Phage r1t holin family

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The Lactococcus lactis Phage r1t Holin (r1t Holin) Family (TC# 1.E.18) 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 (i.e., 168 aa, 4 TMS, uncharacterized holin of Rhodococcus opacus ; TC# 1.E.18.1.9). 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. [1]

Contents

Function and expression

The Lactococcus lactis phage r1t genome includes two adjacent genes, orf48 and orf49, which encode Orf48 (TC# 1.E.18.1.1; 75 aas) and a lysin Orf49 (270 aas), probably an N-acetyl-muramoyl-L-alanine amidase, respectively. Orf48 exhibits 2 putative hydrophobic transmembrane segments (TMSs) separated by a short β-turn region. It also has a hydrophobic N-terminus and a highly charged C-terminus. Orf48/Orf49 constitute the phage r1t lysis cassette. An essential role of Orf49 in cell lysis by Orf48 has been demonstrated. [2]

Orf48 is homologous to the Gp4 holin of Mycobacterium phage Ms6 (TC# 1.E.18.1.2). [3] Like most double-stranded (ds) DNA phages, mycobacteriophage Ms6 uses the holin-endolysin system to achieve lysis of its host. In addition to endolysin (lysA) and holin (hol) genes, Ms6 encodes three accessory lysis proteins. The lysis function of Gp1, encoded by the gp1 gene that lies immediately upstream of lysA, was revealed. [4]

Catalão et al. observed Escherichia coli lysis after coexpression of LysA and Gp1 in the absence of the Ms6 holin. Gp1 does not belong to the holin class of proteins, but it shares several characteristics with molecular chaperones. The authors suggest that Gp1 interacts with LysA, and that this interaction is necessary for LysA delivery to its target. PhoA fusions showed that in Mycobacterium smegmatis , LysA is exported to the extracytoplasmic environment in the presence of Gp1 which is necessary for efficient M. smegmatis lysis, as Ms6 gp1 deletion results in host lysis defects. Catalao et al. proposed that delivery of Ms6 endolysin to the murein layer is assisted by Gp1, a chaperone-like protein, in a holin-independent manner. [4]

The transport reaction catalyzed by phage r1t Orf48 is:

lysin (in) → lysin (out)

See also

Further reading

Related Research Articles

Lysin

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 alternative 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.

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 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 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 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 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 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 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 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 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 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 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 Firmicute 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. ↑ "1.E.18 The Lactococcus lactis Phage r1t Holin (r1t Holin) Family". Transporter Classification Database. Retrieved 2016-03-28.
  2. ↑ van Sinderen, D.; Karsens, H.; Kok, J.; Terpstra, P.; Ruiters, M. H.; Venema, G.; Nauta, A. (1996-03-01). "Sequence analysis and molecular characterization of the temperate lactococcal bacteriophage r1t" (PDF). Molecular Microbiology. 19 (6): 1343–1355. doi:10.1111/j.1365-2958.1996.tb02478.x. ISSN   0950-382X. PMID   8730875. S2CID   10182620.
  3. ↑ Garcia, Miguel; Pimentel, Madalena; Moniz-Pereira, José (2002-06-01). "Expression of Mycobacteriophage Ms6 lysis genes is driven by two sigma(70)-like promoters and is dependent on a transcription termination signal present in the leader RNA". Journal of Bacteriology. 184 (11): 3034–3043. doi:10.1128/jb.184.11.3034-3043.2002. ISSN   0021-9193. PMC   135080 . PMID   12003945.
  4. 1 2 Catalão, Maria João; Gil, Filipa; Moniz-Pereira, José; Pimentel, Madalena (2010-08-01). "The mycobacteriophage Ms6 encodes a chaperone-like protein involved in the endolysin delivery to the peptidoglycan". Molecular Microbiology. 77 (3): 672–686. doi:10.1111/j.1365-2958.2010.07239.x. ISSN   1365-2958. PMID   20545844. S2CID   29630013.

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