Transcript Lysogeny and the prophage
Slide 1
Lysogeny:
Phage Entry into Bacterial Hosts
Bobby Chaggar
Yordanos Teferra
attP and attB regions
attP site of L5 phage used in comparing phages and similar
attB site of M. Smegmatis used in finding other att sites.
Search for Similar attP
regions
Search for similar attB
sites
M. Segmatis: GCGGGCGTAGCTCAATGGTAGAGCCCTAG
TCTTCCAAACTAGCTACGCGGGTTCGATTCCCGTCGCCCGCTC
Msme-155.Msmeg-11642 (4764496 -> 4764566) Aliases:(tRNA-Gly”)
M. Vanbaalenii:
GCGGGCGTAGCTCAATGGTAGAGCCCTAG
TCTTCCAAACTAGCTACGCGGGTTCGATTCCCGTCGCCCGCTCCA
Mvan-PYR-1.Mvan-PYR-1-10996 (4324373 -> 4324446) Aliases:(tRNA-Gly”)
M. SP.JLS:
GCGGGCGTAGCTCAATGGTAGAGCCCTAGTCTTCCAAACTAGCTACGCGGGTTCGATTCCCGTC
GCCCGCTCCA
M-JLS.Mjls-9576 (3780254 -> 3780327) Aliases:(tRNA-Gly”)
The Search for Prophage
DNA in Mycobacteria
Sliding Window
Deviations in GC content
Proteins to Consider
• Tail tape measure protein
• Phage major capsid protein
• Large-subunit terminase
• Integrase
• excisionase
References
Gomathi, N.S. . "In silico analysis of mycobacteriophage Che12 genome: Characterization of genes
required to lysogenise Mycobacterium tuberculosis." ScienceDirect. 31. (2007): 82-91. Web.
Hatful, Graham. "Characterization of the Mycobacteriophage L5 Attachment Site, attp." JMB. 266.
(1997): 76-92.
Canchaya, C., Proux, C., Fournous, G., Bruttin, A., & Brussow, H. (2003). Prophage genomics. Microbiol
Mol Biol Rev. 2003 June; 67(2): 238–276. doi: 10.1128/MMBR.67.2.238-276.2003
Hendrix, R., Smith, M., Burns, R., Ford, M., & Hatfull, G. (1999). Evolutionary relationships among
diverse bacteriophages and prophages: All the world’s a phage. Proc Natl Acad Sci U S A. 1999
March 2; 96(5): 2192–2197. Evolution.
Karlin, S. (2001). Detecting anomalous gene clusters and pathogenicity islands in diverse bacterial
genomes. TRENDS in Microbiology Vol.9 No.7 July 2001
Slide 2
Lysogeny:
Phage Entry into Bacterial Hosts
Bobby Chaggar
Yordanos Teferra
attP and attB regions
attP site of L5 phage used in comparing phages and similar
attB site of M. Smegmatis used in finding other att sites.
Search for Similar attP
regions
Search for similar attB
sites
M. Segmatis: GCGGGCGTAGCTCAATGGTAGAGCCCTAG
TCTTCCAAACTAGCTACGCGGGTTCGATTCCCGTCGCCCGCTC
Msme-155.Msmeg-11642 (4764496 -> 4764566) Aliases:(tRNA-Gly”)
M. Vanbaalenii:
GCGGGCGTAGCTCAATGGTAGAGCCCTAG
TCTTCCAAACTAGCTACGCGGGTTCGATTCCCGTCGCCCGCTCCA
Mvan-PYR-1.Mvan-PYR-1-10996 (4324373 -> 4324446) Aliases:(tRNA-Gly”)
M. SP.JLS:
GCGGGCGTAGCTCAATGGTAGAGCCCTAGTCTTCCAAACTAGCTACGCGGGTTCGATTCCCGTC
GCCCGCTCCA
M-JLS.Mjls-9576 (3780254 -> 3780327) Aliases:(tRNA-Gly”)
The Search for Prophage
DNA in Mycobacteria
Sliding Window
Deviations in GC content
Proteins to Consider
• Tail tape measure protein
• Phage major capsid protein
• Large-subunit terminase
• Integrase
• excisionase
References
Gomathi, N.S. . "In silico analysis of mycobacteriophage Che12 genome: Characterization of genes
required to lysogenise Mycobacterium tuberculosis." ScienceDirect. 31. (2007): 82-91. Web.
Hatful, Graham. "Characterization of the Mycobacteriophage L5 Attachment Site, attp." JMB. 266.
(1997): 76-92.
Canchaya, C., Proux, C., Fournous, G., Bruttin, A., & Brussow, H. (2003). Prophage genomics. Microbiol
Mol Biol Rev. 2003 June; 67(2): 238–276. doi: 10.1128/MMBR.67.2.238-276.2003
Hendrix, R., Smith, M., Burns, R., Ford, M., & Hatfull, G. (1999). Evolutionary relationships among
diverse bacteriophages and prophages: All the world’s a phage. Proc Natl Acad Sci U S A. 1999
March 2; 96(5): 2192–2197. Evolution.
Karlin, S. (2001). Detecting anomalous gene clusters and pathogenicity islands in diverse bacterial
genomes. TRENDS in Microbiology Vol.9 No.7 July 2001
Slide 3
Lysogeny:
Phage Entry into Bacterial Hosts
Bobby Chaggar
Yordanos Teferra
attP and attB regions
attP site of L5 phage used in comparing phages and similar
attB site of M. Smegmatis used in finding other att sites.
Search for Similar attP
regions
Search for similar attB
sites
M. Segmatis: GCGGGCGTAGCTCAATGGTAGAGCCCTAG
TCTTCCAAACTAGCTACGCGGGTTCGATTCCCGTCGCCCGCTC
Msme-155.Msmeg-11642 (4764496 -> 4764566) Aliases:(tRNA-Gly”)
M. Vanbaalenii:
GCGGGCGTAGCTCAATGGTAGAGCCCTAG
TCTTCCAAACTAGCTACGCGGGTTCGATTCCCGTCGCCCGCTCCA
Mvan-PYR-1.Mvan-PYR-1-10996 (4324373 -> 4324446) Aliases:(tRNA-Gly”)
M. SP.JLS:
GCGGGCGTAGCTCAATGGTAGAGCCCTAGTCTTCCAAACTAGCTACGCGGGTTCGATTCCCGTC
GCCCGCTCCA
M-JLS.Mjls-9576 (3780254 -> 3780327) Aliases:(tRNA-Gly”)
The Search for Prophage
DNA in Mycobacteria
Sliding Window
Deviations in GC content
Proteins to Consider
• Tail tape measure protein
• Phage major capsid protein
• Large-subunit terminase
• Integrase
• excisionase
References
Gomathi, N.S. . "In silico analysis of mycobacteriophage Che12 genome: Characterization of genes
required to lysogenise Mycobacterium tuberculosis." ScienceDirect. 31. (2007): 82-91. Web.
Hatful, Graham. "Characterization of the Mycobacteriophage L5 Attachment Site, attp." JMB. 266.
(1997): 76-92.
