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Bacteriophage (PDF) How viruses infect bacteria?

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How viruses infect bacteria?

Article (PDF Available)in The EMBO Journal 28(7):797-8 · May 2009with 108 Reads
DOI: 10.1038/emboj.2009.71 · Source: PubMed

Abstract
Viruses are minuscule infectious particles composed of a protein coat and a nucleic acid core. They exist in a huge variety of forms and infect practically all living creatures: animals, plants, insects and bacteria. Insight into the infection process could facilitate new therapeutic strategies for viral and bacterial diseases as well as food preservation. An article by Aksyuk et al (2009) published in this issue sheds light on the still mysterious infection process. It reports the first crystal structure of a significant portion of the bacteriophages T4 tail sheath protein. Together with fittings into existing cryo-EM reconstructions, it suggests a mechanism of genome delivery into the host cell for the Myoviridae phages.

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Author content

All content in this area was uploaded by E.V. Orlova

Bacteriophage T4. The left panel illustrates the phage in the extended state, whereas the right panel shows the phage in the contracted state. The middle panel shows enlarged fragments of the tail both in extended and contracted states; the upper part of the middle panel demonstrates the fitting of the X-ray structure into EM map. Subunits shadowed in red show their rearrangement in the same helical strand (adapted from figures kindly provided by Petr Leiman and Michael Rossmann).
Bacteriophage T4. The left panel illustrates the phage in the extended state, whereas the right panel shows the phage in the contracted state. The middle panel shows enlarged fragments of the tail both in extended and contracted states; the upper part of the middle panel demonstrates the fitting of the X-ray structure into EM map. Subunits shadowed in red show their rearrangement in the same helical strand (adapted from figures kindly provided by Petr Leiman and Michael Rossmann).
… 
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All content in this area was uploaded by E.V. Orlova on Oct 14, 2014

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Available via license: CC BY-NC-ND 3.0
How viruses infect bacteria?
Elena V Orlova*
School of Crystallography, Birkbeck College, London, UK
*Corresponding author. School of Crystallography, Birkbeck College, Malet Street, London WC1E 7HX, UK.
The EMBO Journal (2009) 28, 797–798. doi:10.1038/emboj.2009.71
Viruses are minuscule infectious particles composed of a
protein coat and a nucleic acid core. They exist in a huge
variety of forms and infect practically all living creatures:
animals, plants, insects and bacteria. Insight into the
infection process could facilitate new therapeutic strate-
gies for viral and bacterial diseases as well as food pre-
servation. An article by Aksyuk et al (2009) published in
this issue sheds light on the still mysterious infection
process. It reports the first crystal structure of a significant
portion of the bacteriophages T4 tail sheath protein.
Together with fittings into existing cryo-EM reconstruc-
tions, it suggests a mechanism of genome delivery into the
host cell for the Myoviridae phages.
Viruses can be considered as mobile genetic particles, containing
instructions for reproducing themselves using foreign cellular re-
sources. The amount of viruses that exist in the biosphere is
enormous, varying in their virion shapes, genomes and lifestyles.
Classification of viruses is defined by host preference, viral mor-
phology, genome type and auxiliary structures such as tails or
envelopes. Viral particles outside a host cell (so called virions)
are inert entities with a genome surrounded by a protective coat.
Viruses that attack bacteria were named ‘bacteriophages’.
The term phage originates from Greek phagein, which translates
as ‘to eat’. The phage infection cycle seems to be simple but
extremely efficient: a single phage injects its genome into a bacterial
cell, switching the cells’ programme in its favour so the host cell
will eventually die and release about 100 new phage particles.
Studies of bacteriophages became an essential part of biology
because their omnipresence was tightly linked to bacteria.
Analyses of bacteriophage genome sequences provide the opportu-
nity to identify basic principles of genome organisation, co-evolu-
tion, as well as model and modify their genome. Novel studies on
the phage life cycle will not only reveal its interaction with
biological barriers during viral transmission and high-level adapta-
tion but might also help to overcome serious clinical problems
caused by the occurrence of multi-resistant bacteria, the so-called
‘superbugs’. This presumption is based on the fact that phages
infecting certain bacteria may recognise and infect these despite
their antibiotic(s) resistance. Indeed, exponential effects of phage
growth in cells has proven very important in combating bacterial
diseases.
The Caudovirales order of bacteriophages is characterised by
double-stranded DNA (dsDNA) genomes, which can be of the size
from 18 to 500 kb in length. The phages, belonging to Caudovirales,
account for 95% of all the phages reported in the scientific
literature, and most likely represent the majority of phages on the
planet (Ackermann, 2006). Although genome sequences vary quite
significantly, the virus particles of this group have a quite similar
organisation: each virion has a polyhedral, predominantly icosahe-
dral, head (capsid) that contains a genome. The head is bound to a
tail through a connector, and the distant end of the tail is equipped
with a special system for piercing a bacterial membrane. The
bacteriophage tail and its related structures are essential tools of
the phage during infectivity process securing the entry of the viral
nucleic acid into the host cell.
Rossmann’s group has been involved for many years with
analysing different viruses and a significant part of their research
is dedicated to the bacterial virus T4 that belongs to the Myoviridae
family (Ackermann, 2006). Myoviridae are a family of bacterio-
phages with contractile tails, comprising B25% of all known phage
populations. Tail contraction is an essential phase of cellular infec-
tion by these phages, resulting in pressing the central tail tube
through the outer cell membrane similar to a syringe, thereby
creating a channel for DNA ejection from the capsid and into the
host cell (Figure 1; Leiman et al, 2003).
Tailed dsDNA phages are characterised by their futility for
crystallisation trials, although crystal structures of some individual
protein components have been determined for T4 bacteriophage by
the Rossmann lab. Structural studies of other phages from the
Myoviridae family were hampered by variation and diversity in
the amino-acid sequences among the tailed bacteriophages, making
prediction of the structural organisation of phage elements unreli-
able. Cryo-EM became the only available tool that allowed structur-
al insight at subnanometer resolution (6–10 A
˚; Jiang et al, 2006;
Lander et al, 2008). Combining EM and crystallography also
allowed the identification of the T4 bacteriophage baseplate pro-
teins, long and short fibres as well as the capsid protein (Leiman
et al, 2004; Kostyuchenko et al, 2005).
The new work by Aksyuk and co-authors published in this issue
of The EMBO Journal further advances our understanding of this
complex biological system. Using a similar hybrid approach,
Aksyuk et al (2009) solve here the crystal structure of a small
protease-resistant fragment (gp18PR) of the sheath protein gp18.
Using molecular replacement, they further determine the structure
Figure 1 Bacteriophage T4. The left panel illustrates the phage in
the extended state, whereas the right panel shows the phage in the
contracted state. The middle panel shows enlarged fragments of the
tail both in extended and contracted states; the upper part of
the middle panel demonstrates the fitting of the X-ray structure
into EM map. Subunits shadowed in red show their rearrangement
in the same helical strand (adapted from figures kindly provided by
Petr Leiman and Michael Rossmann).
The EMBO Journal (2009) 28, 797–798 |
&
2009 European Molecular Biology Organization |Some Rights Reserved 0261-4189/09
www.embojournal.org
&2009 European Molecular Biology Organization The EMBO Journal VOL 28 |NO 7 |2009 797

