Viral Diversity

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 Takeaways

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.

image

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.

image

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).

RNA Bacteriophages

Nineteen families of bacteriophages that infect bacteria and archaea are currently recognized; of these, only two families have RNA genomes.

Learning Objectives

Identify differences between bacterial ssRNA and dsRNA viruses

Key Takeaways

Key Points

  • Cystovirus is a genus of dsRNA virus that infect certain Gram-negative bacteria. All cystoviruses are distinguished by their three strands of dsRNA and their protein and lipid outer layer. No other bacteriophage has any lipid in its outer coat.
  • RNA -dependent RNA polymerases (RdRPs) are critical components in the life cycle of double-stranded RNA (dsRNA) viruses. However, it is not fully understood how these important enzymes function during viral replication.
  • Bacteriophage Φ6 is a member of the Cystoviridae family that infects Pseudomonas bacteria (typically plant-pathogenic P. syringae). It is a lytic phage, though under certain circumstances has been observed to display a delay in lysis that may be described as a “carrier state”.

Key Terms

  • RNA genome: Like DNA, RNA can carry genetic information. RNA viruses have genomes composed of RNA that encodes a number of proteins.

Nineteen families of bacteriophages that infect bacteria and archaea are currently recognized. Of these, only two families have RNA genomes: Cystoviridae (segmented dsRNA) and Leviviridae (linear ssRNA).

The Leviviridae include the genera Allolevivirus (type species: Enterobacteria phage Qβ) and Levivirus (type species: Enterobacteria phage MS2).

Cystovirus is a genus of dsRNA virus that infect certain Gram-negative bacteria. All cystoviruses are distinguished by their three strands (analogous to chromosomes) of dsRNA, totalling ~14 kb in length, and by their protein and lipid outer layer. No other bacteriophage has any lipid in its outer coat, though the Tectiviridae and the Corticoviridae have lipids within their capsids.

image

Structure of bacteriophage PP7 from Pseudomonas aeruginosa: Members of this protein family form the capsid of Pseudomonas phage PP7. They adopt a secondary structure consisting of a six-stranded beta sheet and an alpha helix.

Most identified cystoviruses infect Pseudomonas species, but this is likely biased due to the method of screening and enrichment. The type species is Pseudomonas phage Φ6, but there are many other members of this family: Φ7, Φ8, Φ9, Φ10, Φ11, Φ12, and Φ13 have been identified and named, but other cystoviruses have also been isolated.

Members of the Cystoviridae appear to be most closely related to the Reoviridae, but also share homology with the Totiviridae. Cystoviruses are the only bacteriophage that are more closely related to viruses of eukaryotes than to other phage.

Bacteriophage Φ6 is a member of the Cystoviridae family. It infects Pseudomonas bacteria (typically plant-pathogenic P. syringae). It has a three-part, segmented, double-stranded RNA genome, totalling ~13.5 kb in length. Φ6 and its relatives have a lipid membrane around their nucleocapsid, a rare trait among bacteriophages. It is a lytic phage, though under certain circumstances has been observed to display a delay in lysis that may be described as a “carrier state. ”

Φ6 typically attaches to the Type IV pilus of P. syringae with its attachment protein, P3. It is thought that the cell then retracts its pilus, pulling the phage toward the bacterium. Fusion of the viral envelope with the bacterial outer membrane is facilitated by the phage protein, P6. The muralytic (peptidoglycan-digesting) enzyme, P5, then digests a portion of the cell wall, and the nucleocapsid enters the cell coated with the bacterial outer membrane.

RNA-dependent RNA polymerases (RdRPs) are critical components in the life cycle of double-stranded RNA (dsRNA) viruses. However, it is not fully understood how these important enzymes function during viral replication. Expression and characterization of the purified recombinant RdRP of Φ6 is the first direct demonstration of RdRP activity catalyzed by a single protein from a dsRNA virus. The recombinant Φ6 RdRP is highly active in vitro, possesses RNA replication and transcription activities, and is capable of using both homologous and heterologous RNA molecules as templates.

