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Bacteriophage- Structure, Classification, Application
- The virus that infects only bacterial cells (bacteria eater)
- Known as naturally abundant obligate intracellular parasites
- Niche- present where bacteria or archaea reside
- Diversity is more than the number of bacteria in nature
- Small size causes it to beyond the limits of light microscope resolution
- Smallest bacteriophage: 20 nanometers in diameter, largest bacteriophage: 500 nanometers in diameter
Structure of Bacteriophage
Each bacteriophage consists of the nucleic acid genome that enclosed in a protein coat, known as a capsid or surrounded by a lipid membrane called an envelope. Its capsid consists of repeating protein subunits known as protomers and it is important in packaging the phage genome and transfer of genome into a host cell. Bacteriophage contains only one type of nucleic acid genome, which is either RNA or DNA, but not both. Its genomes can also exist as single-stranded or double-stranded DNA or RNA and they can be also in circular or linear form. In general, the bacteriophage is structurally complex, containing head, tails, collar and other components. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4275845/
Classification of Bacteriophage
In 1967, Bradley proposed the classification of bacteriophage-based on six morphological groups:
- Bacteriophage with hexagonal head and tail with contractile sheath
- Bacteriophage with a hexagonal head and long, flexible tail
- Bacteriophage with a hexagonal head and short, non-contractile tail
- Bacteriophage with only hexagonal head in symmetry with large capsomere on it
- Bacteriophage with a simple regular hexagonal head
- Bacteriophage with no head but with long flexible filament virion
However, The International Committee on Taxonomy of Viruses (ICTV), as the only organization that developed and authorized on the virus taxonomy, had classified the phages based on the nature of their nucleic acid, morphology and physicochemical properties of their virion particles. Currently, ICTV has classified the bacteriophages into nine orders, 48 families with 32 subfamilies, and 317 genera. The types of the nucleic acid genome in the phages can be varied, most of them contain double-stranded DNA, while others can be single-stranded DNA, single-stranded RNA or double-stranded RNA.
By morphology, phages can be tailed phages, polyhedral or cubic, filamentous or pleomorphic phages.
I. Tailed phages (equivalents to 96% of the phages discovered)
-classified as order Caudovirales which further divided into three families: Myoviridae, Siphoviridae, and Podoviridae.
Myoviridae phages- with icosahedral head, contractile tails, double-stranded DNA (dsDNA)
Example: phage T4, phage P1
Siphoviridae phages -with icosahedral head, long and non-contractile tails, double-stranded DNA (dsDNA)
Example: phage λ, Lactococcus phage C2
Podoviridae phages- have the icosahedral head, short tails, double-stranded DNA (dsDNA)
Example: phage T7, phage P22
II. Polyhedral or cubic phages
-classified into Microviridae, Corticoviridae, Tectiviridae, Leviviridae, and Cystoviridae.
Microviridae phages- icosahedral head, virion size 27 nm, with 12 capsomers, single-stranded DNA (ssDNA)
Example: phage φX174
Corticoviridae phages- no envelope, 63 nm in size, complex capsid, lipids, dsDNA
Example: phage PM2
Tectiviridae phages- no envelope, 60 nm, flexible lipid vesicle, pseudo-tail, dsDNA
Example: phage PRD1
Leviviridae phages- no envelope, 23 nm, poliovirus-like, ssRNA
Example: phage MS2
Cystoviridae phages-with enveloped, icosahedral head, 70-80 nm, lipids, dsRNA
Example: Pseudomonas ɸ6
III. Filamentous phages
-Made up of three families known as Inoviridae, Lipothrixviridae, and Rudiviridae.
