Size and Sequence Polymorphism in the Isocitrate Dehydrogenase Kinase/Phosphatase Gene (aceK) and Flanking Regions in Salmonella enterica and Escherichia coli

Abstract

The sequence of aceK, which codes for the regulatory catalytic enzyme isocitrate dehydrogenase kinase/phosphatase (IDH K/P), and sequences of the 5′ flanking region and part or all of the 3′ flanking region were determined for 32 strains of Salmonella enterica and Escherichia coli. In E. coli, the aceK gene was 1734 bp long in 13 strains, but in three strains it was 12 bp shorter and the stop codon was TAA rather than TGA. Strains with the shorter aceK lacked an open reading frame (f728) downstream between aceK and iclR that was present, in variable length, in the other strains. Among the 72 ECOR strains, the truncated aceK gene was present in all isolates of the B2 group and half of those of the D group. Other variant conditions included the presence of IS1 elements in two strains and large deletions in two strains. The aceK-aceA intergenic region varied in length from 48 to 280 bp in E. coli, depending largely on the number of repetitive extragenic palindromic (REP) sequences present. Among the ECOR strains, the number of REP elements showed a high degree of phylogenetic association, and sequencing of the region in the ECOR strains permitted partial reconstruction of its evolutionary history. In S. enterica, the normal length of aceK was 1752 bp, but three other length variants, ranging from 1746 to 1785 bp, were represented in five of the 16 strains examined. The flanking intergenic regions showed relatively minor variation in length and sequence. The occurrence of several nonrandom patterns of distribution of polymorphic synonymous nucleotide sites indicated that intragenic recombination of horizontally exchanged DNA has contributed to the generation of allelic diversity at the aceK locus in both species.

Protein Phosphatases−A Phylogenetic Perspective

“…201 The bifunctional IDH kinase/phosphatase appears to be a highly specialized, 'one of a kind' enzyme with few imitators. Not only has it thus far proved restricted to enteric bacteria such as E. coli and Salmonella enterica, 204 but in the 20 years since its discovery, no evidence has emerged for either additional family members or alternative substrates. Although it is premature to draw equally firm conclusions concerning the HPr kinase/phosphatase, thus far it too has proven to be restricted to a few members of the Bacteria and to the regulation of a single protein substrate, HPr.…”

The “Catalytic” Triad of Isocitrate Dehydrogenase Kinase/Phosphatase from E. coli and Its Relationship with That Found in Eukaryotic Protein Kinases

“…The AspPheGly (Asp-184) and AlaProGlu (Glu-208) motifs which are highly conserved in all ePKs [in 87% and 70% of the 390 sequences registered in the Protein Kinase Resource (41), respectively] are, however, sometimes replaced by AspLeuGly (in 5.6% of the sequences) and AlaIleGlu (in 2%) as reported here for IDHK/P. In the only other IDHK/P sequence found in the Swiss-Prot database (42), from Salmonella typhimurium, the residues highlighted in this partial alignment are totally conserved (43).…”