SEA-PHAGES | Two endolysins?

Link to this post \| posted 19 Feb, 2025 19:02
adiaz	Hello, We are annotated three different phages assigned to Cluster GK, all isolated from Microbacterium paraoxydans, and we're trying to determine if it's possible for podoviridae phages to have two endolysins. As reference, here's the relevant information for the two genes in phage SpiderBri: Gene 11 (Pham 199043) Start 11487, stop 12080 HHPRED: D-alanyl-D-alanine carboxypeptidase; 99.2% probability; 57% coverage; 8.6 e-11 Phagesdb BLAST: Endolysin; Footloose 23; 5 e-14 NCBI BLAST: M23 family metallopeptidase [actinomycetes]; 38% coverage; 20.7% identity; 3.83 e-14 Gene 12 (Pham 214664) Start 12150, stop 12740 HHPRED: Peptidase M23; membrane protein, 99.1% probability, 72% coverage, 2.9 e-8 Phagesdb BLAST: endolysin, protease M23 domain; Trapezoid 12, 7 e-23 NCBI BLAST: M23 family metallopeptidase; 79% coverage; 37% identity; 6.15 e-27 Conserved domain database: Peptidase family M23; 58.6% coverage; 50% identity; 1.13 e-28 Interestingly, gene 13 is a terminase while genes 14 (1 TMD) and 15 (2 TMD) are membrane proteins. Thank you, Arturo

Link to this post | posted 19 Feb, 2025 19:02

Hello,

We are annotated three different phages assigned to Cluster GK, all isolated from Microbacterium paraoxydans, and we're trying to determine if it's possible for podoviridae phages to have two endolysins. As reference, here's the relevant information for the two genes in phage SpiderBri:

Gene 11 (Pham 199043)
Start 11487, stop 12080
HHPRED: D-alanyl-D-alanine carboxypeptidase; 99.2% probability; 57% coverage; 8.6 e-11
Phagesdb BLAST: Endolysin; Footloose 23; 5 e-14
NCBI BLAST: M23 family metallopeptidase [actinomycetes]; 38% coverage; 20.7% identity; 3.83 e-14

Gene 12 (Pham 214664)
Start 12150, stop 12740
HHPRED: Peptidase M23; membrane protein, 99.1% probability, 72% coverage, 2.9 e-8
Phagesdb BLAST: endolysin, protease M23 domain; Trapezoid 12, 7 e-23
NCBI BLAST: M23 family metallopeptidase; 79% coverage; 37% identity; 6.15 e-27
Conserved domain database: Peptidase family M23; 58.6% coverage; 50% identity; 1.13 e-28

Interestingly, gene 13 is a terminase while genes 14 (1 TMD) and 15 (2 TMD) are membrane proteins.

Thank you,

Arturo

Link to this post \| posted 19 Feb, 2025 20:03
debbie	Arturo, Hi. i don't think that the lysis cassette is a reflection of virion morphology. Many phages in our collections have 2 gene that do the function(s) of the endolysins. the mycobacteriophage papers on endolysins are helpful to determine the domains of the endolysins. the exact structure of the cell well is not as clearly understood in the Microbacterium, so we have not seen the gene that corresponds to lysin B. But we have seen the lysin A (endolysin) function to be across 2 separate genes, just like this. Call you genes endolysin, but then list the prominent domain that it is hitting. https://pubmed.ncbi.nlm.nih.gov/22470512/ debie

Link to this post | posted 19 Feb, 2025 20:03

debbie

Arturo,
Hi. i don't think that the lysis cassette is a reflection of virion morphology. Many phages in our collections have 2 gene that do the function(s) of the endolysins. the mycobacteriophage papers on endolysins are helpful to determine the domains of the endolysins. the exact structure of the cell well is not as clearly understood in the Microbacterium, so we have not seen the gene that corresponds to lysin B. But we have seen the lysin A (endolysin) function to be across 2 separate genes, just like this. Call you genes endolysin, but then list the prominent domain that it is hitting.
https://pubmed.ncbi.nlm.nih.gov/22470512/
debie

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