Inoviridae phages- no envelope, long flexible filament or short straight rods, ssDNA
Example: phage M13
Lipothrixviridae phages- enveloped, rod-shaped capsid, lipids, dsDNA
Example: phage TTV1
Rudiviridae phages- Straight uncoated rods, TMV-like, dsDNA
Example: phage SIRV-1
IV. Pleomorphic phages
-phages that contain dsDNA and classified into several families: Plasmaviridae, Fuselloviridae, Guttaviridae, Bicaudaviridae, Ampullaviridae, and Globuloviridae.
Plasmaviridae phages- enveloped, 80nm, with no capsid, lipids
Example: phage MVL2
Fuselloviridae phages- enveloped, tapered capsid with short spikes end, lipids
Example: phage SSV1
Guttaviridae phages- droplet-shaped
Example: phage SNDV
Bicaudaviridae phages- Lemon-shaped virions, 120X 80 nm, long tails
Example: phage ATV
Ampullaviridae phages- enveloped, bottle-shaped virion, 230 nm in length
Example: phage ABV
Globuloviridae phages- spherical virions, 70-100 nm, lipid-containing envelope
Example: phage PSV
Phage therapy is now an alternative route to combat and control the prevalence of bacterial infections including some antibiotics-resistance bacteria. The main issue concerned for antibiotic therapy is the occurrence of antibiotics-resistance microorganisms. Hence, phage therapy had been applied to overcome this problem. By comparing phage therapy and antibiotic therapy, phage therapy has more advantages as phages are naturally-occurring products that bring minimal impact to our environment.
As an example, it was found that TM4 phage is effective to kill extracellular Mycobacterium avium and Mycobacterium tuberculosis when it was delivered through Mycobacterium smegmatis. The result showed a significant decrease in the number of viable bacteria after four days. Hence, it is concluded that this method of delivery should be investigated more as it can be useful in the phage therapy treatment of bacterial.
Phage therapy can also be used to control chronic infection. There was a case documented in 2016 at Eliava Phage Therapy Center in which a phage treatment was being tested on a 16-years-old boy with Netherton syndrome (NS) and it was surprising that the phages have somehow reduced the symptoms brought by Netherton syndrome. After the phage treatment, no side effect or allergy was being observed on the boy, who had allergies to most of the antibiotics.
Application of Phage Display Technology
Phage display technology was first being introduced by Smith in 1985, in which he discovered that when a recombinant protein is incorporated into a phage, the foreign amino acid sequence was susceptible to bind to an antibody. After the discovery of phage display technology, bacteriophage then becomes an interest in research and phage therapy is slowly being developed.
Phage display technology is a technique which involves the introduction of foreign nucleotide sequence into the genome of either capsid protein or tail protein of bacteriophage, which during the expression of the capsid or the tail gene, the foreign nucleotide sequence will be expressed together, results that the foreign protein displays onto the surface of the capsid or the tail of the bacteriophage.
Phage display technology is widely applicable, especially in the immunological and medical field. A study had conducted using the phage display technique on mice with BT-474 tumor cells to select the suitable peptide agent to image the therapy-resistance BT-474 human breast cancer xenografts. The in vivo data of this study proved that In-DOTA-51 is the potential to be used for imaging BT474 human breast cancer tumor xenografts but it was suggested that more research works are still needed to investigate on the specificity of this peptide.
By using biopanning, ELISA method and competitive inhibition assay, a study aimed to screen for a novel peptide specific to CD44v, an isoform of CD44 with variable exons. This study had proved that the specificity and high affinity of CV-1 phage to CD44v3-v10 protein, gastric cancer cells, and tissues, enabled it in the detection of CD44v-positive stomach tumors. Another recent study had been done to identify whether the lambda display phage (LDP) with capsid head protein D had the capability to act as the carrier for peptide epitopes. It was a concern that whether the lambda phage can survive in the intestinal tract as the conditions in the digestive tract were harsh for the survival of phage which involved in oral vaccine delivery system. The successful induction of antibody responses when the lambda D gene is introduced into LDP indicated that the D protein provides T cell epitopes which gave a positive result on inducing the mucosal immune responses.