OBPgp279

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OBPgp279
OBPgp279 Predicted Structure 3.png
Predicted structure of OPBgp279 from Phyre2. Homology model based on 4OK7 .
Identifiers
Organism Pseudomonas phage OBP
SymbolOBP_279
UniProt G9I9L2
Search for
Structures Swiss-model
Domains InterPro

OBPgp279 (OBP genome protein 279) is an endolysin that hydrolyzes peptidoglycan, a major constituent in bacterial membrane. [1] OBPgp279 is found in Pseudomonas fluorescens phage OBP, which belongs in the Myoviridae family of bacteriophages. Because of its role in hydrolyzing the peptidoglycan layer, OBPgp279 is a key enzyme in the lytic cycle of the OBP bacteriophage; it allows the bacteriophage to lyse its host internally to escape. Unlike other endolysins, OBPgp279 does not rely on holins to perforate the inner bacterial membrane in order to reach the peptidoglycan layer. [1] [2] Although OBPgp279 is not a well-studied enzyme, it has garnered interest as a potential antibacterial protein due to its activity against multidrug-resistant gram-negative bacteria. [3]

Contents

Predicted enzyme mechanism

Active site of gycoside hydrolase family 19 papaya chitinase (PDB: 3cql ). Conserved residues are shown surrounding the catalytic acid, Glu67. A GlcNAc2 unit binding in the -1 and +1 subsites is shown in narrow stick representation and an arrow indicates the position of the glycosidic oxygen. Glycoside Hydrolase Family 19 Active Site Detail.PNG
Active site of gycoside hydrolase family 19 papaya chitinase ( PDB: 3cql ​). Conserved residues are shown surrounding the catalytic acid, Glu67. A GlcNAc2 unit binding in the -1 and +1 subsites is shown in narrow stick representation and an arrow indicates the position of the glycosidic oxygen.

The mechanism of OBPgp279 is predicted to be part of glycoside hydrolase family 19 (GH19) due to the presence of a conserved sequence motif (general sequence motif=[FHY]-G-R-G-[AP]-ζ-Q-[IL]-[ST]-[FHYW]-[HN]-[FY]-[NY], ζ= hydrophilic amino acid) in the catalytic domain of the enzyme. [1] [5] GH19 is a group of endo-acting enzymes that hydrolyzes the glycosidic bonds of β-1,4-linked N-Acetylglucosamine (GlcNAc) typically within chitin; however, some enzymes in this family also demonstrate lysozyme activity.[ citation needed ]

Since bacterial cell walls do not contain chitin, OBPgp279 hydrolyzes β-1,4-linked GlcNAc in peptidoglycan. [2] The hydrolysis of β-1,4-linked GlcNAc is catalyzed by two glutamate residues in the active side, one acting as a general acid, and another acting as a general base. [6]

There is limited detail on the catalytic mechanism of OBPgp279. However, because OBPgp279 is part of GH19, it is possible to infer the structure of OBPgp279 binding to peptidoglycan from the substrate binding of glycoside hydrolase family 19. [4] The figure on the right shows an example of a glycoside hydrolase family 19 binding to chitin. OBPgp279 most likely has a similar active site, but it binds to peptidoglycan instead of chitin.

Due to the activity of OBPgp279 on β-1,4-linked GlcNAc, it is likely that OBPgp279 is a N-acetylmuramidase (lysozyme-like) endolysin which hydrolyzes the sugar backbone component of the peptidoglycan on the reducing side of GlcNAc. [7]

Enzyme domain organization

The catalytic domain of the enzyme resides on the C-terminal region of the enzyme. OBPgp279 is also predicted to contain peptidoglycan binding domains; since OBPgp279 contains two peptidoglycan binding domain motifs in its N-terminal region (general sequence motif=D-G-(Pho)2-G-K/N-G/N-T, Pho =  hydrophobic amino acid), it likely contains two peptidoglycan binding domains as shown in the schematic drawing below. [1] [8]

The domain organization of OBPgp279. The E-values for OBP domains predicted by HHpred are shown below the respective domains. OBPgp279 domains.PNG
The domain organization of OBPgp279. The E-values for OBP domains predicted by HHpred are shown below the respective domains.