of the larger gp18M protein comprising three of the four domains of
the protein. Fitting of the gp18M atomic model into existing EM
maps allowed localisation of the individual protein subunits within
the tail sheath and also identified conformational changes
during tail contraction (central panel in Figure 1). These results
suggest the interactions of subunits within the tail, and provide a
mechanistic view on the phage tail contraction during the infection
process.
This first tail sheath protein structure determination, together
with the comparative modelling approach, sheds light on the
process of T4-bacteriophage infection and might similarly be ap-
plied to related structural studies.
References
Ackermann H-W (2006) Classification of bacteriophages. In The
Bacteriophages, Calendar R (ed) 2nd edn, pp 8–16. New York, NY:
Oxford University Press
Aksyuk AA, Leiman PG, Kurochkina LP, Shneider MM,
Kostyuchenko VA, Mesyanzhinov VV, Rossmann MG (2009)
The tail sheath structure of bacteriophage T4: a molecular
machine for infecting bacteria. EMBO J 28:821–829
Jiang W, Chang J, Jakana J, Weigele P, King J, Chiu W (2006) Structure
of epsilon15 bacteriophage reveals genome organization and DNA
packaging/injection apparatus. Nature 439: 612–616
Kostyuchenko VA, Chipman PR, Leiman PG, Arisaka F,
Mesyanzhinov VV, Rossmann MG (2005) The tail structure of
bacteriophage T4 and its mechanism of contraction. Nat Struct
Mol Biol 12: 810–813
Lander GC, Evilevitch A, Jeembaeva M, Potter CS, Carragher B,
Johnson JE. (2008) Bacteriophage lambda stabilization by aux-
iliary protein gpD: timing, location, and mechanism of attach-
ment determined by cryo-EM. Structure 16: 1399–1406
Leiman PG, Chipman PR, Kostyuchenko VA, Mesyanzhinov VV,
Rossmann MG (2004) Three-dimensional rearrangement of
proteins in the tail of bacteriophage T4 on infection of its host.
Cell 118: 419–429
Leiman PG, Kanamaru S, Mesyanzhinov VV, Arisaka F, Rossmann
MG (2003) Structure and morphogenesis of bacteriophage T4.
Cell Mol Life Sci 60: 235
EMBO
open
This is an open-access article distributed
under the terms of the Creative Commons
Attribution License, which permits distri-
bution, and reproduction in any medium, provided the
original author and source are credited. This license does not
permit commercial exploitation without specific permission.
The EMBO Journal is published by Nature
Publishing Group on behalf of European
Molecular Biology Organization. This article is licensed
under a Creative Commons Attribution-Noncommercial-
No Derivative Works 3.0 Licence. [http://creativecommons.
org/licenses/by-nc-nd/3.0]
How viruses infect bacteria?
EV Orlova
The EMBO Journal VOL 28 |NO 7 |2009 &2009 European Molecular Biology Organization798

