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Created 1.25.98, revised 9.10.05.

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A Glossary defining some terms for bacteriophage biology
 
phage picture
 
Words in the text marked glossary icon indicate links to definitions elsewhere in this glossary.
 
Please see our note on web viewing of Greek letters in phage names.
 
To view the illustrations (larger than the thumbnails) in this glossary you must enable your browser for Java. Some of the images are animated.
 
A | B | C | D | E | F | G | H | I/J | K/L | M | N | O | P | Q/R | S | T | U/V | W/X/Y/Z
 
A
A-B type toxins are protein molecules secreted by bacteria, frequently as single polypeptides that are later hydrolyzed to produce a B peptide, which binds specifically to some target cell, linked to an A peptide, which has some enzymatic activity harmful to cells. Details of subunit secretion and composition of the mature toxin vary. It is the job of the B peptide to get the A peptide into the cytoplasm of a particular type of cell, where the A peptide performs its nasty activity to kill the cell. The details of toxin internalization also vary, and not all are as pictured in the illustrations here. It is the particular specificity of the B peptide that determines what type of cell will be the target. Some B peptides bind to nerve cells, others to gut cells, and so on. The actual symptoms experienced by the person exposed to the toxin depend on what type of cells are killed. Killing of nerve cells might cause paralysis, and killing of gut cells might cause intestinal symptoms, for example.

Illustrations for A-B type toxins (line drawings & animated GIF files:
please enable your browser for Java)
1: A-Btoxin Figure 1   2: A-Btoxin Figure 2   3: A-Btoxin Figure 3

Antibiotic therapy consists of treatment of an infected person, animal, or plant with a chemical antimicrobial agent with the intent of controlling an infection. The original definition of an antibiotic included the requirement that the agent be one produced by another microorganism. Although that is still often true, many synthetic derivatives of antibiotics have been made, where modifications improve performance of the agent, and these agents are usually also called antibiotics. The microbe that is the target of the agent can be a fungus (antifungal antibiotic) but is most often a bacterial pathogen (antibacterial antibiotic). Although a few antiviral agents are in use, typically these are not chemicals produced by microorganisms and so are not called antibiotics. The conventional use of the term antibiotic implies that it is antibacterial.
 
Therapeutically successful antibiotics have a property called "selective toxicity". These agents work by killing or interfering with the growth of some parasite we don't want growing in us. But the fundamental chemistry of how cells work is the same whether the cells are bacterial, fungal, plant, bovine, or human. Chemical toxicity that would interfere with chemistry we all have in common would also harm us, causing nasty or even fatal "side effects". Most bacteria and fungi have cell walls that are made of materials that don't occur in humans or our agricultural animals, so we can use antibiotics that target those structures. Protozoa don't have many properties that differ from our own cells' properties, and human viruses work by hijacking our own cells to reproduce themselves. In most cases we do not know of agents that harm them without also harming us. This is why we don't have good (having mild or no side-effects) antibiotic treatments for protozoal parasite infections or virus infections.
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B
Bacteriophage: a virus that must infect bacteria in order to reproduce itself. Synonym: phage.
The burst size of a phage is the average number of new phage produced by a single infected bacterium during the glossary icon lytic growth cycle. This number varies widely for well-studied phages, from only a few to over one hundred.
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C
Coliphage: a bacteriophage that infects E. coli.
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D
A defective prophage is a glossary icon prophage that lacks some function(s) essential to viral reproduction. For example, one or more essential genes might be missing or damaged. Toxin genes present in such a DNA element may or may not be expressed to produce active toxin, depending on how those genes are regulated and where the phage defects are. A bacterium carrying a defective prophage is not usually said to be a lysogen. Probably most bacterial genomes contain fragments of one or more phage genomes, in various stages of decay.
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E
A eukaryote is an organism containing subcellular compartments separated from the cytoplasm by a lipid bilayer membrane. In particular the nucleus is so contained in a separate compartment. Plants, animals, fungi, protozoa, and algae are all eukaryotes.
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F
A protein or gene family is a set of proteins or genes that have sufficient similarity at the amino acid or DNA sequence level that it appears they are evolutionarily related. This is usually taken to mean that the different members of the set function similarly and one can infer properties of a newly recognized member from known properties of other members of the set.
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G
H
I/J
Induction of a glossary icon prophage is an event in which the formerly quiescent genome of the phage becomes activated and expresses the various genes necessary to the production of new progeny phages. By this activation the phage enters the lytic phase of its glossary icon life cycle.
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K/L
Although biologists argue about whether viruses are "alive", it is usual for phage biologists to speak of the life cycle or life style or "growth" of the phage, in reference to the mode of phage replication and exit from the infected cell once replication is accomplished. The three alternatives recognized are
  1. a lytic infection in which replication of virus proceeds immediately and is followed by enzymatic destruction of the bacterial cell wall so that progeny viruses are released,
  2. a persistent infection in which replication of virus proceeds immediately and continuously, and progeny virions are extruded from the cell individually without compromising the physical integrity of the host bacterium, so that virus replication and bacterial replication can both continue, and
  3. a temperate life style in which following each phage infection of a bacterium the phage may choose between going ahead with a lytic infection or becoming established as a glossary icon prophage in the host cell. In the prophage state the phage genome is mostly repressed and inactive, but at some later time can become reactivated (induced), whereupon a lytic or persistent infection ensues.
Illustrations of phage life cycles (animated GIFs illustrating infection, the lytic cycle, and the temperate life style use a tailed dsDNA phage example, the persistent cycle example uses a ssDNA phage example). To view these images please enable your browser for Java.
 
