Arginine decarboxylase (encoded by adi) is induced under conditions of acidic pH, anaerobiosis, and rich medium. The DNA sequence of a 3-kb fragment of the Escherichia coli chromosome encoding biodegradative arginine decarboxylase was determined. This sequence encodes a protein of 755 amino acids with a molecular size of 84,420 daltons. The molecular weight and predicted Adi amino acid composition agree with those found in earlier work. The amino acid sequence of arginine decarboxylase showed homology to those of three other decarboxylases of E. cofi: (i) CadA, encoding lysine decarboxylase; (ii) SpeC, encoding biosynthetic ornithine decarboxylase; and (iii) SpeF, encoding biodegradative ornithine decarboxylase and the lysine decarboxylase of Hafnia alvei. Unlike SpeC and SpeF, Adi is not similar to the biosynthetic arginine decarboxylase, SpeA. adi is also dissimilar to cad4 and speF in that it does not appear to be part of an operon containing a metabolically related transport protein, indicating that it represents a new type of biodegradative decarboxylase regulation. Transcriptional fusions between fragments upstream of adi and lacZ, primer extension, and site-directed mutagenesis experiments defined the pH-regulated promoter. Deletion analysis of the upstream region and cloning of fragments to make adi::lacZ protein fusions implicated a region beyond an upstream SspI site in pH regulation. Induction of adi in the presence of sublethal concentrations of novobiocin or coumermycin Al, inhibitors of DNA gyrase, was dramatically decreased, indicating that DNA supercoiling is involved in adi expression. These results and those of promoter structure studies indicated that acid regulation of adi may involve a mechanism different from that of acid regulation of cad.

Three methods were used to provide information on the identity and phylogenetic relatedness of 19 aerobic, chemoheterotrophic bacteria isolated from topsoil and deep subsurface sediments at a site in South Carolina. These methods were (i) analysis of selected physiological traits, (ii) restriction endonuclease analysis (REA) of genomic DNA, and (iii) analysis of 16S ribosomal RNA sequences. When the 16S rRNA sequences were compared with those for 12 standard strains, two topsoil isolates and six subsurface strains formed a tight group with the high-G+C Gram-positive bacteria and appeared to be most closely related to Arthrobacter globiformis--a coryneform-actinomycete bacterium with unusually effective survival capabilities. The rest of the subsurface isolates were scattered among the standard strains from the Proteobacteria-including the pseudomonads and Agrobacterium tumefaciens--or the low-G+C Gram-positive bacteria.