Purification and characterization of D-serine deaminase activator protein

Roles of serine accumulation and catabolism in the colonization of the murine urinary tract by Escherichia coli CFT073

A D-serine deaminase (DsdA) mutant of uropathogenic Escherichia coli strain CFT073 has a hypercolonization phenotype in a murine model of urinary tract infection (UTI) due to increased virulence gene expression by an unknown mechanism (B. J. Haugen et al., Infect. Immun. 75:278-289, 2007). DsdC is a D-serine-dependent activator of dsdXA transcription. DsdC may regulate the virulence genes responsible for hypercolonization. The loss of DsdA leads to increased intracellular accumulation of D-serine. In this study we show that deletion of the genes encoding L-serine deaminases SdaA and SdaB resulted in a mutant that accumulates higher intracellular levels of L-serine than CFT073. CFT073 sdaA sdaB has a mild competitive colonization defect whereas a CFT073 dsdA sdaA sdaB triple mutant shows a greater loss in competitive colonization ability. Thus, the inability to generate serine-specific catabolic products does not result in hypercolonization and the ability to catabolize serine represents a positive physiological trait during murine UTI. CFT073 dsdC and CFT073 dsdC dsdA mutants continue to outcompete the wild type in the UTI model. These results confirm that loss of DsdA activity results in the hypercolonization phenotype and that DsdC does not play a direct role in the elevated-colonization phenotype. Interestingly, a CFT073 dsdA mutant with deletions of D-serine transporter genes dsdX and cycA shows wild-type colonization levels of the bladder but is attenuated for kidney colonization. Thus, D-serine acts as a signal for hypercolonization and virulence gene expression by CFT073 dsdA, whereas overall catabolism of serine represents a positive Escherichia coli fitness trait during UTI.

Uropathogenic Escherichia coli use d-serine deaminase to modulate infection of the murine urinary tract

Although once thought to be unique to bacteria, d-amino acids are also produced by mammals. For example, d-serine is excreted in human urine at concentrations ranging from 3.0 to 40 micro g ml-1. An epidemiological survey demonstrated that urine isolates of E. coli are more likely to catabolise d-serine via expression of d-serine deaminase, DsdA than enteric disease isolates. The urosepsis strain, CFT073, and an isogenic dsdA mutant have similar growth kinetics in minimal or complex media. However, relative to the wild type, the dsdA mutant has a pleiomorphic cell shape and a prolonged, 4-6 h lag phase when grown in human urine. This suggests that d-serine catabolism provides a growth advantage in the urinary tract. Unexpectedly, in a direct competition model of urinary tract infection, the dsdA mutant was recovered 300-times more frequently than the wild type in the bladders of mice 48 h after infection. A new model of E. coli uropathogenesis is proposed where growth and gene expression are modulated in response to environmental d-serine levels. In support of this, the CFT073 dsdA mutant is hyperflagellated and more motile than the wild type indicating that intracellular levels of d-serine may directly or indirectly influence the expression of regulons associated with E. coli uropathogenesis.

Effects of structural changes in the dsdA-dsdC intergenic region on D-serine deaminase synthesis

Single-base-pair changes well upstream of its transcription initiation site resulted in partially to fully constitutive expression of the D-serine deaminase structural gene, dsdA, independently of the cyclic AMP-cyclic AMP-binding protein complex and of the specific D-serine deaminase activator protein. These promoter mutations appear to define a consensus sequence that is repeated several times. Basal expression of dsdA+ was also strongly enhanced by subcloning on multicopy plasmids, by the DNA gyrase inhibitor novobiocin, and in dsdC(Con) mutants by increasing growth temperature. These results suggest that activation of dsdA+ expression by the dsdC-encoded protein involves distortion of promoter DNA. A dsdA translation start at bp -731 was verified by subcloning of dsdC+. Plasmid-specified activator at a high concentration interfered with chromosomal dsdC(Con) expression, and the interference was enhanced by deletion of most of the intergenic region from the plasmid. Even at a high concentration, however, plasmid-specified activator did not activate expression of chromosomal dsdA+, and in one case it was actually repressive. These results confirm the strong cis tropism of plasmid-specified dsdC-encoded protein and suggest that it is mediated by multiple sites in the dsdA-dsdC intergenic region.

RepA protein- and oriR-dependent initiation of R1 plasmid replication: identification of a rho-dependent transcription terminator required for cis-action of repA protein

Initiation of R1 plasmid replication is dependent on cis-acting repA protein and the 188 base-pair (bp) sequence, oriR. RepA protein synthesized in vitro preferentially activates oriR in cis, regardless of the orientation and location of oriR on the template DNA. RepA protein is not reusable after it activates oriR in the cis-position. Cis-action of repA protein is also dependent on the presence of CIS, a 170 bp sequence, between repA and oriR. CIS contains a rho dependent transcription terminator of the repA transcript, deletion of which results in decrease in transformation efficiency and rapid loss of plasmid in the absence of selection. The significance of transcription termination events in replication was indicated by decreased replication activity in vivo caused by premature termination of the repA transcript between repA and CIS. A model which may account for the role of CIS in mediating the cis-action of the repA protein is presented.

DNA sequence of the D-serine deaminase activator gene dsdC

We have determined the DNA sequence of dsdC, the gene that encodes the D-serine deaminase activator protein of Escherichia coli K-12. The sequence contains a single open reading frame that terminates in a UGA codon. One the basis of the size of the protein, 33 kilodaltons, and the amino acid sequence encoded by the open reading frame, we identified a likely translation initiation codon 731 base pairs upstream of the translation initiation codon for the divergently transcribed D-serine deaminase gene. There is a broad range of codon usage, not surprising in view of the weak expression of the gene. The N-terminal two-thirds of the activator is arginine-lysine rich and quite polar; the remainder is more neutral. The segment of the protein that seems most likely to have potential to form the helix-turn-helix structure characteristic of DNA-regulatory proteins is located near the end of the polar region. The protein contains a region with significant homology to lambda attB.

In vivo D-serine deaminase transcription start sites in wild-type Escherichia coli and in dsdA promoter mutants

The D-serine deaminase structural (dsdA) and regulatory (dsdC) genes are transcribed with opposite polarity from an intergenic region comprising more than 600 base pairs. The order of genes in the dsd region is supN-dsdA-dsdC-aroC---his. The DNA sequence of the intergenic region has been slightly revised from a previously published version (E. McFall and L. Runkel, J. Bacteriol. 154:1508-1512, 1983). The dsdA gene is preceded by a long open reading frame. The dsdA in vivo transcription start sites for the wild type (base pair +1) and for three phenotypically distinct promoter constitutive mutants were determined by the S1 nuclease method. They are identical and are located about 81 base pairs upstream of the translation start site. D-Serine deaminase regulation is normal in rho mutants. Possible mechanisms for dsdA activation are discussed.