A prophage is a bacteriophage (often shortened to "phage")

genome In the fields of molecular biology and genetics, a genome is all the genetic information of an organism. It consists of nucleotide sequences of DNA (or RNA in RNA viruses). The nuclear genome includes protein-coding genes and non-coding g ...

that is integrated into the

circular bacterial chromosome A circular chromosome is a chromosome in bacteria, archaea, mitochondria, and chloroplasts, in the form of a molecule of circular DNA, unlike the linear chromosome of most eukaryotes. Most prokaryote chromosomes contain a circular DNA molecu ...

or exists as an extrachromosomal plasmid within the bacterial

cell Cell most often refers to: * Cell (biology), the functional basic unit of life Cell may also refer to: Locations * Monastic cell, a small room, hut, or cave in which a religious recluse lives, alternatively the small precursor of a monastery ...

. Integration of prophages into the bacterial host is the characteristic step of the

lysogenic cycle Lysogeny, or the lysogenic cycle, is one of two cycles of viral reproduction (the lytic cycle being the other). Lysogeny is characterized by integration of the bacteriophage nucleic acid into the host bacterium's genome or formation of a circu ...

temperate In geography, the temperate climates of Earth occur in the middle latitudes (23.5° to 66.5° N/S of Equator), which span between the tropics and the polar regions of Earth. These zones generally have wider temperature ranges throughout ...

phages. Prophages remain

latent Latency or latent may refer to: Science and technology * Latent heat, energy released or absorbed, by a body or a thermodynamic system, during a constant-temperature process * Latent variable, a variable that is not directly observed but inferred ...

in the genome through multiple cell divisions until activation by an external factor, such as UV light, leading to production of new phage particles that will lyse the cell and spread. As ubiquitous

mobile genetic elements Mobile genetic elements (MGEs) sometimes called selfish genetic elements are a type of genetic material that can move around within a genome, or that can be transferred from one species or replicon to another. MGEs are found in all organisms. In ...

, prophages play important roles in bacterial genetics and evolution, such as in the acquisition of

virulence Virulence is a pathogen's or microorganism's ability to cause damage to a host. In most, especially in animal systems, virulence refers to the degree of damage caused by a microbe to its host. The pathogenicity of an organism—its ability to ...

factors.

Background

Prophages are able to do a multitude of things within their respective bacterial strains. Prophages can increase the virulence potential of bacterial strains in both humans and plant pathogens as well as increase the ability of the bacteria to survive in harsh environments. Pathogens have been able to adapt and thrive in a wide range of environments. Some anaerobic pathogens such as ''

Clostridium perfringens ''Clostridium perfringens'' (formerly known as ''C. welchii'', or ''Bacillus welchii'') is a Gram-positive, rod-shaped, anaerobic, spore-forming pathogenic bacterium of the genus ''Clostridium''. ''C. perfringens'' is ever-present in nature an ...

'' and '' Clostridium difficile'' exist in the intestines and are unable to survive in places with large amounts of oxygen for extended periods of time. Still others can reside in the soil such as B. anthracis, while pathogens such as ''C. difficile'' can even survive in very sterile hospital settings. Prophages can provide these bacteria with both resistance mechanisms as well as metabolic advantages which give the host cell the best chance of survival,. sometimes even completely altering the bacterial genome.

Prophage induction

Upon detection of host cell damage by UV light or certain chemicals, the prophage is excised from the bacterial chromosome in a process called prophage induction. After induction, viral replication begins via the

lytic cycle The lytic cycle ( ) is one of the two cycles of viral reproduction (referring to bacterial viruses or bacteriophages), the other being the lysogenic cycle. The lytic cycle results in the destruction of the infected cell and its membrane. Bacteri ...

. In the lytic cycle, the virus commandeers the cell's reproductive machinery. The cell may fill with new viruses until it lyses or bursts, or it may release the new viruses one at a time in an exocytotic process. The period from infection to lysis is termed the latent period. A virus following a lytic cycle is called a

virulent Virulence is a pathogen's or microorganism's ability to cause damage to a host. In most, especially in animal systems, virulence refers to the degree of damage caused by a microbe to its host. The pathogenicity of an organism—its ability to ...

virus. Prophages are important agents of

horizontal gene transfer Horizontal gene transfer (HGT) or lateral gene transfer (LGT) is the movement of genetic material between unicellular and/or multicellular organisms other than by the ("vertical") transmission of DNA from parent to offspring (reproduction). H ...