Single-Stranded DNA Bacteriophages

Of the viral families with DNA genomes, only two have single-stranded genomes, the Inoviridae and the Microviridae.

Learning Objectives

Illustrate the characteristics and life cycle of ssDNA bacteriophages

Key Takeaways

Key Points

  • The Inoviridae are a family of filamentous bacteriophages. The virons are non-enveloped, rod-shaped, and filamentous. Viron release may involve host lysis, but alternatively productive infection may occur by budding from the host membrane.
  • The Microviridae are a family of bacteriophages with a single-stranded DNA genome. Their genomes are among the smallest of the DNA viruses. Although the majority of species in this family have lytic life cycles, a few may have temperate life cycles.
  • The Microviridae are divided into two subfamilies, Gokushovirinae and Microvirinae. These groups differ in their hosts, genome structure, and viron composition.

Key Terms

  • microviridae: The Microviridae are a family of bacteriophages with a single-stranded DNA genome.
  • virion: A single individual particle of a virus (the viral equivalent of a cell).

Nineteen viral families are currently recognized that infect bacteria and archaea. Of these, only two families have RNA genomes and only five are enveloped. Of the viral families with DNA genomes, only two have single-stranded genomes.

Inoviridae

The Inoviridae are a family of filamentous bacteriophages. The name of the family is derived from the Greek nos, meaning “muscle. ”

image

Citrobacter freundii: Citrobacter freundii, one member of the family Enterobacteriaceae. The genus Inovirus infect species of Enterobacteriaceae.

Taxonomy

There are two genera in this family: Inovirus and Plectrovirus. These genera differ in their host range: Plectovirii infect hosts of the class Mollicutes, while Inovirii infect species of the Enterobacteriaceae, Pseudomonadaceae, Spirillaceae, Xanthomonadaceae, Clostridium, and Propionibacterium classes.

Physical and Genomic Properties

Inoviridae are non-enveloped, rod-shaped, and filamentous. The capsid has a helical symmetry, and in general has a length of 85-280 nm or 760-1950 nm and a width of 10-16 nm or 6-8 nm, respectively. These morphological differences depend on the species.

The genomes are non-segmented, circular, positive-sense, single-stranded DNA, 4.4-8.5 kilobases in length. They encode 4 to 11 proteins. Replication of the genome occurs via a dsDNA intermediate and the rolling circle mechanism. Gene transcription is by the host’s cellular machinery, as each gene has a specific promoter.

Life Cycle

There are six steps in the life cycle of Inoviridae:

  1. Adsorbion to the host via specific receptor(s)
  2. Movement of the viral DNA into the host cell
  3. Conversion of the single-strand form to a double-stranded intermediate
  4. Replication of the viral genome
  5. Synthesis of the new virions
  6. Release of the new virions from the host

Action in Host

Conversion from single-stranded to double-stranded form is carried out by the host’s own DNA polymerase. The host’s RNA polymerase binds to the viral genome and syntheses RNA. Some of this RNA is translated and the remainder is used to initiate DNA replication.

Virion release may involve host lysis, but alternatively productive infection may occur by budding from the host membrane. This pattern is typically seen in the Plectivirus genus. A number of exceptions to this life cycle are known. Lysogenic species, which encode integrases, exist within this family.

Microviridae

The Microviridae are a family of bacteriophages with a single-stranded DNA genome. The name of this family is derived from the Greek micro, meaning “small. ” This refers to the size of their genomes, which are among the smallest of the DNA viruses.

Taxonomy

This family is divided into two subfamilies, Gokushovirinae (derived from the Japanese for “very small”) and Microvirinae. These groups differ in their hosts, genome structure, and virion composition.

Gokushoviruses are currently known to infect only obligate intra-cellular parasites. These species are members of the genera Bdellovibrio, Chlamydia, and Spiroplasma. Subfamily Microvirinae are all of the genus Microvirus. All seven such members infect Enterobacteria.

