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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 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 holin LLH family is a group of transporters belonging to the Holin superfamily VI. The Holin LLH family is found in Bacillota and phage of Bacillota as well as other bacteria. Members are fairly large, between 100 and 160 amino acyl residues in length, and have an N-terminal transmembrane segment (TMS). Some proteins, such as putative holin of Fusobacterium varium, may exhibit 2 TMSs. A representative list of proteins belonging to the Holin LLH family can be found in the Transporter Classification Database.
The Staphylococcusphage P68 Putative Holin Family consists of a single putative holin from Staphylococcus aureus phage P68 that is 92 amino acyl residues (aas) in length and exhibits 2 transmembrane segments (TMSs). While annotated as a holin, this protein has not been functionally characterized.[2]
The Putative 3-4 TMS Transglycosylase-associated Holin Family is believed to be a group of holins that does not belong to one of the seven holin superfamilies. Homologues include thousands of diverse phage and bacterial proteins between 80 and 140 amino acyl residues (aas) in length that exhibit 3 to 4 transmembrane segments (TMSs). These proteins are holin-like in their size and topology and are designated 'Transglycosylase-associated', 'Putative holin', 'Phage-like transmembrane protein', 'YeaQ protein', etc. in the NCBI protein database. As of early 2016, they remain functionally uncharacterized. They derive from a wide range of bacterial and archaeal phyla including both Gram-negative and Gram-positive bacteria. These proteins are related to the RDD family in the conserved domain database. A representative list of proteins belonging to the T-A Hol 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 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 Putative Treponema 4 TMS Holin (Tre4Hol) Family consists of several proteins from Treponema species. They range in size from 100 to 110 amino acyl residues (aas) in length and exhibit 4 transmembrane segments (TMSs). A fragment has been sequenced from Treponema phage Phi td1 (D2ECI8) and was designated a putative holin.
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 Pseudomonadota and caudovirales.
The Putative 3 TMS Holin (3-Hol) Family is large, consisting of many members derived from Pseudomonadota 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 Prophage Hp1 Hol (Hp1Hol) Family consists of a single putative holin of 69 amino acyl residues in length, exhibiting what appears to be a single transmembrane segment (TMS). It is derived from the Bacillota, Clostridium hathewayi DSM 13479. This protein is functionally uncharacterized and does not appear to be homologous to other holins. It does, however, show 31% identity to a heavy metal transporter from Dethiosulfovibrio peptidovorans.
The Enterobacterial Holin (EBHol) Family consists of many closely related proteins of 100 to 120 amino acyl residues (aas) in length with a single C-terminal transmembrane segment (TMS). They derive from γ-proteobacteria of many genera: Salmonella, Escherichia, Klebsiella and Photorhabdus, and their phage. As of March 2016, these proteins have not been functionally characterized. A representative list of proteins belonging to the EBHol family can be found in the Transporter Classififcation Database.
The Putative Acholeplasma Phage L2 Holin Family consists of a putative holin and a homologous uncharacterized protein. These proteins are of particular interest because they may show a link between prokaryotic holins and eukaryotic virus viroporins. While functionally uncharacterized, this putative holin comes up in BLAST searches when members of viroporin families TC# 1.A.95 and TC# 1.A.100 are used as query sequences.
The Putative Archaeal 2 TMS Holin (A2-Hol) Family consists of a few putative holins from Nitrososphaerota 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 Putative Bacterial Archaeal Holin(BAH) Family consists of several uncharacterized proteins. However, these proteins were retrieved when functionally characterized holins from the T-A Hol family were BLASTED against the NCBI database, and thus may be related to the T-A Hol family. Most BAH proteins are between 125 and 140 amino acyl residues (aas) in length and exhibit 4 transmembrane segments (TMSs), although at least one putative holin is almost 260 aas long. A representative list of proteins belonging to the BAH family can be found in the Transporter Classification Database.
The Firmicute PhageφU53 Holin Family consists of putative holins that range in size from 117 to 124 amino acyl residues (aas) in length and exhibit 3 transmembrane segments (TMSs) found in Bacillota phage. While annotated as holins, it appears as though many members of the φU53 holin family are not yet functionally characterized. A representative list of homologues can be found in the Transporter Classification Database.
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
- ↑ Ramadugu, Chandrika; Gabriel, Dean William (Apr 5, 2011), Identification and use of genes encoding holins and holin-like proteins in plants for the control of microbes and pests , retrieved 2016-03-29
- ↑ "BLAST: Basic Local Alignment Search Tool". blast.ncbi.nlm.nih.gov. Retrieved 2016-03-29.
- ↑ "1.E.45 The Xanthomonas Phage Holin (XanPHol) Family". TCDB. Retrieved 2016-03-29.
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