Chapter Summary


  • Transformation is the uptake by living cells of freefloating DNA from dead, lysed cells.
  • Competence for transformation in some organisms is triggered by a genetically programmed physiological change.
  • Conjugation is a DNA transfer process mediated by a transferable plasmid that requires cell-cell contact and formation of a protein complex between mating cells.
  • Pheromone peptides secreted by Gram-positive cocci such as Enterococcus faecalis activate transfer genes in nearby donor cells.
  • Some bacteria can transfer DNA across phylogenetic domains. For example, Agrobacterium tumefaciens conjugates with plant cells.
  • Transduction is the process whereby bacteriophages transfer fragments of bacterial DNA from one bacterium to another. In generalized transduction, a phage preparation can move any gene in a bacterial genome to another bacterium. In specialized transduction, a phage can move only a limited number of bacterial genes.
  • Restriction endonucleases protect bacteria from invasion by foreign DNA. Restriction-modification enzymes methylate restriction target sites in the host DNA to prevent self-digestion.


  • Recombination is the process by which DNA sequences can be exchanged between DNA molecules.
  • General recombination involves large regions of sequence homology between recombining DNA molecules.
  • RecA synaptase mediates generalized recombination.
  • The extremely radiation-resistant Deinococcus radiodurans is thought to use RecA protein to patch together homologous ends of fragmented DNA in a way that reconstructs the chromosome after extreme radiation damage.
  • Site-specific recombination requires little homology between donor and recipient DNA molecules. Site-specific recombination enables phage DNA to integrate into bacterial chromosomes and is a process that can turn on or turn off certain genes, as in flagellar phase variation in Salmonella.


  • A mutation is any heritable change in DNA sequence, regardless of whether there is a change in gene function. Genotype reflects the genetic makeup of an organism, whereas phenotype reflects its physical traits.
  • Classes of mutations include silent mutations, missense mutations, nonsense mutations, point mutations, insertions, deletions, and frameshift mutations.
  • Spontaneous mutations reflect tautomeric shifts in DNA nucleotides during replication, accidental incorporation of noncomplementary nucleotides during replication, or “natural” levels of chemical or physical (irradiation) mutagens in the environment.
  • Chemical mutagens can alter purine and pyrimidine structure and change base-pairing properties.
  • Mutagenicity of a chemical can be assessed by its effect on bacterial cultures.


  • DNA repair pathways in microorganisms include error-proof and error-prone mechanisms.
  • Methyl mismatch repair uses methylation of the parental DNA strand to discriminate it from newly replicated DNA. The premise is that the parental strand will contain the proper DNA sequence.
  • Photoreactivation cleaves the cyclobutane rings of pyrimidine dimers.
  • Nucleotide excision repair (NER) clips out a patch of single-stranded DNA containing certain types of damaged bases.
  • Base excision repair (BER) excises structurally altered bases without cleaving the phosphodiester backbone. The resulting AP (apurinic/apyrimidinic) site is targeted by AP nucleases.
  • Recombinational repair takes place at a replication fork. A “good” strand of DNA is used to replace a homologous damaged strand.
  • Extensive DNA damage leads to induction of the SOS response, producing increased levels of the error-proof repair systems, as well as error-prone.


  • Transposable elements and insertion sequences (“jumping genes”) move from one DNA molecule to another, usually without replicating separately (that is, they are not plasmids).
  • Transposase is an enzyme that forms a transpososome complex with the transposable element and target DNAs.
  • Insertion sequences are simple DNA transposable elements containing a transposase gene flanked by short inverted-repeat sequences.
  • Transposable elements move by nonreplicative or replicative mechanisms.
  • Transposons are complex transposable elements carrying additional genes (for example, drug resistance).
  • Composite transposons have two duplicate insertion sequence elements that flank additional genes. Often the interior inverted repeats of these elements contain mutations.
  • Transposons can carry a variety of genes, including antibiotic resistance genes.


  • Horizontal gene transfers between species are thought to occur by conjugation, transformation, and transduction.
  • A DNA sequence with a GC content different from that of flanking chromosomal DNA is one sign of horizontal gene transfer.
  • Pathogenicity islands are the result of horizontal gene transfers that improve the pathogenicity of a recipient. Fitness islands are similar to pathogenicity islands but improve environmental survival characteristics of the recipient.
  • Superfamilies of functional proteins result from gene duplications and mutations that cause divergent evolution of function.