Physical and Genomic Properties

Members of the subfamily Gokushovirus have only two structural proteins: capsid proteins F (Virus Protein 1) and DNA pilot protein H (Virus Protein 2) and do not use scaffolding proteins. They also possess ‘mushroom-like’ protrusions positioned at the three-fold axes of symmetry of their icosahedral capsids. These are formed by large insertion loops within the protein F of gokushoviruses and are absent in the microviruses. They lack both the external scaffolding protein D and the major spike protein G of the species in the genus Microvirus. The genomes of this group tend to be smaller, about 4.5 kb in length. This subfamily includes the genera Bdellomicrovirus, Chlamydiamicrovirus, and Spiromicrovirus.

Microviridae are non-enveloped and round with an icosahedral symmetry. They have a diameter between 25-27 nanometers and lack tails. Each virion has 60 copies each of the F, G, and J proteins and 12 copies of the H protein. Viruses in this family replicate their genomes via a rolling circle mechanism and encode dedicated RCR initiation proteins. Although the majority of species in this family have lytic life cycles, a few may have temperate life cycles.

Life Cycle

There are a number of steps in the life cycle:

  1. Adsorbion to the host via specific receptor(s)
  2. Movement of the viral DNA into the host cell
  3. Conversion of the single-strand form to a double-stranded intermediate, known as the replicative form I
  4. Transcription of early genes
  5. Replication of the viral genome
  6. Late genes are now transcribed by the host’s RNA polymerase
  7. Synthesis of the new virions
  8. Maturation of the virions in the host cytoplasm
  9. Release from the host

Action in Host

Cell lysis is mediated by the phiX174-encoded protein E, which inhibits the peptidoglycan synthesis, leading to the eventual bursting of the infected cell.

Double-Stranded DNA Bacteriophages

The dsDNA tailed phages, or Caudovirales, account for 95% of all known phages and possibly make up the majority of phages on the planet.

Learning Objectives

Describe dsDNA bacteriophages

Key Takeaways

Key Points

  • The Caudovirales are an order of viruses also known as the tailed bacteriophages. The virus particles have a distinct shape; each virion has an icosohedral head that contains the viral genome, and is attached to a flexible tail by a connector protein.
  • The order encompasses a wide range of viruses, many of which contain genes of similar nucleotide sequence and function. Some tailed bacteriophage genomes can vary quite significantly in nucleotide sequence, even among the same genus. There are at least 350 recognized species in this order.
  • Because of the lack of homology between the amino acid and DNA sequences of these viruses, the three families here are defined based on morphology: the Myoviridae have long contractile tails, the Podoviridae have short noncontractile tails, and the Siphoviridae have long non-contractile tails.

Key Terms

  • Caudovirales: A taxonomic order within the kingdom Virus—the bacteriophages that have tails.

The Double-Stranded DNA (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. Nineteen families that infect bacteria and archaea are currently recognized; of these, 15 have double-stranded DNA genomes.

Under the Baltimore classification scheme, the Caudovirales are group I viruses as they have double-stranded DNA (dsDNA) genomes, which can be anywhere from 18,000 base pairs to 500,000 base pairs in length. The virus particles have a distinct shape; each virion has an icosohedral head that contains the viral genome, and is attached to a flexible tail by a connector protein. The order encompasses a wide range of viruses, many of which contain genes of similar nucleotide sequence and function. Some tailed bacteriophage genomes can vary quite significantly in nucleotide sequence, however, even among the same genus. Due to their characteristic structure and possession of potentially homologous genes, it is believed these bacteriophages possess a common origin. There are at least 350 recognized species in this order.