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    • Victor A Kostyuchenko

      Victor A Kostyuchenko

    • Michael G. Rossmann

      Michael G. Rossmann

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      Paul Chipman

    • Petr Leiman

      Petr Leiman

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    Article
    Full-text available
    • Mar 2006
    • Nature
    • Juan Chang

      Juan Chang

    • Joanita Jakana

      Joanita Jakana

    • Wah Chiu

      Wah Chiu

    • Wen Jiang

      Wen Jiang

    The critical viral components for packaging DNA, recognizing and binding to host cells, and injecting the condensed DNA into the host are organized at a single vertex of many icosahedral viruses. These component structures do not share icosahedral symmetry and cannot be resolved using a conventional icosahedral averaging method. Here we report the structure of the entire infectious Salmonella bacteriophage epsilon15 (ref. 1) determined from single-particle cryo-electron microscopy, without icosahedral averaging. This structure displays not only the icosahedral shell of 60 hexamers and 11 pentamers, but also the non-icosahedral components at one pentameric vertex. The densities at this vertex can be identified as the 12-subunit portal complex sandwiched between an internal cylindrical core and an external tail hub connecting to six projecting trimeric tailspikes. The viral genome is packed as coaxial coils in at least three outer layers with approximately 90 terminal nucleotides extending through the protein core and the portal complex and poised for injection. The shell protein from icosahedral reconstruction at higher resolution exhibits a similar fold to that of other double-stranded DNA viruses including herpesvirus, suggesting a common ancestor among these diverse viruses. The image reconstruction approach should be applicable to studying other biological nanomachines with components of mixed symmetries.

  • Classification of bacteriophages
    • Ackermann H-W
    • Ackermann H-W
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Bacteriophages and Their Structural Organisation

March 2012
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Viruses are extremely small infectious particles that are not visible in a light microscope, and

are able to pass through fine porcelain filters. They exist in a huge variety of forms and

infect practically all living systems: animals, plants, insects and bacteria. All viruses have a

genome, typically only one type of nucleic acid, but it could be one or several molecules of

DNA or RNA, … [Show full abstract] which is surrounded by a protective stable coat (capsid) and sometimes by

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additional proteins. The viruses that have only a protein coat are named “naked”, or non-
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ABSTRACT Bacteriophage T4 is the most well-studied member of Myoviridae, the most complex family of tailed phages. T4 assembly is divided into three independent pathways: the head, the tail and the long tail fibers. The prolate head encapsidates a 172 kbp concatemeric dsDNA genome. The 925 Å-long tail is surrounded by the contractile sheath and ends with a hexagonal baseplate. Six long tail … [Show full abstract] fibers are attached to the baseplate's periphery and are the host cell's recognition sensors. The sheath and the baseplate undergo large conformational changes during infection. X-ray crystallography and cryo-electron microscopy have provided structural information on protein-protein and protein-nucleic acid interactions that regulate conformational changes during assembly and infection of Escherichia coli cells.

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Bacteriophage phiKZ is a giant phage that infects Pseudomonas aeruginosa, a human pathogen. The phiKZ virion consists of a 1450 Å diameter icosahedral head and a 2000 Å-long contractile tail. The structure of the whole virus was previously reported, showing that its tail organization in the extended state is similar to the well-studied Myovirus bacteriophage T4 tail. The crystal structure of a … [Show full abstract] tail sheath protein fragment of phiKZ was determined to 2.4 Å resolution. Furthermore, crystal structures of two prophage tail sheath proteins were determined to 1.9 and 3.3 Å resolution. Despite low sequence identity between these proteins, all of these structures have a similar fold. The crystal structure of the phiKZ tail sheath protein has been fitted into cryo-electron-microscopy reconstructions of the extended tail sheath and of a polysheath. The structural rearrangement of the phiKZ tail sheath contraction was found to be similar to that of phage T4.

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Remarkable progress has been made during the past ten years in elucidating the structure of the bacteriophage T4 tail by a combination of three-dimensional image reconstruction from electron micrographs and X-ray crystallography of the components. Partial and complete structures of nine out of twenty tail structural proteins have been determined by X-ray crystallography and have been fitted into … [Show full abstract] the 3D-reconstituted structure of the "extended" tail. The 3D structure of the "contracted" tail was also determined and interpreted in terms of component proteins. Given the pseudo-atomic tail structures both before and after contraction, it is now possible to understand the gross conformational change of the baseplate in terms of the change in the relative positions of the subunit proteins. These studies have explained how the conformational change of the baseplate and contraction of the tail are related to the tail's host cell recognition and membrane penetration function. On the other hand, the baseplate assembly process has been recently reexamined in detail in a precise system involving recombinant proteins (unlike the earlier studies with phage mutants). These experiments showed that the sequential association of the subunits of the baseplate wedge is based on the induced-fit upon association of each subunit. It was also found that, upon association of gp53 (gene product 53), the penultimate subunit of the wedge, six of the wedge intermediates spontaneously associate to form a baseplate-like structure in the absence of the central hub. Structure determination of the rest of the subunits and intermediate complexes and the assembly of the hub still require further study.

