DNA restriction and modification
ATP and ATP hydrolysis
Adenosine triphosphate (ATP) is a primary repository of energy that is released for other catalytic activities when ATP is hydrolyzed (split) to yield adenosine diphosphate.
Bacteriophages (lambda and T-even)
Bacterial viruses. Phage lambda () is a temperate phage and therefore on infection of a bacterial cell one of two alternative pathways may result; either the lytic pathway in which the bacterium is sacrificed and progeny phages are produced or the temperate (lysogenic) pathway in which the phage genome is repressed and, if it integrates into the host chromosome, will be stably maintained in the progeny of the surviving bacterium. Phage was isolated from Escherichia coli K-12 in which it resided in its temperate (prophage) state. T-even phages (T2, T4, and T6) are virulent coliphages, that is, infection of a sensitive strain of E. coli leads to the production of phages at the inevitable expense of the host. T-even phages share the unusual characteristic that their DNA includes hydroxymethylcytosine rather than cytosine.
Conjugation, conjugational transfer
Gene transfer by conjugation requires cell-to-cell contact. Conjugative, or self-transmissible, plasmids such as the F factor of E.coli encode the necessary functions to mobilize one strand of their DNA with a defined polarity from an origin of transfer determined by a specific nick. The complementary strand is then made in the recipient cell. Some plasmids are transmissible but only on provision in trans of the necessary functions by a conjugative plasmid. A conjugative plasmid, such as the F factor, can mobilize transfer of the bacterial genome following integration of the plasmid into the bacterial chromosome.
DNA methyltransferases
Enzymes (MTases) that catalyze the transfer of a methyl group from the donor S-adenosylmethionine to adenine or cytosine residues in the DNA.
Efficiency of plating
This usually refers to the ratio of the plaque count on a test strain relative to that obtained on a standard, or reference, strain.
Endonucleases
Enzymes that can fragment polynucleotides by the hydrolysis of internal phosphodiester bonds.
Escherichia coli strain K-12
The strain used by Lederberg and Tatum in their discovery of recombination in E.coli.
Glucosylation of DNA
The DNA of T-even phages in addition to the pentose sugar, deoxyribose, contains glucose attached to the hydroxymethyl group of hydroxymethyl-cytosine. Glucosylation of the DNA is mediated by phage-encoded enzymes, but the host provides the glucose donor.
Proteomics
The study of the protein complement, or proteome, of an organism.
Helicases
Enzymes that separate paired strands of polynucleotides.
Recombination pathway
The process by which new combinations of DNA sequences are generated. The general recombination process relies on enzymes that use DNA sequence homology for the recognition of the recombining partner. In the major pathway in E.coli, RecBCD generates the DNA strands for transfer and RecA protein promotes synapsis. The RecBCD enzyme, also recognized as exonuclease V, enters DNA via a double-strand end. It tracks along the DNA, promoting unwinding of the strands but, in response to a special nucleotide sequence termed Chi, it makes a nick, following which strand separation continues and the single-stranded DNA with a 3 end becomes available for synapsis with homologous DNA. In vitro, the mechanism by which RecBCD makes a DNA end is determined by the reaction conditions; its activity as a potent exonuclease is influenced by the relative concentrations of ATP and Mg ions.
SOS response
DNA damage induces expression of a set of genes, the SOS genes, involved in the repair of DNA damage.
Southern transfer
The transfer of denatured DNA from a gel to a solid matrix, such as a nitrocellulose filter, within which the denatured DNA can be maintained and hybridized to labeled probes (single-stranded DNA or RNA molecules). Fragments previously separated by electrophoresis through a gel may be identified by hybridization to a specific probe.
Transformation
The direct assimilation of DNA by a cell, which results in the recipient being changed genetically.
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