Actinobacterial phage holin family

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The Actinobacterial Phage Holin (APH) Family (TC# 1.E.57) 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. [1]

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One of the archetype proteins in this family is the Gp5 holin of mycobacteriophage Ms6. Mycobacteriophage Ms6 is a double-stranded DNA (dsDNA) bacteriophage which, in addition to the predicted endolysin (LysA)-holin (Gp4) lysis system, encodes three additional proteins within its lysis module: Gp1, LysB, and Gp5. [2]

A mycobacteriophage is a member of a group of bacteriophages known to have mycobacteria as host bacterial species. While originally isolated from the bacterial species Mycobacterium smegmatis and Mycobacterium tuberculosis, the causative agent of tuberculosis, more than 4,200 mycobacteriophage have since been isolated from various environmental and clinical sources. Almost 1400 have been completely sequenced. Mycobacteriophages have served as examples of viral lysogeny and of the divergent morphology and genetic arrangement characteristic of many phage types.

Bacteriophage virus that infects and replicates within bacteria. And there are two types of t phage present ,t even phage and t odd phage.

A bacteriophage, also known informally as a phage, is a virus that infects and replicates within bacteria and archaea. The term was derived from "bacteria" and the Greek φαγεῖν, "to devour". Bacteriophages are composed of proteins that encapsulate a DNA or RNA genome, and may have structures that are either simple or elaborate. Their genomes may encode as few as four genes and as many as hundreds of genes. Phages replicate within the bacterium following the injection of their genome into its cytoplasm.

Ms6 Gp4 (TC# 1.E.18.1.2) was previously described as a class II holin-like protein. A second putative holin gene (gp5) encoding a protein (Gp5) with a predicted single N-terminal TMS was identified at the end of the Ms6 lytic operon. Neither the putative class II holin nor the single TMS polypeptide could trigger lysis in pairwise combinations with the endolysin LysA in Escherichia coli . However, further studies have shown that Ms6's Gp4 and Gp5 interact with each other. This suggests that in Ms6 infection, the correct and programmed timing of lysis is achieved by the combined action of Gp4 and Gp5. [2]

Lysis refers to the breaking down of the membrane of a cell, often by viral, enzymic, or osmotic mechanisms that compromise its integrity. A fluid containing the contents of lysed cells is called a lysate. In molecular biology, biochemistry, and cell biology laboratories, cell cultures may be subjected to lysis in the process of purifying their components, as in protein purification, DNA extraction, RNA extraction, or in purifying organelles.

<i>Escherichia coli</i> species of Gram-negative, rod-shaped bacterium

Escherichia coli, also known as E. coli, is a Gram-negative, facultative anaerobic, rod-shaped, coliform bacterium of the genus Escherichia that is commonly found in the lower intestine of warm-blooded organisms (endotherms). Most E. coli strains are harmless, but some serotypes can cause serious food poisoning in their hosts, and are occasionally responsible for product recalls due to food contamination. The harmless strains are part of the normal microbiota of the gut, and can benefit their hosts by producing vitamin K2, and preventing colonization of the intestine with pathogenic bacteria, having a symbiotic relationship. E. coli is expelled into the environment within fecal matter. The bacterium grows massively in fresh fecal matter under aerobic conditions for 3 days, but its numbers decline slowly afterwards.

See also

Actinobacteria phylum of Gram-positive bacteria

The Actinobacteria are a phylum of Gram-positive bacteria. They can be terrestrial or aquatic. They are of great economic importance to humans because agriculture and forests depend on their contributions to soil systems. In soil, they behave much like fungi, helping to decompose the organic matter of dead organisms so the molecules can be taken up anew by plants. In this role the colonies often grow extensive mycelia, like a fungus would, and the name of an important order of the phylum, Actinomycetales, reflects that they were long believed to be fungi. Some soil actinobacteria live symbiotically with the plants whose roots pervade the soil, fixing nitrogen for the plants in exchange for access to some of the plant's saccharides. Other species, such as many members of the genus Mycobacterium, are important pathogens.

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.

Lysin class of enzymes

Lysins, also known as endolysins or murein hydrolases, are hydrolytic enzymes produced by bacteriophages in order to cleave the host's cell wall during the final stage of the lytic cycle. Lysins are highly evolved enzymes that are able to target one of the five bonds in peptidoglycan (murein), the main component of bacterial cell walls, which allows the release of progeny virions from the lysed cell. Cell-wall-containing Archaea are also lysed by specialized pseudomurein-cleaving lysins, while most archaeal viruses employ alternate mechanisms. Similarly, not all bacteriophages synthesize lysins: some small single-stranded DNA and RNA phages produce membrane proteins that activate the host's autolytic mechanisms such as autolysins.

Further reading

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Related Research Articles

The Phi11 Holin Family constitutes the Holin Superfamily I.

The Phage 21 S Family is a member of the Holin Superfamily II.

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 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 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 firmicutes 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 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 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 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 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 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 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 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 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. ↑ "1.E.57. The Actinobacterial Phage Holin (APH) Family". TCDB. Retrieved 2016-03-29.
  2. 1 2 Catalão, Maria João; Gil, Filipa; Moniz-Pereira, José; Pimentel, Madalena (2011-06-01). "Functional analysis of the holin-like proteins of mycobacteriophage Ms6". Journal of Bacteriology. 193 (11): 2793–2803. doi:10.1128/JB.01519-10. ISSN   1098-5530. PMC   3133122 . PMID   21441511.

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