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Bacteriophage

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“Phage” redirects here. For other uses, see Phage (disambiguation) .

The structure of a typical myovirus bacteriophage

Anatomy and infection cycle of phage T4

A bacteriophage ( /bækˈtɪərif/ ), also known informally as a phage ( /f/ ), is a virus that infects and replicates within Bacteria and Archaea . The term was derived from “bacteria” and the Greek φαγεῖν (phagein), “to devour”. Bacteriophages are composed of proteins that encapsulate a DNA or RNA genome , and may have relatively simple or elaborate structures. 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 . Bacteriophages are among the most common and diverse entities in the biosphere . [1] Bacteriophages are ubiquitous viruses, found wherever bacteria exist. It is estimated there are more than 1031 bacteriophages on the planet, more than every other organism on Earth, including bacteria, combined. [2]

Phages are widely distributed in locations populated by bacterial hosts, such as soil or the intestines of animals. One of the densest natural sources for phages and other viruses is seawater, where up to 9×108 virions per millilitre have been found in microbial mats at the surface, [3] and up to 70% of marine bacteria may be infected by phages. [4] They have been used for over 90 years as an alternative to antibiotics in the former Soviet Union and Central Europe as well as in France. [5] They are seen as a possible therapy against multi-drug-resistant strains of many bacteria (see phage therapy ). [6] Nevertheless, phages of Inoviridae have been shown to complicate biofilms involved in pneumonia and cystic fibrosis and shelter the bacteria from drugs meant to eradicate disease, thus promote persistent infection. [7]

Contents

  • 1 Classification
  • 2 History
  • 3 Uses
    • 3.1 Phage therapy
    • 3.2 Dairy industry
    • 3.3 Other
  • 4 Replication
    • 4.1 Attachment and penetration
    • 4.2 Synthesis of proteins and nucleic acid
    • 4.3 Virion assembly
    • 4.4 Release of virions
  • 5 Genome structure
  • 6 Systems biology
  • 7 In the environment
  • 8 Model bacteriophages
  • 9 See also
  • 10 References
  • 11 External links

Classification[ edit ]

Bacteriophages occur abundantly in the biosphere, with different genomes, and lifestyles. Phages are classified by the International Committee on Taxonomy of Viruses (ICTV) according to morphology and nucleic acid.

Nineteen families are currently recognized by the ICTV that infect bacteria and archaea . Of these, only two families have RNA genomes, and only five families are surrounded by an envelope. Of the viral families with DNA genomes, only two have single-stranded genomes. Eight of the viral families with DNA genomes have circular genomes while nine have linear genomes. Nine families infect bacteria only, nine infect archaea only, and one (Tectiviridae) infects both bacteria and archaea.

Bacteriophage P22, a member of the Podoviridae by morphology due to its short, non-contractile tail

ICTV classification of prokaryotic (bacterial and archaeal) viruses [1]
OrderFamilyMorphologyNucleic acidExamples
Caudovirales Myoviridae Non enveloped , contractile tailLinear dsDNA T4 phage , Mu , PBSX, P1Puna-like, P2, I3, Bcep 1, Bcep 43, Bcep 78
Siphoviridae Nonenveloped, noncontractile tail (long)Linear dsDNA λ phage , T5 phage , phi, C2, L5, HK97 , N15
Podoviridae Nonenveloped, noncontractile tail (short)Linear dsDNA T7 phage , T3 phage , Φ29 , P22, P37
Ligamenvirales Lipothrixviridae Enveloped, rod-shapedLinear dsDNA Acidianus filamentous virus 1
Rudiviridae Nonenveloped, rod-shapedLinear dsDNA Sulfolobus islandicus rod-shaped virus 1
Unassigned Ampullaviridae Enveloped, bottle-shapedLinear dsDNA
Bicaudaviridae Nonenveloped, lemon-shapedCircular dsDNA
Clavaviridae Nonenveloped, rod-shapedCircular dsDNA
Corticoviridae Nonenveloped, isometricCircular dsDNA
Cystoviridae Enveloped, sphericalSegmented dsRNA
Fuselloviridae Nonenveloped, lemon-shapedCircular dsDNA
Globuloviridae Enveloped, isometricLinear dsDNA
Guttaviridae Nonenveloped, ovoidCircular dsDNA
Inoviridae Nonenveloped, filamentousCircular ssDNA M13
Leviviridae Nonenveloped, isometricLinear ssRNA MS2 , Qβ
Microviridae Nonenveloped, isometricCircular ssDNA ΦX174
Plasmaviridae Enveloped, pleomorphicCircular dsDNA
Tectiviridae Nonenveloped, isometricLinear dsDNA

History[ edit ]