Canchaya, C., Proux, C., Fournous, G., Bruttin, A., & Brussow, H. (2003). Prophage genomics. Microbiol
Mol Biol Rev. 2003 June; 67(2): 238–276. doi: 10.1128/MMBR.67.2.238-276.2003
Hendrix, R., Smith, M., Burns, R., Ford, M., & Hatfull, G. (1999). Evolutionary relationships among
diverse bacteriophages and prophages: All the world’s a phage. Proc Natl Acad Sci U S A. 1999
March 2; 96(5): 2192–2197. Evolution.
Karlin, S. (2001). Detecting anomalous gene clusters and pathogenicity islands in diverse bacterial
genomes. TRENDS in Microbiology Vol.9 No.7 July 2001
Slide 4
Lysogeny:
Phage Entry into Bacterial Hosts
Bobby Chaggar
Yordanos Teferra
attP and attB regions
attP site of L5 phage used in comparing phages and similar
attB site of M. Smegmatis used in finding other att sites.
Search for Similar attP
regions
Search for similar attB
sites
M. Segmatis: GCGGGCGTAGCTCAATGGTAGAGCCCTAG
TCTTCCAAACTAGCTACGCGGGTTCGATTCCCGTCGCCCGCTC
Msme-155.Msmeg-11642 (4764496 -> 4764566) Aliases:(tRNA-Gly”)
M. Vanbaalenii:
GCGGGCGTAGCTCAATGGTAGAGCCCTAG
TCTTCCAAACTAGCTACGCGGGTTCGATTCCCGTCGCCCGCTCCA
Mvan-PYR-1.Mvan-PYR-1-10996 (4324373 -> 4324446) Aliases:(tRNA-Gly”)
M. SP.JLS:
GCGGGCGTAGCTCAATGGTAGAGCCCTAGTCTTCCAAACTAGCTACGCGGGTTCGATTCCCGTC
GCCCGCTCCA
M-JLS.Mjls-9576 (3780254 -> 3780327) Aliases:(tRNA-Gly”)
The Search for Prophage
DNA in Mycobacteria
Sliding Window
Deviations in GC content
Proteins to Consider
• Tail tape measure protein
• Phage major capsid protein
• Large-subunit terminase
• Integrase
• excisionase
References
Gomathi, N.S. . "In silico analysis of mycobacteriophage Che12 genome: Characterization of genes
required to lysogenise Mycobacterium tuberculosis." ScienceDirect. 31. (2007): 82-91. Web.
Hatful, Graham. "Characterization of the Mycobacteriophage L5 Attachment Site, attp." JMB. 266.
(1997): 76-92.
Canchaya, C., Proux, C., Fournous, G., Bruttin, A., & Brussow, H. (2003). Prophage genomics. Microbiol
Mol Biol Rev. 2003 June; 67(2): 238–276. doi: 10.1128/MMBR.67.2.238-276.2003
Hendrix, R., Smith, M., Burns, R., Ford, M., & Hatfull, G. (1999). Evolutionary relationships among
diverse bacteriophages and prophages: All the world’s a phage. Proc Natl Acad Sci U S A. 1999
March 2; 96(5): 2192–2197. Evolution.
Karlin, S. (2001). Detecting anomalous gene clusters and pathogenicity islands in diverse bacterial
genomes. TRENDS in Microbiology Vol.9 No.7 July 2001
Slide 5
Lysogeny:
Phage Entry into Bacterial Hosts
Bobby Chaggar
Yordanos Teferra
attP and attB regions
attP site of L5 phage used in comparing phages and similar
attB site of M. Smegmatis used in finding other att sites.
Search for Similar attP
regions
Search for similar attB
sites
M. Segmatis: GCGGGCGTAGCTCAATGGTAGAGCCCTAG
TCTTCCAAACTAGCTACGCGGGTTCGATTCCCGTCGCCCGCTC
Msme-155.Msmeg-11642 (4764496 -> 4764566) Aliases:(tRNA-Gly”)
M. Vanbaalenii:
GCGGGCGTAGCTCAATGGTAGAGCCCTAG
TCTTCCAAACTAGCTACGCGGGTTCGATTCCCGTCGCCCGCTCCA
Mvan-PYR-1.Mvan-PYR-1-10996 (4324373 -> 4324446) Aliases:(tRNA-Gly”)
M. SP.JLS:
GCGGGCGTAGCTCAATGGTAGAGCCCTAGTCTTCCAAACTAGCTACGCGGGTTCGATTCCCGTC
GCCCGCTCCA
M-JLS.Mjls-9576 (3780254 -> 3780327) Aliases:(tRNA-Gly”)
The Search for Prophage
DNA in Mycobacteria
Sliding Window
Deviations in GC content
Proteins to Consider
• Tail tape measure protein
• Phage major capsid protein
• Large-subunit terminase
• Integrase
• excisionase
References
Gomathi, N.S. . "In silico analysis of mycobacteriophage Che12 genome: Characterization of genes
required to lysogenise Mycobacterium tuberculosis." ScienceDirect. 31. (2007): 82-91. Web.
Hatful, Graham. "Characterization of the Mycobacteriophage L5 Attachment Site, attp." JMB. 266.
(1997): 76-92.
Canchaya, C., Proux, C., Fournous, G., Bruttin, A., & Brussow, H. (2003). Prophage genomics. Microbiol
Mol Biol Rev. 2003 June; 67(2): 238–276. doi: 10.1128/MMBR.67.2.238-276.2003
Hendrix, R., Smith, M., Burns, R., Ford, M., & Hatfull, G. (1999). Evolutionary relationships among
diverse bacteriophages and prophages: All the world’s a phage. Proc Natl Acad Sci U S A. 1999
March 2; 96(5): 2192–2197. Evolution.
Karlin, S. (2001). Detecting anomalous gene clusters and pathogenicity islands in diverse bacterial
genomes. TRENDS in Microbiology Vol.9 No.7 July 2001
Slide 6
Lysogeny:
Phage Entry into Bacterial Hosts
Bobby Chaggar
Yordanos Teferra
attP and attB regions
attP site of L5 phage used in comparing phages and similar
attB site of M. Smegmatis used in finding other att sites.
Search for Similar attP
regions
Search for similar attB
sites
M. Segmatis: GCGGGCGTAGCTCAATGGTAGAGCCCTAG
TCTTCCAAACTAGCTACGCGGGTTCGATTCCCGTCGCCCGCTC
Msme-155.Msmeg-11642 (4764496 -> 4764566) Aliases:(tRNA-Gly”)
M. Vanbaalenii:
GCGGGCGTAGCTCAATGGTAGAGCCCTAG
TCTTCCAAACTAGCTACGCGGGTTCGATTCCCGTCGCCCGCTCCA
Mvan-PYR-1.Mvan-PYR-1-10996 (4324373 -> 4324446) Aliases:(tRNA-Gly”)
M. SP.JLS:
GCGGGCGTAGCTCAATGGTAGAGCCCTAGTCTTCCAAACTAGCTACGCGGGTTCGATTCCCGTC
GCCCGCTCCA
M-JLS.Mjls-9576 (3780254 -> 3780327) Aliases:(tRNA-Gly”)
The Search for Prophage
DNA in Mycobacteria
Sliding Window
Deviations in GC content
Proteins to Consider
• Tail tape measure protein
• Phage major capsid protein
• Large-subunit terminase
• Integrase
• excisionase
References
Gomathi, N.S. . "In silico analysis of mycobacteriophage Che12 genome: Characterization of genes
required to lysogenise Mycobacterium tuberculosis." ScienceDirect. 31. (2007): 82-91. Web.
