Mycobacterium virus D29

Mycobacterium virus D29
Virus classification
(unranked):	Virus
Realm:	Duplodnaviria
Kingdom:	Heunggongvirae
Phylum:	Uroviricota
Class:	Caudoviricetes
Order:	Caudovirales
Family:	Siphoviridae
Genus:	Fromanvirus
Species:	Mycobacterium virus D29

Last updated August 23, 2023

Mycobacterium virus D29 (D29) is a cluster A mycobacteriophage belonging to the Siphoviridae family of viruses, it was discovered in 1954 by S. Froman.^[1] D29 is notable for its ability to infect M. tuberculosis (the causative agent of tuberculosis). D29 is a double stranded DNA mycobacteriophage. It is a lytic phage, this means that D29 takes the lytic pathway of infection instead of the lysogenic pathway of infection. There are no human associated diseases associated with mycobacterium virus D29.^{[ citation needed ]}

Viral classification

Mycobacterium virus D29 is a Caudovirales virus belonging to the Siphoviridae family.^[2] These are commonly referred to as T5-Like Phages. Mycobacterium phage T5 was the first of the siphoviruses found with the structure consistent throughout the Siphoviridae viruses, which is why they are referred to as T5-Like Phages.^{[ citation needed ]}

Mycobacteriophage are broken up into 33 genomically distinct groups. 26 of these groups are known as clusters (A-Z) and there are 7 singleton groups. D29 belongs to cluster A, subcluster A2. Subcluster A2 has a unique distinction of being one of a few groups known to infect tuberculosis along with A3 and cluster K phages. This is important as it emphasizes these clusters and subclusters for potential importance in dealing with tuberculosis, as it is still one of the leading causes of death in certain parts of the globe.^{[ citation needed ]}

Genome

Mycobacterium virus D29 is a double-stranded DNA mycobacteriophage that has a genome length of 49127 base pairs (bp), coding for a total of 77 protein coding genes. Five tRNA genes are also present in D29's genome (genes 6-9.2). The G+C content of the D29 genome is 63.6%, which is similar to that of other T5-Like Phages.^{[ citation needed ]}

Sequencing of D29 has shown that it is indeed very similar to that of certain T5-Like Phages. L5 and some other siphoviruses have a similar layout to the genomes as D29 does. The attachment site for D29 is at a very similar location on its genome to that of L5. The attachment site divides the genome into the left and right arms of the genome. The left arm of D29 is about 80% identical to L5 in terms of nucleic acids. The right arm is where the differences lie between D29 and L5 (and some of the other T5-Like Phages), sequences of the right arm are highly related between D29 and L5, but "punctuated by segments of unrelated DNA".^[3] The right end of the D29 genome has a 3.6 kb deletion in comparison to that of L5 at the far right end of the arm. This deletion seems to affect the repressor gene 71 and surrounding genes. This would appear to be why D29 is a lytic phage instead of a temperate phage like L5.^{[ citation needed ]}

The left arm of D29 encodes gene 1 through gene 33, some of which are involved in head subunits, tail subunits, the five tRNA genes, and Integrase. The functions for multiple different genes are unknown. The right arm encodes for genes 34.1 through 89. Not all of these genes are protein coding, but the right arm likely encodes for DNA Polymerase, Haloperoxidase, potentially DNA primase, and a few others that are only hypothesized.^{[ citation needed ]}

Replication

Mycobacterium virus D29 is a big DNA phage, this just means that it carries a large genome. With a genome length over 49000 bp long, D29 is considered to have a large genome size. Large genome sizes generally point to a replication process that is commonly referred to as rolling circle model of DNA replication. The DNA is packaged and stored in the protein head of the phage in a linear fashion. But after infecting cells the linear genome is converted into a circle, this allows for continuous DNA synthesis. The length of the circular DNA is equal to that of the linear DNA length except it is missing one terminal repeat section. This form of DNA replication is very common in mycobacteriophages.^{[ citation needed ]}

