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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]]''.<ref>{{cite journal|last1=Gillis|first1=Annika|last2=Mahillon|first2=Jacques|title=Phages Preying on Bacillus anthracis, Bacillus cereus, and Bacillus thuringiensis: Past, Present and Future|journal=Viruses|date=9 July 2014|volume=6|issue=7|pages=2623–2672|doi=10.3390/v6072623|pmid=25010767|pmc=4113786|doi-access=free}}</ref><ref>{{cite journal|last1=Lee|first1=Ju-Hoon|last2=Shin|first2=Hakdong|last3=Ryu|first3=Sangryeol|title=Characterization and comparative genomic analysis of bacteriophages infecting members of the Bacillus cereus group|journal=Archives of Virology|date=22 November 2013|volume=159|issue=5|pages=871–884|doi=10.1007/s00705-013-1920-3|pmid=24264384|s2cid=15058899}}</ref><ref>{{cite journal|last1=Klumpp|first1=Jochen|last2=Lavigne|first2=Rob|last3=Loessner|first3=Martin J.|last4=Ackermann|first4=Hans-Wolfgang|title=The SPO1-related bacteriophages|journal=Archives of Virology|date=17 August 2010|volume=155|issue=10|pages=1547–1561|doi=10.1007/s00705-010-0783-0|pmid=20714761|url=http://doc.rero.ch/record/312164/files/705_2010_Article_783.pdf|hdl=20.500.11850/23338|s2cid=20320784|hdl-access=free}}</ref><ref>{{cite journal|last1=Gentry-Weeks|first1=C|last2=Coburn|first2=PS|last3=Gilmore|first3=MS|title=Phages and other mobile virulence elements in gram-positive pathogens.|journal=Current Topics in Microbiology and Immunology|date=2002|volume=264|issue=2|pages=79–94|pmid=12012871}}</ref>
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]]''.<ref>{{cite journal|last1=Gillis|first1=Annika|last2=Mahillon|first2=Jacques|title=Phages Preying on Bacillus anthracis, Bacillus cereus, and Bacillus thuringiensis: Past, Present and Future|journal=Viruses|date=9 July 2014|volume=6|issue=7|pages=2623–2672|doi=10.3390/v6072623|pmid=25010767|pmc=4113786|doi-access=free}}</ref><ref>{{cite journal|last1=Lee|first1=Ju-Hoon|last2=Shin|first2=Hakdong|last3=Ryu|first3=Sangryeol|title=Characterization and comparative genomic analysis of bacteriophages infecting members of the Bacillus cereus group|journal=Archives of Virology|date=22 November 2013|volume=159|issue=5|pages=871–884|doi=10.1007/s00705-013-1920-3|pmid=24264384|s2cid=15058899}}</ref><ref>{{cite journal|last1=Klumpp|first1=Jochen|last2=Lavigne|first2=Rob|last3=Loessner|first3=Martin J.|last4=Ackermann|first4=Hans-Wolfgang|title=The SPO1-related bacteriophages|journal=Archives of Virology|date=17 August 2010|volume=155|issue=10|pages=1547–1561|doi=10.1007/s00705-010-0783-0|pmid=20714761|url=http://doc.rero.ch/record/312164/files/705_2010_Article_783.pdf|hdl=20.500.11850/23338|s2cid=20320784|hdl-access=free}}</ref><ref>{{cite journal|last1=Gentry-Weeks|first1=C|last2=Coburn|first2=PS|last3=Gilmore|first3=MS|title=Phages and other mobile virulence elements in gram-positive pathogens.|journal=Current Topics in Microbiology and Immunology|date=2002|volume=264|issue=2|pages=79–94|pmid=12012871}}</ref> The genus Bacillus includes the model organism, [[Bacillus subtilis|B. subtilis]], and two widely known human pathogens, [[Bacillus anthracis|B. anthracis]] and [[Bacillus cereus|B. cereus]]. Other strains of Bacillus bacteria that phage are known to infect include B. megaterium, B. mycoides, B. pseudomycoides, [[Bacillus thuringiensis|B. thuringiensis]], and B. weihenstephanensis. More than 1,455 bacillus phage have been discovered from many different environments and areas around the world.<ref>{{Cite web|title=Bacillus Phage Database {{!}} Home|url=http://bacillus.phagesdb.org/|access-date=2021-12-16|website=bacillus.phagesdb.org}}</ref> Only 164 of these phages have been completely sequenced as of December 16, 2021<ref>{{Cite web|title=Bacillus Phage Database {{!}} Home|url=http://bacillus.phagesdb.org/|access-date=2021-12-16|website=bacillus.phagesdb.org}}</ref>.

