9.7A: Overview of Bacterial Viruses

Bacteriophages are viruses that infect bacteria and are among the most common and diverse entities in the biosphere.

Learning Objectives

• Evaluate the complexity of bacteriophages

Key Points

• Phages are obligate intracellular parasites that are able to reproduce only while infecting bacteria. Bacteriophages are comprised of proteins that encapsulate a DNA or RNA genome.
• Bacteriophages occur in over 140 bacterial or archaeal genera. They arose repeatedly in different hosts and there are at least 11 separate lines of descent. Nineteen families are currently recognised that infect bacteria and archaea.
• 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 sea water.
• Bacteriophages may have a lytic cycle or a lysogenic cycle, and a few viruses are capable of carrying out both.
• To enter a host cell, bacteriophages attach to specific receptors on the surface of bacteria. 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.

Key Terms

• bacteriophage: A virus that specifically infects bacteria.
• lysogeny: the process by which a bacteriophage incorporates its nucleic acids into a host bacterium

Bacteriophages

Bacteriophages (phages) are potentially the most numerous “organisms” on Earth. They are among the most common and diverse entities in the biosphere. They are the viruses of bacteria (more generally, of prokaryotes). Phages are obligate intracellular parasites, meaning that they are able to reproduce only while infecting bacteria. Bacteriophages are comprised 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 bacteria following the injection of their genome into the cytoplasm.

Figure: Artistic rendering of a T4 bacteriophage: The structure of a typical myovirus bacteriophage

Phage-ecological interactions are quantitatively vast. Bacteria (along with archaea) are highly diverse, with possibly millions of species. Phage-ecological interactions are also qualitatively diverse. There are huge numbers of environment types, bacterial-host types, and also individual phage types. Bacteriophages occur in over 140 bacterial or archaeal genera. They arose repeatedly in different hosts and there are at least 11 separate lines of descent. Over 5100 bacteriophages have been examined in the electron microscope since 1959. Of these, at least 4950 phages (96%) have tails. Of the tailed phages 61% have long, noncontractile tails (Siphoviridae). Tailed phages appear to be monophyletic and are the oldest known virus group.

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 sea water, where up to 9×108 virions per milliliter have been found in microbial mats at the surface. Up to 70% of marine bacteria may be infected by phages.

The dsDNA tailed phages, or Caudovirales, account for 95% of all the phages reported in the scientific literature, and possibly make up the majority of phages on the planet. However, other phages occur abundantly in the biosphere, with different virions, 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 recognised that infect bacteria and archaea. Of these, only two families have RNA genomes and only five families are enveloped. 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.

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.

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

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 fairly 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 reproduced 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.

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.

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. Budding is associated with certain Mycoplasma phages.

Bacteriophage genomes are especially mosaic: the genome of any one phage species appears 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).