SEA-PHAGES | Lysins in Gordonia

Link to this post \| posted 11 Aug, 2017 03:34
delesall	The Lysin A in Gordonia phage is encoded by two genes, representing two domains. In Gordonia phage Adgers, these two genes correspond to N-acetyl-BetaD-muramidase domain (pfam 01510) and to a peptidase domain (pfam 01551). In Gordonia phage SuperSulley, the two Lysin A genes are ORF 49 (start 37820) and ORF 50 (start 38485) and respectively correspond to a peptidase domain (pfam 13529) and to a glycoside hydrolase (cd00325). See Payne and Hatfull (2012 PlosOne - Mycobactteriophage Endolysins…. pfam 13529 is not listed in Table 1!

Link to this post | posted 11 Aug, 2017 03:34

The Lysin A in Gordonia phage is encoded by two genes, representing two domains.
In Gordonia phage Adgers, these two genes correspond to N-acetyl-BetaD-muramidase domain (pfam 01510) and to a peptidase domain (pfam 01551).
In Gordonia phage SuperSulley, the two Lysin A genes are ORF 49 (start 37820) and ORF 50 (start 38485) and respectively correspond to a peptidase domain (pfam 13529) and to a glycoside hydrolase (cd00325).
See Payne and Hatfull (2012 PlosOne - Mycobactteriophage Endolysins… smile

. pfam 13529 is not listed in Table 1!

Link to this post \| posted 31 Dec, 2017 19:50
smolloy123	Hi All, I have a question about split lysin A genes in the CR1 genomes versus the DM genomes. In Flapper, a cluster CR1 genome, the call was pretty straight forward as the HHPRED matched up wtih the approved functional calls "lysin A, protease M15 domain" and "lysin A, glycosyl hydrolase domain" for Flapper proteins gp52 and 53 in phamerator. But in SallySpecial, a DM phage, the two genes gp5 and 6 are more like the two genes in Strept phage C1 that has Lysin A gene product that encodes the peptidoglycan binding subunit and a second gene that encodes the catalytic gene. I called these genes using the approved functions but in hind sight I don't like the gp 5 call as the protease M15 domain. I attached the HHPRED results of the two SallySpecial genes. Any insight on this Welkin or Veronique or anyone? Thanks! Sally 756Kb

Link to this post | posted 31 Dec, 2017 19:50

smolloy123

Hi All,
I have a question about split lysin A genes in the CR1 genomes versus the DM genomes. In Flapper, a cluster CR1 genome, the call was pretty straight forward as the HHPRED matched up wtih the approved functional calls "lysin A, protease M15 domain" and "lysin A, glycosyl hydrolase domain" for Flapper proteins gp52 and 53 in phamerator.

But in SallySpecial, a DM phage, the two genes gp5 and 6 are more like the two genes in Strept phage C1 that has Lysin A gene product that encodes the peptidoglycan binding subunit and a second gene that encodes the catalytic gene. I called these genes using the approved functions but in hind sight I don't like the gp 5 call as the protease M15 domain. I attached the HHPRED results of the two SallySpecial genes.

Any insight on this Welkin or Veronique or anyone?

Thanks!
Sally

Link to this post \| posted 02 Jan, 2018 13:45
welkin	I am happy to add "lysin A, [insert domain name here]" to the list if you have some specific suggestions?

Link to this post \| posted 02 Jan, 2018 14:04
smolloy123	Hi Welin, Thanks! I suggest "lysin A, peptidoglycan binding domain."

Link to this post \| posted 30 Mar, 2018 17:37
coomansr	All: In Brylie, gp29 and gp30 correspond to the two lysin A genes. These match closely the two in BetterKatz (also 29 & 30). Is the correct annotation lysin A, protease M15 domain and lysin A, glycosyl hydrolase domain as in the approved list of functions or lysin A, N5 cysteine protease domain and lysin A, GH19 glycoside hydrolase domain, as in BetterKatz? Roy

Link to this post \| posted 22 May, 2018 15:46
fogartym1	I am also having problems deciding the best functional calls for Gordonia split lysin A genes. In the singleton phage Octobien14 the first lysin gene product shows evidence for being a peptidase domain - possibly C39-likeA - a subfamily of c39 peptidases. The functional call Lysin A, protease M15 domain just doesn't seem quite right. A more generic 'peptidase domain' might be a better fit? For the second lysin A gene, there is evidence for hydrolase: N-acetylmuramoyl-L-alanine amidase family. Would glycosyl hydrolase be the correct functional call here? Again, a less specific call like hydrolase domain feels safer! Thank you for any advice. HHPRED results are attached. Marie 91Kb

Link to this post | posted 22 May, 2018 15:46

fogartym1

I am also having problems deciding the best functional calls for Gordonia split lysin A genes.
In the singleton phage Octobien14 the first lysin gene product shows evidence for being a peptidase domain - possibly C39-likeA - a subfamily of c39 peptidases. The functional call Lysin A, protease M15 domain just doesn't seem quite right. A more generic 'peptidase domain' might be a better fit?

For the second lysin A gene, there is evidence for hydrolase: N-acetylmuramoyl-L-alanine amidase family. Would glycosyl hydrolase be the correct functional call here? Again, a less specific call like hydrolase domain feels safer!

Thank you for any advice. HHPRED results are attached.
Marie

Link to this post \| posted 22 May, 2018 15:47
fogartym1	the second Octobien lysin A HHPRED result 114Kb

Link to this post \| posted 23 May, 2018 13:28
welkin	Hi MArie, Do you have any BLAST results for lysins in the Mycobacteriophages? The lysin A domains were extensively characterized by Kim Payne in Graham's lab. My favorite way to assign the domains is to align the gordonia lysins with the phages from the Payne and Hatfull paper in 2012 about lysins. Kim really did that bench work, so if you have sequence alignment to those domains, you can feel confident about being more specific. Thanks!

Link to this post | posted 23 May, 2018 13:28

welkin

Hi MArie,
Do you have any BLAST results for lysins in the Mycobacteriophages? The lysin A domains were extensively characterized by Kim Payne in Graham's lab.
My favorite way to assign the domains is to align the gordonia lysins with the phages from the Payne and Hatfull paper in 2012 about lysins. Kim really did that bench work, so if you have sequence alignment to those domains, you can feel confident about being more specific.

Thanks!

Link to this post \| posted 24 May, 2018 02:05
fogartym1	Hi Welkin - This article is helpful, thank you. Based on this article, I would like to call Octobien14_gp36 as lysin A, N-acetyl-β-D-muramidase" - it has conserved domain pfam01510 as does phage BPs and BXZ1. It shows a 164 blast p score alignment (64 % query coverage) with lysin A of BPs. For Octobien_gp35, I would call it as lysin A, peptidase as does Supersulley mentioned in the first post above. Like Supersulley, it has conserved domain pfam 13529 and when blasted against Supersulley's lysin A, it has a score alignment of 129 (81% query coverage). Does this seem reasonable? Thanks Marie

Link to this post | posted 24 May, 2018 02:05

fogartym1

Hi Welkin - This article is helpful, thank you.

Based on this article, I would like to call Octobien14_gp36 as lysin A, N-acetyl-β-D-muramidase" - it has conserved domain pfam01510 as does phage BPs and BXZ1. It shows a 164 blast p score alignment (64 % query coverage) with lysin A of BPs.

For Octobien_gp35, I would call it as lysin A, peptidase as does Supersulley mentioned in the first post above.
Like Supersulley, it has conserved domain pfam 13529 and when blasted against Supersulley's lysin A, it has a score alignment of 129 (81% query coverage).

Does this seem reasonable?
Thanks
Marie

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