== Diversity and Genomes ==
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%<ref>{{Cite web|title=Bacillus Phage Database {{!}} Detail for Phage pHS181|url=http://bacillus.phagesdb.org/phages/pHS181/|access-date=2021-12-16|website=bacillus.phagesdb.org}}</ref>.


Within Bacillus phage there are 12 clusters (A-L), 28 subclusters, and 14 singletons. Singletons are phage that have no nucleotide similarity to others. The 12 clusters show at least 50% homology between phage<ref>{{Cite journal|last=Grose|first=Julianne H.|last2=Jensen|first2=Garrett L.|last3=Burnett|first3=Sandra H.|last4=Breakwell|first4=Donald P.|date=2014-10-04|title=Genomic comparison of 93 Bacillus phages reveals 12 clusters, 14 singletons and remarkable diversity|url=https://doi.org/10.1186/1471-2164-15-855|journal=BMC Genomics|volume=15|issue=1|pages=855|doi=10.1186/1471-2164-15-855|issn=1471-2164|pmc=PMC4197329|pmid=25280881}}</ref>. The most conserved genes within the Bacillus phage include those that encode tail proteins and other structural proteins, holin, and a site-specific recombinase<ref>{{Cite journal|last=Grose|first=Julianne H.|last2=Jensen|first2=Garrett L.|last3=Burnett|first3=Sandra H.|last4=Breakwell|first4=Donald P.|date=2014-10-04|title=Genomic comparison of 93 Bacillus phages reveals 12 clusters, 14 singletons and remarkable diversity|url=https://doi.org/10.1186/1471-2164-15-855|journal=BMC Genomics|volume=15|issue=1|pages=855|doi=10.1186/1471-2164-15-855|issn=1471-2164|pmc=PMC4197329|pmid=25280881}}</ref>. 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.
[[File:Bacillus Phage Cluster Dot-Plot.png|thumb|Nucleotide and amino acid dot plot analysis of 93 fully sequenced Bacillus phages reveals 12 clusters (A-L) and 14 singletons. Nucleotide (A) and amino acid (C) dot plot of Bacillus genomes of less than 100 kb organized by similarity reveals 10 clusters of related phages. Nucleotide (B) and amino acid (D) 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). Dot plots were produced using Gepard and whole genome amino acid sequences were retrieved from Phamerator.]]
{| class="wikitable sortable mw-collapsible"
|'''Cluster'''
|'''Sub.'''
|'''Phages'''
|'''Hosts'''
|'''Genome size'''
|'''%GC'''
|'''# ORFS (tRNA)'''
|'''Type'''
|-
|A
|2
|5
|A                    T    
|~15000
|~39.0
|~30.0
|T
|-
|B
|3
|6
|    B    S   
|~20000
|~37.0
|~28.0
|P
|-
|C
|2
|2
|   B        W
|~26000
|~30.5
|~39.5
|S
|-
|D
|1
|3
|  M   
|~40000
|~41.0
|~49.5
|P
|-
|E
|1
|3
|      C        T    
|~40000
|~38.0
|~49.0
|S
|-
|F
|3
|11
|A    B    C        T    
|~40000
|~35.0
|~53.5
|S
|-
|G
|1
|2
|   C        T    
|~55000
|~36.5
|~70.0
|S
|-
|H
|1
|10
|   B        M    P   
|~48000
|~42.0
|~74.5
|S
|-
|I
|1
|2
|   B   
|~65000
|~47.5
|~112.5
|UK
|-
|J
|2
|3
|   C    M   
|~81000
|~35.0
|~122.0
|S
|-
|K
|2
|5
|   B    C       S   
|~140500
|~40.0
|~223.0
|M
|-
|L
|8
|27
|   B    C        P    S    T    
|~160000
|~39.1
|~270.0
|M
|}


==Applications==
==Applications==

Revision as of 20:04, 16 December 2021

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[6].