Upon encountering a host bacterium, the tail section of the virion binds to receptors on the cell surface and delivers the DNA into the cell by use of an injectisome-like mechanism (an injectisome is a nanomachine that evolved for the delivery of proteins by type III secretion). The tail section of the virus punches a hole through the bacterial cell wall and plasma membrane and the genome passes down the tail into the cell. Once inside, the genes are expressed from transcripts made by the host machinery, using host ribosomes. Typically, the genome is replicated by use of concatemers, in which overlapping segments of DNA are made, and then put together to form the whole genome.

Viral capsid proteins come together to form a precursor prohead, into which the genome enters. Once this has occurred, the prohead undergoes maturation by cleavage of capsid subunits to form an icosohedral phage head with 5-fold symmetry. After the head maturation, the tail is joined in one of two ways: either the tail is constructed separately and joined with the connector, or the tail is constructed directly onto the phage head. The tails consist of helix-based proteins with 6-fold symmetry. After maturation of virus particles, the cell is lysed by lysins, holins, or a combination of the two.

Because the lack of homology between the amino acid and DNA sequences of these viruses precludes these from being used as taxonomic markers (as is common for other organisms), the three families here are defined on the basis of morphology. This classification scheme was originated by Bradley in 1969 and has since been extended. All viruses in this order have icosahedral or oblate heads, but differ in the length and contractile abilities of their tails. The Myoviridae have long tails that are contractile, the Podoviridae have short noncontractile tails, and the Siphoviridae have long non-contractile tails. Siphoviridae constitute the majority of the known tailed viruses.

image

Siphovirus phages: Electron micrographs of bacteriophages from P. acnes. Phages were negatively stained with 0.75% uranyl formate and subjected to transmission electron microscopy. The phages have a head of approximately 55 nm in diameter, loaded with genetic material. Their tails have a size of 150 × 10 nm and are flexible and non-contractile. In the lower micrograph, PAD25 is adhering to bacterial cell debris, and two phages have lost their heads. At the attachment site between the phage and the cell debris, a base plate with attached spikes can be observed. All phages were classified as Siphoviruses based on their morphology.

Mu: A Double-Stranded Transposable DNA Bacteriophage

Bacteriophage Mu is a temperate bacteriophage that uses DNA-based transposition in its lysogenic cycle.

Learning Objectives

Outline the life cycle of Mu phages

Key Takeaways

Key Points

  • All of the known temperate phages employ one of only three different systems for their lysogenic cycle: lambda-like integration/excision, Mu-like transposition, or the plasmid-like partitioning of phage N15.
  • Phage Mu uses DNA -based transposition to integrate its genome into the genome of the host cell that it is infecting. It can then use transposition to initiate its viral DNA replication.
  • Mu phage transposition is the best-known example of replicative transposition. Its transposition mechanism is somewhat similar to a homologous recombination.

Key Terms

  • replicative transposition: A mechanism of transposition in which the transposable element is duplicated during the reaction, so that the transposing entity is a copy of the original element.

Bacteriophage Mu, or phage Mu, is a temperate bacteriophage, a type of virus that infects bacteria. It belongs to the family Myoviridae, and consists of an icosahedral head, a contractile tail, and six tail fibers.

image

Myoviridae: Structural overview of the T4 phage, from the same family (Myoviridae) as Mu bacteriophage.

All of the known temperate phages employ one of only three different systems for their lysogenic cycle: lambda-like integration/excision, Mu-like transposition, or the plasmid-like partitioning of phage N15.

Mu bacteriophage uses DNA-based transposition to integrate its genome into the genome of the host cell that it is infecting. It can then use transposition to initiate its viral DNA replication. Once the viral DNA is inserted into the bacteria, the Mu’s transposase protein/enzyme in the cell recognizes the recombination sites at the ends of the viral DNA (gix-L and gix-R sites) and binds to them, allowing the process of replicating the viral DNA or embedding it into the host genome. A transposable element (TE) is a DNA sequence that can change its relative position (self-transpose) within the genome of a single cell. The mechanism of transposition can be either “copy and paste” or “cut and paste. ” Transposition can create phenotypically significant mutations and alter the cell’s genome size.