Release of phage

The release of mycobacteriophages from the host is done through a procedure working throughout the replication and assembly period of the phage. Since D29 only takes the lytic pathway of infecting hosts, a D29 infection of a mycobacterium always results in the death of the host. Lysis is a procedure in which after the phage has irreversibly attached to the cell and injected its DNA into the host, and after phage particles have been assembled, the cell wall is broken, or lysed releasing the phage into the environment for further infection. D29 has three genes which operate together to achieve this. Gene gp10 which encodes for the protein Lysin A, gene gp11 which encodes for the holin protein, and gene gp12 which encodes for Lysin B.^[4] Together these three proteins have a lethal effect on the infected bacteria. Essentially, the holins form pores in the cell membrane of the host. These pores allow for the Lysin A and Lysin B to cooperate to reach and breach the peptidoglycan to bust open the cell walls. This process releases the newly assembled phage particles into the environment but also kills the cell.^{[ citation needed ]}

Structure

The morphotype of mycobacterium virus D29 is that of siphoviridae. The family is known to have an icosahedral head, with long, flexible, non-contractile, thin tails. D29 has an average head diameter of around 80 nm. The tails vary between 3 different sizes, the tails can be about 150, 300, or 450 nm in length.^[5] The tail has an average diameter of approximately 12 nm. The tail leads to a site at the distal end where three L-shaped tail fibers exist, at this point, the "tubular tail undergoes a transition at the tail fiber attachment site to a conical form, which tapers into a single straight tail fiber". These structural measurements are common throughout the T5-Like Phages. As T5-Like phages refers to the morphology of the phage, or the structure and outward appearance. Some of the T5-Like phages are extremely similar to D29 in other respects though, such as the mentioned L5 phage.^{[ citation needed ]}

There are 6 structural polypeptide proteins in the viral structure, three larger polypeptides named polypeptide III, polypeptide IV, and polypeptide VI. There are three minor polypeptides known as polypeptide I, polypeptide II, and polypeptide V. There are no lipids present in the virus or that the virus requires.^{[ citation needed ]}

Tropism

D29 can infect a large variety of mycobacterium.^[6] The host range of D29 is known to be broad indicating the ability to bind to receptors that are common among many types of mycobacteria. These receptors are not well documented or studied at this time though, some are known, but few. These mycobacterial species include both pathogenic bacteria (e.g. M. tuberculosis), and non-pathogenic bacteria (e.g. M. smegmatis).

This makes D29 a rather effective control phage in studies involving mycobacteriophages. Mycobacteriophages are not dangerous to humans as they cannot affect the cells of the human body nor can they affect the bacteria living in the human biome.^{[ citation needed ]}

Phage therapy

D29 serves as a potential candidate for bacteriophage used in phage therapy. With its broad host range, and ability to infect M. tuberculosis , it is heavily thought that D29 could be used effectively in combating dangerous pathogens in a safe manner. For example, D29 would be able to infect M. tuberculosis without really affecting the human host. This is because of the non-lysogenic abilities of D29. Since D29 only engages in the lytic cycle, D29 kills the infected bacteria which is the desired effect in terms of phage therapy.^{[ citation needed ]}

It has also been suggested that instead of using D29 and other such phages for actively combating current infection (of tuberculosis for example), phage be given to family members and other working in constant close proximity to the infected individual to hold off the acquiring of the pathogen. This as an effective method has only been suggested and the actual effectiveness of the strategy has yet to be tested.^{[ citation needed ]}

Related Research Articles

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". Bacteriophages are composed of proteins that encapsulate a DNA or RNA genome, and may have structures that are either simple or elaborate. Their genomes may encode as few as four genes and as many as hundreds of genes. Phages replicate within the bacterium following the injection of their genome into its cytoplasm.

Enterobacteria phage λ is a bacterial virus, or bacteriophage, that infects the bacterial species Escherichia coli. It was discovered by Esther Lederberg in 1950. The wild type of this virus has a temperate life cycle that allows it to either reside within the genome of its host through lysogeny or enter into a lytic phase, during which it kills and lyses the cell to produce offspring. Lambda strains, mutated at specific sites, are unable to lysogenize cells; instead, they grow and enter the lytic cycle after superinfecting an already lysogenized cell.