Hatful, Graham. "Characterization of the Mycobacteriophage L5 Attachment Site, attp." JMB. 266.
(1997): 76-92.
Canchaya, C., Proux, C., Fournous, G., Bruttin, A., & Brussow, H. (2003). Prophage genomics. Microbiol
Mol Biol Rev. 2003 June; 67(2): 238–276. doi: 10.1128/MMBR.67.2.238-276.2003
Hendrix, R., Smith, M., Burns, R., Ford, M., & Hatfull, G. (1999). Evolutionary relationships among
diverse bacteriophages and prophages: All the world’s a phage. Proc Natl Acad Sci U S A. 1999
March 2; 96(5): 2192–2197. Evolution.
Karlin, S. (2001). Detecting anomalous gene clusters and pathogenicity islands in diverse bacterial
genomes. TRENDS in Microbiology Vol.9 No.7 July 2001
Slide 7
Lysogeny:
Phage Entry into Bacterial Hosts
Bobby Chaggar
Yordanos Teferra
attP and attB regions
attP site of L5 phage used in comparing phages and similar
attB site of M. Smegmatis used in finding other att sites.
Search for Similar attP
regions
Search for similar attB
sites
M. Segmatis: GCGGGCGTAGCTCAATGGTAGAGCCCTAG
TCTTCCAAACTAGCTACGCGGGTTCGATTCCCGTCGCCCGCTC
Msme-155.Msmeg-11642 (4764496 -> 4764566) Aliases:(tRNA-Gly”)
M. Vanbaalenii:
GCGGGCGTAGCTCAATGGTAGAGCCCTAG
TCTTCCAAACTAGCTACGCGGGTTCGATTCCCGTCGCCCGCTCCA
Mvan-PYR-1.Mvan-PYR-1-10996 (4324373 -> 4324446) Aliases:(tRNA-Gly”)
M. SP.JLS:
GCGGGCGTAGCTCAATGGTAGAGCCCTAGTCTTCCAAACTAGCTACGCGGGTTCGATTCCCGTC
GCCCGCTCCA
M-JLS.Mjls-9576 (3780254 -> 3780327) Aliases:(tRNA-Gly”)
The Search for Prophage
DNA in Mycobacteria
Sliding Window
Deviations in GC content
Proteins to Consider
• Tail tape measure protein
• Phage major capsid protein
• Large-subunit terminase
• Integrase
• excisionase
References
Gomathi, N.S. . "In silico analysis of mycobacteriophage Che12 genome: Characterization of genes
required to lysogenise Mycobacterium tuberculosis." ScienceDirect. 31. (2007): 82-91. Web.
Hatful, Graham. "Characterization of the Mycobacteriophage L5 Attachment Site, attp." JMB. 266.
(1997): 76-92.
Canchaya, C., Proux, C., Fournous, G., Bruttin, A., & Brussow, H. (2003). Prophage genomics. Microbiol
Mol Biol Rev. 2003 June; 67(2): 238–276. doi: 10.1128/MMBR.67.2.238-276.2003
Hendrix, R., Smith, M., Burns, R., Ford, M., & Hatfull, G. (1999). Evolutionary relationships among
diverse bacteriophages and prophages: All the world’s a phage. Proc Natl Acad Sci U S A. 1999
March 2; 96(5): 2192–2197. Evolution.
Karlin, S. (2001). Detecting anomalous gene clusters and pathogenicity islands in diverse bacterial
genomes. TRENDS in Microbiology Vol.9 No.7 July 2001
Slide 8
Lysogeny:
Phage Entry into Bacterial Hosts
Bobby Chaggar
Yordanos Teferra
attP and attB regions
attP site of L5 phage used in comparing phages and similar
attB site of M. Smegmatis used in finding other att sites.
Search for Similar attP
regions
Search for similar attB
sites
M. Segmatis: GCGGGCGTAGCTCAATGGTAGAGCCCTAG
TCTTCCAAACTAGCTACGCGGGTTCGATTCCCGTCGCCCGCTC
Msme-155.Msmeg-11642 (4764496 -> 4764566) Aliases:(tRNA-Gly”)
M. Vanbaalenii:
GCGGGCGTAGCTCAATGGTAGAGCCCTAG
TCTTCCAAACTAGCTACGCGGGTTCGATTCCCGTCGCCCGCTCCA
Mvan-PYR-1.Mvan-PYR-1-10996 (4324373 -> 4324446) Aliases:(tRNA-Gly”)
M. SP.JLS:
GCGGGCGTAGCTCAATGGTAGAGCCCTAGTCTTCCAAACTAGCTACGCGGGTTCGATTCCCGTC
GCCCGCTCCA
M-JLS.Mjls-9576 (3780254 -> 3780327) Aliases:(tRNA-Gly”)
The Search for Prophage
DNA in Mycobacteria
Sliding Window
Deviations in GC content
Proteins to Consider
• Tail tape measure protein
• Phage major capsid protein
• Large-subunit terminase
• Integrase
• excisionase
References
Gomathi, N.S. . "In silico analysis of mycobacteriophage Che12 genome: Characterization of genes
required to lysogenise Mycobacterium tuberculosis." ScienceDirect. 31. (2007): 82-91. Web.
Hatful, Graham. "Characterization of the Mycobacteriophage L5 Attachment Site, attp." JMB. 266.
(1997): 76-92.
Canchaya, C., Proux, C., Fournous, G., Bruttin, A., & Brussow, H. (2003). Prophage genomics. Microbiol
Mol Biol Rev. 2003 June; 67(2): 238–276. doi: 10.1128/MMBR.67.2.238-276.2003
Hendrix, R., Smith, M., Burns, R., Ford, M., & Hatfull, G. (1999). Evolutionary relationships among
diverse bacteriophages and prophages: All the world’s a phage. Proc Natl Acad Sci U S A. 1999
March 2; 96(5): 2192–2197. Evolution.
Karlin, S. (2001). Detecting anomalous gene clusters and pathogenicity islands in diverse bacterial
genomes. TRENDS in Microbiology Vol.9 No.7 July 2001
Slide 9
Lysogeny:
Phage Entry into Bacterial Hosts
Bobby Chaggar
Yordanos Teferra
attP and attB regions
attP site of L5 phage used in comparing phages and similar
attB site of M. Smegmatis used in finding other att sites.
