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Studying phage codon adaptation is important not only for understanding the process of translation elongation, but also for reengineering phages for medical and industrial purposes. To evaluate the effect of mutation and selection on phage codon usage, we developed an index to measure selection imposed by host translation machinery, based on the difference in codon usage between all host genes and highly expressed host genes. We developed linear and nonlinear models to estimate the C → T mutation bias in different phage lineages and to evaluate the relative effect of mutation and host selection on phage codon usage. C → T-biased mutations occur more frequently in single-stranded DNA (ssDNA) phages than in double-stranded DNA (dsDNA) phages and affect not only synonymous codon usage, but also nonsynonymous substitutions at second codon positions, especially in ssDNA phages. The host translation machinery affects codon adaptation in both dsDNA and ssDNA phages, with a stronger effect on dsDNA phages than on ssDNA phages. Strand asymmetry with the associated local variation in mutation bias can significantly interfere with codon adaptation in both dsDNA and ssDNA phages. [ABSTRACT FROM AUTHOR]

Pseudomonas fluorescens is a model for the study of adaptive radiation. When propagated in a spatially structured environment, the bacterium rapidly diversifies into a range of niche specialist genotypes. Here we present a genetic dissection and phenotypic characterization of the fuzzy spreader (FS) morphotype--a type that arises repeatedly during the course of the P. fluorescens radiation and appears to colonize the bottom of static broth microcosms. The causal mutation is located within gene fuzY (pflu0478)--the fourth gene of the five-gene fuzVWXYZ operon. fuzY encodes a b-glycosyltransferase that is predicted to modify lipopolysaccharide (LPS) O antigens. The effect of the mutation is to cause cell flocculation. Analysis of 92 independent FS genotypes showed each to have arisen as the result of a loss-of-function mutation in fuzY, although different mutations have subtly different phenotypic and fitness effects. Mutations within fuzY were previously shown to suppress the phenotype of mat-forming wrinkly spreader (WS) types. This prompted a reinvestigation of FS niche preference. Time-lapse photography showed that FS colonizes the meniscus of broth microcosms, forming cellular rafts that, being too flimsy to form a mat, collapse to the vial bottom and then repeatably reform only to collapse. This led to a reassessment of the ecology of the P. fluorescens radiation. Finally, we show that ecological interactions between the three dominant emergent types (smooth, WS, and FS), combined with the interdependence of FS and WS on fuzY, can, at least in part, underpin an evolutionary arms race with bacteriophage SBW25F2, to which mutation in fuzY confers resistance. [ABSTRACT FROM AUTHOR]

Experimental evolution of bacteriophage provides a powerful means of studying the genetics of adaptation, as every substitution contributing to adaptation can be identified and characterized. Here, I use experimental evolution of MS2, an RNA bacteriophage, to study its adaptive response to a novel environment. To this end, three lines of MS2 were adapted to rapid growth and lysis at cold temperature for a minimum of 50 phage generations and subjected to whole-genome sequencing. Using this system, I identified adaptive substitutions, monitored changes in frequency of adaptive mutations through the course of the experiment, and measured the effect on phage growth rate of each substitution. All three lines showed a substantial increase in fitness (a two- to threefold increase in growth rate) due to a modest number of substitutions (three to four). The data show some evidence that the substitutions occurring early in the experiment have larger beneficial effects than later ones, in accordance with the expected diminishing returns relationship between the fitness effects of a mutation and its order of substitution. Patterns of molecular evolution seen here-primarily a paucity of hitchhiking mutations-suggest an abundant supply of beneficial mutations in this system. Nevertheless, some beneficial mutations appear to have been lost, possibly due to accumulation of beneficial mutations on other genetic backgrounds, clonal interference, and negatively epistatic interactions with other beneficial mutations. [ABSTRACT FROM AUTHOR]

Parallel evolution is the acquisition of identical adaptive traits in independently evolving populations. Understanding whether the genetic changes underlying adaptation to a common selective environment are parallel within and between species is interesting because it sheds light on the degree of evolutionary constraints. If parallel evolution is perfect, then the implication is that forces such as functional constraints, epistasis, and pleiotropy play an important role in shaping the outcomes of adaptive evolution. In addition, population genetic theory predicts that the probability of parallel evolution will decline with an increase in the number of adaptive solutions--if a single adaptive solution exists, then parallel evolution will be observed among highly divergent species. For this reason, it is predicted that close relatives--which likely overlap more in the details of their adaptive solutions--will show more parallel evolution. By adapting three related bacteriophage species to a novel environment we find (1) a high rate of parallel genetic evolution at orthologous nucleotide and amino acid residues within species, (2) parallel beneficial mutations do not occur in a common order in which they fix or appear in an evolving population, (3) low rates of parallel evolution and convergent evolution between species, and (4) the probability of parallel and convergent evolution between species is strongly effected by divergence. [ABSTRACT FROM AUTHOR]

Examines the genetics of cosQ, the DNA-packaging termination site of phage. Local suppressors and methylation effects; Results of experiments indicating that EcoO1091 methylation has an impact on cosQ function; Description of cis-acting suppressors that overcome methylation-associated defects, including a methylation-dependent suppressor; General recombinant DNA techniques.

Investigates the effects of temperature-sensitive Escherichia coli DNA ligase on the short-homology-dependent illegitimate recombination that generates lambdabio-transducing phages. Distribution of recombination sites in lambdabio-transducing phages; Analysis of recombination junctions of lambdabio phages isolated from lambda lysogens.

Investigates the morphogenetic pathway of bacteriophage phiX174 in rep mutant hosts that specifically block stage III single-stranded DNA synthesis. Mutant rep protein's effect on the formation of the 50S complex; Ogr (rep) mutations; Localization of four of the six coat protein substitutions.

Examines the effects of nucleotide sequence changes on DNA secondary structure formation in Escherichia coli. DNA palindromes' potential to adopt cruciform structures; Construction of a set of palindromes with paired changes in the central sequence; Plating behavior of palindrome phage; Implications of cruciform extrusions in wild-type hosts.

Examines bacteriophage recombination in vivo. Use of lambda phages with restriction site morphisms; Infection with phage variants; Measurement by Southern blotting and hybridization with a substitution sequence-specific probe; Observed high frequency recombination.

Describes the isolation and characterization of second-site suppressors of a cold-sensitive (cs) external scaffolding protein, gpD, of bacteriophage phi-X174. Absence of allele specificity; Location within the major coat protein of the virus; Structural and stoichiometric phenomena.

Describes the genetic analysis of a phage mutation, tdx-1, that eliminates the formation of abortive transductants and implicates injected phage proteins in the formation of abortive transductants. Impairment of high-transducing phage HT12/4 for the formation of abortive transductants; Genetic basis for the HT12/4-transducing phenotype.