Mycobacterium is a genus of over 190 species in the phylum Actinomycetota, assigned its own family, Mycobacteriaceae. This genus includes pathogens known to cause serious diseases in mammals, including tuberculosis and leprosy in humans. The Greek prefix myco- means 'fungus', alluding to this genus' mold-like colony surfaces. Since this genus has cell walls with a waxy lipid-rich outer layer that contains high concentrations of mycolic acid, acid-fast staining is used to emphasize their resistance to acids, compared to other cell types.

A prophage is a bacteriophage genome that is integrated into the circular bacterial chromosome or exists as an extrachromosomal plasmid within the bacterial cell. Integration of prophages into the bacterial host is the characteristic step of the lysogenic cycle of temperate phages. Prophages remain latent in the genome through multiple cell divisions until activation by an external factor, such as UV light, leading to production of new phage particles that will lyse the cell and spread. As ubiquitous mobile genetic elements, prophages play important roles in bacterial genetics and evolution, such as in the acquisition of virulence factors.

Transduction is the process by which foreign DNA is introduced into a cell by a virus or viral vector. An example is the viral transfer of DNA from one bacterium to another and hence an example of horizontal gene transfer. Transduction does not require physical contact between the cell donating the DNA and the cell receiving the DNA, and it is DNase resistant. Transduction is a common tool used by molecular biologists to stably introduce a foreign gene into a host cell's genome.

<span class="mw-page-title-main">Lytic cycle</span> Cycle of viral reproduction

The lytic cycle is one of the two cycles of viral reproduction, the other being the lysogenic cycle. The lytic cycle results in the destruction of the infected cell and its membrane. Bacteriophages that only use the lytic cycle are called virulent phages.

Escherichia virus T4 is a species of bacteriophages that infect Escherichia coli bacteria. It is a double-stranded DNA virus in the subfamily Tevenvirinae from the family Myoviridae. T4 is capable of undergoing only a lytic life cycle and not the lysogenic life cycle. The species was formerly named T-even bacteriophage, a name which also encompasses, among other strains, Enterobacteria phage T2, Enterobacteria phage T4 and Enterobacteria phage T6.

Myoviridae is a family of bacteriophages in the order Caudovirales. Bacteria and archaea serve as natural hosts. There are 625 species in this family, assigned to eight subfamilies and 217 genera.

Podoviridae is a family of bacteriophage in the order Caudovirales often associated with T-7 like phages. There are 130 species in this family, assigned to 3 subfamilies and 52 genera. This family is characterized by having very short, noncontractile tails. Podoviradae are largely understudied and most new isolates are of the phicbkviruses genus, a group of giant viruses that appear to be Caulobacter specific.

Caudoviricetes is a class of viruses known as the tailed bacteriophages. Under the Baltimore classification scheme, the Caudoviricetes are group I viruses as they have double stranded DNA (dsDNA) genomes, which can be anywhere from 18,000 base pairs to 500,000 base pairs in length. The virus particles have a distinct shape; each virion has an icosahedral head that contains the viral genome, and is attached to a flexible tail by a connector protein. The order encompasses a wide range of viruses, many containing genes of similar nucleotide sequence and function. However, some tailed bacteriophage genomes can vary quite significantly in nucleotide sequence, even among the same genus. Due to their characteristic structure and possession of potentially homologous genes, it is believed these bacteriophages possess a common origin.

<span class="mw-page-title-main">Lysogenic cycle</span> Process of virus reproduction

Lysogeny, or the lysogenic cycle, is one of two cycles of viral reproduction. Lysogeny is characterized by integration of the bacteriophage nucleic acid into the host bacterium's genome or formation of a circular replicon in the bacterial cytoplasm. In this condition the bacterium continues to live and reproduce normally, while the bacteriophage lies in a dormant state in the host cell. The genetic material of the bacteriophage, called a prophage, can be transmitted to daughter cells at each subsequent cell division, and later events can release it, causing proliferation of new phages via the lytic cycle. Lysogenic cycles can also occur in eukaryotes, although the method of DNA incorporation is not fully understood. For instance the AIDS viruses can either infect humans lytically, or lay dormant (lysogenic) as part of the infected cells' genome, keeping the ability to return to lysis at a later time. The rest of this article is about lysogeny in bacterial hosts.