Diversity and Genomes

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%[7].


Within Bacillus phage there are 12 clusters (A-L), 28 subclusters, and 14 singletons. Singletons are phage that have no nucleotide similarity to others. The 12 clusters show at least 50% homology between phage[8]. The most conserved genes within the Bacillus phage include those that encode tail proteins and other structural proteins, holin, and a site-specific recombinase[9]. 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.

Nucleotide and amino acid dot plot analysis of 93 fully sequenced Bacillus phages reveals 12 clusters (A-L) and 14 singletons. Nucleotide (A) and amino acid (C) dot plot of Bacillus genomes of less than 100 kb organized by similarity reveals 10 clusters of related phages. Nucleotide (B) and amino acid (D) 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). Dot plots were produced using Gepard and whole genome amino acid sequences were retrieved from Phamerator.
Cluster Sub. Phages Hosts Genome size %GC # ORFS (tRNA) Type
A 2 5 A                    T     ~15000 ~39.0 ~30.0 T
B 3 6     B    S    ~20000 ~37.0 ~28.0 P
C 2 2    B        W ~26000 ~30.5 ~39.5 S
D 1 3   M    ~40000 ~41.0 ~49.5 P
E 1 3       C        T     ~40000 ~38.0 ~49.0 S
F 3 11 A    B    C        T     ~40000 ~35.0 ~53.5 S
G 1 2    C        T     ~55000 ~36.5 ~70.0 S
H 1 10    B        M    P    ~48000 ~42.0 ~74.5 S
I 1 2    B    ~65000 ~47.5 ~112.5 UK
J 2 3    C    M    ~81000 ~35.0 ~122.0 S
K 2 5    B    C       S    ~140500 ~40.0 ~223.0 M
L 8 27    B    C        P    S    T     ~160000 ~39.1 ~270.0 M

Applications

The DNA polymerase of Bacillus phage phi29 is a unique and efficient polymerase with proofreading activity.[10][11]

References

  1. ^ Gillis, Annika; Mahillon, Jacques (9 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, Ju-Hoon; Shin, Hakdong; Ryu, Sangryeol (22 November 2013). "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, Jochen; Lavigne, Rob; Loessner, Martin J.; Ackermann, Hans-Wolfgang (17 August 2010). "The SPO1-related bacteriophages" (PDF). 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. ^ "Bacillus Phage Database | Home". bacillus.phagesdb.org. Retrieved 2021-12-16.
  6. ^ "Bacillus Phage Database | Home". bacillus.phagesdb.org. Retrieved 2021-12-16.
  7. ^ "Bacillus Phage Database | Detail for Phage pHS181". bacillus.phagesdb.org. Retrieved 2021-12-16.
  8. ^ Grose, Julianne H.; Jensen, Garrett L.; Burnett, Sandra H.; Breakwell, Donald P. (2014-10-04). "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. ISSN 1471-2164. PMC 4197329. PMID 25280881.{{cite journal}}: CS1 maint: PMC format (link) CS1 maint: unflagged free DOI (link)
  9. ^ Grose, Julianne H.; Jensen, Garrett L.; Burnett, Sandra H.; Breakwell, Donald P. (2014-10-04). "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. ISSN 1471-2164. PMC 4197329. PMID 25280881.{{cite journal}}: CS1 maint: PMC format (link) CS1 maint: unflagged free DOI (link)
  10. ^ 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): 5325–9. Bibcode:1984PNAS...81.5325B. doi:10.1073/pnas.81.17.5325. PMC 391696. PMID 6433348.
  11. ^ Salas, Margarita; Blanco, Luis; Lázaro, José M.; de Vega, Miguel (12 December 2007). "The bacteriophage ϕ29 DNA polymerase". IUBMB Life. 60 (1): 82–85. doi:10.1002/iub.19. PMID 18379997. S2CID 39622915.

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