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Holins are a diverse group of small proteins produced by dsDNA bacteriophages in order to trigger and control the degradation of the host's cell wall at the end of the lytic cycle. Holins form pores in the host's cell membrane, allowing lysins to reach and degrade peptidoglycan, a component of bacterial cell walls. Holins have been shown to regulate the timing of lysis with great precision. Over 50 unrelated gene families encode holins, making them the most diverse group of proteins with common function. Together with lysins, holins are being studied for their potential use as antibacterial agents.
The HP1 Holin Family is a member of the Holin Superfamily II. Proteins in this family are typically found to contain two transmembrane segments (TMSs) and range between 70 and 80 amino acyl residues (aas) in length. A representative list of proteins belonging to the HP1 holin family can be found in the Transporter Classification Database.
The LydA Holin Family, named after the lydA gene which codes for its prototype member, belongs to the Holin Superfamily III. Members of this family have 3 transmembrane segments (TMSs) and appear to possess between 90 and 120 amino acyl residues (aas). A representative list of proteins belonging to this family can be found in the Transporter Classification Database.
The PRD1 Phage P35 Holin Family is a member of Holin Superfamily III. The prototype for this family is the lipid-containing PRD1 enterobacterial phage holin protein P35 encoded by gene XXXV (orfT). It is a component of a typical holin-endolysin system which functions to lyse the host bacterial cell.
The Bacillus subtilis φ29 Holin Family is a group of transporters belonging to the Holin Superfamily IV. A representative list of members belonging to the φ29 holin family can be found in the Transporter Classification Database.
The CidA/LrgA Holin Family is a group of proteins named after CidA and LrgA of Staphylococcus aureus. CidA and LrgA are homologous holin and anti-holin proteins, each with 4 putative transmembrane segments (TMSs). Members of the CidA/LrgA holin family also include putative murine hydrolase exporters from a wide range of Gram-positive and Gram-negative bacteria as well as archaea. Most CidA/LrgA holin family proteins vary in size between 100 and 160 amino acyl residues (aas) in length although a few are larger.
The SPP1 Holin Family consists of proteins of between 90 and 160 amino acyl residues (aas) in length that exhibit two transmembrane segments (TMSs). SPP1 is a double-stranded DNA phage that infects the Gram-positive bacteria. Although annotated as holins, members of the SPP1 family are not yet functionally characterized. A representative list of proteins belonging to the SPP1 Holin family can be found in Transporter Classification Database.
The 2 or 3 TMS Putative Holin Family consists of many proteobacterial proteins ranging in size from about 70 to 120 amino acyl residues (aas) in length that exhibit 2 or 3 predicted transmembrane segments (TMSs). Although annotated as holins, these proteins are not yet functionally characterized. A representative list of proteins belonging to the 2/3 Holin family can be found in the Transporter Classification Database.
The Putative Lactococcus lactis Holin (LLHol) Family consists of just a few proteins from Lactococcus lactis species and their phage. These proteins are small, between 61 and 78 amino acyl residues (aas) in length, and exhibit one or two transmembrane segments (TMSs). As of March 2016, LLHol proteins remain functionally uncharacterized. They are not demonstrably homologous to members of other holin families and thus do not belong to one of the seven holin superfamilies. A representative list of proteins belonging to the LLHol family can be found in the Transporter Classification Database.
The XanthomonasPhage Holin (XanPHol) Family consists of a single protein of 64 amino acyl residues (aas) in length with 2 transmembrane segments (TMSs). It is a putative uncharacterized protein from Xanthomonas phage Xp15. This protein corresponds to sequence 68 from patent US 7919601. As of March 2016, this protein does not show appreciable sequence similarity to any other proteins in the NCBI protein database.
The CaulobacterPhage Holin (CauHol) Family consists of several putative holins of 157 to 159 amino acyl residues (aas) in length that exhibit 2 transmembrane segments (TMSs). They derive from phage specific for Caulobacter species. These proteins are not functionally characterized. A representative list of proteins belonging to the CauHol family can be found in the Transporter Classification Database.
The β-proteobacterial holin (BP-Hol) family is a small family that includes members derived from a number of Burkholderia phage as well as a Poloromonas species. As of April 3, 2016, this family belongs to the Holin superfamily II. Members of Saier Bioinformatics Lab at University of California, San Diego found that the BP-Hol family is most closely related to the T7 holin family. These proteins are of 60 to 110 amino acyl residues (aas) in length and exhibit 1 or 2 transmembrane segments (TMSs). Some are annotated as type II hollins and may be related to members of the T7 Holin family, although BP-Hol proteins remain functionally uncharacterized. A representative list of the proteins belonging to the BP-Hol family can be found in the Transporter Classification Database.
