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What is a bacteriophage?

Discovered in 1915 by Frederick W. Twort, and independently in 1917 by Félix d’Herelle (a then somewhat obscure researcher at the Pasteur Institute in Paris), bacteriophages are ubiquitous and in numbers difficult to comprehend, but estimated at around 10 in total. Their importance in ecosystems, particularly marine ecosystems, has only recently been comprehended.

In the simplest terms, bacteriophages or "phages" are viruses which attack only bacteria. Like all viruses, bacteriophages share broad similarities of structure and function. There are differences, however, based on the particular strain of virus or the mode of reproduction (lytic or lysogenic, or a combination of these). All phages are obligate parasites of bacteria. All, in some form or another, possess genes (which code for structural proteins as well various enzymes) enclosed in a capsid, as well as tails and other structures used to penetrate the host.

Phages can be divided according to what form their genetic material is stored (RNA or DNA, single-stranded or double-stranded, circular or linear). There are some general patterns and loose rules regarding relationships between lifestyle and structure. Filamentous phages (which lack tails and appear as thin tubes) are always lysogenic. T4, the most commonly recognized phage (at least to non-specialists), exhibits a prolate head and a contractile tail in the classical “spaceship” form, often (and mistakenly) seen as the epitome of the viral shape. T4 is lytic, but not all lytic phages exhibit a similar structure. Many are spherical or icosahedral, lacking any discernable tail. These globular phages tend to possess the greatest quantity of genetic information, but again, this is not a concrete pattern.

Phage biology: lysis mechanisms

With few exceptions (e.g. filamentous temperate phages), all viruses of bacteria ultimately lyse their hosts to release virion particles. The phenomenon of lysis is therefore universal. However, as will be evidenced, this does not mean that the process is simple or even similar among phage species. Temperate (lysogenic) phages appear to utilize a relatively recently evolved life strategy toward mutualism. Interestingly, they still retain the genetic capacity to produce endolytic enzymes along with concomitant or accessory molecules (which control the timing and strength of lysis).

Broadly speaking, there are two methods by which bacteriophages lyse their hosts. Both weaken and ultimately destroy the bacterial cell wall by interfering with the protein murein.

The first method, and by far the most common, is to actively degrade the protein murein, causing the localized weakness and eventual rupturing of the entire bacterium by internal osmotic pressure. To date, four independently evolved muralytic enzymes have been identified: endopeptidase, amidase, glycosidase, and transglycosylase. Some phages of gram-positive bacteria use forms of lysozymic endopeptidase to attack peptide linkages in oligopeptide cross-links. Others express the T7 lysozyme, gp3.5, which acts as an amidase to destroy the molecular connection between MurNac and the cross-linking oligopeptide. The phage λ utilizes the lysis gene e, which expresses glycosidase. This is related to and shares a cell-wall substrate with transglycosylase, which is expressed by the T4 lysis gene R. Glycosidase hydrolyzes the GlcNac-MurNac glycosidic bond, whereas transglycosylase degrades the same bond using an internal nucleophile rather than water (producing cyclic end-products in the process.

The second, least common and perhaps more genetically complicated method, is to prohibit or prevent the bacterium from repairing or synthesizing the cell wall. In this sense, then, the phage directs its attack not on the cell wall but on the bacterial mechanisms for murein production. Three phages have been shown to lack endolytic activity: single-stranded RNA Фx174, as well as the alloleviruses Qβ and MS2. Instead, with the exception of MS2 (whose function remains a mystery) they express amurins, which act to inhibit various enzymes in the murein synthesis pathway.

With regard to active bacterial cell wall degradation, phage mechanisms are not as straightforward or simple as involving the expression of lytic enzymes alone. An essential component is lysis timing and the means which have evolved to control it. Phages express a very diverse family of proteins known as holins, which act to stimulate or aid the secretion of endolytic enzymes across the bacterial plasma membrane(s), allowing active lysis.

The “logic” of evolution indicates the utility of these proteins. Slow, steady production and secretion of lytic enzymes would allow only the localized or slow secretion of virions because cell-wall degradation would be countered by the repair efforts of the bacterium. Instead of countering these efforts, exhausting the host in the process and possibly lowering virion assembly rates, the phage induces (through holin production) a build-up of muralytic enzymes behind the cytosolic plasma membrane. Upon the appropriate timing or environmental signal (such as a chemotactic indication that there are more hosts in the vicinity ripe for infection) holins trigger a massive release of enzymes from the plasma membrane. The cell wall is bombarded by this influx, causing an immediate and irreparable lysis.

