| Item (concept) | Evidence summary | Key experimental/bioinformatic support | Implication for y13J/P39503 | Primary source (author year) | DOI/URL | Publication date (month year) |
|---|---|---|---|---|---|---|
| Spanins definition | Spanins are the phage lysis proteins responsible for the final disruption of the outer membrane in Gram-negative hosts; two-component systems comprise an inner-membrane i-spanin and an outer-membrane lipoprotein o-spanin that bridge the periplasm and act after peptidoglycan degradation (pqac-00000003, pqac-00000004, pqac-00000007). | Review synthesis of genetic, cell biological, and biochemical data across phages; spanins defined as a third lysis function beyond holin and endolysin (pqac-00000003, pqac-00000004). | Supports annotating y13J/P39503 specifically as an outer-membrane lysis factor, not an enzyme or structural virion protein. | Cahill & Young 2019; Young 2014; Kongari et al. 2018 | https://doi.org/10.1016/bs.aivir.2018.09.003; https://doi.org/10.1007/s12275-014-4087-z; https://doi.org/10.1186/s12859-018-2342-8 | Jan 2019; Mar 2014; Sep 2018 |
| T4 pseT.2/pseT.3 identification | T4 genes pseT.3 and pseT.2 were identified as the T4 Rz/Rz1-equivalent spanin pair; T4 is cited as a separated two-component spanin architecture, with pseT.2 corresponding to the o-spanin and pseT.3 to the i-spanin (pqac-00000000, pqac-00000007, pqac-00000008, pqac-00000009). | Bioinformatic signatures: one product has an N-terminal transmembrane domain, the other an outer-membrane lipoprotein signal; gene arrangement is head-to-tail with overlapping stop/start codons but separated coding regions (pqac-00000008, pqac-00000009). | Verifies that UniProt P39503 / y13J (pseT.2) is the T4 o-spanin in the correct organism, Enterobacteria phage T4. | Summer et al. 2007; Young 2014; Kongari et al. 2018 | https://doi.org/10.1016/j.jmb.2007.08.045; https://doi.org/10.1007/s12275-014-4087-z; https://doi.org/10.1186/s12859-018-2342-8 | Nov 2007; Mar 2014; Sep 2018 |
| Δ(pseT.2 pseT.3) phenotype | Deletion of the T4 pseT.2/pseT.3 pair caused a classic spanin-null phenotype: a Mg2+-dependent lysis defect with infected cells becoming spherical, indicating failure of outer-membrane disruption after peptidoglycan loss (pqac-00000008, pqac-00000009). | Direct T4 mutant construction and phenotyping in lysis assays; phenotype matched known Rz−/Rz1− defects (pqac-00000008, pqac-00000009). | Strong experimental evidence that y13J/P39503 is required for the final lysis step, specifically outer-membrane disruption. | Summer et al. 2007 | https://doi.org/10.1016/j.jmb.2007.08.045 | Nov 2007 |
| Predicted topology | Two-component spanins have complementary topologies: i-spanins carry an N-terminal TMD in the inner membrane, whereas o-spanins carry an N-terminal lipoprotein signal/lipobox and are anchored in the outer membrane (pqac-00000002, pqac-00000003, pqac-00000008). For T4, pseT.3 has the TMD signature and pseT.2 the lipoprotein signal (pqac-00000008). | Topology prediction and comparative annotation across Rz/Rz1-like systems; T4-specific bioinformatic assignment reported by Summer et al. (pqac-00000008). | y13J/P39503 is best annotated as an outer-membrane lipoprotein subunit of a periplasm-spanning complex, rather than a soluble periplasmic protein. | Summer et al. 2007; Rajaure et al. 2015; Cahill & Young 2019 | https://doi.org/10.1016/j.jmb.2007.08.045; https://doi.org/10.1073/pnas.1420588112; https://doi.org/10.1016/bs.aivir.2018.09.003 | Nov 2007; Apr 2015; Jan 2019 |
| Role in membrane fusion model | Spanins are proposed to trigger fusion of inner and outer membranes once peptidoglycan is degraded; figure-based and textual evidence shows the i-/o-spanin complex bridging IM and OM and then collapsing/fusing the membranes to release virions (pqac-00000002, pqac-00000011, pqac-00000012). | Primary PNAS study plus figure evidence for spanin topology and fusion model; reviews synthesize that PG removal relieves a topological constraint and allows fusion (pqac-00000001, pqac-00000002, pqac-00000011, pqac-00000012). | y13J/P39503 most likely functions mechanistically in membrane fusion as the OM-anchored partner of the T4 spanin complex. | Rajaure et al. 2015; Cahill & Young 2019 | https://doi.org/10.1073/pnas.1420588112; https://doi.org/10.1016/bs.aivir.2018.09.003 | Apr 2015; Jan 2019 |