Mu phage transposition is the best known example of replicative transposition. Its transposition mechanism is somewhat similar to a homologous recombination. Replicative transposition is a mechanism of transposition in molecular biology, proposed by James A. Shapiro in 1979, in which the transposable element is duplicated during the reaction, so that the transposing entity is a copy of the original element. In this mechanism, the donor and receptor DNA sequences form a characteristic intermediate “theta” configuration, sometimes called a “Shapiro intermediate. ” Replicative transposition is characteristic to retrotransposons and occurs from time to time in class II transposons.

Virulent Bacteriophages and T4

T-4 bacteriophage is a virulent bacteriophage that infects E. coli bacteria; virulent bacteriophages have a lytic life cycle.

Learning Objectives

Summarize how the T4 life cycle serves as a model for viral virulence

Key Takeaways

Key Points

  • Virulence is the degree of pathogenicity within a group or species of parasites as indicated by case fatality rates and/or the ability of the organism to invade the tissues of the host. The pathogenicity of an organism is determined by its virulence factors.
  • A key difference between the lytic and lysogenic phage cycles is that in the lytic phage, the viral DNA exists as a separate molecule within the bacterial cell, and replicates separately from the host bacterial DNA.
  • The T-4’s tail fibres allow attachment to a host cell, and the T4’s tail is hollow so that it can pass its nucleic acid to the cell it is infecting during attachment. T4 is capable of undergoing only a lytic lifecycle and not the lysogenic lifecycle.

Key Terms

  • lytic cycle: The normal process of viral reproduction involving penetration of the cell membrane, nucleic acid synthesis, and lysis of the host cell.
  • virulence: the degree of pathogenicity within a group or species of parasites as indicated by case fatality rates and/or the ability of the organism to invade the tissues of the host.

Virulence is the degree of pathogenicity within a group or species of parasites as indicated by case fatality rates and/or the ability of the organism to invade the tissues of the host. The pathogenicity of an organism is determined by its virulence factors. Virus virulence factors determine whether an infection will occur and how severe the resulting viral disease symptoms are. Viruses often require receptor proteins on host cells to which they specifically bind. Typically, these host cell proteins are endocytosed and the bound virus then enters the host cell. Virulent viruses such as HIV, which causes AIDS, have mechanisms for evading host defenses.

Some viral virulence factors confer ability to replicate during the defensive inflammation responses of the host such as during virus-induced fever. Many viruses can exist inside a host for long periods during which little damage is done. Extremely virulent strains can eventually evolve by mutation and natural selection within the virus population inside a host. The term “neurovirulent” is used for viruses such as rabies and herpes simplex which can invade the nervous system and cause disease there.

Model organisms of virulent viruses that have been extensively studied include virus T4 and other T-even bacteriophages which infect Escherichia coli and a number of related Bacteria.

The lytic cycle is one of the two cycles of viral reproduction, the other being the lysogenic cycle. The lytic cycle is typically considered the main method of viral replication, since it results in the destruction of the infected cell. A key difference between the lytic and lysogenic phage cycles is that in the lytic phage, the viral DNA exists as a separate molecule within the bacterial cell, and replicates separately from the host bacterial DNA. The location of viral DNA in the lysogenic phage cycle is within the host DNA, therefore in both cases the virus/phage replicates using the host DNA machinery, but in the lytic phage cycle, the phage is a free floating separate molecule to the host DNA.

image

Cycles of viral reproduction: Comparison of the bacteriophage lysogenic and lytic cycles.

The lytic cycle is a six-stage cycle. In the first stage, called “penetration,” the virus injects its own nucleic acids into a host cell. Then the viral acids form a circle in the center of the cell. The cell then mistakenly copies the viral acids instead of its own nucleic acids. Then the viral DNA organize themselves as viruses inside the cell. When the number of viruses inside becomes too much for the cell to hold, the membrane splits and the viruses are free to infect other cells. Some viruses escape the host cell without bursting the cell membrane; instead, they bud off from it by taking a portion of the membrane with them. Because it otherwise is characteristic of the lytic cycle in other steps, it still belongs to this category, although it is sometimes named the Productive Cycle. HIV, influenza and other viruses that infect eukaryotic organisms generally use this method.

