1.E.5 The PRD1 Phage P35 Holin (P35 Holin) Family The prototype for this family is the lipid-containing PRD1 enterobacterial phage holin protein P35 (12.8 kDa) encoded by gene XXXV (orfT) (Rydman and Bamford, 2003). It is a component of a typical holin-endolysin system which functions to lyse the host bacterial cell. The autolysin is the gene XV product, P15, a soluble β1,4-N-acetylmuramidase that causes lysis following digestion of the Gram-negative bacterial cell wall. A defect in its structural gene can be corrected by expression of the lambda phage S gene encoding the lambda holin. P35 holin has 3 TMSs with 5 positively charged residues between TMSs 1 and 2 and 4 at the C-terminus (Rydman and Bamford, 2003). It is therefore likely that the N-terminus is in the periplasm and the C-terminus is in the cytoplasm. Homologues of 109 aa, which also have 3 putative TMSs, are encoded in the genomes of Xylella fastidiosa strains (25% identity; 46% similarity; no gaps). PRD1 infects gram-negative cells harboring a conjugative IncP plasmid. Here we studied the lytic functions of PRD1. Using infected cells and plasmid-borne lysis genes, we demonstrated that a two-component lysis system (holin-endolysin) operates to release progeny phage particles from the host cell. Monitoring of ion fluxes and the ATP content of the infected cells allowed us to build a model of the sequence of lysis-related physiological changes. A decrease in the intracellular level of ATP is the earliest indicator of cell lysis, followed by the leakage of K+ from the cytosol approximately 20 min prior to the decrease in culture turbidity. However, the K+ efflux does not immediately lead to the depolarization of the cytoplasmic membrane or leakage of the intracellular ATP. These effects are observed only approximately 5 to 10 min prior to cell lysis. Similar results were obtained using cells expressing the holin and endolysin genes from plasmids. The reaction catalyzed by P35 holin is: autolysin (in) → autolysin (out)
This family belongs to the Holin III Superfamily .
References:
Quinones-Olvera, N., S.V. Owen, L.M. McCully, M.G. Marin, E.A. Rand, A.C. Fan, O.J. Martins Dosumu, K. Paul, C.E. Sanchez Castaño, R. Petherbridge, J.S. Paull, and M. Baym. (2024). Diverse and abundant phages exploit conjugative plasmids. Nat Commun 15: 3197.
Rydman, P.S. and D.H. Bamford. (2003). Identification and mutational analysis of bacteriophage PRD1 holin protein P35. J. Bacteriol. 185: 3795-3803.
Sänger, P.A., M. Knüpfer, M. Kegel, B. Spanier, E.M. Liebler-Tenorio, and T.M. Fuchs. (2023). Regulation and Functionality of a Holin/Endolysin Pair Involved in Killing of Galleria mellonella and Caenorhabditis elegans by Yersinia enterocolitica. Appl. Environ. Microbiol. e0003623. [Epub: Ahead of Print]
Springer, K., S. Reuter, M. Knüpfer, L. Schmauder, P.A. Sänger, A. Felsl, and T.M. Fuchs. (2018). Activity of a Holin-Endolysin System in the Insecticidal Pathogenicity Island of Yersinia enterocolitica. J. Bacteriol. 200:.
Zhang, X., Y. Chen, T. Yan, H. Wang, R. Zhang, Y. Xu, Y. Hou, Q. Peng, and F. Song. (2024). Cell death dependent on holins LrgAB repressed by a novel ArsR family regulator CdsR. Cell Death Discov 10: 173.
Ziedaite, G., R. Daugelavicius, J.K. Bamford, and D.H. Bamford. (2005). The Holin protein of bacteriophage PRD1 forms a pore for small-molecule and endolysin translocation. J. Bacteriol. 187: 5397-5405.
Examples:
TC#	Name	Organismal Type	Example
1.E.5.1.1	P35 holin of phage PRD1 (Rydman and Bamford 2003; Ziedaite et al. 2005). This holin is up to 98% identical to the holins of plasmid-dependent tectiviruses (Quinones-Olvera et al. 2024). Cell death can be dependent on holins LrgAB repressed by a novel ArsR family regulator CdsR (Zhang et al. 2024).	Phage	*P35 protein of Bacteriophage PRD1* (Q3T4L9)**

