1.E.64. The P7 Phage Holin LydD (LydD) Family P1 and P7 are model temperate myoviruses. They infect different Enterobacteriaceae and can develop lytically or form lysogens. Only some P1 adaptation strategies to propagate in different hosts are known. An atypical feature of P1 is the number and organization of cell lysis-associated genes. In addition to SAR-endolysin Lyz, holin LydA, and antiholin LydB, P1 encodes other predicted holins, LydC and LydD (Bednarek et al. 2022). LydD is encoded within the same operon as Lyz; LydA and LydB are encoded withiin an unlinked operon, and LydC is encoded within an operon preceding the lydA gene. By analyzing the phenotypes of P1 mutants in known or predicted holin genes, Bednarek et al. 2022 showed that all of the products of these genes cooperate with the P1 SAR-endolysin in cell lysis and that LydD is a pinholin. The contributions of holins/pinholins to cell lysis by P1 appear to vary depending on the host of P1 and the bacterial growth conditions. The pattern of morphological transitions characteristic of SAR-endolysin-pinholin action dominates during lysis by wild-type P1, but in the case of a lydC lydD mutant, it changes to that characteristic of classical endolysin-pinholin action. The complex lytic system facilitates P1 adaptation to various hosts and their growth conditions (Bednarek et al. 2022).
References:
Bednarek, A., A. Cena, W. Izak, J. Bigos, and M. Łobocka. (2022). Functional Dissection of P1 Bacteriophage Holin-like Proteins Reveals the Biological Sense of P1 Lytic System Complexity. Int J Mol Sci 23:.
Rodea M, G.E., E. González-Villalobos, M.D.R. Espinoza-Mellado, U. Hernández-Chiñas, C.A. Eslava-Campos, J.L. Balcázar, and J. Molina-López. (2024). Genomic analysis of a novel phage vB_SenS_ST1UNAM with lytic activity against Salmonella enterica serotypes. Diagn Microbiol Infect Dis 109: 116305.
Examples:
TC#	Name	Organismal Type	Example
1.E.64.1.1	Enterobacterial phage P7 holin, LydD of 84 aas and 2 TMSs .		LydD holin of Phage P7

1.E.64.1.2	Holin of 84 aas and 2 TMSs.		*Holin of Pantoea* sp. PSNIH6**

1.E.64.1.3	*Uncharacterized putative holin of 71 aas and 2 TMSs. This protein is 92% identical to a putative holin of 70 aas and 2 TMSs from Aeromonas* phage vB_AsaM-56.**		*UP of Aeromonas* phage 2_D05**

1.E.64.1.4	Uncharacterized protein of 77 aas and 2 TMSs. This protein interconnects 1.E.64.1, 1.E.64.2 and 1.E.53.2.6.		*UP of Methylobacterium* sp. WL12**

1.E.64.1.5	Uncharacterized protein of 68 aas and 2 TMSs.		*UP of Mesorhizobium* sp. (plant metagenome)**

Examples:
TC#	Name	Organismal Type	Example
1.E.64.2.1	Uncharacterized putative holin of 73 aas and 2 TMSs.		Putative holin of Hyphomicrobiales bacterium

1.E.64.2.2	Uncharacterized protein of 73 aas and 2 TMSs.		UP of Rhizobium leguminosarum

1.E.64.2.3	Uncharacterized protein, putative holin of 77 aas and 2 TMSs.		UP of Pleomorphomonas carboxyditropha

1.E.64.2.4	Uncharacterized protein of 72 aas and 2 TMSs.		UP of Achromobacter pulmoni

1.E.64.2.5	Fusion protein with a holin domain at the N-terminus and a lysozyme domain at the C-terminus. The holin domain includes 2 TMSs, while there is a single TMS at the N-terminus of the lysozyme domain.		Holin-Lysozyme fusion protein of Leisingera daeponensis

1.E.64.2.6	Uncharacterized protein of 77 aas asnd 2 TMSs.		*UP of Pseudomonas* sp. GV047**

1.E.64.2.7	Putative class II holin of 69 aas and 2 TMSs.		*Holin of Alteromonas* phage vB_AmeP_R8W**

Examples:
TC#	Name	Organismal Type	Example
1.E.64.3.1	*Holin of Acinetobacter* phage Loki of 80 aas and 2 TMSs.**		*Holin of Acinetobacter* baumannii phage Loki**

1.E.64.3.10	Uncharacterized protein of 84 aas and 2 TMSs.		UP of Zavarzinia aquatilis

1.E.64.3.2	Burkholderia phage BcepNazgul holin of 127 aas and 3 TMSs.		*Holin of Burkholderia* phage BcepNazgul**

1.E.64.3.3	Uncharacterized protein of 93 aas and 2 probable TMSs.		UP of Achromobacter dolens

1.E.64.3.4	Putative holin of 79 aas and 2 TMSs. This protein is 86% idetical and the same length as the holin from phage vB_SenS_ST1UNAM which has lytic activity against Salmonella typhimurium (Rodea M et al. 2024).		*Holin of Salmonella* phage Akira**

1.E.64.3.5	Putative holin of 114 aas and 3 TMSs.		Holin of Klebsiella oxytoca

1.E.64.3.6	Uncharacterized protein of 90 aas and 2 TMSs.		UP of Acinetobacter baumannii

1.E.64.3.7	Uncharacterized protein (putative holn) of 88 aas and 2 TMSs.		UP of Cupriavidus alkaliphilus

1.E.64.3.8	Uncharacterized protein of 90 aas and 2 TMSs.		*UP of Sphingomonas* sp. RIT328**

1.E.64.3.9	Uncharacterized protein of 87 aas and 2 TMSs.		UP of Achromobacter marplatensis (Achromobacter spiritinus)