SEA-PHAGES | lysZ-like proteins?

Link to this post \| posted yesterday, 13:04
nic.vega	After Tom Bernhardt's talk at the symposium, is there an annotation we can use for lysZ-like proteins? For example, we have Atlantica gp21 (CDS 16204-16494): Canonical structure (per Tom's talk) is a N-terminal TMD + a variable-length helical domain. gp21 has a N-terminal TMD (approx. residues 5-25, annotated as "TMD" rather than "signal" by DeepTMHMMM, confirmed with SOSUI); AlphaFold predicts extended alpha helical domain High-probability, near-full-length hits on HHPred to bacterial FtsB (e.g. 6H9N_B; cell division protein with one TMD; sticks N terminal domain in the membrane & associates other cell division complex stuff on the C terminal domain) and to phage spanins (e.g. P39504). Similar length (97 aa) to these proteins (94-121 aa). Located at the end of the tail assembly genes, immediately before endolysin Amino acid sequence: MSPELLTAILGAGGLAAIVPKLIDGWKAWRSGRAAEEKDKNKGLVDRLAAAEVRLEAEIMWRRANEEYAATLRRLLIEVYGVPADKLPPWPVRRTS

Link to this post | posted yesterday, 13:04

After Tom Bernhardt's talk at the symposium, is there an annotation we can use for lysZ-like proteins? For example, we have Atlantica gp21 (CDS 16204-16494):

predicts

hits on HHPred

Located at the end of the tail assembly genes, immediately before endolysin
Amino acid sequence: MSPELLTAILGAGGLAAIVPKLIDGWKAWRSGRAAEEKDKNKGLVDRLAAAEVRLEAEIMWRRANEEYAATLRRLLIEVYGVPADKLPPWPVRRTS

Link to this post \| posted yesterday, 13:04
nic.vega	whoops forgot the .dnam5 33Kb

Link to this post \| posted today, 11:46
Pollenz	Hello Our lab at USF has been working on these cool TM genes now since 2022 (see: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0276603) and also have wet lab data supporting a lysis function for these 1TMD proteins in phages that infect M. smeg. In Arthrobacter phages, we also noted that the 1TMD appears to be upstream of the putative endolysins and that there are also 1-2 other TMD genes in the vicinity. We have also found up to 4 TMD encoding genes in phages that infect smeg and Gordonia as well as similar 1TMD encoded proteins that are NOT in the lysis cassette area with lysins. My opinion at the moment is that calling a LysZ function needs to wait until 1) the data is actually published and 2) that the function observed in the Corynebacterium is also confirmed in smeg and our other hosts. The 1TMD is clearly involved in lysis, but there are also other functions for very similar proteins described in the literature (see: https://journals.asm.org/doi/10.1128/mbio.00813-22?url_ver=Z39.88-2003&rfr_id=ori:rid:crossref.org&rfr_dat=cr_pub%20%200pubmed). RS Pollenz

Link to this post | posted today, 11:46

Pollenz

Hello

Our lab at USF has been working on these cool TM genes now since 2022 (see: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0276603) and also have wet lab data supporting a lysis function for these 1TMD proteins in phages that infect M. smeg. In Arthrobacter phages, we also noted that the 1TMD appears to be upstream of the putative endolysins and that there are also 1-2 other TMD genes in the vicinity. We have also found up to 4 TMD encoding genes in phages that infect smeg and Gordonia as well as similar 1TMD encoded proteins that are NOT in the lysis cassette area with lysins. My opinion at the moment is that calling a LysZ function needs to wait until 1) the data is actually published and 2) that the function observed in the Corynebacterium is also confirmed in smeg and our other hosts. The 1TMD is clearly involved in lysis, but there are also other functions for very similar proteins described in the literature (see: https://journals.asm.org/doi/10.1128/mbio.00813-22?url_ver=Z39.88-2003&rfr_id=ori:rid:crossref.org&rfr_dat=cr_pub%20%200pubmed).

RS Pollenz

Link to this post \| posted today, 14:25
nic.vega	Thanks for the papers, this is very helpful! I agree it's probably lysis associated based on synteny - the cassette in these AS3 phage seems to be [4 TMD protein][1 TMD protein, spanin-like][endolysin][2 TMD protein, pretty canonical-looking phage holin] at the end of the structural genes & terminating at the back end of the reverse-strand block, not dissimilar to some of the Gordonia cassettes I think. If the function is conserved in other phage, I'd be surprised if it isn't similar here.

Link to this post | posted today, 14:25

nic.vega

Thanks for the papers, this is very helpful! I agree it's *probably* lysis associated based on synteny - the cassette in these AS3 phage seems to be [4 TMD protein][1 TMD protein, spanin-like][endolysin][2 TMD protein, pretty canonical-looking phage holin] at the end of the structural genes & terminating at the back end of the reverse-strand block, not dissimilar to some of the Gordonia cassettes I think. If the function is conserved in other phage, I'd be surprised if it isn't similar here.

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lysZ-like proteins?