T4 holin

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The T4 Holin Family (TC# 1.E.8) 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 (Lysozyme E) was identified in 1961, the holin (product of gene t and called T-holin) was not characterized until 2001. [1] A representative list of proteins belonging to the T4 holin family can be found in the Transporter Classification Database. [2]

Contents

Structure

T4 holin is fairly large, about 218 amino acyl residues (aas) in length. The protein is highly hydrophilic with 49 acidic and basic residues distributed along its length and a single putative transmembrane segment (TMS) near its N-terminus, leaving most of the protein in the periplasm. [3]

Function

The large periplasmic domain is a major determinant in the timing mechanism and is involved in lysis inhibition (LIN). [4] LIN involves the antiholin rI protein of T4 (See TC# 1.E.8.1.1). [5] Lysis inhibition is an effective strategy to coordinate lysis timing with phage particle maturation and to exclude other phage. [6] The C-terminal periplasmic domain of T4 holin binds the periplasmic domain of T4 antiholin (RI; 97 aas) which like the holin, spans the membrane once. [3] T-holin of T4 phage forms a 1:1 complex with the RI inhibitor which block aggregation and pore formation. [7]

Homology

The phage T4 T-holin (lysis protein) is identical to the holin from phage K3 and nearly identical to that from phage ARI. Residues 35-96 are 28% identical to residues 436-495 of a K+ uptake protein of Lactococcus lactis (gbAAK04721; TC# 2.A.72; KUP), suggesting an evolutionary relationship between a holin and a transporter. Holins have 1 to 4 TMSs and a short C-terminal domain rich in basic residues.

See also

Related Research Articles

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 T7 Holin family is a member of the Holin Superfamily II. Members of this family are predominantly found in Caudovirales and Proteobacteria. They typically have only 1 transmembrane segment (TMS) and vary from 60 to 130 amino acyl residues in length. A representative list of proteins belonging to this family can be found in the Transporter Classification Database.

The Lambda Holin S Family is a group of integral membrane transporter proteins belonging to the Holin Superfamily III. Members of this family generally consist of the characteristic three transmembrane segments (TMSs) and are of 110 amino acyl residues (aas) in length, on average. A representative list of members belonging to this 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 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 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 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 Mycobacterial Phage PBI1 Gp36 Holin Family consists of a single protein, Gp36 of Mycobacterial phage PBI1 identified by Castalao et al. (2012). Gp36 is 116 amino acyl residues (aas) in length and exhibits 2 transmembrane segments (TMSs). While annotated as a holin, this protein has not been functionally characterized.

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 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 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 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.

References

  1. ↑ Ramanculov, E.; Young, R. (2001-04-01). "Functional analysis of the phage T4 holin in a lambda context". Molecular Genetics and Genomics. 265 (2): 345–353. doi:10.1007/s004380000422. ISSN   1617-4615. PMID   11361346. S2CID   40455691.
  2. ↑ "1.E.8 The T4 Holin (T4 Holin) Family". Transporter Classification Database. Retrieved 2016-03-26.
  3. 1 2 Tran, Tram Anh T.; Struck, Douglas K.; Young, Ry (2005-10-01). "Periplasmic domains define holin-antiholin interactions in t4 lysis inhibition". Journal of Bacteriology. 187 (19): 6631–6640. doi:10.1128/JB.187.19.6631-6640.2005. ISSN   0021-9193. PMC   1251592 . PMID   16166524.
  4. ↑ Ramanculov, E.; Young, R. (2001-03-07). "Genetic analysis of the T4 holin: timing and topology". Gene. 265 (1–2): 25–36. doi:10.1016/s0378-1119(01)00365-1. ISSN   0378-1119. PMID   11255004.
  5. ↑ Ramanculov, E.; Young, R. (2001-08-01). "An ancient player unmasked: T4 rI encodes a t-specific antiholin". Molecular Microbiology. 41 (3): 575–583. doi: 10.1046/j.1365-2958.2001.02491.x . ISSN   0950-382X. PMID   11532126. S2CID   25273199.
  6. ↑ Miller, Eric S.; Kutter, Elizabeth; Mosig, Gisela; Arisaka, Fumio; Kunisawa, Takashi; Rüger, Wolfgang (2003-03-01). "Bacteriophage T4 genome". Microbiology and Molecular Biology Reviews. 67 (1): 86–156, table of contents. doi:10.1128/mmbr.67.1.86-156.2003. ISSN   1092-2172. PMC   150520 . PMID   12626685.
  7. ↑ Moussa, Samir H.; Kuznetsov, Vladimir; Tran, Tram Anh T.; Sacchettini, James C.; Young, Ry (2012-04-01). "Protein determinants of phage T4 lysis inhibition". Protein Science. 21 (4): 571–582. doi:10.1002/pro.2042. ISSN   1469-896X. PMC   3375757 . PMID   22389108.

Further reading

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