Félix d’Herelle

In 1896, Ernest Hanbury Hankin reported that something in the waters of the Ganges and Yamuna rivers in India had marked antibacterial action against cholera and could pass through a very fine porcelain filter. [8] In 1915, British bacteriologist Frederick Twort , superintendent of the Brown Institution of London, discovered a small agent that infected and killed bacteria. He believed the agent must be one of the following:

  1. a stage in the life cycle of the bacteria;
  2. an enzyme produced by the bacteria themselves; or
  3. a virus that grew on and destroyed the bacteria. [9]

Twort’s work was interrupted by the onset of World War I and shortage of funding. Independently, French-Canadian microbiologist Félix d’Hérelle , working at the Pasteur Institute in Paris , announced on 3 September 1917, that he had discovered “an invisible, antagonistic microbe of the dysentery bacillus”. For d’Hérelle, there was no question as to the nature of his discovery: “In a flash I had understood: what caused my clear spots was in fact an invisible microbe … a virus parasitic on bacteria.” [10] D’Hérelle called the virus a bacteriophage or bacteria-eater (from the Greek phagein meaning “to devour”). He also recorded a dramatic account of a man suffering from dysentery who was restored to good health by the bacteriophages. [11] It was D’Herelle who conducted much research into bacteriophages and introduced the concept of phage therapy . [12]

In 1969, Max Delbrück , Alfred Hershey and Salvador Luria were awarded the Nobel Prize in Physiology or Medicine for their discoveries of the replication of viruses and their genetic structure. [13]

Uses[ edit ]

Phage therapy[ edit ]

Main article: Phage therapy

Phages were discovered to be antibacterial agents and were used in the former Soviet Republic of Georgia (pioneered there by Giorgi Eliava with help from the co-discoverer of bacteriophages, Félix d’Herelle ) during the 1920s and 1930s for treating bacterial infections. They had widespread use, including treatment of soldiers in the Red Army. However, they were abandoned for general use in the West for several reasons:

  • Antibiotics were discovered and marketed widely. They were easier to make, store and to prescribe.
  • Medical trials of phages were carried out, but a basic lack of understanding raised questions about the validity of these trials. [14]
  • Publication of research in the Soviet Union was mainly in the Russian or Georgian languages and were not followed internationally for many years.

The use of phages has continued since the end of the Cold War in Georgia and elsewhere in Central and Eastern Europe. The first regulated, randomized, double-blind clinical trial was reported in the Journal of Wound Care in June 2009, which evaluated the safety and efficacy of a bacteriophage cocktail to treat infected venous ulcers of the leg in human patients. [15] The FDA approved the study as a Phase I clinical trial. The study’s results demonstrated the safety of therapeutic application of bacteriophages but did not show efficacy. The authors explain that the use of certain chemicals that are part of standard wound care (e.g. lactoferrin or silver) may have interfered with bacteriophage viability. [15] Another controlled clinical trial in Western Europe (treatment of ear infections caused by Pseudomonas aeruginosa) was reported shortly after this in the journal Clinical Otolaryngology in August 2009. [16] The study concludes that bacteriophage preparations were safe and effective for treatment of chronic ear infections in humans. Additionally, there have been numerous animal and other experimental clinical trials evaluating the efficacy of bacteriophages for various diseases, such as infected burns and wounds, and cystic fibrosis associated lung infections, among others. [17] Meanwhile, bacteriophage researchers are developing engineered viruses to overcome antibiotic resistance , and engineering the phage genes responsible for coding enzymes which degrade the biofilm matrix, phage structural proteins and also the enzymes responsible for lysis of the bacterial cell wall. [3] [4] [5] There have been results showing that T4 phages that are small in size and short-tailed can be helpful in detecting E.coli in the human body. [18]

D’Herelle “quickly learned that bacteriophages are found wherever bacteria thrive: in sewers, in rivers that catch waste runoff from pipes, and in the stools of convalescent patients.” [19] This includes rivers traditionally thought to have healing powers, including India’s Ganges River. [20]

In 2015, a psychology professor whose wife is a professor of public health at University of California, San Diego, became ill with a resistant strain of Acinetobacter baumanii, a deadly strain of bacteria especially prevalent in the Middle East. The psychology professor, Tom Patterson, became ill while traveling in Egypt, and eventually fell into a coma. Patterson’s wife, Steffanie Strathdee , began working with the head of infectious diseases at UCSD. In her search for alternatives to antibiotics, Strathdee had discovered bacteriophages, and concentrated on reaching out to various institutions to find an appropriate treatment for her husband’s infection. According to an article by Laura Kahn in the Bulletin of the Atomic Scientists , “The US Food and Drug Administration (FDA) provided emergency approval for experimental intravenous and intra-abdominal-cavity treatments. The phage cocktail crafted to attack the professor’s infection needed several adjustments, but after three days of treatment in the intensive care unit at Thornton Hospital, part of UC San Diego Health, he woke from his coma.” [21]

Dairy industry[ edit ]

Bacteriophages present in the environment can cause fermentation failures of cheese starter cultures. In order to avoid this, mixed-strain starter cultures and culture rotation regimes can be used. [22]

