Bacillus phage

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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 . [1] [2] [3] [4] 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. [5] Only 164 of these phages have been completely sequenced as of December 16, 2021. [5]

Contents

Genome diversity

Bacillus phage are classified based on their genome sequences. The total sequence length ranges from 7,826 (in phage pMC8) to 509,170 bp (in phage pHS181) with the GC content of these phage being an average of 38.25%. [6]

Within Bacillus phage there are 12 clusters (A-L), 28 subclusters, and 14 singletons. Clusters are groups of related genomes with the 12 clusters showing at least 50% homology between phage. [7] Singletons are phage that have no significant nucleotide similarity to others. The most conserved genes within the Bacillus phage include those that encode tail proteins and other structural proteins, holin, and a site-specific recombinase. [7] One group of gene that is highly variable between Bacillus phage are tRNA genes. The role of phage tRNAs largely depend on their bacterial host, hence the number could widely differ depending on the specific strain of bacteria.[ citation needed ]

Nucleotide and amino acid dot plot analysis of 93 fully sequenced Bacillus phages reveals 12 clusters (A-L) and 14 singletons. Nucleotide (top-left) and amino acid (top-right) dot plot of Bacillus genomes of less than 100 kb organized by similarity reveals 10 clusters of related phages. Nucleotide (bottom-left) and amino acid (bottom-right) dot plot of Bacillus genomes of greater than 100 kb organized by similarity reveals 2 clusters of related phages. Thick lines indicate cluster assignments, which are provided on the Y-axis (A-L). Bacillus Phage Cluster Dot-Plot.png
Nucleotide and amino acid dot plot analysis of 93 fully sequenced Bacillus phages reveals 12 clusters (A-L) and 14 singletons. Nucleotide (top-left) and amino acid (top-right) dot plot of Bacillus genomes of less than 100 kb organized by similarity reveals 10 clusters of related phages. Nucleotide (bottom-left) and amino acid (bottom-right) dot plot of Bacillus genomes of greater than 100 kb organized by similarity reveals 2 clusters of related phages. Thick lines indicate cluster assignments, which are provided on the Y-axis (A-L).
ClusterSub.PhagesHostsGenome size%GC# ORFS (tRNA)Type
A25A                    T    ~15000~39.0~30.0T
B36    B    S   ~20000~37.0~28.0P
C22   B        W~26000~30.5~39.5S
D13  M   ~40000~41.0~49.5P
E13      C        T    ~40000~38.0~49.0S
F311A    B    C        T    ~40000~35.0~53.5S
G12   C        T    ~55000~36.5~70.0S
H110   B        M    P   ~48000~42.0~74.5S
I12   B   ~65000~47.5~112.5UK
J23   C    M   ~81000~35.0~122.0S
K25   B    C       S   ~140500~40.0~223.0M
L827   B    C        P    S    T    ~160000~39.1~270.0M

Characteristics given are cluster assignment, number of subclusters (Sub.), number of phages in the cluster, host species from which the phages were isolated, the average genome size, average percent GC content, average number of ORFS, and the morphotype. Species abbreviations are Bacillus anthracis (A), Bacillus cereus (C), Bacillus sp. (B), Bacillus megaterium (M), Bacillus pumulis (P), Bacillus subtilis (S), Bacillus thuringiensis (T), and Bacillus westenstephanensis MG1, (W). Family/morphotype abbreviations are Tectiviridae (T), Podoviridae (P), Siphoviridae (S), and Myoviridae (M). UK is unknown/unreported. [7]

Applications

The DNA polymerase of Bacillus phage phi29 is a unique and efficient polymerase with proofreading activity. [8] [9]

Related Research Articles

<i>Bacillus</i> Genus of bacteria

Bacillus is a genus of Gram-positive, rod-shaped bacteria, a member of the phylum Bacillota, with 266 named species. The term is also used to describe the shape (rod) of other so-shaped bacteria; and the plural Bacilli is the name of the class of bacteria to which this genus belongs. Bacillus species can be either obligate aerobes which are dependent on oxygen, or facultative anaerobes which can survive in the absence of oxygen. Cultured Bacillus species test positive for the enzyme catalase if oxygen has been used or is present.

<i>Bacillus cereus</i> Species of bacterium

Bacillus cereus is a Gram-positive rod-shaped bacterium commonly found in soil, food, and marine sponges. The specific name, cereus, meaning "waxy" in Latin, refers to the appearance of colonies grown on blood agar. Some strains are harmful to humans and cause foodborne illness due to their spore-forming nature, while other strains can be beneficial as probiotics for animals, and even exhibit mutualism with certain plants. B. cereus bacteria may be anaerobes or facultative anaerobes, and like other members of the genus Bacillus, can produce protective endospores. They have a wide range of virulence factors, including phospholipase C, cereulide, sphingomyelinase, metalloproteases, and cytotoxin K, many of which are regulated via quorum sensing. B. cereus strains exhibit flagellar motility.

<i>Podoviridae</i> Family of viruses

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.

<span class="mw-page-title-main">Caudovirales</span> Class of viruses

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.

<span class="mw-page-title-main">Mycobacteriophage</span> Virus infecting mycobacteria

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">Bacillus virus phi29</span> Species of virus

Bacillus virus Φ29 is a double-stranded DNA (dsDNA) bacteriophage with a prolate icosahedral head and a short tail that belongs to the genus Salasvirus, order Caudovirales, and family Salasmaviridae. They are in the same order as phages PZA, Φ15, BS32, B103, M2Y (M2), Nf, and GA-1. First discovered in 1965, the Φ29 phage is the smallest Bacillus phage isolated to date and is among the smallest known dsDNA phages.

