Bacteriophage experimental evolution

Last updated March 12, 2019

Experimental evolution studies are a means of testing evolutionary theory under carefully designed, reproducible experiments. Given enough time, space, and money, any organism could be used for experimental evolution studies. However, those with rapid generation times, high mutation rates, large population sizes, and small sizes increase the feasibility of experimental studies in a laboratory context. For these reasons, bacteriophages (i.e. viruses that infect bacteria) are especially favored by experimental evolutionary biologists. Bacteriophages, and microbial organisms, can be frozen in stasis, facilitating comparison of evolved strains to ancestors. Additionally, microbes are especially labile from a molecular biologic perspective. Many molecular tools have been developed to manipulate the genetic material of microbial organisms, and because of their small genome sizes, sequencing the full genomes of evolved strains is trivial. Therefore, comparisons can be made for the exact molecular changes in evolved strains during adaptation to novel conditions.

Experimental evolution is the use of laboratory experiments or controlled field manipulations to explore evolutionary dynamics. Evolution may be observed in the laboratory as individuals/populations adapt to new environmental conditions by natural selection. There are two different ways in which adaptation can arise in experimental evolution. One is via an individual organism gaining a novel beneficial mutation. The other is from allele frequency change in standing genetic variation already present in a population of organisms. Other evolutionary forces outside of mutation and natural selection can also play a role or be incorporated into experimental evolution studies, such as genetic drift and gene flow. The organism used is decided by the experimenter, based on whether the hypothesis to be tested involves adaptation through mutation or allele frequency change. A large number of generations are required for adaptive mutation to occur, and experimental evolution via mutation is carried out in viruses or unicellular organisms with rapid generation times, such as bacteria and asexual clonal yeast. Polymorphic populations of asexual or sexual yeast, and multicellular eukaryotes like Drosophila, can adapt to new environments through allele frequency change in standing genetic variation. Organisms with longer generations times, although costly, can be used in experimental evolution. Laboratory studies with foxes and with rodents have shown that notable adaptations can occur within as few as 10–20 generations and experiments with wild guppies have observed adaptations within comparable numbers of generations. More recently, experimentally evolved individuals or populations are often analyzed using whole genome sequencing, an approach known as Evolve and Resequence (E&R). E&R can identify mutations that lead to adaptation in clonal individuals or identify alleles that changed in frequency in polymorphic populations, by comparing the sequences of individuals/populations before and after adaptation. The sequence data makes it possible to pinpoint the site in a DNA sequence that a mutation/allele frequency change occurred to bring about adaptation. The nature of the adaptation and functional follow up studies can shed insight into what effect the mutation/allele has on phenotype.

Evolution is change in the heritable characteristics of biological populations over successive generations. These characteristics are the expressions of genes that are passed on from parent to offspring during reproduction. Different characteristics tend to exist within any given population as a result of mutation, genetic recombination and other sources of genetic variation. Evolution occurs when evolutionary processes such as natural selection and genetic drift act on this variation, resulting in certain characteristics becoming more common or rare within a population. It is this process of evolution that has given rise to biodiversity at every level of biological organisation, including the levels of species, individual organisms and molecules.

In population biology and demography, the generation time is the average time between two consecutive generations in the lineages of a population. In human populations, the generation time typically ranges from 22 to 33 years. Historians sometimes use this to date events, by converting generations into years to obtain rough estimates of time.

Experimental studies, by category
Laboratory phylogenetics
Epistasis
Experimental adaptation
Impact of sex/coinfection
Muller’s ratchet
Prisoner’s dilemma
Coevolution
References
Bibliography
Laboratory phylogenetics 2
Epistasis 2
Experimental adaptation 2
Impact of sex/coinfection 2
Muller’s ratchet 2
Prisoner’s dilemma 2
Coevolution 2

Experimental studies, by category

Laboratory phylogenetics

Phylogenetics is the study of the evolutionary relatedness of organisms. Laboratory phylogenetics is the study of the evolutionary relatedness of laboratory-evolved organisms. An advantage of laboratory phylogenetics is the exact evolutionary history of an organism is known, rather than estimated as is the case for most organisms.