Application

OBPgp279 has gained attention as a potential antibiotic because of the increasing prevalence of multidrug resistant gram-negative bacteria. [9] Typically, most endolysins rely on holin to reach the peptidoglycan layer of gram-negative bacteria. This limits their efficacy as standalone antibiotics; without holins or any membrane permeabilizers, they have low membrane penetration. In contrast, OBPgp279 is capable of penetrating the bacterial outer membrane to reach the peptidoglycan layer without needing holins or any membrane permeabilizers. [2]

In addition, unlike most endolysins, OBPgp279 demonstrates high efficacy against a variety of bacteria instead of being species-specific. [1] Compared to small molecule antibiotics, OBPgp279 also has the advantages of a low chance of bacterial resistance, specificity towards pathogen-causing bacteria, and efficacy on mucosal surfaces. [10]

In 2013, Katholieke Universiteit Leuven (KU Leuven) professor Rob Lavigne modified OBPgp279 by adding a polycationic nonapeptide to its C-terminus, thereby improving its efficacy as an antibiotic. [9] The addition of the polycationic nonapeptide improved OBPgp279’s log reduction against various gram-negative and gram-positive bacteria by as much as three logs. This improvement is likely because of increased outer membrane penetration, in turn caused by favorable electrostatic interaction between the cationic nonapeptide and the negatively charged bacterial membrane. [11] The engineered OBPgp279, along with the engineering technology platform, is currently owned by Boehringer Ingelheim Vetmedica. [12]

The major drawback of working with OBPgp279 and other endolysins is their immunogenicity. Although studies show that antibodies do not affect the efficacy of endolysins in animal models, immunogenicity must be monitored if OBPgp279 is pursued for medical use. [13]

Related Research Articles

<span class="mw-page-title-main">Cell wall</span> Outermost layer of some cells

A cell wall is a structural layer that surrounds some cell types, found immediately outside the cell membrane. It can be tough, flexible, and sometimes rigid. Primarily, it provides the cell with structural support, shape, protection, and functions as a selective barrier. Another vital role of the cell wall is to help the cell withstand osmotic pressure and mechanical stress. While absent in many eukaryotes, including animals, cell walls are prevalent in other organisms such as fungi, algae and plants, and are commonly found in most prokaryotes, with the exception of mollicute bacteria.

<span class="mw-page-title-main">Gram-positive bacteria</span> Bacteria that give a positive result in the Gram stain test

In bacteriology, gram-positive bacteria are bacteria that give a positive result in the Gram stain test, which is traditionally used to quickly classify bacteria into two broad categories according to their type of cell wall.

<span class="mw-page-title-main">Gram-negative bacteria</span> Group of bacteria that do not retain the Gram stain used in bacterial differentiation

Gram-negative bacteria are bacteria that, unlike gram-positive bacteria, do not retain the crystal violet stain used in the Gram staining method of bacterial differentiation. Their defining characteristic is their cell envelope, which consists of a thin peptidoglycan cell wall sandwiched between an inner (cytoplasmic) membrane and an outer membrane. These bacteria are found in all environments that support life on Earth.

<span class="mw-page-title-main">Penicillin</span> Group of antibiotics derived from Penicillium fungi

Penicillins are a group of β-lactam antibiotics originally obtained from Penicillium moulds, principally P. chrysogenum and P. rubens. Most penicillins in clinical use are synthesised by P. chrysogenum using deep tank fermentation and then purified. A number of natural penicillins have been discovered, but only two purified compounds are in clinical use: penicillin G and penicillin V. Penicillins were among the first medications to be effective against many bacterial infections caused by staphylococci and streptococci. They are still widely used today for various bacterial infections, though many types of bacteria have developed resistance following extensive use.