1.E.5.1.2	Phage holin	γ-Proteobacteria	Phage holin of of Providencia stuartii

1.E.5.1.3	Putative holin	γ-Proteobacterial viruses	*Putative holin of Xanthomonas* phage vB_XSVEM_DIBBI**

1.E.5.1.4	Putative holin (106 aas)	γ-Proteobacteria	Putative holin of Pantoea stewartii

1.E.5.1.5	Uncharacterized protein	β-Proteobacteria	Uncharacterized protein of Methyloversatilis universalis

1.E.5.1.6	putative phage holin pg30	β-Proteobacterial viruses	*gp30 of Burkholderia* phage Bcep43**

1.E.5.1.7	Uncharacterized protein of 112 aas and 3 TMSs		UP of Parcubacteria group bacterium

Examples:
TC#	Name	Organismal Type	Example
1.E.5.2.1	Phage-related protein (105 aas)	ε-Proteobacteria	*Phage-related protein of Nitratiruptor* sp. strain SB155-2**

1.E.5.2.2	Uncharacterized protein	γ-Proteobacteria	Uncharacterized protein of Vibrio mimicus

1.E.5.2.3	Putative holin	γ-Proteobacterial viruses	Putative holin of proteobacterial phage

1.E.5.2.4	Uncharacterized protein	β-Proteobacteria	Uncharacterized protein of Nitrosomonas eutropha

1.E.5.2.5	Putative holin of 134 aas and 3 TMSs.		Holin of E. coli

1.E.5.2.6	Putative holin of 107 aas and 3 TMSs.		*Hol of Citrobacter* sp. TSA-1**

1.E.5.2.7	Phage holin family protein of 138 aas and 3 TMSs in a 1 + 2 TMS arrangement.		Holin of Marinomonas shanghaiensis

1.E.5.2.8	*Holin, HolY of 103 aas and 3 TMSs. It is found in a holin-endolysin cassette in Y. enterocolitica, and has been adapted via evolution to export a large bacterial toxin (Sänger et al.* 2023).**		HolY of Yersinia enterocolitica

1.E.5.2.9	Holin, Stm0015, of 114 aas and 3 TMSs. This holin, together with a peptidoglycan hydrolase, Stm0016, comprises a secretion system (type 10) for an exo-chitinase of 699 aas (Stm0018) (partially homologous to the protein listed under TC# 9.B.29.2.7 (Chi1)).		*Holin of Salmonella enterica* (subsp. Typhimurium)**

Examples:
TC#	Name	Organismal Type	Example
1.E.5.3.1	Uncharacterized protein	δ-Proteobacteria	Uncharacterized protein of Desulfovibrio vulgaris

1.E.5.3.2	Putative holin	Synergistetes	Putative holin of Aminobacterium colombiense

1.E.5.3.3	Uncharacterized protein	Synergistetes	Uncharacterized protein of Dethiosulfovibrio peptidovorans

1.E.5.3.4	Putative holin	Synergistetes	Putative holin of Jonquetella anthopi

1.E.5.3.5	Putative holin	Synergistetes	Putative holin of Pyramidobacter piscolens

Examples:
TC#	Name	Organismal Type	Example
1.E.5.4.1	Phage holin family protein of 108 aas and 3 TMSs.		*Holin of Rhizobium* sp.**

1.E.5.4.2	Phage holin family protein of 108 aas and 2 or 3 TMSs.		Holin of Chitinibacter tainanensis

1.E.5.4.3	Phage holin family protein of 111 aas and 3 TMSs.		Holin of Azospirillum oryzae

1.E.5.4.4	Phage holin family protein of 117 aas and 3 TMSs.		Holin of Elstera litoralis

1.E.5.4.5	Putative holin of 117 aas and 3 TMSs.		Holin of Halomonas qiaohouensis

1.E.5.4.6	Uncharacterized putative holin protein of 108 aas and 3 TMSs.		*UP of Parvibaculum* sp.**

1.E.5.4.7	Uncharacterized putative holin of 121 aas and 3 TMSs.		UP of Hoeflea sp.

Examples:
TC#	Name	Organismal Type	Example
1.E.5.5.1	Holin of 96 aas with 3 TMSs.		*Holin of Serratia* phage Serbin**

Examples:
TC#	Name	Organismal Type	Example