Curation Notes: Bacteriophage T4 y13K (UniProt P39504)

Identity and Nomenclature

• Gene symbol: y13K (synonym: pseT.3)
• UniProt accession: P39504 (SPAN1_BPT4)
• Protein name: Spanin, inner membrane subunit (i-spanin)
• Length: 117 AA (13,135 Da)
• Organism: Enterobacteria phage T4 (NCBITaxon:10665)

Summary of Experimental Evidence

• Identification and Genetic Validation in T4 (Summer et al. 2007): [PMID:17900620, "In the case of T4, a deletion of a non-overlapping gene pair pseT.2 and pseT.3 identified as Rz/Rz1 equivalents resulted in the same divalent cation-dependent lysis phenotype."] y13K (pseT.3) encodes the 117-amino-acid inner-membrane spanin subunit (i-spanin) of the T4 two-component spanin complex, paired with the adjacent outer-membrane lipoprotein gene y13J (pseT.2, o-spanin). Deletion of pseT.3 and pseT.2 in T4 produces the classical divalent cation ($Mg^{2+}$)-dependent lysis defect in which infected E. coli cells form spherical bodies bounded by an intact outer membrane after holin-endolysin action.
• Topology, Subcellular Localization, and Mechanism: y13K (pseT.3) is a single-pass type II inner membrane protein (SUBCELLULAR LOCATION: Host cell inner membrane {ECO:0000250}; Single-pass type II membrane protein {ECO:0000250}; Periplasmic side {ECO:0000250}.) with an N-terminal transmembrane signal-anchor helix (residues 3-23) and a periplasmic coiled-coil domain (residues 24-93; total periplasmic region 24-117). Its C-terminus binds the C-terminus of the outer-membrane o-spanin y13J (pseT.2) across the periplasm (These proteins were named "spanins," since their protein products are predicted to span the periplasm providing a physical connection between the inner and outer membranes. PMID:17900620). Following peptidoglycan degradation by T4 endolysin, the spanin complex undergoes conformational collapse to fuse the inner and outer membranes and complete host cell lysis.

Review of Existing GO Annotations

1. GO:0020002 (host cell plasma membrane, IEA GO_REF:0000044): ACCEPT. In Gram-negative bacteria (E. coli), the inner membrane (UniProtKB-SubCell:SL-0373, Host cell inner membrane) is the host cell plasma membrane, where Y13K is anchored via its N-terminal transmembrane helix.
2. GO:0044659 (viral release from host cell by cytolysis, IGI PMID:17900620): ACCEPT. Directly supported by the $\Delta(\text{pseT.3 pseT.2})$ lysis defect in T4 PMID:17900620.
3. GO:0031640 (killing of cells of another organism, IEA GO_REF:0000043): MODIFY to GO:0044659 (viral release from host cell by cytolysis), which is the specific descendant process already experimentally annotated on the gene.