or template strand, which doe ...

of the large genome segment (6374 bases) is then synthesized (

transcription Transcription refers to the process of converting sounds (voice, music etc.) into letters or musical notes, or producing a copy of something in another medium, including: Genetics * Transcription (biology), the copying of DNA into RNA, the fir ...

) 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 synthesizes RNA from a DNA template. Using the enzyme helicase, RNAP locally opens the ...

, 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 Translation is the communication of the meaning of a source-language text by means of an equivalent target-language text. The English language draws a terminological distinction (which does not exist in every language) between ''transla ...

from the large segment spontaneously assemble into procapsids, which then package a large segment sense strand, polymerizing its

complement A complement is something that completes something else. Complement may refer specifically to: The arts * Complement (music), an interval that, when added to another, spans an octave ** Aggregate complementation, the separation of pitch-class ...

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 ( ) 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 ''lysate''. In molecular bio ...

RNA-dependent RNA polymerase

RNA-dependent RNA polymerase RNA-dependent RNA polymerase (RdRp) or RNA replicase is an enzyme that catalyzes the replication of RNA from an RNA template. Specifically, it catalyzes synthesis of the RNA strand complementary to a given RNA template. This is in contrast to t ...

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 Enzymes () are proteins that act as biological catalysts by accelerating chemical reactions. The molecules upon which enzymes may act are called substrates, and the enzyme converts the substrates into different molecules known as products. A ...

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 residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, respo ...

from a

dsRNA virus Baltimore classification is a system used to classify viruses based on their manner of messenger RNA (mRNA) synthesis. By organizing viruses based on their manner of mRNA production, it is possible to study viruses that behave similarly as a dis ...

. The recombinant Φ6 RdRP is highly active ''in vitro'', possesses RNA replication and

activities, and is capable of using both homologous and

heterologous The term heterologous has several meanings in biology. Gene expression In cell biology and protein biochemistry, heterologous expression means that a protein is experimentally put into a cell that does not normally make (i.e., express) that ...

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

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 in bacteria. It is a bacterial transcription initiation factor that enables specific binding of RNA polymerase (RNAP) to gene promoters. It is ho ...

/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 ''Orthornavirae'' is a kingdom of viruses that have genomes made of ribonucleic acid (RNA), those genomes encoding an RNA-dependent RNA polymerase (RdRp). The RdRp is used to transcribe the viral RNA genome into messenger RNA (mRNA) and to repli ...

package their genomes, its structure has been studied by scientists interested in

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

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

evolutionary Evolution is change in the heredity, heritable Phenotypic trait, characteristics of biological populations over successive generations. These characteristics are the Gene expression, expressions of genes, which are passed on from parent to ...

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 through which, in the absence of recombination (especially in an asexual population), an accumulation of irreversible d ...

. Phage Φ6 has been used extensively in additional phage

experimental evolution Experimental evolution is the use of laboratory experiments or controlled field manipulations to explore evolutionary dynamics. Evolution may be observed in the laboratory as individuals/populations adapt to new environmental conditions by natura ...

studies.

References

External links