Epistasis

Epistasis is the dependence of the effect of one gene or mutation on the presence of another gene or mutation. Theoretically epistasis can be of three forms: no epistasis (additive inheritance), synergystic (or positive) epistasis and antagonistic (or negative) epistasis. In synergystic epistasis, each additional mutation has increasing negative impact on fitness. In antagonistic epistasis, the effect of each mutation declines with increasing numbers of mutation. Understanding whether the majority of genetic interactions are synergistic or antagonistic will help solve such problems as the evolution of sex.

In biology, a mutation is the permanent alteration of the nucleotide sequence of the genome of an organism, virus, or extrachromosomal DNA or other genetic elements.

Physical fitness is a state of health and well-being and, more specifically, the ability to perform aspects of sports, occupations and daily activities. Physical fitness is generally achieved through proper nutrition, moderate-vigorous physical exercise, and sufficient rest.

The phage literature provides many examples of epistasis which are not studied under the context of experimental evolution nor necessarily described as examples of epistasis.

Experimental adaptation

Experimental adaptation involves selection of organisms either for specific traits or under specific conditions. For example, strains could be evolved under conditions of high temperatures to observe the molecular changes that facilitate survival and reproduction under those conditions.

A phenotypic trait, simply trait, or character state is a distinct variant of a phenotypic characteristic of an organism; it may be either inherited or determined environmentally, but typically occurs as a combination of the two. For example, eye color is a character of an organism, while blue, brown and hazel are traits.

Reproduction is the biological process by which new individual organisms – "offspring" – are produced from their "parents". Reproduction is a fundamental feature of all known life; each individual organism exists as the result of reproduction. There are two forms of reproduction: asexual and sexual.

The reader should be aware that numerous phage experimental adaptations were performed in the early decades of phage study.

Adaptation to usual hosts.

Adaptation to new or modified hosts.

The older phage literature, e.g., pre-1950s, contains numerous examples of phage adaptations to different hosts.

Adaptation to modified conditions

The older phage literature, e.g., pre-1950s, also contains examples of phage adaptations to different culture conditions, such as phage T2 adaptation to low salt conditions.

Adaptation to high temperatures.

Adaptation as compensation for deleterious mutations.

There are many examples in early phage literature of bacteriophages adapting and compensating for deleterious mutations.

Adaptation as toward change in phage virulence

Virulence is the negative impact that a pathogen (or parasite) has on the Darwinian fitness of a harboring organism (host). For phage, virulence results either in reduction of bacterial division rates or, more typically, in the death (via lysis) of individual bacteria. A number of theory papers exist on this subject, especially as it applies to the evolution of phage latent period.

In biology, a pathogen, in the oldest and broadest sense, is anything that can produce disease. A pathogen may also be referred to as an infectious agent, or simply a germ.

Lysis refers to the breaking down of the membrane of a cell, often by viral, enzymic, or osmotic mechanisms that compromise its integrity. A fluid containing the contents of lysed cells is called a lysate. In molecular biology, biochemistry, and cell biology laboratories, cell cultures may be subjected to lysis in the process of purifying their components, as in protein purification, DNA extraction, RNA extraction, or in purifying organelles.

Incubation period is the time elapsed between exposure to a pathogenic organism, a chemical, or radiation, and when symptoms and signs are first apparent. In a typical infectious disease, incubation period signifies the period taken by the multiplying organism to reach a threshold necessary to produce symptoms in the host.

The older phage literature contains numerous references to phage virulence, and phage virulence evolution. However, the reader should be warned that virulence is often used as a synonym for "not temperature", a usage which is neither employed here nor to be encouraged generally.

Impact of sex/coinfection

More than one phage can coinfect the same bacterial cell. When this happens, the phage can exchange genes, which is equivalent to "sex." Note that a number of the immediately following studies employ sex to overcome Muller's ratchet while papers that demonstrate Muller's ratchet (i.e., without employing sex to overcome the result) are instead presented under that heading.