Bacteriophage T7 is a bacteriophage, a virus that infects bacteria. It infects most strains of Escherichia coli and relies on these hosts to propagate. Bacteriophage T7 has a lytic life cycle, meaning that it destroys the cell it infects. It also possesses several properties that make it an ideal phage for experimentation: its purification and concentration have produced consistent values in chemical analyses; it can be rendered noninfectious by exposure to UV light; and it can be used in phage display to clone RNA binding proteins.

A Bacillus phage is a member of a group of bacteriophages known to have bacteria in the genus Bacillus as host species. These bacteriophages have been found to belong to the families Myoviridae, Siphoviridae, Podoviridae, or Tectiviridae. The genus Bacillus includes the model organism, B. subtilis, and two widely known human pathogens, B. anthracis and B. cereus. Other strains of Bacillus bacteria that phage are known to infect include B. megaterium, B. mycoides, B. pseudomycoides, B. thuringiensis, and B. weihenstephanensis. More than 1,455 bacillus phage have been discovered from many different environments and areas around the world. Only 164 of these phages have been completely sequenced as of December 16, 2021.

A mycobacteriophage is a member of a group of bacteriophages known to have mycobacteria as host bacterial species. While originally isolated from the bacterial species Mycobacterium smegmatis and Mycobacterium tuberculosis, the causative agent of tuberculosis, more than 4,200 mycobacteriophage have since been isolated from various environmental and clinical sources. 2,042 have been completely sequenced. Mycobacteriophages have served as examples of viral lysogeny and of the divergent morphology and genetic arrangement characteristic of many phage types.

<span class="mw-page-title-main">Cyanophage</span> Virus that infects cyanobacteria

Cyanophages are viruses that infect cyanobacteria, also known as Cyanophyta or blue-green algae. Cyanobacteria are a phylum of bacteria that obtain their energy through the process of photosynthesis. Although cyanobacteria metabolize photoautotrophically like eukaryotic plants, they have prokaryotic cell structure. Cyanophages can be found in both freshwater and marine environments. Marine and freshwater cyanophages have icosahedral heads, which contain double-stranded DNA, attached to a tail by connector proteins. The size of the head and tail vary among species of cyanophages. Cyanophages infect a wide range of cyanobacteria and are key regulators of the cyanobacterial populations in aquatic environments, and may aid in the prevention of cyanobacterial blooms in freshwater and marine ecosystems. These blooms can pose a danger to humans and other animals, particularly in eutrophic freshwater lakes. Infection by these viruses is highly prevalent in cells belonging to Synechococcus spp. in marine environments, where up to 5% of cells belonging to marine cyanobacterial cells have been reported to contain mature phage particles.

P1 is a temperate bacteriophage that infects Escherichia coli and some other bacteria. When undergoing a lysogenic cycle the phage genome exists as a plasmid in the bacterium unlike other phages that integrate into the host DNA. P1 has an icosahedral head containing the DNA attached to a contractile tail with six tail fibers. The P1 phage has gained research interest because it can be used to transfer DNA from one bacterial cell to another in a process known as transduction. As it replicates during its lytic cycle it captures fragments of the host chromosome. If the resulting viral particles are used to infect a different host the captured DNA fragments can be integrated into the new host's genome. This method of in vivo genetic engineering was widely used for many years and is still used today, though to a lesser extent. P1 can also be used to create the P1-derived artificial chromosome cloning vector which can carry relatively large fragments of DNA. P1 encodes a site-specific recombinase, Cre, that is widely used to carry out cell-specific or time-specific DNA recombination by flanking the target DNA with loxP sites.

Corticovirus is a genus of viruses in the family Corticoviridae. Corticoviruses are bacteriophages; that is, their natural hosts are bacteria. The genus contains two species. The name is derived from Latin cortex, corticis. However, prophages closely related to PM2 are abundant in the genomes of aquatic bacteria, suggesting that the ecological importance of corticoviruses might be underestimated. Bacteriophage PM2 was first described in 1968 after isolation from seawater sampled from the coast of Chile.

<span class="mw-page-title-main">Bacteriophage P2</span> Species of virus

Bacteriophage P2, scientific name Escherichia virus P2, is a temperate phage that infects E. coli. It is a tailed virus with a contractile sheath and is thus classified in the genus Peduovirus, subfamily Peduovirinae, family Myoviridae within order Caudovirales. This genus of viruses includes many P2-like phages as well as the satellite phage P4.