Search for Similar attP
regions
Search for similar attB
sites
M. Segmatis: GCGGGCGTAGCTCAATGGTAGAGCCCTAG
TCTTCCAAACTAGCTACGCGGGTTCGATTCCCGTCGCCCGCTC
Msme-155.Msmeg-11642 (4764496 -> 4764566) Aliases:(tRNA-Gly”)
M. Vanbaalenii:
GCGGGCGTAGCTCAATGGTAGAGCCCTAG
TCTTCCAAACTAGCTACGCGGGTTCGATTCCCGTCGCCCGCTCCA
Mvan-PYR-1.Mvan-PYR-1-10996 (4324373 -> 4324446) Aliases:(tRNA-Gly”)
M. SP.JLS:
GCGGGCGTAGCTCAATGGTAGAGCCCTAGTCTTCCAAACTAGCTACGCGGGTTCGATTCCCGTC
GCCCGCTCCA
M-JLS.Mjls-9576 (3780254 -> 3780327) Aliases:(tRNA-Gly”)
The Search for Prophage
DNA in Mycobacteria
Sliding Window
Deviations in GC content
Proteins to Consider
• Tail tape measure protein
• Phage major capsid protein
• Large-subunit terminase
• Integrase
• excisionase
References
Gomathi, N.S. . "In silico analysis of mycobacteriophage Che12 genome: Characterization of genes
required to lysogenise Mycobacterium tuberculosis." ScienceDirect. 31. (2007): 82-91. Web.
Hatful, Graham. "Characterization of the Mycobacteriophage L5 Attachment Site, attp." JMB. 266.
(1997): 76-92.
Canchaya, C., Proux, C., Fournous, G., Bruttin, A., & Brussow, H. (2003). Prophage genomics. Microbiol
Mol Biol Rev. 2003 June; 67(2): 238–276. doi: 10.1128/MMBR.67.2.238-276.2003
Hendrix, R., Smith, M., Burns, R., Ford, M., & Hatfull, G. (1999). Evolutionary relationships among
diverse bacteriophages and prophages: All the world’s a phage. Proc Natl Acad Sci U S A. 1999
March 2; 96(5): 2192–2197. Evolution.
Karlin, S. (2001). Detecting anomalous gene clusters and pathogenicity islands in diverse bacterial
genomes. TRENDS in Microbiology Vol.9 No.7 July 2001
Slide 10
Lysogeny:
Phage Entry into Bacterial Hosts
Bobby Chaggar
Yordanos Teferra
attP and attB regions
attP site of L5 phage used in comparing phages and similar
attB site of M. Smegmatis used in finding other att sites.
Search for Similar attP
regions
Search for similar attB
sites
M. Segmatis: GCGGGCGTAGCTCAATGGTAGAGCCCTAG
TCTTCCAAACTAGCTACGCGGGTTCGATTCCCGTCGCCCGCTC
Msme-155.Msmeg-11642 (4764496 -> 4764566) Aliases:(tRNA-Gly”)
M. Vanbaalenii:
GCGGGCGTAGCTCAATGGTAGAGCCCTAG
TCTTCCAAACTAGCTACGCGGGTTCGATTCCCGTCGCCCGCTCCA
Mvan-PYR-1.Mvan-PYR-1-10996 (4324373 -> 4324446) Aliases:(tRNA-Gly”)
M. SP.JLS:
GCGGGCGTAGCTCAATGGTAGAGCCCTAGTCTTCCAAACTAGCTACGCGGGTTCGATTCCCGTC
GCCCGCTCCA
M-JLS.Mjls-9576 (3780254 -> 3780327) Aliases:(tRNA-Gly”)
The Search for Prophage
DNA in Mycobacteria
Sliding Window
Deviations in GC content
Proteins to Consider
• Tail tape measure protein
• Phage major capsid protein
• Large-subunit terminase
• Integrase
• excisionase
References
Gomathi, N.S. . "In silico analysis of mycobacteriophage Che12 genome: Characterization of genes
required to lysogenise Mycobacterium tuberculosis." ScienceDirect. 31. (2007): 82-91. Web.
Hatful, Graham. "Characterization of the Mycobacteriophage L5 Attachment Site, attp." JMB. 266.
(1997): 76-92.
Canchaya, C., Proux, C., Fournous, G., Bruttin, A., & Brussow, H. (2003). Prophage genomics. Microbiol
Mol Biol Rev. 2003 June; 67(2): 238–276. doi: 10.1128/MMBR.67.2.238-276.2003
Hendrix, R., Smith, M., Burns, R., Ford, M., & Hatfull, G. (1999). Evolutionary relationships among
diverse bacteriophages and prophages: All the world’s a phage. Proc Natl Acad Sci U S A. 1999
March 2; 96(5): 2192–2197. Evolution.
Karlin, S. (2001). Detecting anomalous gene clusters and pathogenicity islands in diverse bacterial
genomes. TRENDS in Microbiology Vol.9 No.7 July 2001
Slide 11
Lysogeny:
Phage Entry into Bacterial Hosts
Bobby Chaggar
Yordanos Teferra
attP and attB regions
attP site of L5 phage used in comparing phages and similar
attB site of M. Smegmatis used in finding other att sites.
Search for Similar attP
regions
Search for similar attB
sites
M. Segmatis: GCGGGCGTAGCTCAATGGTAGAGCCCTAG
TCTTCCAAACTAGCTACGCGGGTTCGATTCCCGTCGCCCGCTC
Msme-155.Msmeg-11642 (4764496 -> 4764566) Aliases:(tRNA-Gly”)
M. Vanbaalenii:
GCGGGCGTAGCTCAATGGTAGAGCCCTAG
TCTTCCAAACTAGCTACGCGGGTTCGATTCCCGTCGCCCGCTCCA
Mvan-PYR-1.Mvan-PYR-1-10996 (4324373 -> 4324446) Aliases:(tRNA-Gly”)
M. SP.JLS:
GCGGGCGTAGCTCAATGGTAGAGCCCTAGTCTTCCAAACTAGCTACGCGGGTTCGATTCCCGTC
GCCCGCTCCA
M-JLS.Mjls-9576 (3780254 -> 3780327) Aliases:(tRNA-Gly”)
The Search for Prophage
DNA in Mycobacteria
Sliding Window
Deviations in GC content
Proteins to Consider
• Tail tape measure protein
• Phage major capsid protein
• Large-subunit terminase
• Integrase
• excisionase
References
Gomathi, N.S. . "In silico analysis of mycobacteriophage Che12 genome: Characterization of genes
required to lysogenise Mycobacterium tuberculosis." ScienceDirect. 31. (2007): 82-91. Web.
Hatful, Graham. "Characterization of the Mycobacteriophage L5 Attachment Site, attp." JMB. 266.
(1997): 76-92.
Canchaya, C., Proux, C., Fournous, G., Bruttin, A., & Brussow, H. (2003). Prophage genomics. Microbiol
Mol Biol Rev. 2003 June; 67(2): 238–276. doi: 10.1128/MMBR.67.2.238-276.2003
Hendrix, R., Smith, M., Burns, R., Ford, M., & Hatfull, G. (1999). Evolutionary relationships among
diverse bacteriophages and prophages: All the world’s a phage. Proc Natl Acad Sci U S A. 1999
March 2; 96(5): 2192–2197. Evolution.
