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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 Mycobacterial 4 TMS Phage Holin Family is a group of transporters belonging to Holin superfamily IV. A representative list of members belonging to the MP4 holin family 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 Firmicutes and phage of Firmicutes 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 Mycobacterial 2 TMS Phage Holin Family is a group of transporters belonging to the Holin Superfamily VII. The Mycobactrerial 2 transmembrane segment (TMS) Holins have been identified and recognized by Catalao et al (2012). The Mycobacterium phage D29 gp11 protein is a holin that, upon expression, rapidly kills both E. coli and Mycobacterium smegmatis. Shortening gp11 from its C-terminus resulted in diminished cytotoxicity and smaller holes. The two TMSs at the N-terminus alone do not integrate into the cytoplasmic membrane and do not show toxicity. Fusion of the two TMSs and a small C-terminal coiled-coil region resulted in restoration of cell killing. The second TMS is dispensable for toxicity. The gp11 C-terminal region is therefore necessary but not sufficient for toxicity.
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 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 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 holin-like toxin (Hol-Tox) family consists of many small proteins, between 34 and 48 amino acyl residues (aas) with a single transmembrane segment (TMSs). Rajesh et al. first identified the gene and designated it tmp1, which coded for a 34 amino acyl peptide that acts as an antibacterial agent on gram-positive bacteria. This peptide exhibits a single transmembrane domain (TMD) that is believed to play a role in facilitating the antibacterial activity. A representative list of proteins belonging to the Hol-Tox 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 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 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 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.
The Flp/Fap Pilin Putative Holin (FFPP-Hol) Family is a large diverse family with members from many bacterial phyla. Some members are annotated as Flp or Fap pilin subunits; others are identified as Holin BlyA family members. They range in size of 50 to 80 amino acyl residues (aas) with a single N-terminal transmembrane segment (TMS) although one member has 99 aas and 2 TMSs. Flp homologues are included in TCDB under TC# 3.A.7.13.1 (pXO1-63) and TC# 3.A.7.15.1 (Flp-1). As in March 2016, their precise functions appear to be unknown. A representative list of proteins belonging to the FFPP-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 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 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 firmicute, 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 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.
References
- ↑ Catalão, Maria João; Gil, Filipa; Moniz-Pereira, José; São-José, Carlos; Pimentel, Madalena (2013-07-01). "Diversity in bacterial lysis systems: bacteriophages show the way". FEMS Microbiology Reviews. 37 (4): 554–571. doi: 10.1111/1574-6976.12006 . ISSN 1574-6976. PMID 23043507.
- ↑ "Mycobacterial Phage PBI1 Gp36 Holin (Gp36 Hol) Family". TCDB. Retrieved 2016-03-28.
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