Other[ edit ]

Food industry. Since 2006, the United States Food and Drug Administration (FDA) and United States Department of Agriculture (USDA) have approved several bacteriophage products. LMP-102 (Intralytix) was approved for treating ready-to-eat (RTE) poultry and meat products. In that same year, the FDA approved LISTEX (developed and produced by Micreos ) using bacteriophages on cheese to kill Listeria monocytogenes bacteria, giving them generally recognized as safe (GRAS) status. [23] In July 2007, the same bacteriophage were approved for use on all food products. [24] In 2011 USDA confirmed that LISTEX is a clean label processing aid and is included in USDA. [25] Research in the field of food safety is continuing to see if lytic phages are a viable option to control other food-borne pathogens in various food products.

Diagnostics. In 2011, the FDA cleared the first bacteriophage-based product for in vitro diagnostic use. [26] The KeyPath MRSA/MSSA Blood Culture Test uses a cocktail of bacteriophage to detect Staphylococcus aureus in positive blood cultures and determine methicillin resistance or susceptibility. The test returns results in about 5 hours, compared to 2–3 days for standard microbial identification and susceptibility test methods. It was the first accelerated antibiotic susceptibility test approved by the FDA. [27]

Counteracting bioweapons and toxins. Government agencies in the West have for several years been looking to Georgia and the former Soviet Union for help with exploiting phages for counteracting bioweapons and toxins, such as anthrax and botulism . [28] Developments are continuing among research groups in the US. Other uses include spray application in horticulture for protecting plants and vegetable produce from decay and the spread of bacterial disease. Other applications for bacteriophages are as biocides for environmental surfaces, e.g., in hospitals, and as preventative treatments for catheters and medical devices before use in clinical settings. The technology for phages to be applied to dry surfaces, e.g., uniforms, curtains, or even sutures for surgery now exists. Clinical trials reported in Clinical Otolaryngology [29] show success in veterinary treatment of pet dogs with otitis .

The SEPTIC bacterium sensing and identification method uses the ion emission and its dynamics during phage infection and offers high specificity and speed for detection. [30]

Phage display is a different use of phages involving a library of phages with a variable peptide linked to a surface protein. Each phage’s genome encodes the variant of the protein displayed on its surface (hence the name), providing a link between the peptide variant and its encoding gene. Variant phages from the library can be selected through their binding affinity to an immobilized molecule (e.g., botulism toxin) to neutralize it. The bound, selected phages can be multiplied by reinfecting a susceptible bacterial strain, thus allowing them to retrieve the peptides encoded in them for further study. [31]

Antimicrobial drug discovery. Phage proteins often have antimicrobial activity and may serve as leads for peptidomimetics , i.e. drugs that mimic peptides. [32] Phage-ligand technology makes use of phage proteins for various applications such as binding of bacteria and bacterial components (e.g. endotoxin ) and lysis of bacteria. [33]

Basic research. Bacteriophages are also important model organisms for studying principles of evolution and ecology . [34]

Replication[ edit ]

Diagram of the DNA injection process

Bacteriophages may have a lytic cycle or a lysogenic cycle , and a few viruses are capable of carrying out both. With lytic phages such as the T4 phage , bacterial cells are broken open (lysed) and destroyed after immediate replication of the virion. As soon as the cell is destroyed, the phage progeny can find new hosts to infect. Lytic phages are more suitable for phage therapy . Some lytic phages undergo a phenomenon known as lysis inhibition, where completed phage progeny will not immediately lyse out of the cell if extracellular phage concentrations are high. This mechanism is not identical to that of temperate phage going dormant and is usually temporary.

In contrast, the lysogenic cycle does not result in immediate lysing of the host cell. Those phages able to undergo lysogeny are known as temperate phages . Their viral genome will integrate with host DNA and replicate along with it relatively harmlessly, or may even become established as a plasmid . The virus remains dormant until host conditions deteriorate, perhaps due to depletion of nutrients; then, the endogenous phages (known as prophages ) become active. At this point they initiate the reproductive cycle, resulting in lysis of the host cell. As the lysogenic cycle allows the host cell to continue to survive and reproduce, the virus is replicated in all of the cell’s offspring.
An example of a bacteriophage known to follow the lysogenic cycle and the lytic cycle is the phage lambda of E. coli. [35]

Sometimes prophages may provide benefits to the host bacterium while they are dormant by adding new functions to the bacterial genome in a phenomenon called lysogenic conversion . Examples are the conversion of harmless strains of Corynebacterium diphtheriae or Vibrio cholerae by bacteriophages to highly virulent ones, which cause diphtheria or cholera , respectively. [36] [37] Strategies to combat certain bacterial infections by targeting these toxin-encoding prophages have been proposed. [38]

Attachment and penetration[ edit ]

In this electron micrograph of bacteriophages attached to a bacterial cell, the viruses are the size and shape of coliphage T1.