Karlin, S. (2001). Detecting anomalous gene clusters and pathogenicity islands in diverse bacterial
genomes. TRENDS in Microbiology Vol.9 No.7 July 2001
Lysogeny:
Phage Entry into Bacterial Hosts
Bobby Chaggar
Yordanos Teferra
attP and attB regions
attP site of L5 phage used in comparing phages and similar
attB site of M. Smegmatis used in finding other att sites.
Search for Similar attP
regions
Search for similar attB
sites
M. Segmatis: GCGGGCGTAGCTCAATGGTAGAGCCCTAG
TCTTCCAAACTAGCTACGCGGGTTCGATTCCCGTCGCCCGCTC
Msme-155.Msmeg-11642 (4764496 -> 4764566) Aliases:(tRNA-Gly”)
M. Vanbaalenii:
GCGGGCGTAGCTCAATGGTAGAGCCCTAG
TCTTCCAAACTAGCTACGCGGGTTCGATTCCCGTCGCCCGCTCCA
Mvan-PYR-1.Mvan-PYR-1-10996 (4324373 -> 4324446) Aliases:(tRNA-Gly”)
M. SP.JLS:
GCGGGCGTAGCTCAATGGTAGAGCCCTAGTCTTCCAAACTAGCTACGCGGGTTCGATTCCCGTC
GCCCGCTCCA
M-JLS.Mjls-9576 (3780254 -> 3780327) Aliases:(tRNA-Gly”)
The Search for Prophage
DNA in Mycobacteria
Sliding Window
Deviations in GC content
Proteins to Consider
• Tail tape measure protein
• Phage major capsid protein
• Large-subunit terminase
• Integrase
• excisionase
References
Gomathi, N.S. . "In silico analysis of mycobacteriophage Che12 genome: Characterization of genes
required to lysogenise Mycobacterium tuberculosis." ScienceDirect. 31. (2007): 82-91. Web.
Hatful, Graham. "Characterization of the Mycobacteriophage L5 Attachment Site, attp." JMB. 266.
(1997): 76-92.
Canchaya, C., Proux, C., Fournous, G., Bruttin, A., & Brussow, H. (2003). Prophage genomics. Microbiol
Mol Biol Rev. 2003 June; 67(2): 238–276. doi: 10.1128/MMBR.67.2.238-276.2003
Hendrix, R., Smith, M., Burns, R., Ford, M., & Hatfull, G. (1999). Evolutionary relationships among
diverse bacteriophages and prophages: All the world’s a phage. Proc Natl Acad Sci U S A. 1999
March 2; 96(5): 2192–2197. Evolution.
Karlin, S. (2001). Detecting anomalous gene clusters and pathogenicity islands in diverse bacterial
genomes. TRENDS in Microbiology Vol.9 No.7 July 2001
Slide 2
Lysogeny:
Phage Entry into Bacterial Hosts
Bobby Chaggar
Yordanos Teferra
attP and attB regions
attP site of L5 phage used in comparing phages and similar
attB site of M. Smegmatis used in finding other att sites.
Search for Similar attP
regions
Search for similar attB
sites
M. Segmatis: GCGGGCGTAGCTCAATGGTAGAGCCCTAG
TCTTCCAAACTAGCTACGCGGGTTCGATTCCCGTCGCCCGCTC
Msme-155.Msmeg-11642 (4764496 -> 4764566) Aliases:(tRNA-Gly”)
M. Vanbaalenii:
GCGGGCGTAGCTCAATGGTAGAGCCCTAG
TCTTCCAAACTAGCTACGCGGGTTCGATTCCCGTCGCCCGCTCCA
Mvan-PYR-1.Mvan-PYR-1-10996 (4324373 -> 4324446) Aliases:(tRNA-Gly”)
M. SP.JLS:
GCGGGCGTAGCTCAATGGTAGAGCCCTAGTCTTCCAAACTAGCTACGCGGGTTCGATTCCCGTC
GCCCGCTCCA
M-JLS.Mjls-9576 (3780254 -> 3780327) Aliases:(tRNA-Gly”)
The Search for Prophage
DNA in Mycobacteria
Sliding Window
Deviations in GC content
Proteins to Consider
• Tail tape measure protein
• Phage major capsid protein
• Large-subunit terminase
• Integrase
• excisionase
References
Gomathi, N.S. . "In silico analysis of mycobacteriophage Che12 genome: Characterization of genes
required to lysogenise Mycobacterium tuberculosis." ScienceDirect. 31. (2007): 82-91. Web.
Hatful, Graham. "Characterization of the Mycobacteriophage L5 Attachment Site, attp." JMB. 266.
(1997): 76-92.
Canchaya, C., Proux, C., Fournous, G., Bruttin, A., & Brussow, H. (2003). Prophage genomics. Microbiol
Mol Biol Rev. 2003 June; 67(2): 238–276. doi: 10.1128/MMBR.67.2.238-276.2003
Hendrix, R., Smith, M., Burns, R., Ford, M., & Hatfull, G. (1999). Evolutionary relationships among
diverse bacteriophages and prophages: All the world’s a phage. Proc Natl Acad Sci U S A. 1999
March 2; 96(5): 2192–2197. Evolution.
Karlin, S. (2001). Detecting anomalous gene clusters and pathogenicity islands in diverse bacterial
genomes. TRENDS in Microbiology Vol.9 No.7 July 2001
Slide 3
Lysogeny:
Phage Entry into Bacterial Hosts
Bobby Chaggar
Yordanos Teferra
attP and attB regions
attP site of L5 phage used in comparing phages and similar
attB site of M. Smegmatis used in finding other att sites.
Search for Similar attP
regions
Search for similar attB
sites
M. Segmatis: GCGGGCGTAGCTCAATGGTAGAGCCCTAG
TCTTCCAAACTAGCTACGCGGGTTCGATTCCCGTCGCCCGCTC
Msme-155.Msmeg-11642 (4764496 -> 4764566) Aliases:(tRNA-Gly”)
M. Vanbaalenii:
GCGGGCGTAGCTCAATGGTAGAGCCCTAG
TCTTCCAAACTAGCTACGCGGGTTCGATTCCCGTCGCCCGCTCCA
Mvan-PYR-1.Mvan-PYR-1-10996 (4324373 -> 4324446) Aliases:(tRNA-Gly”)
M. SP.JLS:
GCGGGCGTAGCTCAATGGTAGAGCCCTAGTCTTCCAAACTAGCTACGCGGGTTCGATTCCCGTC
GCCCGCTCCA
M-JLS.Mjls-9576 (3780254 -> 3780327) Aliases:(tRNA-Gly”)
The Search for Prophage
DNA in Mycobacteria
Sliding Window
Deviations in GC content
Proteins to Consider
• Tail tape measure protein
• Phage major capsid protein
• Large-subunit terminase
• Integrase
• excisionase
References
Gomathi, N.S. . "In silico analysis of mycobacteriophage Che12 genome: Characterization of genes
required to lysogenise Mycobacterium tuberculosis." ScienceDirect. 31. (2007): 82-91. Web.
Hatful, Graham. "Characterization of the Mycobacteriophage L5 Attachment Site, attp." JMB. 266.
(1997): 76-92.