Infection: phage infecting a bacterium   Lytic: lytic phage infection   Persistent: persistent phage infection   Temperate: the temperate life style
The adjective "lysogenic" describes a bacterium as containing the genome of a bacterial virus that is in the prophage state. Such a bacterium is said to be "a lysogen", or said to be lysogenic for (name of the phage). See also glossary icon temperate and glossary icon prophage.
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M
A moron (in bacteriophage biology) is a DNA element inserted between a pair of genes in one phage genome when the genes of this same pair are adjacent in a related phage genome. The name derives from the fact that one phage contains "more" DNA than the other at this particular spot (see illustration 1). Many virulence factors of pathogenic bacteria are actually encoded in the morons of integrated prophages (see illustration 2).

Illustrations for morons: to see larger versions of drawings please enable your browser for Java

 
 
Illustrations 1: morons in phages gifsy-1 & gifsy-2   2: morons in lambda family late operon
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N
O
An operon is a cluster of adjacent genes that are all expressed from a single promoter, generating a single mRNA transcript from which individual proteins are translated. This type of gene organization is found only in prokaryotic organisms and some viruses, as far as we know. It allows coordinate regulation of all the genes in the cluster, and minimizes the space needed for the genes. In bacteriophages, it is common for specific groups of genes to be clustered in operons.
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P
A pathogenicity island (PAI) is a region of a bacterial chromosome that contains a cluster of virulence factor genes associated with pathogenicity of that bacterium. To be so designated the PAI must show internal (sequence) evidence that the gene cluster has at some time in the past been horizontally transferred from some other organism.
Pathovar: Pathogenic variety. A group of subspecies of bacteria (all members of the same species) that share a specific cluster of pathogenic behaviors. Abbreviation: pv. Example: in bacteria that are pathogenic for plants the designation is based on which type of plants are infected, such as Xanthomonas campestris pv. citri.
A bacteriophage is said to cause a persistent infection when infection leads to virus replication but mature virions are extruded individually from the host cell without killing the cell. See glossary icon life cycle.
Phage: a virus that must infect bacteria in order to reproduce itself. Synonym: bacteriophage.
Probiotic is an adjective referring to a live microorganism product used to protect or support the health of animals or people, usually by feeding the organism orally. "Live cultures" in yogurt are an example. Modified definitions are emerging as technology develops.
A prokaryote is an organism in which the genetic material is not separated from the cytoplasm by a conventional lipid bilayer membrane. The cells of these organisms do not separate their metabolic functions into membrane-bounded compartments: although specialized membranes may be present these are continuous extensions of the cytoplasmic membrane that separates the cell from its environment. Known archaea and virtually all known bacteria are prokaryotes (see also glossary icon eukaryotes).
A prophage is a bacterial virus the genome of which is residing in a bacterial host in a passive state, not expressing many viral functions or producing progeny virions. It may be incorporated into the bacterial DNA or it may be a separately replicated molecule within the bacterial cytoplasm. In some cases toxin genes present in prophage genomes have gene expression signals that allow their independent function when the viral genome is otherwise passive.
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Q/R
Recombinant DNA is a term used specifically to mean DNA that has been linked enzymatically in the laboratory ("in vitro", literal meaning "in glass") to DNA from a different cell, sometimes a different type of organism, and then reintroduced into a living cell, where the new combination of DNA sequences may give expression to properties not observed in either of the contributing sources. Since bacteriophages are in the business of carrying genetic information from one bacterium to another, bacteriophage sequences are often used as a carrier (usually termed "vector") to move other types of sequences around in such procedures.
