SEA-PHAGES | lysin A

Link to this post \| posted 24 Apr, 2018 14:26
welkin	BD phages have a single endolysin, it should be labeled "lysin A".

Link to this post \| posted 09 Mar, 2020 00:38
cdshaffer	Based on this posting from Feb 2020: https://seaphages.org/forums/topic/5000/ Which I will repost here: `Just looked at 2 cluster AO2 phages, JKerns and StevieBAY. StevieBAY's gene 28 is an endolysin. It possesses all of domains we expect to see in an endolysin. Gene 64 codes for the CHAP endopeptidase domain of LysK (a Staphylococcus phage lysin gene). It is reported out as an endolysin also. We won't call either of them lysin A (Reserved only for mycobacteriophages for now, unless the phage genomes contains a lysin A and a lysin B.` And this in the approved terms (as of Feb 2020): `some arthrobacter and streptomyces phages have a single endolysin with domains not found in the Mycobacteriophages (like the CHAP domain). use "endolysin" rather than lysin A if the phage does not infect Mycobacterium and no lysin b can be identified.` The BD6 phage appear to have a lysin which is a very high quality HHpred hit (99.8 Prob, 97.2 coverage) to the N-ACETYLMURAMOYL-L-ALANINE AMIDASE crystal (2WKX_A) should annotation be the approved term "endolysin" or "lysin A, N-acetylmuramoyl-L-alanine amidase domain" Edited 09 Mar, 2020 00:50

Link to this post | posted 09 Mar, 2020 00:38

cdshaffer

Based on this posting from Feb 2020:
https://seaphages.org/forums/topic/5000/

Which I will repost here:

Just looked at 2 cluster AO2 phages, JKerns and StevieBAY. StevieBAY's
gene 28 is an endolysin. It possesses all of domains we expect to see in an
endolysin. Gene 64 codes for the CHAP endopeptidase domain of LysK (a
Staphylococcus phage lysin gene). It is reported out as an endolysin also.
We won't call either of them lysin A (Reserved only for mycobacteriophages
for now, unless the phage genomes contains a lysin A and a lysin B.

And this in the approved terms (as of Feb 2020):

some arthrobacter and streptomyces phages have a single endolysin
with domains not found in the Mycobacteriophages (like the CHAP domain).
use "endolysin" rather than lysin A if the phage does not infect
Mycobacterium and no lysin b can be identified.

The BD6 phage appear to have a lysin which is a very high quality HHpred hit (99.8 Prob, 97.2 coverage) to the N-ACETYLMURAMOYL-L-ALANINE AMIDASE crystal (2WKX_A)

should annotation be the approved term "endolysin" or "lysin A, N-acetylmuramoyl-L-alanine amidase domain"

Edited 09 Mar, 2020 00:50

Link to this post \| posted 09 Mar, 2020 12:33
welkin	Thanks Chris. This should be "endolysin". According to my most recent conversation with Graham about this, the Lysin A and B designations arose because there are two in the Mycobacteriophages. Other phages, which just have one, have historically just used the term "endolysin". So we will be changing all of the non-Mycobacteriophage lysins to "endolysin" except in cases in which we can identify a clear lysin B (I think this only applies to some of the Gordonia phages). I haven't gotten to updating the Streptomyces yet.

Link to this post | posted 09 Mar, 2020 12:33

welkin

Thanks Chris.
This should be "endolysin". According to my most recent conversation with Graham about this, the Lysin A and B designations arose because there are two in the Mycobacteriophages. Other phages, which just have one, have historically just used the term "endolysin". So we will be changing all of the non-Mycobacteriophage lysins to "endolysin" except in cases in which we can identify a clear lysin B (I think this only applies to some of the Gordonia phages).

I haven't gotten to updating the Streptomyces yet.

Link to this post \| posted 09 Mar, 2020 13:00
scaruso	I appreciate this conversation, by the way, and the new notes on the approved functions list. There was a lot written on lysin A structure (in Mycos) but not the limit on using the designation. So it's good to get the clarification. Steve

Link to this post \| posted 09 Mar, 2020 16:28
cdshaffer	OK the rule that "you must have a B, in order to have an A" makes sense to me. Thanks for the clarification.

Link to this post \| posted 09 Mar, 2020 18:52
lhughes	I think we've been trying to use "endolysin" unless it was specifically the Lysin A and B situation, so hopefully most of our more recent ones are already correct. Good to have the clarification.

Link to this post \| posted 17 Mar, 2020 00:42
debbie	Lee, Do you have any Streptomyces phage genomes with a lysin B? debbie

Link to this post \| posted 17 Mar, 2020 18:37
cdshaffer	I just searched the phamerator database. There are no genes from amy phage with host streptomyces that have lysin B as an annotation.

Link to this post \| posted 17 Mar, 2020 19:14
debbie	Chris, Thanks! Someday I will learn how to do the queries. debbie

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lysin A