T-4 bacteriophage is a bacteriophage that infects E. coli bacteria. Its double-stranded DNA genome is about 169 kbp long and is held in an icosahedral head, also known as a capsid. T4 is a relatively large phage, at approximately 90 nm wide and 200 nm long (most phages range from 25 to 200 nm in length). Its tail fibres allow attachment to a host cell, and the T4’s tail is hollow so that it can pass its nucleic acid to the cell it is infecting during attachment. T4 is capable of undergoing only a lytic lifecycle and not the lysogenic lifecycle.

The T4 Phage initiates an E. coli infection by recognizing cell surface receptors of the host with its long tail fibers (LTF). A recognition signal is sent through the LTFs to the baseplate. This unravels the short tail fibers (STF) that bind irreversibly to the E. coli cell surface. The baseplate changes conformation and the tail sheath contracts causing GP5 at the end of the tail tube to puncture the outer membrane of the cell. The lysozyme domain of GP5 is activated and degrades the periplasmic peptidoglycan layer. The remaining part of the membrane is degraded and then DNA from the head of the phage can travel through the tail tube and enter the E. coli.

The lytic lifecycle (from entering a bacterium to its destruction) takes approximately 30 minutes (at 37 °C) and consists of:

  • Adsorption and penetration (starting immediately)
  • Arrest of host gene expression (starting immediately)
  • Enzyme synthesis (starting after 5 minutes)
  • DNA replication (starting after 10 minutes)
  • Formation of new virus particles (starting after 12 minutes)

After the life cycle is complete, the host cell bursts open and ejects the newly built viruses into the environment, destroying the host cell. T4 has a burst size of approximately 100-150 viral particles per infected host. Complementation, deletion, and recombination tests can be used to map out the rII gene locus by using T4. These bacteriophage infect a host cell with their information and then blow up the host cell, thereby propagating themselves.

The T4 phage has some unique features, including:

  • Eukaryote-like introns
  • High speed DNA copying mechanism, with only 1 error in 300 copies
  • Special DNA repair mechanisms
  • It infects E. coli O157:H7

Temperate Bacteriophages: Lambda and P1

In virology, temperate refers to the ability of some bacteriophages to display a lysogenic life cycle.

Learning Objectives

Evaluate the differences between the temperate phages, P1, and lambda

Key Takeaways

Key Points

  • Many temperate phages can integrate their genomes into their host bacterium ‘s chromosome, together becoming a lysogen as the phage genome becomes a prophage. A temperate phage is also able to undergo a productive, typically-lytic life cycle.
  • P1 is a temperate bacteriophage (phage) that infects Escherichia coli and some other bacteria. A unique feature of phage P1 is that during lysogeny its genome is not incorporated into the bacterial chromosome, as is commonly observed during lysogeny of other bacteriophage.
  • Enterobacteria phage λ ( lambda phage, coliphage λ) is a bacterial virus, or bacteriophage, that infects the bacterial species Escherichia coli.
  • With the infection of a bacteria by phage, a lytic cycle usually ensues where the lambda DNA is replicated many times and the genes for head, tail, and lysis proteins are expressed. Under certain conditions the phage DNA may integrate itself into the host cell chromosome in the lysogenic pathway.

Key Terms

  • lytic life cycle: One of the two cycles of viral reproduction (the other being the lysogenic cycle). The lytic cycle is typically considered the main method of viral replication and it results in the destruction of the infected cell.
  • temperate bacteriophage: Phages able to undergo lysogeny.

