Citrate utilization under anaerobic environment in Escherichia coli is under direct control of Fnr and indirect control of ArcA and Fnr via CitA-CitB system

Most Escherichia coli (E. coli) strains do not cause disease, naturally living in the lower intestine and is expelled into the environment within faecal matter. Escherichia coli can utilize citrate under anaerobic conditions but not aerobic conditions. However, the underlying regulatory mechanisms are poorly understood. In this study, we explored regulatory mechanisms of citrate fermentation genes by global regulators ArcA and Fnr under anaerobic conditions. A gel mobility shift assay showed that the regulator proteins ArcA and Fnr binded to the promoter region localized between the citAB and citCDEFXGT operons. Subsequent assays confirmed that ArcA indirectly controled the expression of citrate fermentation genes via regulating CitA-CitB system, while Fnr directly regulated but also indirectly modulated citrate fermentation genes via controling CitA-CitB system. Deletions of arcA and fnr significantly reduced the growth of Escherichia coli in M9 medium with a citrate carbon source. We conclude that both ArcA and Fnr can indirectly control the citrate utilization via CitA-CitB system, while Fnr can also directly regulate the expression of citrate fermentation genes in E. coli under anaerobic conditions.     

MutY is Down-regulated by Oxidative Stress in E. coli

In Escherichia coli, MutM (8-oxoG DNA glycosylase/lyase or Fpg protein), MutY (adenine DNA glycosylase) and MutT (8-oxodGTPase) function cooperatively to prevent mutation due to 7, 8-dihydro-8-oxoguanine (8-oxoG), a highly mutagenic oxidative DNA adduct. MutM activity has been demonstrated to be induced by oxidative stress. Its regulation is under the negative control of the global regulatory genes, fur, fnr and arcA. However, interestingly the presence of MutY increases the mutation frequency in mutT- background because of MutY removes adenine (A) from 8-oxoG:A which arises from the misincorporation of 8-oxoG against A during DNA replication. Accordingly we hypothesized that the response of MutY to oxidative stress is opposite to that of MutM and compared the regulation of MutY activity with MutM under various oxidative stimuli. Unlike MutM, MutY activity was reduced by oxidative stress. Its activity was reduced to 30% of that of the control when E. coli was treated with paraquat (0.5 mM) or H₂O₂ (0.1 mM) and induced under anaerobic conditions to more than twice that observed under aerobic conditions. The reduced mRNA level of MutY coincided with its reduced activity by paraquat treatment. Also, the increased activity of MutY in anaerobic conditions was reduced further in E. coli strains with mutations in fur, fnr and arcA and the maximum reduction in activity was when all mutations were present in combination, indicating that MutY is under the positive control of these regulatory genes. Therefore, the down-regulation of MutY suggests that there has been complementary mechanism for its mutagenic activity under special conditions. Moreover, the efficacy of anti-mutagenic action should be enhanced by the reciprocal co-regulation of MutM.     

Two-dimensional gel electrophoretic analysis of Escherichia coli proteins: influence of various anaerobic growth conditions and the fnr gene product on cellular protein composition

Two-dimensional gel electrophoresis was used to examine the response of the cellular proteins of Escherichia coli to various anaerobic growth conditions and to the presence or absence of a functional Fnr protein. The steady-state levels of 125 polypeptides were found to vary in either a positive or negative manner, with many polypeptides being affected under a number of conditions. A large number (21) of the anaerobically inducible polypeptides were shown to be totally independent of the presence of Fnr while 22 were shown to be reduced in a fnr mutant under all anaerobic growth conditions tested. A total of 8 proteins were shown to be reduced in a fnr mutant only in aerobically grown cells indicating that the Fnr protein has a function in the presence of oxygen. This was further confirmed by the observation that 15 anaerobically inducible polypeptides were also found to show an increase in aerobically grown cells, however, only in a fnr strain. This latter finding implies that Fnr may also exhibit repressor function. This effect of Fnr-dependent repression was also observed with several polypeptides in anaerobically grown cells.Abbreviation CRP cyclic AMP receptor protein     

Characterization oftrans-acting regulatory elements affecting the expression of Mn-superoxide dismutase (sodA) inEscherichia coli

