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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 Phage 21 S Family is a member of the Holin Superfamily II.
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 putative actinobacterial holin-X (Hol-X) family was retrieved as a distant member of TC family 1.E.20, suggesting membership of the holin superfamily III. Most Hol-X proteins are less than 200 amino acyl residues (aas) in length and possess two transmembrane segments (TMSs). A representative list of proteins belonging to this family can be found in the Transporter Classification Database.
The Listeria Phage A118 Holin (Hol118) Family is a group of transporters belonging to the Holin Superfamily V. A representative list of proteins belonging to the Hol118 family can be found in the Transporter Classification Database.
The Holin Hol44 (Hol44) Family is a group of transporters belonging to the Holin Superfamily V. A representative list of proteins belonging to the Hol44 family from caudovirales and Bacillota can be found in the Transporter Classification Database.
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 T4 Holin Family is a group of putative pore-forming proteins that does not belong to one of the seven holin superfamilies. T-even phage such as T4 use a holin-endolysin system for host cell lysis. Although the endolysin of phage T4 encoded by the e gene was identified in 1961, the holin was not characterized until 2001. A representative list of proteins belonging to the T4 holin family can be found in the Transporter Classification Database.
The Lactococcus lactis Phage r1t Holin Family is a family of putative pore-forming proteins that typically range in size between about 65 and 95 amino acyl residues (aas) in length, although a few r1t holins have been found to be significantly larger. Phage r1t holins exhibit between 2 and 4 transmembrane segments (TMSs), with the 4 TMS proteins resulting from an intragenic duplication of a 2 TMS region. A representative list of the proteins belonging to the r1t holin family can be found in the Transporter Classification Database.
The Neisserial Phage-associated Holin (NP-Holin) Family is a family of small proteins, between 47–53 amino acyl residues in length, that exhibit a single N-terminal transmembrane segment (TMS). Although annotated as phage proteins or holins, NP-Holin proteins are not yet functionally characterized, thus more research is needed to confirm holin activity. A representative list of proteins belonging to the NP-Holin family can be found in the Transporter Classification Database.
The Bacterophase Dp-1 Holin Family is a family of proteins present in several Gram-positive bacteria and their phage. The genes coding for the lytic system of the pneumococcal phage, Dp-1, has been cloned and characterized. The holin of phage Dp-1 is 74 amino acyl residues (aas) long with two putative transmembrane segments (TMSs). The lytic enzyme of Dp-1 (Pal), an N-acetyl-muramoyl-L-alanine amidase, shows a modular organization similar to that described for the lytic enzymes of Streptococcus pneumoniae and its bacteriophage in which change in the order of the functional domains changes the enzyme specificity. A representative list of proteins belonging to the Dp-1 family can be found in the Transporter Classification Database.
The Actinobacterial 1 TMS Holin Family consists of proteins found in actinobacteria, their conjugative plasmids and their phage. They are usually between 90 and 140 amino acyl residues (aas) in length and exhibit 1 or sometimes even 2 transmembrane segments despite the families name. Although some are annotated as phage proteins or holins, members of the A-1 family are not yet functionally characterized. A representative list of proteins belonging to the A-1 Holin family can be found in the Transporter Classification Database (TCDB).
The Mycobacterial 1 TMS Phage Holin Family was identified and recognized by Catalao et al. (2012). Members of this family are found in mycobacterial phage, exhibit a single transmembrane segment (TMSs), and are about 75 to 95 amino acyl residues in length. Although annotated as holins, members of this family are not yet functionally characterized. A representative list of proteins belonging to this family can be found in the Transporter Classification Database.
The Phage T1 Holin Family is represented in enterobacterial phages T1, RTP and F20, Klebsiella phage KP36, and Escherichia phage ADB-2. All of these possess a putative holin that share a high level of identity. Additionally, Gp9 of E. coli phage phiE49 is similar in sequence. These proteins are short, 55 to 71 amino acyl residues (aas) in length, and exhibit a single transmembrane segment (TMS). A representative list of proteins belonging to the T1 Holin family can be found in the Transporter Classification Database.
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 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 Holin-2 (PH-2) Family is a large family with members from a wide variety of bacteria. As of early 2016, functional data is not available for members of the PH-2 family, but based on their size and topology, it is believed they act as holins to facilitate cell lysis. PH-2 family proteins are of 130 to 210 amino acyl residues (aas) in length and may exhibit 1 or 2 transmembrane segments (TMSs). A representative list of proteins belonging to the PH-2 family can be found in the Transporter Classification Database.
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 BhlA Holin Family is named after putative holin-like peptides encoded in bacteria with bacteriocin similarities. BhlA proteins are generally about 67 to 80 amino acyl residues (aas) in length and exhibit a single N-terminal transmembrane segment (TMS). BhlA. It has an antibacterial activity against Gram-positive bacteria. A representative list of proteins belonging to this 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.
References
- ↑ "1.E.30 The Vibrio Holin (Vibrio Holin) Family". Transporter Classification Database. Retrieved 2016-03-28.
- ↑ Krupovic, Mart; Daugelavicius, Rimantas; Bamford, Dennis H. (2007-06-01). "A novel lysis system in PM2, a lipid-containing marine double-stranded DNA bacteriophage". Molecular Microbiology. 64 (6): 1635–1648. doi: 10.1111/j.1365-2958.2007.05769.x . ISSN 0950-382X. PMID 17555443. S2CID 21319342.
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