In virology, temperate refers to the ability of some bacteriophages (notable coliphage λ) to display a lysogenic life cycle. Many (but not all) temperate phages can integrate their genomes into their host bacterium’s chromosome, together becoming a lysogen as the phage genome becomes a prophage. A temperate phage is also able to undergo a productive, typically-lytic life cycle, where the prophage is expressed, replicates the phage genome, and produces phage progeny, which then leave the bacterium. With phage the term virulent is often used as an antonym to temperate, but more strictly a virulent phage is one that has lost its ability to display lysogeny through mutation, rather than a phage lineage with no genetic potential to ever display lysogeny (which more properly would be described as an obligately lytic phage).

P1 is a temperate bacteriophage (phage) that infects Escherichia coli and some other bacteria. When undergoing a lysogenic cycle, the phage genome exists as a plasmid in the bacterium, unlike other phages (e.g., the lambda phage) that integrate into the host DNA. P1 has an icosahedral “head” containing the DNA, attached to a contractile tail with six tail fibers.

The virion is similar in structure to the T4 phage, but simpler. It has an icosahedral head containing the genome attached at one vertex to the tail. The tail has a tube surrounded by a contractile sheath, and ends in a base plate with six tail fibers. The tail fibers are involved in attaching to the host and providing specificity.

At around 93Kbp in length, the genome of the P1 phage is moderately large compared to the genomes of others, like T4 (169Kbp), lambda (48Kbp), and Ff (6.4Kbp). In the viral particle it is in the form of a linear double-stranded DNA molecule. Once inserted into the host, it circularizes and replicates as a plasmid.

Temperate phage, such as P1, have the ability to exist within the bacterial cell they infect in two different ways. In lysogeny, P1 can exist within a bacterial cell as a circular DNA, in that it exists by replicating as if it were a plasmid and does not cause cell death. Alternatively, in its lytic phase, P1 can promote cell lysis during growth, resulting in host cell death. During lysogeny, new phage particles are not produced. In contrast, during lytic growth many new phage particles are assembled and released from the cell. By alternating between these two modes of infection, P1 can survive during extreme nutritional conditions that may be imposed upon the bacterial host in which it exists.

A unique feature of phage P1 is that during lysogeny its genome is not incorporated into the bacterial chromosome, as is commonly observed during lysogeny of other bacteriophage. Instead, P1 exists independently within the bacterial cell, much like a plasmid would. P1 replicates as a 90 kilobase (kb) plasmid in the lysogenic state and is partitioned equally into two new daughter cells during normal cell division.

Enterobacteria phage λ (lambda phage, coliphage λ) is a bacterial virus, or bacteriophage, that infects the bacterial species Escherichia coli. This virus is temperate and may reside within the genome of its host through lysogeny.

Lambda phage consists of a virus particle including a head (also known as a capsid), a tail, and tail fibers. The head contains the phage’s double-stranded circular DNA genome. The phage particle recognizes and binds to its host, E. coli, causing DNA in the head of the phage to be ejected through the tail into the cytoplasm of the bacterial cell. Usually, a “lytic cycle” ensues, where the lambda DNA is replicated many times and the genes for head, tail, and lysis proteins are expressed. This leads to assembly of multiple new phage particles within the cell and subsequent cell lysis, releasing the cell contents, including virions that have been assembled, into the environment. However, under certain conditions the phage DNA may integrate itself into the host cell chromosome in the lysogenic pathway. In this state, the λ DNA is called a prophage and stays resident within the host’s genome without apparent harm to the host. The host can be termed a lysogen when a prophage is present.

image

Insertion of the bacteriophage lambda: Schematic representation of the insertion of the bacteriophage lambda. Note how sib is displaced by the recombination event from the N extended PL promoter open reading frame.

The virus particle consists of a head and a tail that can have tail fibers. The head contains 48,490 base pairs of double-stranded, linear DNA, with 12-base single-stranded segments at both 5′ ends. These two single-stranded segments are the “sticky ends” of what is called the cos site. The cos site circularizes the DNA in the host cytoplasm. In its circular form, the phage genome therefore is 48,502 base pairs in length. The prophage exists as a linear section of DNA inserted into the host chromosome.