In evolutionary genetics, Muller's ratchet is a process by which the genomes of an asexual population accumulate deleterious mutations in an irreversible manner. Muller proposed this mechanism as one reason why sexual reproduction may be favored over asexual reproduction. The negative effect of accumulating irreversible deleterious mutations may not be prevalent in organisms, which, while they reproduce asexually, also undergo other forms of recombination. This effect has also been observed in those regions of the genomes of sexual organisms that do not undergo recombination.

Muller’s ratchet

Muller’s ratchet is the gradual, but irreversible accumulation of deleterious mutations in asexual organisms. Asexual organisms do not undergo gene exchange and therefore can't recreate mutation-free genomes. Chao, 1997, provides a phage-emphasizing review of the subject.

Prisoner’s dilemma

Prisoner's dilemma is a part of game theory which involves two individuals choosing to cooperate or defect, reaping differential rewards. During phage coinfection, it pertains to viruses which produce more protein products than they use (cooperators) and viruses which use more protein products than they produce (defectors).

Coevolution

Coevolution is the study of the evolutionary influence that two species have upon each other. Phage-bacterial coevolution is typically studied within the context of phage community ecology.

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Bacteriophage virus that infects and replicates within bacteria

A bacteriophage, also known informally as a phage, is a virus that infects and replicates within bacteria and archaea. The term was derived from "bacteria" and the Greek φαγεῖν (phagein), "to devour". Bacteriophages are composed 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 the bacterium following the injection of their genome into its cytoplasm. Bacteriophages are among the most common and diverse entities in the biosphere. Bacteriophages are ubiquitous viruses, found wherever bacteria exist. It is estimated there are more than 10³¹ bacteriophages on the planet, more than every other organism on Earth, including bacteria, combined.

Population genetics is a subfield of genetics that deals with genetic differences within and between populations, and is a part of evolutionary biology. Studies in this branch of biology examine such phenomena as adaptation, speciation, and population structure.

Escherichia virus T4 is a species of bacteriophages that infect Escherichia coli bacteria. It is a member of virus subfamily Tevenvirinae and includes among other strains Enterobacteria phage T2, Enterobacteria phage T4 and Enterobacteria phage T6. T4 is capable of undergoing only a lytic lifecycle and not the lysogenic lifecycle.

Microviridae is a family of bacteriophages with a single-stranded DNA genome. The name of this family is derived from the ancient Greek word μικρός (mikrós), meaning "small". This refers to the size of their genomes, which are among the smallest of the DNA viruses. Enterobacteria, intracellular parasitic bacteria, and spiroplasma serve as natural hosts. There are currently 12 species in this family, divided among 7 genera and one subfamily.

Genetics, a discipline of biology, is the science of heredity and variation in living organisms.

The phi X 174 bacteriophage is a single-stranded DNA (ssDNA) virus that infects Escherichia coli, and the first DNA-based genome to be sequenced. This work was completed by Fred Sanger and his team in 1977. In 1962, Walter Fiers and Robert Sinsheimer had already demonstrated the physical, covalently closed circularity of ΦX174 DNA. Nobel prize winner Arthur Kornberg used ΦX174 as a model to first prove that DNA synthesized in a test tube by purified enzymes could produce all the features of a natural virus, ushering in the age of synthetic biology. In 1972-1974, Jerard Hurwitz, Sue Wickner, and Reed Wickner with collaborators identified the genes required to produce the enzymes to catalyze conversion of the single stranded form of the virus to the double stranded replicative form. In 2003, it was reported by Craig Venter's group that the genome of ΦX174 was the first to be completely assembled in vitro from synthesized oligonucleotides. The ΦX174 virus particle has also been successfully assembled in vitro. Recently, it was shown how its highly overlapping genome can be fully decompressed and still remain functional.

Bacteriophage T7 is a bacteriophage, a virus that infects susceptible bacterial cells, that is composed of DNA and infects most strains of Escherichia coli. Bacteriophage T7 has a lytic life cycle and several properties that make it an ideal phage for experimentation.

The Enterobacteria phage P22 is a bacteriophage that infects Salmonella typhimurium. Like many phage viruses, it has been used in molecular biology to induce mutations in cultured bacteria and to introduce foreign genetic material. Upon its discovery, P22 has been used in generalized transduction and is an important tool for Salmonella genetics.