The Actinobacterial Phage Holin (APH) Family is a fairly large family of proteins between 105 and 180 amino acyl residues in length, typically exhibiting a single transmembrane segment (TMS) near the N-terminus. A representative list of proteins belonging to the APH family can be found in the Transporter Classification Database.

Escherichia virus CC31, formerly known as Enterobacter virus CC31, is a dsDNA bacteriophage of the subfamily Tevenvirinae responsible for infecting the bacteria family of Enterobacteriaceae. It is one of two discovered viruses of the genus Karamvirus, diverging away from the previously discovered T4virus, as a clonal complex (CC). CC31 was first isolated from Escherichia coli B strain S/6/4 and is primarily associated with Escherichia, even though is named after Enterobacter.

References

↑ "The Actinobacteriophage Database | Phage D29". phagesdb.org. Retrieved 2 November 2017.
↑ Granoff, Allan; Webster, Robert (1999). Encyclopedia of Virology (Second ed.). Academic Press. ISBN 978-0-12-227033-8.
↑ Ford, Michael E; Sarkis, Gary J; Belanger, Aimee E; Hendrix, Roger W; Hatfull, Graham F (1998). "Genome structure of mycobacteriophage D29: implications for phage evolution". Journal of Molecular Biology. 279 (1): 143–164. doi:10.1006/jmbi.1997.1610. PMID 9636706.
↑ Amol Arunrao Pohane; Himanshu Joshi; Vikas Jain (13 February 2014). "Molecular dissection of phage endolysin: An interdomain interaction confers host specificity in Lysin A of Mycobacterium phage D29" (PDF). Retrieved 2 November 2017.
↑ Schäfer, R; Huber, U; Franklin, RM (1977). "Chemical and physical properties of mycobacteriophage D29". Eur J Biochem. 73 (1): 239–46. doi:10.1111/j.1432-1033.1977.tb11312.x. PMID 837938.
↑ Swift, Benjamin M. C.; Gerrard, Zara E.; Huxley, Jonathan N.; Rees, Catherine E. D. (2014). "Factors Affecting Phage D29 Infection: A Tool to Investigate Different Growth States of Mycobacteria". PLOS ONE. 9 (9): e106690. Bibcode:2014PLoSO...9j6690S. doi: 10.1371/journal.pone.0106690 . PMC 4153674 . PMID 25184428.

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[phagesdb-1] "The Actinobacteriophage Database | Phage D29". phagesdb.org. Retrieved 2 November 2017.

[2] Granoff, Allan; Webster, Robert (1999). Encyclopedia of Virology (Second ed.). Academic Press. ISBN 978-0-12-227033-8.

[sciencedirect-3] Ford, Michael E; Sarkis, Gary J; Belanger, Aimee E; Hendrix, Roger W; Hatfull, Graham F (1998). "Genome structure of mycobacteriophage D29: implications for phage evolution". Journal of Molecular Biology. 279 (1): 143–164. doi:10.1006/jmbi.1997.1610. PMID 9636706.

[jbc-4] Amol Arunrao Pohane; Himanshu Joshi; Vikas Jain (13 February 2014). "Molecular dissection of phage endolysin: An interdomain interaction confers host specificity in Lysin A of Mycobacterium phage D29" (PDF). Retrieved 2 November 2017.

[nih-5] Schäfer, R; Huber, U; Franklin, RM (1977). "Chemical and physical properties of mycobacteriophage D29". Eur J Biochem. 73 (1): 239–46. doi:10.1111/j.1432-1033.1977.tb11312.x. PMID 837938.

[plos-6] Swift, Benjamin M. C.; Gerrard, Zara E.; Huxley, Jonathan N.; Rees, Catherine E. D. (2014). "Factors Affecting Phage D29 Infection: A Tool to Investigate Different Growth States of Mycobacteria". PLOS ONE. 9 (9): e106690. Bibcode:2014PLoSO...9j6690S. doi: 10.1371/journal.pone.0106690 . PMC 4153674 . PMID 25184428.

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