SEA-PHAGES | Repressor vs HTH DNA binding proteins

Link to this post \| posted 23 Aug, 2018 14:38
debbie	At this time (8-23-18 ), we felt it prudent to call the DNA binding proteins around the integrases "helix-turn-helix DNA binding proteins", even thought 2 of them are hitting Lambda's CI. (Genome used in this evaluation are Nandita and Ryan). Edited 23 Aug, 2018 14:39

Link to this post \| posted 13 May, 2021 18:50
Pollenz	Given that these FF cluster phage have genes in PHAM 54987 (92 members and majority calls are immunity repressor) that hit to numerous repressors such as 5FD4_B (ComR; Streptococcus, Competence, Quorum sensing, ComR, TRANSCRIPTION REGULATOR; 2.9A {Streptococcus suis (strain 05ZYH33), 6H49_A (Orf20; SaPI, Repressor, STRUCTURAL PROTEIN; HET: SO4; 1.8A {Staphylococcus aureus}) and 5D50_D (Repressor; Repressor, Anti-repressor, complex, DNA BINDING PROTEIN; 2.49A {Salmonella phage SPC32H}) an immunity repressor call is consistent with the data and the location of the genes within an immunity cluster (gp35 in Popper, gp37 in Nandita and gp37 in Ryan). RS Pollenz Edited 13 May, 2021 19:16

Link to this post | posted 13 May, 2021 18:50

Pollenz

Given that these FF cluster phage have genes in PHAM 54987 (92 members and majority calls are immunity repressor) that hit to numerous repressors such as 5FD4_B (ComR; Streptococcus, Competence, Quorum sensing, ComR, TRANSCRIPTION REGULATOR; 2.9A {Streptococcus suis (strain 05ZYH33), 6H49_A (Orf20; SaPI, Repressor, STRUCTURAL PROTEIN; HET: SO4; 1.8A {Staphylococcus aureus}) and 5D50_D (Repressor; Repressor, Anti-repressor, complex, DNA BINDING PROTEIN; 2.49A {Salmonella phage SPC32H}) an immunity repressor call is consistent with the data and the location of the genes within an immunity cluster (gp35 in Popper, gp37 in Nandita and gp37 in Ryan).

RS Pollenz

Edited 13 May, 2021 19:16

Link to this post \| posted 05 Jun, 2023 17:55
MSMC	Pollenz Given that these FF cluster phage have genes in PHAM 54987 (92 members and majority calls are immunity repressor) that hit to numerous repressors such as 5FD4_B (ComR; Streptococcus, Competence, Quorum sensing, ComR, TRANSCRIPTION REGULATOR; 2.9A {Streptococcus suis (strain 05ZYH33), 6H49_A (Orf20; SaPI, Repressor, STRUCTURAL PROTEIN; HET: SO4; 1.8A {Staphylococcus aureus}) and 5D50_D (Repressor; Repressor, Anti-repressor, complex, DNA BINDING PROTEIN; 2.49A {Salmonella phage SPC32H}) an immunity repressor call is consistent with the data and the location of the genes within an immunity cluster (gp35 in Popper, gp37 in Nandita and gp37 in Ryan). Rick, do you still believe these should be called as immunity repressor? I'm QCing an FF phage now, and I've got two genes back to back that align well with the immunity repressor and excisionase. There are two tyrosine integrases present in the genome. I'm inclined to call this immunity repressor and excisionase (taking into account your argument above), but I don't know if there has been a change in consensus since this thread (https://seaphages.org/forums/topic/4785/).

Link to this post | posted 05 Jun, 2023 17:55

MSMC

Pollenz
Given that these FF cluster phage have genes in PHAM 54987 (92 members and majority calls are immunity repressor) that hit to numerous repressors such as 5FD4_B (ComR; Streptococcus, Competence, Quorum sensing, ComR, TRANSCRIPTION REGULATOR; 2.9A {Streptococcus suis (strain 05ZYH33), 6H49_A (Orf20; SaPI, Repressor, STRUCTURAL PROTEIN; HET: SO4; 1.8A {Staphylococcus aureus}) and 5D50_D (Repressor; Repressor, Anti-repressor, complex, DNA BINDING PROTEIN; 2.49A {Salmonella phage SPC32H}) an immunity repressor call is consistent with the data and the location of the genes within an immunity cluster (gp35 in Popper, gp37 in Nandita and gp37 in Ryan).

Rick, do you still believe these should be called as immunity repressor? I'm QCing an FF phage now, and I've got two genes back to back that align well with the immunity repressor and excisionase. There are two tyrosine integrases present in the genome. I'm inclined to call this immunity repressor and excisionase (taking into account your argument above), but I don't know if there has been a change in consensus since this thread (https://seaphages.org/forums/topic/4785/).