Canchaya, C., Proux, C., Fournous, G., Bruttin, A., & Brussow, H. (2003). Prophage genomics. Microbiol
Mol Biol Rev. 2003 June; 67(2): 238–276. doi: 10.1128/MMBR.67.2.238-276.2003
Hendrix, R., Smith, M., Burns, R., Ford, M., & Hatfull, G. (1999). Evolutionary relationships among
diverse bacteriophages and prophages: All the world’s a phage. Proc Natl Acad Sci U S A. 1999
March 2; 96(5): 2192–2197. Evolution.
Karlin, S. (2001). Detecting anomalous gene clusters and pathogenicity islands in diverse bacterial
genomes. TRENDS in Microbiology Vol.9 No.7 July 2001
Slide 4
Lysogeny:
Phage Entry into Bacterial Hosts
Bobby Chaggar
Yordanos Teferra
attP and attB regions
attP site of L5 phage used in comparing phages and similar
attB site of M. Smegmatis used in finding other att sites.
Search for Similar attP
regions
Search for similar attB
sites
M. Segmatis: GCGGGCGTAGCTCAATGGTAGAGCCCTAG
TCTTCCAAACTAGCTACGCGGGTTCGATTCCCGTCGCCCGCTC
Msme-155.Msmeg-11642 (4764496 -> 4764566) Aliases:(tRNA-Gly”)
M. Vanbaalenii:
GCGGGCGTAGCTCAATGGTAGAGCCCTAG
TCTTCCAAACTAGCTACGCGGGTTCGATTCCCGTCGCCCGCTCCA
Mvan-PYR-1.Mvan-PYR-1-10996 (4324373 -> 4324446) Aliases:(tRNA-Gly”)
M. SP.JLS:
GCGGGCGTAGCTCAATGGTAGAGCCCTAGTCTTCCAAACTAGCTACGCGGGTTCGATTCCCGTC
GCCCGCTCCA
M-JLS.Mjls-9576 (3780254 -> 3780327) Aliases:(tRNA-Gly”)
The Search for Prophage
DNA in Mycobacteria
Sliding Window
Deviations in GC content
Proteins to Consider
• Tail tape measure protein
• Phage major capsid protein
• Large-subunit terminase
• Integrase
• excisionase
References
Gomathi, N.S. . "In silico analysis of mycobacteriophage Che12 genome: Characterization of genes
required to lysogenise Mycobacterium tuberculosis." ScienceDirect. 31. (2007): 82-91. Web.
Hatful, Graham. "Characterization of the Mycobacteriophage L5 Attachment Site, attp." JMB. 266.
(1997): 76-92.
Canchaya, C., Proux, C., Fournous, G., Bruttin, A., & Brussow, H. (2003). Prophage genomics. Microbiol
Mol Biol Rev. 2003 June; 67(2): 238–276. doi: 10.1128/MMBR.67.2.238-276.2003
Hendrix, R., Smith, M., Burns, R., Ford, M., & Hatfull, G. (1999). Evolutionary relationships among
diverse bacteriophages and prophages: All the world’s a phage. Proc Natl Acad Sci U S A. 1999
March 2; 96(5): 2192–2197. Evolution.
Karlin, S. (2001). Detecting anomalous gene clusters and pathogenicity islands in diverse bacterial
genomes. TRENDS in Microbiology Vol.9 No.7 July 2001
Slide 5
Lysogeny:
Phage Entry into Bacterial Hosts
Bobby Chaggar
Yordanos Teferra
attP and attB regions
attP site of L5 phage used in comparing phages and similar
attB site of M. Smegmatis used in finding other att sites.
Search for Similar attP
regions
Search for similar attB
sites
M. Segmatis: GCGGGCGTAGCTCAATGGTAGAGCCCTAG
TCTTCCAAACTAGCTACGCGGGTTCGATTCCCGTCGCCCGCTC
Msme-155.Msmeg-11642 (4764496 -> 4764566) Aliases:(tRNA-Gly”)
M. Vanbaalenii:
GCGGGCGTAGCTCAATGGTAGAGCCCTAG
TCTTCCAAACTAGCTACGCGGGTTCGATTCCCGTCGCCCGCTCCA
Mvan-PYR-1.Mvan-PYR-1-10996 (4324373 -> 4324446) Aliases:(tRNA-Gly”)
M. SP.JLS:
GCGGGCGTAGCTCAATGGTAGAGCCCTAGTCTTCCAAACTAGCTACGCGGGTTCGATTCCCGTC
GCCCGCTCCA
M-JLS.Mjls-9576 (3780254 -> 3780327) Aliases:(tRNA-Gly”)
The Search for Prophage
DNA in Mycobacteria
Sliding Window
Deviations in GC content
Proteins to Consider
• Tail tape measure protein
• Phage major capsid protein
• Large-subunit terminase
• Integrase
• excisionase
References
Gomathi, N.S. . "In silico analysis of mycobacteriophage Che12 genome: Characterization of genes
required to lysogenise Mycobacterium tuberculosis." ScienceDirect. 31. (2007): 82-91. Web.
Hatful, Graham. "Characterization of the Mycobacteriophage L5 Attachment Site, attp." JMB. 266.
(1997): 76-92.
Canchaya, C., Proux, C., Fournous, G., Bruttin, A., & Brussow, H. (2003). Prophage genomics. Microbiol
Mol Biol Rev. 2003 June; 67(2): 238–276. doi: 10.1128/MMBR.67.2.238-276.2003
Hendrix, R., Smith, M., Burns, R., Ford, M., & Hatfull, G. (1999). Evolutionary relationships among
diverse bacteriophages and prophages: All the world’s a phage. Proc Natl Acad Sci U S A. 1999
March 2; 96(5): 2192–2197. Evolution.
Karlin, S. (2001). Detecting anomalous gene clusters and pathogenicity islands in diverse bacterial
genomes. TRENDS in Microbiology Vol.9 No.7 July 2001
Slide 6
Lysogeny:
Phage Entry into Bacterial Hosts
Bobby Chaggar
Yordanos Teferra
attP and attB regions
attP site of L5 phage used in comparing phages and similar
attB site of M. Smegmatis used in finding other att sites.
Search for Similar attP
regions
Search for similar attB
sites
M. Segmatis: GCGGGCGTAGCTCAATGGTAGAGCCCTAG
TCTTCCAAACTAGCTACGCGGGTTCGATTCCCGTCGCCCGCTC
Msme-155.Msmeg-11642 (4764496 -> 4764566) Aliases:(tRNA-Gly”)
M. Vanbaalenii:
GCGGGCGTAGCTCAATGGTAGAGCCCTAG
TCTTCCAAACTAGCTACGCGGGTTCGATTCCCGTCGCCCGCTCCA
Mvan-PYR-1.Mvan-PYR-1-10996 (4324373 -> 4324446) Aliases:(tRNA-Gly”)
M. SP.JLS:
GCGGGCGTAGCTCAATGGTAGAGCCCTAGTCTTCCAAACTAGCTACGCGGGTTCGATTCCCGTC
GCCCGCTCCA
M-JLS.Mjls-9576 (3780254 -> 3780327) Aliases:(tRNA-Gly”)
The Search for Prophage
DNA in Mycobacteria
Sliding Window
Deviations in GC content
Proteins to Consider
• Tail tape measure protein
• Phage major capsid protein
• Large-subunit terminase
• Integrase
• excisionase
References
Gomathi, N.S. . "In silico analysis of mycobacteriophage Che12 genome: Characterization of genes
required to lysogenise Mycobacterium tuberculosis." ScienceDirect. 31. (2007): 82-91. Web.