<i>Bacillus anthracis</i> Species of bacterium

Bacillus anthracis is a gram-positive and rod-shaped bacterium that causes anthrax, a deadly disease to livestock and, occasionally, to humans. It is the only permanent (obligate) pathogen within the genus Bacillus. Its infection is a type of zoonosis, as it is transmitted from animals to humans. It was discovered by a German physician Robert Koch in 1876, and became the first bacterium to be experimentally shown as a pathogen. The discovery was also the first scientific evidence for the germ theory of diseases.

Pathema was one of the eight bioinformatics resource centers funded by the National Institute of Allergy and Infectious Diseases (NIAID), a component of the National Institute of Health (NIH), which is an agency of the United States Department of Health and Human Services.

Φ29 DNA polymerase is an enzyme from the bacteriophage Φ29. It is being increasingly used in molecular biology for multiple displacement DNA amplification procedures, and has a number of features that make it particularly suitable for this application. It was discovered and characterized by Spanish scientists Luis Blanco and Margarita Salas.

Enquatrovirus is a genus of bacteriophages in the order Caudovirales, in the family Podoviridae. Bacteria serve as natural hosts. There is currently only one species in this genus: the type species Escherichia virus N4.

Bacillus virus AP50 is a species of bacteriophage that infects Bacillus anthracis bacteria. Originally thought to be an RNA phage, it contains a DNA genome of about 14,000 base pairs in an icosahedral capsid with a two-layer capsid shell.

Pseudomonas virus phiCTX is a virus of the family Myoviridae, genus Citexvirus.

Ralstonia virus RSA1 is a virus of the family Myoviridae, genus Aresaunavirus.

Mycobacterium virus D29 (D29) is a cluster A mycobacteriophage belonging to the Siphoviridae family of viruses, it was discovered in 1954 by S. Froman. D29 is notable for its ability to infect M. 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.

Arbitrium is a viral peptide produced by bacteriophages to communicate with each other and decide host cell fate. It is six amino acids(aa) long, and so is also referred to as a hexapeptide. It is produced when a phage infects a bacterial host. and signals to other phages that the host has been infected.

Metabacillus is a genus of rod-shaped bacteria exhibiting Gram-positive or Gram-variable staining in the family Bacillaceae within the order Bacillales. The type species for this genus is Metabacillus fastidiosus.

Evansella is a genus of Gram-positive rod-shaped bacteria in the family Bacillaceae within the order Bacillales. The type species for this genus is Evansella cellulosilytica.

Ferdinandcohnia is a genus of rod-shaped bacteria that generally display Gram-positive staining in the family Bacillaceae within the order Bacillales. The type species for this genus is Ferdinandcohnia humi.

<i>Microbacterium virus MuffinTheCat</i> Species of virus

Microbacterium virus MuffinTheCat is a species of bacteriophage in the family Tectiviridae. It was collected and identified by Darcy Reimer on 1 October 2019. It is part of the Microbacterium testaceum NRRL B-24232 viral strand and the GE viral cluster. Microbacterium of the Microbacterium testaceum species serve as natural hosts. Microbacterium virus MuffinTheCat is morphologically almost indistinguishable from its sibling species in the Tectiviridae family, but it along with its sibling species in the GE cluster are different enough from other Tectiviridae members that the GE cluster may soon be identified as a new genus. Microbacterium virus MuffinTheCat is identified from other GE cluster members by its genome differences.

References

  1. ↑ Gillis A, Mahillon J (July 2014). "Phages preying on Bacillus anthracis, Bacillus cereus, and Bacillus thuringiensis: past, present and future". Viruses. 6 (7): 2623–2672. doi: 10.3390/v6072623 . PMC   4113786 . PMID   25010767.
  2. ↑ Lee JH, Shin H, Ryu S (May 2014). "Characterization and comparative genomic analysis of bacteriophages infecting members of the Bacillus cereus group". Archives of Virology. 159 (5): 871–884. doi:10.1007/s00705-013-1920-3. PMID   24264384. S2CID   15058899.
  3. ↑ Klumpp J, Lavigne R, Loessner MJ, Ackermann HW (October 2010). "The SPO1-related bacteriophages". Archives of Virology. 155 (10): 1547–1561. doi:10.1007/s00705-010-0783-0. hdl: 20.500.11850/23338 . PMID   20714761. S2CID   20320784.
  4. ↑ Gentry-Weeks C, Coburn PS, Gilmore MS (2002). "Phages and other mobile virulence elements in gram-positive pathogens". Current Topics in Microbiology and Immunology. 264 (2): 79–94. PMID   12012871.
  5. 1 2 "Bacillus Phage Database | Home". bacillus.phagesdb.org. Retrieved 2021-12-16.
  6. ↑ "Bacillus Phage Database | Detail for Phage pHS181". bacillus.phagesdb.org. Retrieved 2021-12-16.
  7. 1 2 3 4 Grose JH, Jensen GL, Burnett SH, Breakwell DP (October 2014). "Genomic comparison of 93 Bacillus phages reveals 12 clusters, 14 singletons and remarkable diversity". BMC Genomics. 15 (1): 855. doi: 10.1186/1471-2164-15-855 . PMC   4197329 . PMID   25280881.
  8. ↑ Blanco L, Salas M (September 1984). "Characterization and purification of a phage phi 29-encoded DNA polymerase required for the initiation of replication". Proceedings of the National Academy of Sciences of the United States of America. 81 (17): 5325–5329. Bibcode:1984PNAS...81.5325B. doi: 10.1073/pnas.81.17.5325 . PMC   391696 . PMID   6433348.
  9. ↑ Salas M, Blanco L, Lázaro JM, de Vega M (January 2008). "The bacteriophage phi29 DNA polymerase". IUBMB Life. 60 (1): 82–85. doi: 10.1002/iub.19 . PMID   18379997. S2CID   39622915.
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