Link to this post \| posted 11 Jun, 2023 13:58
Pollenz	The "immunity cassette" region of the FF phages is rather complex and not canonical as it contains several integrases and various DNA binding proteins. Although there are proteins from these phages grouped to pham 88787 (as of 6/11/23) that have a majority call of immunity repressor, a deeper look at the size of the FF cluster proteins in pham 88787 show that the FF phages all have proteins that are <90 amino acids. Thus, they all contain a clear N-terminal HTH domain that maps to both C1 and C2 repressors, but they all LACK the important C-terminal dimerization domain that is essential to the function of the canonical C1/C2 proteins from lambda and other phages. Note that the great majority of other proteins in the pham are from G1 phages that have 1) a much more clearly defined immunity cassette and 2) HTH proteins that have the C-terminal dimerization domain and can be better defined as immunity represors. So, a more conservative HTH DNA binding domain call for the FF phages is probably warranted at this time for these smaller proteins until clear wet lab data can identify the precise function of these smaller proteins and their exact role in lysogeny. RS Pollenz

Link to this post | posted 11 Jun, 2023 13:58

Pollenz

The "immunity cassette" region of the FF phages is rather complex and not canonical as it contains several integrases and various DNA binding proteins. Although there are proteins from these phages grouped to pham 88787 (as of 6/11/23) that have a majority call of immunity repressor, a deeper look at the size of the FF cluster proteins in pham 88787 show that the FF phages all have proteins that are <90 amino acids. Thus, they all contain a clear N-terminal HTH domain that maps to both C1 and C2 repressors, but they all LACK the important C-terminal dimerization domain that is essential to the function of the canonical C1/C2 proteins from lambda and other phages. Note that the great majority of other proteins in the pham are from G1 phages that have 1) a much more clearly defined immunity cassette and 2) HTH proteins that have the C-terminal dimerization domain and can be better defined as immunity represors. So, a more conservative HTH DNA binding domain call for the FF phages is probably warranted at this time for these smaller proteins until clear wet lab data can identify the precise function of these smaller proteins and their exact role in lysogeny.

RS Pollenz

Link to this post \| posted 12 Jun, 2023 14:56
MSMC	Pollenz The "immunity cassette" region of the FF phages is rather complex and not canonical as it contains several integrases and various DNA binding proteins. Although there are proteins from these phages grouped to pham 88787 (as of 6/11/23) that have a majority call of immunity repressor, a deeper look at the size of the FF cluster proteins in pham 88787 show that the FF phages all have proteins that are <90 amino acids. Thus, they all contain a clear N-terminal HTH domain that maps to both C1 and C2 repressors, but they all LACK the important C-terminal dimerization domain that is essential to the function of the canonical C1/C2 proteins from lambda and other phages. Note that the great majority of other proteins in the pham are from G1 phages that have 1) a much more clearly defined immunity cassette and 2) HTH proteins that have the C-terminal dimerization domain and can be better defined as immunity represors. So, a more conservative HTH DNA binding domain call for the FF phages is probably warranted at this time for these smaller proteins until clear wet lab data can identify the precise function of these smaller proteins and their exact role in lysogeny. Thanks Rick, I was wondering about the C-terminal domains when I was looking at this. I agree, I'll stick with the HTH domain call.

Link to this post | posted 12 Jun, 2023 14:56

MSMC

Pollenz
The "immunity cassette" region of the FF phages is rather complex and not canonical as it contains several integrases and various DNA binding proteins. Although there are proteins from these phages grouped to pham 88787 (as of 6/11/23) that have a majority call of immunity repressor, a deeper look at the size of the FF cluster proteins in pham 88787 show that the FF phages all have proteins that are <90 amino acids. Thus, they all contain a clear N-terminal HTH domain that maps to both C1 and C2 repressors, but they all LACK the important C-terminal dimerization domain that is essential to the function of the canonical C1/C2 proteins from lambda and other phages. Note that the great majority of other proteins in the pham are from G1 phages that have 1) a much more clearly defined immunity cassette and 2) HTH proteins that have the C-terminal dimerization domain and can be better defined as immunity represors. So, a more conservative HTH DNA binding domain call for the FF phages is probably warranted at this time for these smaller proteins until clear wet lab data can identify the precise function of these smaller proteins and their exact role in lysogeny.

Thanks Rick, I was wondering about the C-terminal domains when I was looking at this. I agree, I'll stick with the HTH domain call.

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Repressor vs HTH DNA binding proteins