| Lipobox processing and Lol sorting evidence from paradigm λ Rz1 | In the λ model system, the o-spanin Rz1 has a signal peptidase II lipobox, is acylated on the N-terminal Cys, and sorting to the OM depends on Lol-targeting determinants; mutating key +1/+2 residues can redirect localization away from the OM (pqac-00000001, pqac-00000002, pqac-00000010). | Biochemical labeling, membrane fractionation, and targeting-mutant analyses in λ Rz1; mature o-spanin is OM-anchored via three fatty acyl chains (pqac-00000001, pqac-00000002, pqac-00000010). | Although shown in λ rather than T4, these class-defining data strongly support that T4 y13J/P39503, identified as an o-spanin, is processed as a lipoprotein and sorted to the OM. | Rajaure et al. 2015; Cahill & Young 2019; Young 2014 | https://doi.org/10.1073/pnas.1420588112; https://doi.org/10.1016/bs.aivir.2018.09.003; https://doi.org/10.1007/s12275-014-4087-z | Apr 2015; Jan 2019; Mar 2014 |
| Spheroplast fusion assay evidence | Coexpression of i-spanin and o-spanin in λ drives fusion of labeled spheroplasts, whereas lysis-defective spanin alleles fail to fuse, directly linking spanins to membrane fusion rather than nonspecific damage (pqac-00000001, pqac-00000002). | In vitro/heterologous spheroplast fusion assay with fluorescent markers; allele dependence tied fusion to functional spanin complexes (pqac-00000002). | Provides the strongest mechanistic precedent for inferring that T4 y13J/P39503 acts in an analogous two-component fusion machine with pseT.3. | Rajaure et al. 2015; Cahill & Young 2019 | https://doi.org/10.1073/pnas.1420588112; https://doi.org/10.1016/bs.aivir.2018.09.003 | Apr 2015; Jan 2019 |
| Diversity databases/statistics | Large-scale spanin mining identified 528 two-component spanins and 58 unimolecular spanins; using a 40% identity/40% length threshold, these grouped into 143 i-spanin, 125 o-spanin, and 13 u-spanin families, with >40% of families being singletons (pqac-00000007). | SpaninDataBase bioinformatic survey and family clustering across phage genomes; T4 cited as a separated two-component architecture exemplar (pqac-00000007). | Indicates y13J/P39503 belongs to a widespread but highly diverse class of outer-membrane lysis proteins, explaining limited direct sequence-based annotation outside contextual gene architecture. | Kongari et al. 2018 | https://doi.org/10.1186/s12859-018-2342-8 | Sep 2018 |
| 2024 application paper using T1 spanin as antimicrobial | A 2024 study reported potent bactericidal activity of T1 spanin and used phage delivery of the spanin gene as an antimicrobial strategy; T1-spanin showed activity against 111 E. coli clinical isolates and additional Acinetobacter, Klebsiella, and Pseudomonas isolates (pqac-00000001). | Experimental comparison of phage-derived lytic enzymes in cells; engineered non-proliferative phage delivery of T1-spanin for antibacterial activity (paper-search result summarized in conversation; conceptually aligned with spanin mechanism in pqac-00000001). | While not T4-specific, this demonstrates real-world translational interest in spanin biology, supporting the relevance of accurate annotation of y13J/P39503. | Yamashita et al. 2024 | https://doi.org/10.34133/bdr.0028 | Jan 2024 |
| 2024 programmed autolysis review mentioning holin-endolysin-spanin modules | A 2024 review on engineered bacterial autolysis states that λ and T4 require holin-endolysin-spanin modules for complete lysis of Gram-negative cells, highlighting use of phage lysis systems in biotechnology (paper-search result summarized in conversation; mechanistic background in pqac-00000003, pqac-00000004). | Review of applied autolysis platforms for manufacturing and biomedicine; cites phage lysis modules as programmable tools. | Reinforces that T4 y13J/P39503 should be considered part of a complete lysis cassette relevant to synthetic biology, not an isolated accessory gene. | Dong et al. 2024 | https://doi.org/10.1186/s12934-024-02566-z | Oct 2024 |


*Table: This table summarizes the evidence supporting annotation of Enterobacteria phage T4 y13J (pseT.2; UniProt P39503) as the o-spanin outer-membrane lipoprotein. It integrates T4-specific genetics with broader spanin mechanistic and application literature.*