Characterization of the Escherichia coli K-12 ydhYVWXUT operon: regulation by FNR, NarL and NarP

Abstract

In Escherichia coli K-12 the expression of many genes is controlled by the oxygen-responsive transcription factor FNR and the nitrate-and nitrite-responsive two-component systems NarXL and NarPQ. Here, the ydhY gene is shown to be the first gene of a six-gene operon (ydhYVWXUT) that encodes proteins predicted to be components of an oxidoreductase. Mapping the ydhY-T transcript start and site-directed mutagenesis confirmed that the ydhY-T genes are transcribed from an FNR-dependent class II promoter and showed that the FNR site is centred at "42.5. In the presence of nitrate or nitrite, NarXL and NarPQ repressed ydhY-T expression. Analysis of the DNA sequence of the ydhY promoter region (PydhY) revealed the presence of four heptameric sequences similar to NarL/P binding sites centred at "42, "16, +6 and +15. The latter heptamers are arranged as a 7-2-7 inverted repeat, which is required for recognition by NarP. Accordingly, NarP protected the 7-2-7 region in DNase I footprints, and mutation of either heptamer +6 or heptamer +15 impaired nitrite-mediated repression, whereas mutation of heptamer "42 and heptamer "16 did not affect the response to nitrite. The NarL protein also protected the 7-2-7 region, but in contrast to NarP, the NarL footprint extended further upstream to encompass the "16 heptamer. The extended NarL footprint was consistent with the presence of multiple NarL-PydhY complexes in gel retardation assays. Mutation of heptamer "42, which is located within the FNR binding site, or heptamer +6 (but not heptamers "16 or +15) impaired nitrate-mediated repression. Thus, although the region of the ydhY-T promoter containing the "16 and +15 heptamers was recognized by NarL in vitro, mutation of these heptamers did not affect NarL-mediated repression in vivo.

New Insights into the Formation of Viable but Nonculturable Escherichia coli O157:H7 Induced by High-Pressure CO 2

“…Cytochrome b561 is an electron-transferring component of the respiratory chain (25). YdhY is predicted to be a ferredoxin-like protein and is possibly involved in electron transfer reactions (26). These results suggest that the ability to transfer electrons was enhanced upon VBNC state formation, which might increase the ATP level and thus provide energy for the survival of the cell.…”

Genomic Comparison of Two O111:H − Enterohemorrhagic Escherichia coli Isolates from a Historic Hemolytic-Uremic Syndrome Outbreak in Australia

“…These regions include the ferric aerobactin operon of 11128's second integrative element (IE02), which encodes a potential iron-scavenging siderophore, and part of the ydhYVWXUT oxidoreductase operon ( Fig. 2; see also Table S5 in the supplemental material) (38,39). The majority of differences were related to prophage genes, with some genes being without coverage (e.g., within P11 and P13) and other genes exhibiting more than 1ϫ coverage (e.g., within P02 and P05).…”

Molybdenum Cofactor-Containing Enzymes and Pathways

“…This family is distinguished by the presence of a W-bisPPT cofactor and the best-characterized examples are found in the hyperthermophilic archaeon P. furiosus, with examples glyceraldehyde-3-phosphate:ferredoxin oxidoreductase (GAPOR) (Reher et al 2007), aldehyde oxidoreductase (AOR) (Bevers et al 2005), as well as the YdhV subunit of the E. coli YdhYVXU operon (Partridge et al 2008). It is notable that the first structure determined of a mononuclear Mo/W enzyme was that of the P. furiosus AOR (Chan et al 1995;Roy and Adams 2002).…”