To enter a host cell, bacteriophages attach to specific receptors on the surface of bacteria, including lipopolysaccharides , teichoic acids , proteins , or even flagella . This specificity means a bacteriophage can infect only certain bacteria bearing receptors to which they can bind, which in turn determines the phage’s host range. Host growth conditions also influence the ability of the phage to attach and invade them. [39] As phage virions do not move independently, they must rely on random encounters with the right receptors when in solution (blood, lymphatic circulation, irrigation, soil water, etc.).

Myovirus bacteriophages use a hypodermic syringe -like motion to inject their genetic material into the cell. After making contact with the appropriate receptor, the tail fibers flex to bring the base plate closer to the surface of the cell; this is known as reversible binding. Once attached completely, irreversible binding is initiated and the tail contracts, possibly with the help of ATP present in the tail, [4] injecting genetic material through the bacterial membrane. The injection is done through a sort of bending motion in the shaft by going to the side, contracting closer to the cell and pushing back up.
Podoviruses lack an elongated tail sheath similar to that of a myovirus, so they instead use their small, tooth-like tail fibers enzymatically to degrade a portion of the cell membrane before inserting their genetic material.

Synthesis of proteins and nucleic acid[ edit ]

Within minutes, bacterial ribosomes start translating viral mRNA into protein. For RNA-based phages, RNA replicase is synthesized early in the process. Proteins modify the bacterial RNA polymerase so it preferentially transcribes viral mRNA. The host’s normal synthesis of proteins and nucleic acids is disrupted, and it is forced to manufacture viral products instead. These products go on to become part of new virions within the cell, helper proteins that help assemble the new virions, or proteins involved in cell lysis . Walter Fiers ( University of Ghent , Belgium ) was the first to establish the complete nucleotide sequence of a gene (1972) and of the viral genome of bacteriophage MS2 (1976). [40]

Virion assembly[ edit ]

In the case of the T4 phage , the construction of new virus particles involves the assistance of helper proteins. The base plates are assembled first, with the tails being built upon them afterward. The head capsids, constructed separately, will spontaneously assemble with the tails. The DNA is packed efficiently within the heads. The whole process takes about 15 minutes.

Diagram of a typical tailed bacteriophage structure

Release of virions[ edit ]

Phages may be released via cell lysis, by extrusion, or, in a few cases, by budding. Lysis, by tailed phages, is achieved by an enzyme called endolysin , which attacks and breaks down the cell wall peptidoglycan . An altogether different phage type, the filamentous phages , make the host cell continually secrete new virus particles. Released virions are described as free, and, unless defective, are capable of infecting a new bacterium. Budding is associated with certain Mycoplasma phages. In contrast to virion release, phages displaying a lysogenic cycle do not kill the host but, rather, become long-term residents as prophage .

Genome structure[ edit ]

Given the millions of different phages in the environment, phages’ genomes come in a variety of forms and sizes. RNA phage such as MS2 have the smallest genomes of only a few kilobases. However, some DNA phages such as T4 may have large genomes with hundreds of genes; the size and shape of the capsid varies along with the size of the genome. [41]

Bacteriophage genomes can be highly mosaic , i.e. the genome of many phage species appear to be composed of numerous individual modules. These modules may be found in other phage species in different arrangements. Mycobacteriophages – bacteriophages with mycobacterial hosts – have provided excellent examples of this mosaicism. In these mycobacteriophages, genetic assortment may be the result of repeated instances of site-specific recombination and illegitimate recombination (the result of phage genome acquisition of bacterial host genetic sequences). [42] Evolutionary mechanisms shaping the genomes of bacterial viruses vary between different families and depend on the type of the nucleic acid, characteristics of the virion structure, as well as the mode of the viral life cycle. [43]

Systems biology[ edit ]

Phages often have dramatic effects on their hosts. As a consequence, the transcription pattern of the infected bacterium may change considerably. For instance, infection of Pseudomonas aeruginosa by the temperate phage PaP3 changed the expression of 38% (2160/5633) of its host’s genes. Many of these effects are probably indirect, hence the challenge becomes to identify the direct interactions among bacteria and phage. [44]

Several attempts have been made to map Protein–protein interactions among phage and their host. For instance, bacteriophage lambda was found to interact with its host E. coli by 31 interactions. However, a large-scale study revealed 62 interactions, most of which were new. Again, the significance of many of these interactions remains unclear, but these studies suggest that there are most likely several key interactions and many indirect interactions whose role remains uncharacterized. [45]

In the environment[ edit ]

Main article: Marine bacteriophage

Metagenomics has allowed the in-water detection of bacteriophages that was not possible previously. [46]

Bacteriophages have also been used in hydrological tracing and modelling in river systems, especially where surface water and groundwater interactions occur. The use of phages is preferred to the more conventional dye marker because they are significantly less absorbed when passing through ground waters and they are readily detected at very low concentrations. [47] Non-polluted water may contain ca. 2×108 bacteriophages per mL. [48]

Bacteriophages are thought to extensively contribute to horizontal gene transfer in natural environments, principally via transduction but also via transformation . [49] Metagenomics -based studies have also revealed that viromes from a variety of environments harbor antibiotic resistance genes, including those that could confer multidrug resistance . [50]