Peptidoglycan or murein is a unique large macromolecule, a polysaccharide, consisting of sugars and amino acids that forms a mesh-like layer (sacculus) that surrounds the bacterial cytoplasmic membrane. The sugar component consists of alternating residues of β-(1,4) linked N-acetylglucosamine (NAG) and N-acetylmuramic acid (NAM). Attached to the N-acetylmuramic acid is an oligopeptide chain made of three to five amino acids. The peptide chain can be cross-linked to the peptide chain of another strand forming the 3D mesh-like layer. Peptidoglycan serves a structural role in the bacterial cell wall, giving structural strength, as well as counteracting the osmotic pressure of the cytoplasm. This repetitive linking results in a dense peptidoglycan layer which is critical for maintaining cell form and withstanding high osmotic pressures, and it is regularly replaced by peptidoglycan production. Peptidoglycan hydrolysis and synthesis are two processes that must occur in order for cells to grow and multiply, a technique carried out in three stages: clipping of current material, insertion of new material, and re-crosslinking of existing material to new material.

Autolysins are endogenous lytic enzymes that break down the peptidoglycan components of biological cells which enables the separation of daughter cells following cell division. They are involved in cell growth, cell wall metabolism, cell division and separation, as well as peptidoglycan turnover and have similar functions to lysozymes.

<span class="mw-page-title-main">Teichoic acid</span>

Teichoic acids are bacterial copolymers of glycerol phosphate or ribitol phosphate and carbohydrates linked via phosphodiester bonds.

A spheroplast is a microbial cell from which the cell wall has been almost completely removed, as by the action of penicillin or lysozyme. According to some definitions, the term is used to describe Gram-negative bacteria. According to other definitions, the term also encompasses yeasts. The name spheroplast stems from the fact that after the microbe's cell wall is digested, membrane tension causes the cell to acquire a characteristic spherical shape. Spheroplasts are osmotically fragile, and will lyse if transferred to a hypotonic solution.

The periplasm is a concentrated gel-like matrix in the space between the inner cytoplasmic membrane and the bacterial outer membrane called the periplasmic space in Gram-negative bacteria. Using cryo-electron microscopy it has been found that a much smaller periplasmic space is also present in Gram-positive bacteria, between cell wall and the plasma membrane. The periplasm may constitute up to 40% of the total cell volume of gram-negative bacteria, but is a much smaller percentage in gram-positive bacteria.

<span class="mw-page-title-main">Lytic cycle</span> Cycle of viral reproduction

The lytic cycle is one of the two cycles of viral reproduction, the other being the lysogenic cycle. The lytic cycle results in the destruction of the infected cell and its membrane. Bacteriophages that can only go through the lytic cycle are called virulent phages.

<span class="mw-page-title-main">Pseudopeptidoglycan</span>

Pseudopeptidoglycan is a major cell wall component of some Archaea that differs from bacterial peptidoglycan in chemical structure, but resembles bacterial peptidoglycan in function and physical structure. Pseudopeptidoglycan, in general, is only present in a few methanogenic archaea. The basic components are N-acetylglucosamine and N-acetyltalosaminuronic acid, which are linked by β-1,3-glycosidic bonds.

<span class="mw-page-title-main">Penicillin-binding proteins</span> Class of proteins

Penicillin-binding proteins (PBPs) are a group of proteins that are characterized by their affinity for and binding of penicillin. They are a normal constituent of many bacteria; the name just reflects the way by which the protein was discovered. All β-lactam antibiotics bind to PBPs, which are essential for bacterial cell wall synthesis. PBPs are members of a subgroup of transpeptidase enzymes called DD-transpeptidases.

<span class="mw-page-title-main">Lysin</span>

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.