Holins are small membrane proteins, divided into three classes based on topology. Class I holins possess three transmembrane domains (TMD) with the amino group (N) out, and the carboxyl group (C) in. Class II holins possess two TMDs (N out; C in), while class III holins reveal one TMD (N in; C out). Each phage typically expresses but one class of holin, which is incorporated into the bacterial plasma membrane during virion morphogenesis and muralytic enzyme production. These accumulate within the plasma membrane at the same time as muralytic enzymes amass in the cytoplasm. At the trigger point (determined by holin concentration), the plasma membrane lyses, allowing migration of muralytic enzymes and subsequent contact with wall substrates.

Holins are unique in that, unlike other cytolytic toxins, they are able to accumulate within the cytoplasm of the host until the appropriate environmental or timing cue is received. Both the biochemical means by which holins transform from harmless molecules to cytolytic enzymes (based on conformational changes) and the mechanism controlling the timing of the process remain unclear at present.

Experiments which have studied the in vitro lyse rate of particular phage treatments against their natural bacterial hosts always reveal a massive and instantaneous lysis of the host bacteria, causing immediate, observable plaques to form on prepared cultures.

The microbial loop

Under construction

Ecology of marine bacteriophages

If they can be described as being “alive,” marine phages, although invisible and essentially unnoticed by scientists until very recently, are the most abundant and diverse form of life on the planet. They influence biogeochemical cycles globally, provide and regulate microbial diversity, cycle carbon through marine food webs, and are essential in preventing bacterial population explosions.

Aquatic phages in general are evident in historical accounts: the mythical healing powers of the Ganges River, for example, were not fictional. However, their curative effects were less the benevolence of a Hindu deity than bacteriolytic phages.

Because there are estimated to be on average 10 phages per mL sea water (with 10 phage infections occurring in the world per second), and because every one of these infections allows the opportunity for genetic recombination, it may be concluded that both phage and bacteria have evolved effective and successful means of maintaining and exploiting environmentally-adaptive alleles.

Bacteria are continually exposed, in the form of bacteriophage infections, to selective pressures encouraging better defences against viral attack. They undergo genetic recombination by three seemingly improvised, if effective, mechanisms: transformation (whereby the bacterium transports genetic material into its genome from the external environment), conjugation (in which the transfer of genetic material between bacteria), and transduction (whereby genetic material is passed from bacterium to bacterium by bacteriophages).

Phages, which generally reproduce clonally, depend for genetic recombination on utilizing strands of genetic material found in their hosts. These are derived from prophages already present in the host genome. It is also possible that different lytic phages which infect the bacterium at similar times (i.e. before lysis occurs) are able to trade genes. Such notions are bolstered by the fact that bacteriophages exhibit genetic mosaicism, whereby comparative analysis of different phages reveals strands of closely related genes intermittently broken by strands of different genes. The comparative ratio of phage to bacteria makes phage genetic recombination highly successful. It also allows greater degree of adaptability: those virions which transcribe adaptive genes are bestowed an immediate selective advantage compared to other virions released by the same lytic event, which transcribe less adaptive genes.

Besides this apparent benefit, phages are slightly advantaged in their coevolutionary relationship with bacteria (but obviously not excessively so) because they are much smaller than their hosts, because they have shorter generation times, and because there are so many more of them.

Marine phage applications and geoengineering

As scientists begin to understand phages, their potential becomes clearer. Bacteriophages have been suggested primarily as an organic alternative to antibiotics. However, they may also be utilized in future geoengineering experiments.

Marine cyanophages can be used to prevent or reverse eutrophication, for example, if properly utilized against blue-green algae.

External bacteriophage links

Marine Microbiology Group at the College of Marine Science, University of South Florida

Bacteriophage Ecology Group, Ohio State University

Viral Bioinformatics Resource Center, University of Victoria

References

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See also

• Virus
• Bacteriophage
• Marine Biology
• Ecology
• Phage ecology
• RNA viruses
• DNA viruses
• Phage monographs
• Misplaced Pages: WikiProject Viruses