Hatful, Graham. "Characterization of the Mycobacteriophage L5 Attachment Site, attp." JMB. 266.
(1997): 76-92.
Canchaya, C., Proux, C., Fournous, G., Bruttin, A., & Brussow, H. (2003). Prophage genomics. Microbiol
Mol Biol Rev. 2003 June; 67(2): 238–276. doi: 10.1128/MMBR.67.2.238-276.2003
Hendrix, R., Smith, M., Burns, R., Ford, M., & Hatfull, G. (1999). Evolutionary relationships among
diverse bacteriophages and prophages: All the world’s a phage. Proc Natl Acad Sci U S A. 1999
March 2; 96(5): 2192–2197. Evolution.
Karlin, S. (2001). Detecting anomalous gene clusters and pathogenicity islands in diverse bacterial
genomes. TRENDS in Microbiology Vol.9 No.7 July 2001
Slide 7
Lysogeny:
Phage Entry into Bacterial Hosts
Bobby Chaggar
Yordanos Teferra
attP and attB regions
attP site of L5 phage used in comparing phages and similar
attB site of M. Smegmatis used in finding other att sites.
Search for Similar attP
regions
Search for similar attB
sites
M. Segmatis: GCGGGCGTAGCTCAATGGTAGAGCCCTAG
TCTTCCAAACTAGCTACGCGGGTTCGATTCCCGTCGCCCGCTC
Msme-155.Msmeg-11642 (4764496 -> 4764566) Aliases:(tRNA-Gly”)
M. Vanbaalenii:
GCGGGCGTAGCTCAATGGTAGAGCCCTAG
TCTTCCAAACTAGCTACGCGGGTTCGATTCCCGTCGCCCGCTCCA
Mvan-PYR-1.Mvan-PYR-1-10996 (4324373 -> 4324446) Aliases:(tRNA-Gly”)
M. SP.JLS:
GCGGGCGTAGCTCAATGGTAGAGCCCTAGTCTTCCAAACTAGCTACGCGGGTTCGATTCCCGTC
GCCCGCTCCA
M-JLS.Mjls-9576 (3780254 -> 3780327) Aliases:(tRNA-Gly”)
The Search for Prophage
DNA in Mycobacteria
Sliding Window
Deviations in GC content
Proteins to Consider
• Tail tape measure protein
• Phage major capsid protein
• Large-subunit terminase
• Integrase
• excisionase
References
Gomathi, N.S. . "In silico analysis of mycobacteriophage Che12 genome: Characterization of genes
required to lysogenise Mycobacterium tuberculosis." ScienceDirect. 31. (2007): 82-91. Web.
Hatful, Graham. "Characterization of the Mycobacteriophage L5 Attachment Site, attp." JMB. 266.
(1997): 76-92.
Canchaya, C., Proux, C., Fournous, G., Bruttin, A., & Brussow, H. (2003). Prophage genomics. Microbiol
Mol Biol Rev. 2003 June; 67(2): 238–276. doi: 10.1128/MMBR.67.2.238-276.2003
Hendrix, R., Smith, M., Burns, R., Ford, M., & Hatfull, G. (1999). Evolutionary relationships among
diverse bacteriophages and prophages: All the world’s a phage. Proc Natl Acad Sci U S A. 1999
March 2; 96(5): 2192–2197. Evolution.
Karlin, S. (2001). Detecting anomalous gene clusters and pathogenicity islands in diverse bacterial
genomes. TRENDS in Microbiology Vol.9 No.7 July 2001
Slide 8
Lysogeny:
Phage Entry into Bacterial Hosts
Bobby Chaggar
Yordanos Teferra
attP and attB regions
attP site of L5 phage used in comparing phages and similar
attB site of M. Smegmatis used in finding other att sites.
Search for Similar attP
regions
Search for similar attB
sites
M. Segmatis: GCGGGCGTAGCTCAATGGTAGAGCCCTAG
TCTTCCAAACTAGCTACGCGGGTTCGATTCCCGTCGCCCGCTC
Msme-155.Msmeg-11642 (4764496 -> 4764566) Aliases:(tRNA-Gly”)
M. Vanbaalenii:
GCGGGCGTAGCTCAATGGTAGAGCCCTAG
TCTTCCAAACTAGCTACGCGGGTTCGATTCCCGTCGCCCGCTCCA
Mvan-PYR-1.Mvan-PYR-1-10996 (4324373 -> 4324446) Aliases:(tRNA-Gly”)
M. SP.JLS:
GCGGGCGTAGCTCAATGGTAGAGCCCTAGTCTTCCAAACTAGCTACGCGGGTTCGATTCCCGTC
GCCCGCTCCA
M-JLS.Mjls-9576 (3780254 -> 3780327) Aliases:(tRNA-Gly”)
The Search for Prophage
DNA in Mycobacteria
Sliding Window
Deviations in GC content
Proteins to Consider
• Tail tape measure protein
• Phage major capsid protein
• Large-subunit terminase
• Integrase
• excisionase
References
Gomathi, N.S. . "In silico analysis of mycobacteriophage Che12 genome: Characterization of genes
required to lysogenise Mycobacterium tuberculosis." ScienceDirect. 31. (2007): 82-91. Web.
Hatful, Graham. "Characterization of the Mycobacteriophage L5 Attachment Site, attp." JMB. 266.
(1997): 76-92.
Canchaya, C., Proux, C., Fournous, G., Bruttin, A., & Brussow, H. (2003). Prophage genomics. Microbiol
Mol Biol Rev. 2003 June; 67(2): 238–276. doi: 10.1128/MMBR.67.2.238-276.2003
Hendrix, R., Smith, M., Burns, R., Ford, M., & Hatfull, G. (1999). Evolutionary relationships among
diverse bacteriophages and prophages: All the world’s a phage. Proc Natl Acad Sci U S A. 1999
March 2; 96(5): 2192–2197. Evolution.
Karlin, S. (2001). Detecting anomalous gene clusters and pathogenicity islands in diverse bacterial
genomes. TRENDS in Microbiology Vol.9 No.7 July 2001
Slide 9
Lysogeny:
Phage Entry into Bacterial Hosts
Bobby Chaggar
Yordanos Teferra
attP and attB regions
attP site of L5 phage used in comparing phages and similar
attB site of M. Smegmatis used in finding other att sites.
