SEA-PHAGES | Superinfection Immunity Protein

Link to this post \| posted 25 Jan, 2018 14:28
ClaireRinehart	I am working with gene 72 from Niza, which is an A1 Mycobacteriophage. None of the phagesdb genes show a function but the top HHPred match is to pfam 14373, which is an Immunity Superfection protein based on the E.coli T4 gene described in J. Virol 1989 63:3472-8. Abstract below: "The immunity (imm) gene of the Escherichia coli bacteriophage T4 effects exclusion of phage superinfecting cells already infected with T4. A candidate for this gene was placed under the control of the lac regulatory elements in a pUC plasmid. DNA sequencing revealed the presence of an open reading frame encoding a very lipophilic 83-residue (or 73-residue, depending on the unknown site of translation initiation) polypeptide which most likely represents a plasma membrane protein. This gene could be identified as the imm gene because expression from the plasmid caused exclusion of T4 and because interruption of the gene in the phage genome resulted in a phage no longer effecting superinfection immunity. It was found that the fraction of phage which was excluded upon infection of cells possessing the plasmid-encoded Imm protein ejected only about one-half of their DNA. Therefore, the Imm protein inhibited, directly or indirectly, DNA ejection." The pfam14373 description is: "This family includes the E. coli bacteriophage T4 superinfection immunity (imm) protein. When E. coli is sequentially infected with two T-even type bacteriophage the DNA of the superinfecting phage is excluded from the host, into the periplasmic space. The immunity protein plays a role in this process." Looking at Niza-72, the TMHMM predicts three transmembrane domains that covers 71 residues. The total length of the T4 protein is 76 amino acids and Niza-72 is 104 residues. Finally, NCBI has chosen to recently add the pfam14373 region note to all of the top BLAST hits to Niza-72. A decision for inclusion or exclusion of "superinfection immunity protein" in the accepted function list needs to be made since all future annotators of this Cluster A1 protein will want to include this as a function. It looks like Acinetobacter Baumannii (WP_062937363) has already included it as a function. I didn't attach a DNA Master file since it is readily available on PECAAN. Thanks, Claire

Link to this post | posted 25 Jan, 2018 14:28

I am working with gene 72 from Niza, which is an A1 Mycobacteriophage. None of the phagesdb genes show a function but the top HHPred match is to pfam 14373, which is an Immunity Superfection protein based on the E.coli T4 gene described in J. Virol 1989 63:3472-8. Abstract below:
"The immunity (imm) gene of the Escherichia coli bacteriophage T4 effects exclusion of phage superinfecting cells already infected with T4. A candidate for this gene was placed under the control of the lac regulatory elements in a pUC plasmid. DNA sequencing revealed the presence of an open reading frame encoding a very lipophilic 83-residue (or 73-residue, depending on the unknown site of translation initiation) polypeptide which most likely represents a plasma membrane protein. This gene could be identified as the imm gene because expression from the plasmid caused exclusion of T4 and because interruption of the gene in the phage genome resulted in a phage no longer effecting superinfection immunity. It was found that the fraction of phage which was excluded upon infection of cells possessing the plasmid-encoded Imm protein ejected only about one-half of their DNA. Therefore, the Imm protein inhibited, directly or indirectly, DNA ejection."

The pfam14373 description is: "This family includes the E. coli bacteriophage T4 superinfection immunity (imm) protein. When E. coli is sequentially infected with two T-even type bacteriophage the DNA of the superinfecting phage is excluded from the host, into the periplasmic space. The immunity protein plays a role in this process."

Looking at Niza-72, the TMHMM predicts three transmembrane domains that covers 71 residues. The total length of the T4 protein is 76 amino acids and Niza-72 is 104 residues.

Finally, NCBI has chosen to recently add the pfam14373 region note to all of the top BLAST hits to Niza-72.

A decision for inclusion or exclusion of "superinfection immunity protein" in the accepted function list needs to be made since all future annotators of this Cluster A1 protein will want to include this as a function. It looks like Acinetobacter Baumannii (WP_062937363) has already included it as a function.

I didn't attach a DNA Master file since it is readily available on PECAAN.

Thanks,
Claire

Link to this post \| posted 06 Mar, 2018 21:11
welkin	Sorry, I don't think we are putting this one in any time soon. There are too many different types of unrelated proteins that could provide a similar effect. For now, stick to membrane protein. once we start getting a better handle on the proteins and their classes, maybe we can come up with something more detailed.

Link to this post \| posted 11 Jul, 2020 23:59
ClaireRinehart	Well, here we are again. This time the Cluster A1 phage is STLscum and it has all of the features described above. I notice that there are now others that fit the criteria above that have called this superinfection immunity protein or superinfection exclusion protein including Swag_38, LastResort_38, Jabith_72, and Niza_72. All of these have 2-3 transmembrane domains and are good matches to pfam 14373. Would you reconsider naming this group of proteins "superinfection exclusion protein" after JSwag_38. This seems more appropriate since this protein contributes to the exclusion of super-infecting genomes to the periplasmic space? Thanks, Claire

Link to this post | posted 11 Jul, 2020 23:59

ClaireRinehart

Well, here we are again. This time the Cluster A1 phage is STLscum and it has all of the features described above. I notice that there are now others that fit the criteria above that have called this superinfection immunity protein or superinfection exclusion protein including Swag_38, LastResort_38, Jabith_72, and Niza_72. All of these have 2-3 transmembrane domains and are good matches to pfam 14373. Would you reconsider naming this group of proteins "superinfection exclusion protein" after JSwag_38. This seems more appropriate since this protein contributes to the exclusion of super-infecting genomes to the periplasmic space?
Thanks,
Claire

Link to this post \| posted 13 Jul, 2020 20:29
debbie	Claire, I sent this on to Graham. Because of the hit and significance to T4, he is incline to call this gene "Imm-like superinfection immunity protein". Please call it in your current genome. I added it to the approved functions list. Edited 15 Jul, 2020 20:32

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Superinfection Immunity Protein