Bacteriophages (phages), potentially the most numerous "organisms" on Earth, are the viruses of bacteria. Phage ecology is the study of the interaction of bacteriophages with their environments.

A viral quasispecies is a group of viruses related by a similar mutation or mutations, competing within a highly mutagenic environment. The theory predicts that a viral quasispecies at a low but evolutionarily neutral and highly connected region in the fitness landscape will outcompete a quasispecies located at a higher but narrower fitness peak in which the surrounding mutants are unfit. This phenomenon has been called 'the quasispecies effect' or, more recently, the 'survival of the flattest'.

A suppressor mutation is a second mutation that alleviates or reverts the phenotypic effects of an already existing mutation in a process defined synthetic rescue. Genetic suppression therefore restores the phenotype seen prior to the original background mutation. Suppressor mutations are useful for identifying new genetic sites which affect a biological process of interest. They also provide evidence between functionally interacting molecules and intersecting biological pathways.

The bacteriophage MS2 is an icosahedral, positive-sense single-stranded RNA virus that infects the bacterium Escherichia coli and other members of the Enterobacteriaceae. MS2 is a member of a family of closely related bacterial viruses that includes bacteriophage f2, bacteriophage Qβ, R17, and GA.

Professor Lin Chao is a Chinese Brazilian American evolutionary biologist and geneticist. Professor Chao gained his PhD in 1977 from the University of Massachusetts Amherst, as a student of Bruce R. Levin, and was a NIH postdoctoral fellow at Princeton University in the laboratory of Edward C. Cox. He spent most of his career in the Department of Biology of the University of Maryland, College Park and is currently at the Ecology, Behavior and Evolution Section of the University of California, San Diego.

The phage group was an informal network of biologists centered on Max Delbrück that contributed heavily to bacterial genetics and the origins of molecular biology in the mid-20th century. The phage group takes its name from bacteriophages, the bacteria-infecting viruses that the group used as experimental model organisms. In addition to Delbrück, important scientists associated with the phage group include: Salvador Luria, Alfred Hershey, Seymour Benzer, Gunther Stent, James D. Watson, Frank Stahl, and Renato Dulbecco.

Bacteriophage P2, scientific name Escherichia virus P2, is a temperate phage that infects E. coli. It is a tailed virus with a contractile sheath and is thus classified in the genus P2virus, subfamily Peduovirinae, family Myoviridae within order Caudovirales. This genus of viruses includes many P2-like phages as well as the satellite phage P4.

Host–parasite coevolution is a special case of coevolution, the reciprocal adaptive genetic change of a host and a parasite through reciprocal selective pressures.

Epistasis is the phenomenon where the effect of one gene (locus) is dependent on the presence of one or more 'modifier genes', i.e. the genetic background. Originally the term meant that the phenotypic effect of one gene is masked by a different gene (locus). Thus, epistatic mutations have different effects in combination than individually. It was originally a concept from genetics but is now used in biochemistry, computational biology and evolutionary biology. It arises due to interactions, either between genes, or within them, leading to non-linear effects. Epistasis has a large influence on the shape of evolutionary landscapes, which leads to profound consequences for evolution and evolvability of phenotypic traits.

Endogenosymbiosis is an evolutionary process, proposed by the evolutionary and environmental biologist Roberto Cazzolla Gatti, in which "gene carriers" and symbiotic prokaryotic cells could share parts or all of their genomes in an endogenous symbiotic relationship with their hosts.

References

This article incorporates material from the Citizendium article "Bacteriophage experimental evolution", which is licensed under the Creative Commons Attribution-ShareAlike 3.0 Unported License but not under the GFDL.

Breitbart, M., F. Rohwer, and S. T. Abedon. 2005. Phage ecology and bacterial pathogenesis, p. 66-91. In M. K. Waldor, D. I. Friedman, and S. L. Adhya (eds.), Phages: Their Role in Bacterial Pathogenesis and Biotechnology. ASM Press, Washington DC. ISBN 1-55581-307-0

d'Hérelle, F., and G. H. Smith. 1924. Immunity in Natural Infectious Disease. Williams & Wilkins Co., Baltimore.