Search for Similar attP
regions
Search for similar attB
sites
M. Segmatis: GCGGGCGTAGCTCAATGGTAGAGCCCTAG
TCTTCCAAACTAGCTACGCGGGTTCGATTCCCGTCGCCCGCTC
Msme-155.Msmeg-11642 (4764496 -> 4764566) Aliases:(tRNA-Gly”)
M. Vanbaalenii:
GCGGGCGTAGCTCAATGGTAGAGCCCTAG
TCTTCCAAACTAGCTACGCGGGTTCGATTCCCGTCGCCCGCTCCA
Mvan-PYR-1.Mvan-PYR-1-10996 (4324373 -> 4324446) Aliases:(tRNA-Gly”)
M. SP.JLS:
GCGGGCGTAGCTCAATGGTAGAGCCCTAGTCTTCCAAACTAGCTACGCGGGTTCGATTCCCGTC
GCCCGCTCCA
M-JLS.Mjls-9576 (3780254 -> 3780327) Aliases:(tRNA-Gly”)
The Search for Prophage
DNA in Mycobacteria
Sliding Window
Deviations in GC content
Proteins to Consider
• Tail tape measure protein
• Phage major capsid protein
• Large-subunit terminase
• Integrase
• excisionase
References
Gomathi, N.S. . "In silico analysis of mycobacteriophage Che12 genome: Characterization of genes
required to lysogenise Mycobacterium tuberculosis." ScienceDirect. 31. (2007): 82-91. Web.
Hatful, Graham. "Characterization of the Mycobacteriophage L5 Attachment Site, attp." JMB. 266.
(1997): 76-92.
Canchaya, C., Proux, C., Fournous, G., Bruttin, A., & Brussow, H. (2003). Prophage genomics. Microbiol
Mol Biol Rev. 2003 June; 67(2): 238–276. doi: 10.1128/MMBR.67.2.238-276.2003
Hendrix, R., Smith, M., Burns, R., Ford, M., & Hatfull, G. (1999). Evolutionary relationships among
diverse bacteriophages and prophages: All the world’s a phage. Proc Natl Acad Sci U S A. 1999
March 2; 96(5): 2192–2197. Evolution.
Karlin, S. (2001). Detecting anomalous gene clusters and pathogenicity islands in diverse bacterial
genomes. TRENDS in Microbiology Vol.9 No.7 July 2001
Slide 10
Lysogeny:
Phage Entry into Bacterial Hosts
Bobby Chaggar
Yordanos Teferra
attP and attB regions
attP site of L5 phage used in comparing phages and similar
attB site of M. Smegmatis used in finding other att sites.
Search for Similar attP
regions
Search for similar attB
sites
M. Segmatis: GCGGGCGTAGCTCAATGGTAGAGCCCTAG
TCTTCCAAACTAGCTACGCGGGTTCGATTCCCGTCGCCCGCTC
Msme-155.Msmeg-11642 (4764496 -> 4764566) Aliases:(tRNA-Gly”)
M. Vanbaalenii:
GCGGGCGTAGCTCAATGGTAGAGCCCTAG
TCTTCCAAACTAGCTACGCGGGTTCGATTCCCGTCGCCCGCTCCA
Mvan-PYR-1.Mvan-PYR-1-10996 (4324373 -> 4324446) Aliases:(tRNA-Gly”)
M. SP.JLS:
GCGGGCGTAGCTCAATGGTAGAGCCCTAGTCTTCCAAACTAGCTACGCGGGTTCGATTCCCGTC
GCCCGCTCCA
M-JLS.Mjls-9576 (3780254 -> 3780327) Aliases:(tRNA-Gly”)
The Search for Prophage
DNA in Mycobacteria
Sliding Window
Deviations in GC content
Proteins to Consider
• Tail tape measure protein
• Phage major capsid protein
• Large-subunit terminase
• Integrase
• excisionase
References
Gomathi, N.S. . "In silico analysis of mycobacteriophage Che12 genome: Characterization of genes
required to lysogenise Mycobacterium tuberculosis." ScienceDirect. 31. (2007): 82-91. Web.
Hatful, Graham. "Characterization of the Mycobacteriophage L5 Attachment Site, attp." JMB. 266.
(1997): 76-92.
Canchaya, C., Proux, C., Fournous, G., Bruttin, A., & Brussow, H. (2003). Prophage genomics. Microbiol
Mol Biol Rev. 2003 June; 67(2): 238–276. doi: 10.1128/MMBR.67.2.238-276.2003
Hendrix, R., Smith, M., Burns, R., Ford, M., & Hatfull, G. (1999). Evolutionary relationships among
diverse bacteriophages and prophages: All the world’s a phage. Proc Natl Acad Sci U S A. 1999
March 2; 96(5): 2192–2197. Evolution.
Karlin, S. (2001). Detecting anomalous gene clusters and pathogenicity islands in diverse bacterial
genomes. TRENDS in Microbiology Vol.9 No.7 July 2001
Slide 11
Lysogeny:
Phage Entry into Bacterial Hosts
Bobby Chaggar
Yordanos Teferra
attP and attB regions
attP site of L5 phage used in comparing phages and similar
attB site of M. Smegmatis used in finding other att sites.
Search for Similar attP
regions
Search for similar attB
sites
M. Segmatis: GCGGGCGTAGCTCAATGGTAGAGCCCTAG
TCTTCCAAACTAGCTACGCGGGTTCGATTCCCGTCGCCCGCTC
Msme-155.Msmeg-11642 (4764496 -> 4764566) Aliases:(tRNA-Gly”)
M. Vanbaalenii:
GCGGGCGTAGCTCAATGGTAGAGCCCTAG
TCTTCCAAACTAGCTACGCGGGTTCGATTCCCGTCGCCCGCTCCA
Mvan-PYR-1.Mvan-PYR-1-10996 (4324373 -> 4324446) Aliases:(tRNA-Gly”)
M. SP.JLS:
GCGGGCGTAGCTCAATGGTAGAGCCCTAGTCTTCCAAACTAGCTACGCGGGTTCGATTCCCGTC
GCCCGCTCCA
M-JLS.Mjls-9576 (3780254 -> 3780327) Aliases:(tRNA-Gly”)
The Search for Prophage
DNA in Mycobacteria
Sliding Window
Deviations in GC content
Proteins to Consider
• Tail tape measure protein
• Phage major capsid protein
• Large-subunit terminase
• Integrase
• excisionase
References
Gomathi, N.S. . "In silico analysis of mycobacteriophage Che12 genome: Characterization of genes
required to lysogenise Mycobacterium tuberculosis." ScienceDirect. 31. (2007): 82-91. Web.
Hatful, Graham. "Characterization of the Mycobacteriophage L5 Attachment Site, attp." JMB. 266.
(1997): 76-92.
Canchaya, C., Proux, C., Fournous, G., Bruttin, A., & Brussow, H. (2003). Prophage genomics. Microbiol
Mol Biol Rev. 2003 June; 67(2): 238–276. doi: 10.1128/MMBR.67.2.238-276.2003
Hendrix, R., Smith, M., Burns, R., Ford, M., & Hatfull, G. (1999). Evolutionary relationships among
diverse bacteriophages and prophages: All the world’s a phage. Proc Natl Acad Sci U S A. 1999
March 2; 96(5): 2192–2197. Evolution.
Karlin, S. (2001). Detecting anomalous gene clusters and pathogenicity islands in diverse bacterial
genomes. TRENDS in Microbiology Vol.9 No.7 July 2001