<span class="mw-page-title-main">Plasmid-mediated resistance</span> Antibiotic resistance caused by a plasmid

Plasmid-mediated resistance is the transfer of antibiotic resistance genes which are carried on plasmids. Plasmids possess mechanisms that ensure their independent replication as well as those that regulate their replication number and guarantee stable inheritance during cell division. By the conjugation process, they can stimulate lateral transfer between bacteria from various genera and kingdoms. Numerous plasmids contain addiction-inducing systems that are typically based on toxin-antitoxin factors and capable of killing daughter cells that don't inherit the plasmid during cell division. Plasmids often carry multiple antibiotic resistance genes, contributing to the spread of multidrug-resistance (MDR). Antibiotic resistance mediated by MDR plasmids severely limits the treatment options for the infections caused by Gram-negative bacteria, especially family Enterobacteriaceae. The global spread of MDR plasmids has been enhanced by selective pressure from antimicrobial medications used in medical facilities and when raising animals for food.

<i>Autographiviridae</i> Subfamily of viruses

Autographiviridae is a family of viruses in the order Caudovirales. Bacteria serve as natural hosts. There are 373 species in this family, assigned to 9 subfamilies and 133 genera.

The bacterial cell wall provides strength and rigidity to counteract internal osmotic pressure, and protection against the environment. The peptidoglycan layer gives the cell wall its strength, and helps maintain the overall shape of the cell. The basic peptidoglycan structure of both Gram-positive and Gram-negative bacteria comprises a sheet of glycan chains connected by short cross-linking polypeptides. Biosynthesis of peptidoglycan is a multi-step process comprising three main stages:

  1. formation of UDP-N-acetylmuramic acid (UDPMurNAc) from N-acetylglucosamine (GlcNAc).
  2. addition of a short polypeptide chain to the UDPMurNAc.
  3. addition of a second GlcNAc to the disaccharide-pentapeptide building block and transport of this unit through the cytoplasmic membrane and incorporation into the growing peptidoglycan layer.
<span class="mw-page-title-main">Enzybiotics</span> Experimental antibacterial therapy

Enzybiotics are an experimental antibacterial therapy. The term is derived from a combination of the words “enzyme” and “antibiotics.” Enzymes have been extensively utilized for their antibacterial and antimicrobial properties. Proteolytic enzymes called endolysins have demonstrated particular effectiveness in combating a range of bacteria and are the basis for enzybiotic research. Endolysins are derived from bacteriophages and are highly efficient at lysing bacterial cells. Enzybiotics are being researched largely to address the issue of antibiotic resistance, which has allowed for the proliferation of drug-resistant pathogens posing great risk to animal and human health across the globe.

<span class="mw-page-title-main">Epimerox</span> Chemical compound

Epimerox is an experimental broad-spectrum antibiotic compound being developed by scientists at the Rockefeller University and Astex Pharmaceuticals. It is a small molecule inhibitor compound that blocks the activity of the enzyme UDP-N-acetylglucosamine 2-epimerase, an epimerase enzyme that is called 2-epimerase for short.

<span class="mw-page-title-main">Lipid II</span> Chemical compound

Lipid II is a precursor molecule in the synthesis of the cell wall of bacteria. It is a peptidoglycan, which is amphipathic and named for its bactoprenol hydrocarbon chain, which acts as a lipid anchor, embedding itself in the bacterial cell membrane. Lipid II must translocate across the cell membrane to deliver and incorporate its disaccharide-pentapeptide "building block" into the peptidoglycan mesh. Lipid II is the target of several antibiotics.

<span class="mw-page-title-main">Peptidoglycan recognition protein 3</span>

Peptidoglycan recognition protein 3 is an antibacterial and anti-inflammatory innate immunity protein that in humans is encoded by the PGLYRP3 gene.

