We present a procedure for efficient random mutagenesis of selected genes in a bacterial chromosome. The method combines PCR replication errors with the uptake of PCR-amplified DNA via natural transformation. Cloning of PCR fragments is not required, since mutations are transferred directly to the chromosome via homologous recombination. Random mutations were introduced into the Acinetobacter chromosomal pobR gene encoding the transcriptional activator of pobA, the structural gene for 4-hydroxybenzoate 3-hydroxylase. Mutant strains with strongly reduced PobR activity were selected by demanding the inability to convert 4-hydroxybenzoate to a toxic metabolite. Of spontaneous pobR mutants, 80% carry the insertion element IS1236, rendering them inappropriate for structure-function studies. Transformation with Taq-amplified pobR DNA increased the mutation frequency 240-fold and reduced the proportion of IS1236 inserts to undetectable levels. The relative fidelity of Pfu polymerase compared with Taq polymerase was illustrated by a reduced effect on the mutation frequency; a procedure for rapid assessment of relative polymerase fidelity in PCR follows from this observation. Over 150 independent mutations were localized by transformation with DNA fragments containing nested deletions of wild-type pobR. Sequence analysis of 89 of the mutant pobR alleles showed that the mutations were predominantly single-nucleotide substitutions broadly distributed within pobR. Promoter mutations were recovered, as were two mutations that are likely to block pobR translation. One-third of the recovered mutations conferred a leaky or temperature-sensitive phenotype, whereas the remaining null mutations completely blocked growth with 4-hydroxybenzoate. Strains containing two different nonsense mutations in pobR were transformed with PCR-amplified DNA to identify permissible codon substitutions. Independently, second-site suppressor mutations were recovered within pcaG, another member of the supraoperonic pca-quipob cluster on the Acinetobacter chromosome. This shows that combining PCR mutagenesis with natural transformation is of general utility.Amplification of DNA by thermostable polymerases in the PCR introduces mutations (2,23,34,36,41). This is an inconvenience when the fidelity of replication is a concern, but in some cases, the randomness of nucleotide substitutions introduced by PCR can facilitate genetic analysis. For example, defects caused by a wide spectrum of independent mutations within a gene can give insight into how structure influences the function of the encoded protein. The efficiency of such structure-function studies is determined in large part by the ease with which the phenotype conferred by altered DNA can be observed. In this regard, oxygenative pathways for dissimilation of aromatic compounds by Acinetobacter calcoaceticus (18) provide a convenient genetic system allowing ready selection of defective genes (4, 8, 13) introduced by natural transformation (18).An intriguing target for genetic investigation is Acine...