Modified DNA in Phages DNA Modification Adenine methylation

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Modified DNA in Phages

Modified DNA in Phages

DNA Modification Adenine methylation Cytosine methylation

DNA Modification Adenine methylation Cytosine methylation

Uses of DNA Modification Protection against restriction

Uses of DNA Modification Protection against restriction

Uses of DNA Modification Protection against restriction Kobayashi I (2001). Nucl Acids Res 29:

Uses of DNA Modification Protection against restriction Kobayashi I (2001). Nucl Acids Res 29: 3742 -3756

Uses of DNA Modification Protection against restriction Kobayashi I (2001). Nucl Acids Res 29:

Uses of DNA Modification Protection against restriction Kobayashi I (2001). Nucl Acids Res 29: 3742 -3756

Uses of DNA Modification Protection against restriction Kobayashi I (2001). Nucl Acids Res 29:

Uses of DNA Modification Protection against restriction Kobayashi I (2001). Nucl Acids Res 29: 3742 -3756

Uses of DNA Modification Protection against restriction Kobayashi I (2001). Nucl Acids Res 29:

Uses of DNA Modification Protection against restriction Kobayashi I (2001). Nucl Acids Res 29: 3742 -3756 = DNA methyltransferase

Uses of DNA Modification Protection against restriction Kobayashi I (2001). Nucl Acids Res 29:

Uses of DNA Modification Protection against restriction Kobayashi I (2001). Nucl Acids Res 29: 3742 -3756

Goal Identify DNA methyltransferases (MT) in phages

Goal Identify DNA methyltransferases (MT) in phages

Goal Identify DNA methyltransferases (MT) in phages Focus on Cytosine MT

Goal Identify DNA methyltransferases (MT) in phages Focus on Cytosine MT

Cytosine methyltransferases What are they? Proven cases M. Bsa. HI M. Npu. ORFC 228

Cytosine methyltransferases What are they? Proven cases M. Bsa. HI M. Npu. ORFC 228 P M. Spl. ZORFNP M. Hind. V M. Nla. CORFDP M. Hgi. D 1 M. Hae. III Neely RK, Roberts RJ (2008). BMC Mol Biol 9: 48

Cytosine methyltransferases What are they? Proven cases Neely RK, Roberts RJ (2008). BMC Mol

Cytosine methyltransferases What are they? Proven cases Neely RK, Roberts RJ (2008). BMC Mol Biol 9: 48

Cytosine methyltransferases Find candidates Proven cases All phage proteins Query Targets Blast 44 phage

Cytosine methyltransferases Find candidates Proven cases All phage proteins Query Targets Blast 44 phage proteins, E < 0. 001 Meme Examples: Two mycobacteriophage proteins Blue 7 -0086 Babsiella-0054

Cytosine methyltransferases Do candidates have usual motifs? Proven cases I IV VIII IX X

Cytosine methyltransferases Do candidates have usual motifs? Proven cases I IV VIII IX X

Cytosine methyltransferases Do candidates have usual motifs? I p-Blue 7 -0086 IV VIII IX

Cytosine methyltransferases Do candidates have usual motifs? I p-Blue 7 -0086 IV VIII IX X

Cytosine methyltransferases Do candidates have usual motifs? I p-Babsiella-0054 IV VIII IX X

Cytosine methyltransferases Do candidates have usual motifs? I p-Babsiella-0054 IV VIII IX X

Cytosine methyltransferases Is C-terminus of Babsiella-0054 conserved? p-Babsiella-0054

Cytosine methyltransferases Is C-terminus of Babsiella-0054 conserved? p-Babsiella-0054

Cytosine methyltransferases Is C-terminus of Babsiella-0054 conserved? p-Babsiella-0054 All phage proteins Query Targets Blast

Cytosine methyltransferases Is C-terminus of Babsiella-0054 conserved? p-Babsiella-0054 All phage proteins Query Targets Blast

Cytosine methyltransferases Is C-terminus of Babsiella-0054 conserved? p-Babsiella-0054 p-Blue 7 -0086 All phage proteins

Cytosine methyltransferases Is C-terminus of Babsiella-0054 conserved? p-Babsiella-0054 p-Blue 7 -0086 All phage proteins Targets Query Blast Babsiella Blue 7 Eric. B Eagle I IV VIII X X I IV VIII X

Cytosine methyltransferases Why are C-MTases sometimes in two parts? • Nonessential connection Normal Babsiella

Cytosine methyltransferases Why are C-MTases sometimes in two parts? • Nonessential connection Normal Babsiella Blue 7 • Intron Babsiella Blue 7 Eric. B Eagle I IV VIII X X Intron boundaries?

Protection against restriction How? Site-specific modification

Protection against restriction How? Site-specific modification

Protection against restriction How? Site-specific modification Kobayashi I (2001). Nucl Acids Res 29: 3742

Protection against restriction How? Site-specific modification Kobayashi I (2001). Nucl Acids Res 29: 3742 -3756

Protection against restriction How? Site-specific modification • Adenine-specific methyltransferases • Cytosine-specific methyltransferases Kobayashi I

Protection against restriction How? Site-specific modification • Adenine-specific methyltransferases • Cytosine-specific methyltransferases Kobayashi I (2001). Nucl Acids Res 29: 3742 -3756

Protection against restriction How? Site-specific modification • Adenine-specific methyltransferases • Cytosine-specific methyltransferases Incorporation of

Protection against restriction How? Site-specific modification • Adenine-specific methyltransferases • Cytosine-specific methyltransferases Incorporation of modification nucleotides • d. CMP hydroxymethyl transferase d. CMP 5'-. . . T GCCATATCGCC. . . 3'-. . . ACGGTATAGCGG. . .

Protection against restriction How? Site-specific modification • Adenine-specific methyltransferases • Cytosine-specific methyltransferases Incorporation of

Protection against restriction How? Site-specific modification • Adenine-specific methyltransferases • Cytosine-specific methyltransferases Incorporation of modification nucleotides • d. CMP hydroxymethyl transferase • d. UMP hydroxymethyl transferase d. UMP 5'-. . . T GCCATATCGCC. . . 3'-. . . ACGGTATAGCGG. . . (U = hydroxy thymine)