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 .



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.


TC#NameOrganismal TypeExample

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).


P35 protein of Bacteriophage PRD1 (Q3T4L9)


Phage holin


Phage holin of of Providencia stuartii


Putative holin

γ-Proteobacterial viruses

Putative holin of Xanthomonas phage vB_XSVEM_DIBBI


Putative holin (106 aas)


Putative holin of Pantoea stewartii


Uncharacterized protein


Uncharacterized protein of Methyloversatilis universalis


putative phage holin pg30

β-Proteobacterial viruses

gp30 of Burkholderia phage Bcep43


Uncharacterized protein of 112 aas and 3 TMSs

UP of Parcubacteria group bacterium


TC#NameOrganismal TypeExample

Phage-related protein (105 aas)


Phage-related protein of Nitratiruptor sp. strain SB155-2


Uncharacterized protein


Uncharacterized protein of Vibrio mimicus


Putative holin

γ-Proteobacterial viruses

Putative holin of proteobacterial phage


Uncharacterized protein


Uncharacterized protein of Nitrosomonas eutropha


Putative holin of 134 aas and 3 TMSs.

Holin of E. coli


Putative holin of 107 aas and 3 TMSs.

Hol of Citrobacter sp. TSA-1


Phage holin family protein of 138 aas and 3 TMSs in a 1 + 2 TMS arrangement.

Holin of Marinomonas shanghaiensis


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


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)


TC#NameOrganismal TypeExample

Uncharacterized protein


Uncharacterized protein of Desulfovibrio vulgaris


Putative holin


Putative holin of Aminobacterium colombiense


Uncharacterized protein


Uncharacterized protein of Dethiosulfovibrio peptidovorans


Putative holin


Putative holin of Jonquetella anthopi


Putative holin


Putative holin of Pyramidobacter piscolens


TC#NameOrganismal TypeExample

Phage holin family protein of 108 aas and 3 TMSs.

Holin of Rhizobium sp.


Phage holin family protein of 108 aas and 2 or 3 TMSs.

Holin of Chitinibacter tainanensis


Phage holin family protein of 111 aas and 3 TMSs.

Holin of Azospirillum oryzae


Phage holin family protein of 117 aas and 3 TMSs.

Holin of Elstera litoralis


Putative holin of 117 aas and 3 TMSs.

Holin of Halomonas qiaohouensis


Uncharacterized putative holin protein of 108 aas and 3 TMSs.

UP of Parvibaculum sp.


Uncharacterized putative holin of 121 aas and 3 TMSs.

UP of Hoeflea sp.


TC#NameOrganismal TypeExample

Holin of 96 aas with 3 TMSs. 

Holin of Serratia phage Serbin


TC#NameOrganismal TypeExample