Model bacteriophages[ edit ]

The following bacteriophages are extensively studied:

  • 186 phage
  • λ phage
  • Φ6 phage
  • Φ29 phage
  • ΦX174
  • G4 phage
  • M13 phage
  • MS2 phage (23–28 nm in size [51] )
  • N4 phage
  • P1 phage
  • P2 phage
  • P4 phage
  • R17 phage
  • T2 phage
  • T4 phage (169 kbp genome, [52] 200 nm long [53] )
  • T7 phage
  • T12 phage

See also[ edit ]

  • icon Viruses portal
  • Bacterivore
  • CrAssphage
  • DNA viruses
  • Phage ecology
  • Phage monographs (a comprehensive listing of phage and phage-associated monographs, 1921 – present)
  • Polyphage
  • RNA viruses
  • Transduction
  • Viriome
  • CRISPR

References[ edit ]

  1. ^ a b Mc Grath S and van Sinderen D (editors). (2007). Bacteriophage: Genetics and Molecular Biology (1st ed.). Caister Academic Press. ISBN   978-1-904455-14-1 . [1] .

  2. ^ “Novel Phage Therapy Saves Patient with Multidrug-Resistant Bacterial Infection” . UC Health – UC San Diego. Retrieved 2018-05-13.
  3. ^ a b Wommack, K. E.; Colwell, R. R. (2000). “Virioplankton: Viruses in Aquatic Ecosystems” . Microbiology and Molecular Biology Reviews. 64 (1): 69–114. doi : 10.1128/MMBR.64.1.69-114.2000 . PMC   98987 . PMID   10704475 .
  4. ^ a b c Prescott, L. (1993). Microbiology, Wm. C. Brown Publishers, ISBN   0-697-01372-3
  5. ^ a b BBC Horizon (1997): The Virus that Cures – Documentary about the history of phage medicine in Russia and the West
  6. ^ Keen, E. C. (2012). “Phage Therapy: Concept to Cure” . Frontiers in Microbiology. 3: 238. doi : 10.3389/fmicb.2012.00238 . PMC   3400130 . PMID   22833738 .
  7. ^ “Bacteria and bacteriophages collude in the formation of clinically frustrating biofilms” .
  8. ^ Hankin E H. (1896). “L’action bactericide des eaux de la Jumna et du Gange sur le vibrion du cholera” . Annales de l’Institut Pasteur (in French). 10: 511–523.
  9. ^ Twort, F. W. (1915). “An Investigation on the Nature of Ultra-Microscopic Viruses”. The Lancet. 186 (4814): 1241–1243. doi : 10.1016/S0140-6736(01)20383-3 .
  10. ^ Félix d’Hérelles (1917). “Sur un microbe invisible antagoniste des bacilles dysentériques” (PDF). Comptes Rendus de l’Académie des Sciences de Paris. 165: 373–5. Archived (PDF) from the original on 4 December 2010. Retrieved 5 September 2010.
  11. ^ Félix d’Hérelle (1949). “The bacteriophage” (PDF). Science News. 14: 44–59. Retrieved 5 September 2010.
  12. ^ Keen EC (2012). “Felix d’Herelle and Our Microbial Future”. Future Microbiology. 7 (12): 1337–1339. doi : 10.2217/fmb.12.115 . PMID   23231482 .
  13. ^ “The Nobel Prize in Physiology or Medicine 1969” . Nobel Foundation. Retrieved 2007-07-28.
  14. ^ Kutter, Elizabeth; De Vos, Daniel; Gvasalia, Guram; Alavidze, Zemphira; Gogokhia, Lasha; Kuhl, Sarah; Abedon, Stephen (1 January 2010). “Phage Therapy in Clinical Practice: Treatment of Human Infections”. Current Pharmaceutical Biotechnology. 11 (1): 69–86. doi : 10.2174/138920110790725401 . PMID   20214609 .
  15. ^ a b Rhoads, DD; Wolcott, RD; Kuskowski, MA; Wolcott, BM; Ward, LS; Sulakvelidze, A (June 2009). “Bacteriophage therapy of venous leg ulcers in humans: results of a phase I safety trial”. Journal of Wound Care. 18 (6): 237–8, 240–3. doi : 10.12968/jowc.2009.18.6.42801 . PMID   19661847 .
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External links[ edit ]

  • Häusler, T. (2006) “Viruses vs. Superbugs”, Macmillan
  • Animation of bacteriophage targeting E. coli bacteria
  • Phage.org general information on bacteriophages
  • bacteriophages illustrations and genomics
  • Bacteriophages get a foothold on their prey
  • NPR Science Friday podcast, “Using ‘Phage’ Viruses to Help Fight Infection”, April 2008
  • Animation by Hybrid Animation Medical for a T4 Bacteriophage targeting E. coli bacteria.
  • Bacteriophages: What are they. Presentation by Professor Graham Hatfull, University of Pittsburgh on YouTube
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