The Putative Listeria Phage Holin (LP-Hol) Family consists of several small proteins of 41 amino acyl residues (aas) and 1 transmembrane segment (TMS). They can be found in several Listeria phage as well as in Listeria monocytogenes. While annotated as holins, these proteins remain functionally uncharacterized. A representative list of proteins belonging to the LP-Hol family can be found in the Transporter Classification Database.
Gene transfer agent-release holins are holins which are believed to facilitate the lysis-dependent release of a gene transfer agent. Particularly the gene transfer agent of Rhodobacter capsulatus (RcGTA), which is known to be a bacteriophage-like genetic element that induces horizontal gene transfer. The promoter of the RcGTA gene was identified by Westbye et al. in 2013. A representative list of members belonging to the GTA-Hol family can be found in the Transporter Classification Database with homologues found in proteobacteria and caudovirales.
The Brachyspira holin (B-Hol) Family consists of several proteins from the GTA holin of Brachyspira hyodysenteriae, which facilitates gene transfer agent-release to VSH-1 holin of Brachyspira pilosicoli. VSH-1 is thought to participate in cell lysis. These proteins range in size from about 85 to 145 amino acyl residues (aas) and exhibit between 2 and 4 transmembrane segments (TMSs). A representative list of proteins belonging to the B-Hol family can be found in the Transporter Classification Database.
The Putative 3 TMS Holin (3-Hol) Family is large, consisting of many members derived from proteobacteria and their phage, all of small size and usually with 3 transmembrane segments (TMSs). A representative list of the proteins belonging to this family can be found in the Transporter Classification Database. While many of the proteins belonging to this family are annotated in holins, they remain functionally uncharacterized.
The Actinobacterial Phage Holin (APH) Family is a fairly large family of proteins between 105 and 180 amino acyl residues in length, typically exhibiting a single transmembrane segment (TMS) near the N-terminus. A representative list of proteins belonging to the APH family can be found in the Transporter Classification Database.
The ErwiniaPhage Phi-Ea1h Holin (EPPE-Hol) Family consists of a single protein, holin of Erwinia Phage Phi-Ea1h, which is 119 amino acyl residues in length and exhibits a single transmembrane segment (TMS). Out of three open reading frames sequenced from bacteriophage Phi-Ea1h, the second ORF encodes this holin. Kim and Geider found that no signal sequence was observed at the N-terminus of the enzyme and suggested that the holin possibly facilities the export of an which may export a lysozyme and EPS depolymerase that carries out extracellular polysaccharide (EPS)-degrading activity.
The Putative Archaeal 2 TMS Holin (A2-Hol) Family consists of a few putative holins from Thaumarchaeota ranging in size from about 130 to 165 amino acyl residues (aas) and exhibiting 2 transmembrane segments (TMSs). A representative list of proteins belonging to the A2-Hol family can be found in the Transporter Classification Database. The archaeon, Candidatus Nitrosoarchaeum limnia, encodes adjacent genes designated Toxin Secretion/Lysis Holin. The "toxin" gene encodes a soluble protein of 325 aas stated as belonging to the "Glycosyltransferase GBT-type Superfamily". This protein brings up other glycosyltransferases in a NCBI BLAST search. The adjacent gene encodes a small protein of 132 aas and 2 TMSs that could be a holin, based on its size and topology. This protein has the UniProt accession number of S2E3C4. Paralogues are found in this same organism and other closely related species.
The ArpQ Holin Family consists of a single holin-like protein 58 amino acyl residues (aas) in length with 2 transmembrane segments (TMSs). This protein is encoded by the arpQ gene in Enterococcus hirae. While annotated as a holin, it is not functionally characterized.
References
- ↑ Real, Gonçalo; Pinto, Sérgio M.; Schyns, Ghislain; Costa, Teresa; Henriques, Adriano O.; Moran, Charles P. (2005-09-01). "A gene encoding a holin-like protein involved in spore morphogenesis and spore germination in Bacillus subtilis". Journal of Bacteriology. 187 (18): 6443–6453. doi:10.1128/JB.187.18.6443-6453.2005. ISSN 0021-9193. PMC 1236627 . PMID 16159778.
- ↑ "1.E.23 The Bacillus Spore Morphogenesis and Germination Holin (BSH) Family". Transporter Classification Database. Retrieved 2016-03-28.
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