Viruses of Archaea

Most viruses infecting Archaea are double-stranded DNA viruses that are unrelated to any other form of virus.

Learning Objectives

Illustrate the typical characteristics of archaea-infecting viruses

Key Takeaways

Key Points

  • Archaea can be infected by double-stranded DNA viruses that are unrelated to any other form of virus and have a variety of unusual shapes. These viruses have been studied in most detail in thermophilics, particularly the orders Sulfolobales and Thermoproteales.
  • Although around 50 archaeal viruses are known, all but two have double stranded genomes; two groups of single-stranded DNA viruses that infect archaea have been recently isolated.
  • Defenses against these ssDNA viruses may involve RNA interference from repetitive DNA sequences that are related to the genes of the viruses.

Key Terms

  • DNA virus: A DNA virus is a virus that has DNA as its genetic material and replicates using a DNA-dependent DNA polymerase. The nucleic acid is usually double-stranded DNA (dsDNA) but may also be single-stranded DNA (ssDNA).

A virus infecting archaea was first described in 1974. Several others have been described since then. Most have head-tail morphologies and linear double-stranded DNA genomes. Other morphologies have also been described including spindle shaped, rod shaped, filamentous, icosahedral, and spherical. Additional morphological types may exist.

Archaea can be infected by double-stranded DNA viruses that are unrelated to any other form of virus and have a variety of unusual shapes. These viruses have been studied in the most detail in thermophilics, particularly the orders Sulfolobales and Thermoproteales. Two groups of single-stranded DNA viruses that infect archaea have been recently isolated. One group is exemplified by the Halorubrum pleomorphic virus 1 (“Pleolipoviridae”) infecting halophilic archaea and the other one by the Aeropyrum coil-shaped virus.

image

Archaeal viral infection: Cell of Sulfolobus infected by virus STSV1 observed under microscopy. Two spindle-shaped viruses were being released from the host cell. The strain of Sulfolobus and STSV1 (Sulfolobus tengchongensis Spindle-shaped Virus 1) were isolated by Xiaoyu Xiang and his colleagues in an acidic hot spring in Yunnan Province, China. At present, STSV1 is the largest archaeal virus to have been isolated and studied. Its genome sequence has been sequenced.

Double-stranded DNA viruses infecting archaea:

  • Bacteriophages (viruses infecting bacteria) belonging to the families Tectiviridae and Corticoviridae have a lipid bilayer membrane inside the icosahedral protein capsid and the membrane surrounds the genome. The crenarchaeal virus Sulfolobus turreted icosahedral virus has a similar structure.
  • Species of the order Ligamenvirales and the families Ampullaviridae, Bicaudaviridae, Clavaviridae, Fuselloviridae, Globuloviridae, and Guttaviridae infect hyperthermophilic archaea species of the Crenarchaeota.
  • Species of the genus Salterprovirus infect halophilic archaea species of the Euryarchaeota.

Single-stranded DNA viruses infecting archaea:

Although around 50 archaeal viruses are known, all but two have double stranded genomes. The first archaeal ssDNA virus to be isolated is the Halorubrum pleomorphic virus 1, which has a pleomorphic enveloped virion and a circular genome. Defenses against these viruses may involve RNA interference from repetitive DNA sequences that are related to the genes of the viruses.

The second single stranded DNA virus infecting Archaea is Aeropyrum coil-shaped virus (ACV). The genome is circular and with 24,893 nucleotides is currently the largest known ssDNA genome. The viron is nonenveloped, hollow, cylindrical, and formed from a coiling fiber. The morphology and the genome appear to be unique. ACV has been suggested to represent a new viral family tentatively called “Spiraviridae” (from Latin spira, “a coil”). The Aeropyrum coil-shaped virus infects a hyperthermophilic (optimal growth at 90-95°C) host. Notably, the latter virus has the largest currently reported ssDNA genome.