References

  1. 1 2 3 4 5 6 Walmagh M, Briers Y, dos Santos SB, Azeredo J, Lavigne R (2012-05-15). "Characterization of modular bacteriophage endolysins from Myoviridae phages OBP, 201φ2-1 and PVP-SE1". PLOS One . 7 (5): e36991. Bibcode:2012PLoSO...736991W. doi: 10.1371/journal.pone.0036991 . PMC   3352856 . PMID   22615864.
  2. 1 2 3 Nelson DC, Schmelcher M, Rodriguez-Rubio L, Klumpp J, Pritchard DG, Dong S, Donovan DM (2012-01-01). Łobocka M, Szybalski W (eds.). "Endolysins as antimicrobials". Advances in Virus Research. Bacteriophages, Part B. 83. Academic Press: 299–365. doi:10.1016/b978-0-12-394438-2.00007-4. hdl: 10261/80868 . ISBN   9780123944382. PMID   22748813.
  3. ↑ "The Rockefeller University » Hospital Centennial". centennial.rucares.org. Retrieved 2016-03-01.
  4. 1 2 Eijsink V, Hoell I, Vaaje-Kolstada G (2010-01-01). "Structure and function of enzymes acting on chitin and chitosan". Biotechnology & Genetic Engineering Reviews. 27 (1): 331–66. doi: 10.1080/02648725.2010.10648156 . PMID   21415904.
  5. ↑ Udaya Prakash NA, Jayanthi M, Sabarinathan R, Kangueane P, Mathew L, Sekar K (May 2010). "Evolution, homology conservation, and identification of unique sequence signatures in GH19 family chitinases". Journal of Molecular Evolution. 70 (5): 466–78. Bibcode:2010JMolE..70..466U. doi:10.1007/s00239-010-9345-z. PMID   20480157. S2CID   2202745.
  6. ↑ Huet J, Rucktooa P, Clantin B, Azarkan M, Looze Y, Villeret V, Wintjens R (August 2008). "X-ray structure of papaya chitinase reveals the substrate binding mode of glycosyl hydrolase family 19 chitinases". Biochemistry. 47 (32): 8283–91. doi:10.1021/bi800655u. PMID   18636748.
  7. ↑ Schmelcher M, Donovan DM, Loessner MJ (October 2012). "Bacteriophage endolysins as novel antimicrobials". Future Microbiology. 7 (10): 1147–71. doi:10.2217/fmb.12.97. PMC   3563964 . PMID   23030422.
  8. ↑ Briers Y, Volckaert G, Cornelissen A, Lagaert S, Michiels CW, Hertveldt K, Lavigne R (September 2007). "Muralytic activity and modular structure of the endolysins of Pseudomonas aeruginosa bacteriophages phiKZ and EL". Molecular Microbiology. 65 (5): 1334–44. doi: 10.1111/j.1365-2958.2007.05870.x . PMID   17697255.
  9. 1 2 Briers Y, Walmagh M, Van Puyenbroeck V, Cornelissen A, Cenens W, Aertsen A, et al. (July 2014). "Engineered endolysin-based "Artilysins" to combat multidrug-resistant gram-negative pathogens". mBio. 5 (4): e01379-14. doi:10.1128/mBio.01379-14. PMC   4161244 . PMID   24987094.
  10. ↑ Fischetti VA (August 2010). "Bacteriophage endolysins: a novel anti-infective to control Gram-positive pathogens". International Journal of Medical Microbiology. 300 (6): 357–62. doi:10.1016/j.ijmm.2010.04.002. PMC   3666336 . PMID   20452280.
  11. ↑ Silhavy TJ, Kahne D, Walker S (May 2010). "The bacterial cell envelope". Cold Spring Harbor Perspectives in Biology. 2 (5): a000414. doi:10.1101/cshperspect.a000414. PMC   2857177 . PMID   20452953.
  12. ↑ "Boehringer Ingelheim Vetmedica Acquires Licensing Rights for Artilysin Technology from Lysando AG". Business Wire . 2014-08-12. Retrieved 2016-03-01.
  13. ↑ Fischetti VA (October 2008). "Bacteriophage lysins as effective antibacterials". Current Opinion in Microbiology. 11 (5): 393–400. doi:10.1016/j.mib.2008.09.012. PMC   2597892 . PMID   18824123.
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