Escherichia coli strains harboringtrans-acting mutations affecting the expression of Mn-superoxide dismutase (SOD) gene (sodA) were used to studysodA regulation. Complementation studies revealed that eitherarc (aerobic respiratory control) orfur (ferric uptake regulation) loci independently complemented anaerobic expression of asodA::lacZ protein fusion in one mutant strain (UV16). This mutant exhibited phenotypes (i.e., elevated outer membrane proteins, enzyme activity, and dye sensitivity) typical offur andarc mutants. When these mutations were introduced into an otherwise wild-type background, anaerobicsodA expression occurred only when botharc andfur mutations were present simultaneously, suggesting cooperative roles of Fur and Arc insodA repression. The reconstructedfur arcA andfur arcB double mutants were still inducible by iron chelators, suggesting the possible involvement of another iron-containing repressor protein. A second independent mutant strain harboring atrans-acting regulatory mutation (UV14) was only partially complemented by multicopy plasmids carryingfur ⁺ orarc ⁺ genes, implicating other genetic elements insodA regulation.     

Regulation ofEscherichia coli catalases by anaerobiosis and catabolite repression

Escherichia coli has two forms of catalases, HPI and HPII. Both enzymes, but mainly HPII, are induced in cells reaching the stationary growth phase or under anaerobic conditions and are repressed in the presence of glucose. The induction at the stationary phase is dependent onfnr, a gene that regulates the expression of anaerobically induced proteins. The inhibition by glucose is not affected by cyclic AMP (cAMP) but is reduced in acrp mutant. The results show that HPII belongs to the group of genes controlled by the Fnr protein and is catabolically repressed in a manner that is independent of cAMP.     

Involvement of ArcA and Fnr in expression of Escherichia coli thiol peroxidase gene

To explore the oxygen response regulators involved in thiol peroxidase gene (tpx) expression in Escherichia coli, we constructed a single-copy tpx-lacZ operon fusion and monitored tpx-lacZ expression in various genetic backgrounds. Expression of the tpx-lacZ fusion was increased 4-fold by aerobic growth. Anaerobic expression of tpx-lacZ in either (delta)arcA or delta(fnr) strains was 2.5-fold depressed compared with that of the wild-type strain. The results of immunoblotting experiments also demonstrated that ArcA and Fnr regulatory proteins repressed thiol peroxidase gene expression during anaerobic growth. Inspection of the tpx promoter region revealed putative binding sites for ArcA and Fnr. It thus appears that ArcA and Fnr function as repressors by blocking the binding of RNA polymerase to the tpx promoter in E. coli under anaerobic growth conditions.     

Genomics of the<Emphasis Type="Italic"> ccoNOQP</Emphasis>-encoded<Emphasis Type="Italic"> cbb</Emphasis><Subscript>3</Subscript> oxidase complex in bacteria

Many bacteria adapt to microoxic conditions by synthesizing a particular cytochrome c oxidase (cbb ₃) complex with a high affinity for O₂, encoded by the ccoNOQP operon. A survey of genome databases indicates that ccoNOQP sequences are widespread in all sub-branches of Proteobacteria but otherwise are found only in bacteria of the CFB group (Cytophaga, Flexibacter, Bacteroides). Our analysis of available genome sequences suggests four major strategies of regulating ccoNOQP expression in response to O₂. The most widespread strategy involves direct regulation by the O₂-responsive protein Fnr. The second strategy involves an O₂-insensitive paralogue of Fnr, FixK, whose expression is regulated by the O₂-responding FixLJ two-component system. A third strategy of mixed regulation operates in bacteria carrying both fnr and fixLJ-fixK genes. Another, not yet identified, strategy is likely to operate in the -Proteobacteria Helicobacter pylori and Campylobacter jejuni which lack fnr and fixLJ-fixK genes. The FixLJ strategy appears specific for the -subclass of Proteobacteria but is not restricted to rhizobia in which it was originally discovered.     

Regulation of Escherichia coli superoxide dismutase genes (sodA and sodB) by oxygen

Summary Two types of superoxide dismutase genes, sodA and sodB, were fused to -galactosidase gene (lacZ), in order to quantitatively study the effect of oxygen concentration on the gene expression of sodA and sodB. -Galactosidase activity derived from the sodA-lacZ fusion was induced by shifting from anaerobic condition to aerobic condition. Maximum activity (9.4×10³ U/OD₆₆₀) was observed when oxygen partial pressure was. 0.6 atm. On the contrary, gene expression level for the sodB-lacZ gene fusion was about two times higher during anaerobic condition than that during aerobic condition. From these results it was concluded that oxygen positively affected the gene expression of sodA and negatively affected the gene expression of sodB. An inducible expression vector using the sodA regulatory region was also constructed.