Respiratory burst, also called "oxidative burst", refers to one of our bodily defense mechanisms by which we fight microbial infections. The offending microbes are engulfed by a type of blood cell called a "phagocyte", where they are sequestered in an internal compartment called a "phagolysosome". Here the microbes are attacked in various ways, including by the cell producing, via their own metabolic activity, a sudden increase in concentration (a burst) of highly reactive forms of oxygen such as peroxides and superoxides. These oxygen radicals attack and destroy microbial cells. Some pathogenic bacteria can protect themselves against this type of attack by making enzymes, called peroxidase and superoxide dismutase (Sod), that break down the oxygen radicals into harmless products.
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S
Serovar: Serological variety. A subspecies (variety) of some pathogen that can be specifically recognized by its behavior in some serological test (literally: an immunological test conducted using serum), such as a test for reaction with a particular antibody. Abbreviation: sv. Example: Salmonella enterica sv. typhimurium.
Shigatoxin can refer to a toxin produced either by bacteria in the genus Shigella, or by certain strains of E. coli such as O157:H7. When produced by E. coli, the toxin is sometimes referred to as a "shiga-like" toxin or as glossary icon "Verotoxin". Shigatoxin is an glossary icon A-B type toxin.
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T
A bacteriophage is called temperate when it is capable of establishing a lysogenic state in a susceptible bacterial host. This is a quiescent state in which virus replication does not occur. If this option is not available to the phage, the phage is referred to as "lytic" or sometimes as glossary icon "virulent". See also glossary icon life style.
Bacterial strains are called toxigenic when they are capable of producing toxin. This terminology is typically used to indicate that a bacterial (potential) pathogen is infected with or lysogenic for a phage encoding toxin genes that are capable of expression.
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U/V
(1) In molecular biology a vector is a set of bacteriophage or plasmid sequences that can be used to move other DNA of interest, such as bacterial, human, or mouse genes, from one organism to another during glossary icon recombinant DNA procedures. In general the vector DNA will have the properties that it can easily be moved into and out of, and maintain itself, in the organism in which we wish to study the DNA of interest. For example we might use bacteriophage lambda DNA as a vector for replicating and studying fragments of mouse DNA in the bacterium E. coli. (2) In medical microbiology a vector is an intermediate host, often an insect, in which a pathogenic microbe such as a bacterium or virus, can remain alive while being transferred from a reservoir host to an alternate host. For example, in Lyme disease the disease-causing bacteria Borrelia bergdorferi are transferred among several hosts such as mouse, deer, and human, when a tick takes a blood meal on one host, picking up the bacteria, and then takes another blood meal in a different host, infecting that second animal. The tick is said to a vector of Lyme disease.
Verotoxin, a synonym for glossary icon shigatoxin, is so-called because this toxin can kill African green monkey kidney cells, also known as Vero cells.
A virulence factor is a feature of a pathogenic organism that enhances its ability to cause disease. This might be a structure, an enzyme, a transport system, or any other cellular function that makes the bacteria more successful in infecting some other organism. A glossary icon PAI that includes genes of some type known to be associated (in other contexts) with phage is assumed to represent, at least in part, a cryptic phage genome or genome fragment.
The adjective "virulent", (1) when applied to a bacteriophage, means that infection of a bacterium by the phage always proceeds to virus replication and lysis of the host (for alternative phage life styles see glossary icon life cycle). (2) When applied to a bacterium "virulent" means that the bacterium can cause disease in some animal or plant.
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W/X/Y/Z