P35 holin family

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The PRD1 Phage P35 Holin (P35 Holin) Family (TC# 1.E.5) is a member of Holin Superfamily III. [1] The prototype for this family is the lipid-containing PRD1 enterobacterial phage holin protein P35 (12.8 kDa; TC# 1.E.5.1.1) encoded by gene XXXV (orfT). [2] It is a component of a typical holin-endolysin system which functions to lyse the host bacterial cell.

The Holin Superfamily III is a superfamily of integral membrane transport proteins. It is one of the seven different holin superfamilies in total. In general, these proteins are thought to play a role in regulated cell death, although functionality varies between families and individual members.

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.

Contents

Structure

P35 holin (TC# 1.E.5.1.1) has 3 transmembrane segments (TMSs) with 5 positively charged residues between TMSs 1 and 2. It has 4 positively charged residues at the C-terminus. [2] It is therefore thought that the N-terminus is in the periplasm and the C-terminus is in the cytoplasm. Homologues of 109 amino acyl residues (aas), which also have 3 putative TMSs, are encoded in the genomes of Xylella fastidiosa strains. [2]

The C-terminus is the end of an amino acid chain, terminated by a free carboxyl group (-COOH). When the protein is translated from messenger RNA, it is created from N-terminus to C-terminus. The convention for writing peptide sequences is to put the C-terminal end on the right and write the sequence from N- to C-terminus.

The N-terminus (also known as the amino-terminus, NH2-terminus, N-terminal end or amine-terminus) is the start of a protein or polypeptide referring to the free amine group (-NH2) located at the end of a polypeptide. Normally the amine group is bonded to another carboxylic group in a protein to make it a chain, but since the end of a protein has only 1 out of 2 areas chained, the free amine group is referred to the N-terminus. By convention, peptide sequences are written N-terminus to C-terminus, left to right in LTR languages. This correlates the translation direction to the text direction (because when a protein is translated from messenger RNA, it is created from N-terminus to C-terminus - amino acids are added to the carbonyl end).

Xylella fastidiosa is an aerobic, Gram-negative bacterium of the monotypic genus Xylella. It is a plant pathogen, and is transmitted exclusively by xylem fluid feeding sap insects. Many plant diseases are due to symptomatic infections of X. fastidiosa, including bacterial leaf scorch, oleander leaf scorch, coffee leaf scorch (CLS), alfalfa dwarf, phony peach disease, and the economically important Pierce's disease of grapes (PD) and citrus variegated chlorosis (CVC). In Europe it has attacked olive trees in the Salento area of Southern Italy causing the olive quick decline syndrome (OQDS). While distributions of X. fastidiosa–related diseases are mostly limited to the Americas, outbreaks have occurred in Taiwan, Slovakia, and other countries worldwide.

Function

The reaction catalyzed by P35 holin is:

autolysin (in) → autolysin (out)

See also

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.

Phage typing

Phage typing is a method used for detecting single strains of bacteria. It is used to trace the source of outbreaks of infections. The viruses that infect bacteria are called bacteriophages and some of these can only infect a single strain of bacteria. These phages are used to identify different strains of bacteria within a single species.

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.

Related Research Articles

Tectivirus family of viruses

Tectiviridae is a family of viruses with three genera. Gram-negative bacteria serve as natural hosts. There are currently four species in this genus including the type species Enterobacteria phage PRD1. Tectiviruses have no head-tail structure, but are capable of producing tail-like tubes of ~ 60×10 nm upon adsorption or after chloroform treatment. The name is derived from Latin tectus.

The Phi11 Holin Family constitutes the Holin Superfamily I.

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

The HP1 Holin Family is a member of the Holin Superfamily II. Proteins in this family are typically found to contain two transmembrane segments (TMSs) and range between 70 to 80 amino acyl residues (aas) in length. A representative list of proteins belonging to the HP1 holin 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 Pseudomonas aeruginosa Hol Holin Family is a group of transporters belonging to the Holin Superfamily III.

The Holin superfamily IV is a superfamily of integral membrane transport proteins. It is one of the seven different holin superfamilies in total.

The Holin superfamily V is a superfamily of integral membrane transport proteins. It is one of the seven different holin superfamilies in total. In general, these proteins are thought to play a role in regulated cell death, although functionality varies between families and individual members. The Holin superfamily V includes the TC families:

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 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 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 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 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 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 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.

References

  1. ↑ Reddy, Bhaskara L.; Saier, Milton H. (2013-11-01). "Topological and phylogenetic analyses of bacterial holin families and superfamilies". Biochimica et Biophysica Acta. 1828 (11): 2654–2671. doi:10.1016/j.bbamem.2013.07.004. ISSN   0006-3002. PMC   3788059 . PMID   23856191.
  2. 1 2 3 Rydman, Pia S.; Bamford, Dennis H. (2003-07-01). "Identification and mutational analysis of bacteriophage PRD1 holin protein P35". Journal of Bacteriology. 185 (13): 3795–3803. doi:10.1128/jb.185.13.3795-3803.2003. ISSN   0021-9193. PMC   161566 . PMID   12813073.

As of 10 March 2016, this article is derived in whole or in part from Transporter Classification Database (TCDB). The copyright holder has licensed the content in a manner that permits reuse under CC BY-SA 3.0 and GFDL. All relevant terms must be followed. The original text was at "1.E.5 The PRD1 Phage P35 Holin (P35 Holin) Family".


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