, and are considered part of the

mobilome The mobilome is the entire set of mobile genetic elements in a genome. Mobilomes are found in eukaryotes, prokaryotes, and viruses. The compositions of mobilomes differ among lineages of life, with transposable elements being the major mobile elem ...

. All families of bacterial viruses that have circular (single-stranded or double-stranded) DNA genomes or replicate their genomes through

rolling circle replication Rolling circle replication (RCR) is a process of unidirectional nucleic acid replication that can rapidly synthesize multiple copies of circular molecules of DNA or RNA, such as plasmids, the genomes of bacteriophages, and the circular RNA ...

(e.g.,

Caudovirales ''Caudovirales'' is an order of viruses known as the tailed bacteriophages (''cauda'' is Latin for "tail"). Under the Baltimore classification scheme, the ''Caudovirales'' are group I viruses as they have double stranded DNA (dsDNA) genomes ...

) have temperate members.

Zygotic induction

Zygotic induction occurs when a bacterial cell carrying the DNA of a bacterial virus transfers its own DNA along with the viral DNA (prophage) into the new host cell. This has the effect of causing the host cell to break apart. The DNA of the bacterial cell is silenced before entry into the cell by a repressor protein which is encoded for by the prophage. Upon the transfer of the bacterial cell's DNA into the host cell, the repressor protein is no longer encoded for, and the bacterial cell's original DNA is then turned on in the host cell. This mechanism eventually will lead to the release of the virus as the host cell splits open and the viral DNA is able to spread. This new discovery provided key insights into bacterial conjugation and contributed to the early repression model of gene regulation, which provided an explanation as to how the

lac operon The ''lactose'' operon (''lac'' operon) is an operon required for the transport and metabolism of lactose in ''E. coli'' and many other enteric bacteria. Although glucose is the preferred carbon source for most bacteria, the ''lac'' operon allow ...

and λ bacteriophage genes are negatively regulated.

Prophage reactivation

Bacteriophage λ is able to undergo a type of recombinational repair called prophage reactivation.Bernstein C. Deoxyribonucleic acid repair in bacteriophage. Microbiol Rev. 1981;45(1):72-98 Prophage reactivation can occur by recombination between a UV-damaged infecting phage λ chromosome and a homologous phage

integrated into the bacterial DNA and existing in a prophage state. Prophage reactivation in the case of phage λ appears to be an accurate recombinational repair process that is mediated by the

recA RecA is a 38 kilodalton protein essential for the repair and maintenance of DNA. A RecA structural and functional homolog has been found in every species in which one has been seriously sought and serves as an archetype for this class of homolog ...

+ and red+ gene products.

Applications

Prophages can tell researchers a lot about the relationship between a bacterium and a host. With data from more nonpathogenic bacteria, researchers will be able to gather evidence as to whether or not prophages contribute to the survival value of the host. Prophage genomics has the potential to lead to ecological adaptations of the relationships between bacteria. Another important area of interest is the control of prophage gene expression with many of the lysogenic conversion genes (

gene conversion Gene conversion is the process by which one DNA sequence replaces a homologous sequence such that the sequences become identical after the conversion event. Gene conversion can be either allelic, meaning that one allele of the same gene replaces a ...

) being tightly regulated. This process is capable of converting non-pathogenic bacteria into pathogenic bacteria that can now produce harmful toxins such as in staph infections. Since the specific mechanisms of prophage are not yet detailed, this research could provide the community with this tool for future research.

Economic impact

Exotoxins An exotoxin is a toxin secreted by bacteria. An exotoxin can cause damage to the host by destroying cells or disrupting normal cellular metabolism. They are highly potent and can cause major damage to the host. Exotoxins may be secreted, or, simi ...

encoded by prophages cause pathogenic outcomes in

agriculture Agriculture or farming is the practice of cultivating plants and livestock. Agriculture was the key development in the rise of sedentary human civilization, whereby farming of domesticated species created food surpluses that enabled people t ...

and aquaculture.