Bacillus subtilis aconitase is an RNA-binding protein

Contrasting sensitivities of Escherichia coli aconitases A and B to oxidation and iron depletion

Superoxide damages dehydratases that contain catalytic [4Fe-4S](2+) clusters. Aconitases are members of that enzyme family, and previous work showed that most aconitase activity is lost when Escherichia coli is exposed to superoxide stress. More recently it was determined that E. coli synthesizes at least two isozymes of aconitase, AcnA and AcnB. Synthesis of AcnA, the less-abundant enzyme, is positively controlled by SoxS, a protein that is activated in the presence of superoxide-generating chemicals. We have determined that this arrangement exists because AcnA is resistant to superoxide in vivo. Surprisingly, purified AcnA is extremely sensitive to superoxide and other chemical oxidants unless it is combined with an uncharacterized factor that is present in cell extracts. In contrast, AcnB is highly sensitive to a variety of chemical oxidants in vivo, in extracts, and in its purified form. Thus, the induction of AcnA during oxidative stress provides a mechanism to circumvent a block in the tricarboxylic acid cycle. AcnA appears to be as catalytically competent as AcnB, so the retention of the latter as the primary housekeeping enzyme must provide some other advantage. We observed that the [4Fe-4S] cluster of AcnB is in dynamic equilibrium with the surrounding iron pool, so that AcnB is rapidly demetallated when intracellular iron pools drop. AcnA and other dehydratases do not show this trait. Demetallated AcnB is known to bind its cognate mRNA. The absence of AcnB activity also causes the accumulation and excretion of citrate, an iron chelator for which E. coli synthesizes a transport system. Thus, AcnB may be retained as the primary aconitase because the lability of its exposed cluster allows E. coli to sense and respond to iron depletion.

Staphylococcus aureus aconitase inactivation unexpectedly inhibits post-exponential-phase growth and enhances stationary-phase survival

Staphylococcus aureus preferentially catabolizes glucose, generating pyruvate, which is subsequently oxidized to acetate under aerobic growth conditions. Catabolite repression of the tricarboxylic acid (TCA) cycle results in the accumulation of acetate. TCA cycle derepression coincides with exit from the exponential growth phase, the onset of acetate catabolism, and the maximal expression of secreted virulence factors. These data suggest that carbon and energy for post-exponential-phase growth and virulence factor production are derived from the catabolism of acetate mediated by the TCA cycle. To test this hypothesis, the aconitase gene was genetically inactivated in a human isolate of S. aureus, and the effects on physiology, morphology, virulence factor production, virulence for mice, and stationary-phase survival were examined. TCA cycle inactivation prevented the post-exponential growth phase catabolism of acetate, resulting in premature entry into the stationary phase. This phenotype was accompanied by a significant reduction in the production of several virulence factors and alteration in host-pathogen interaction. Unexpectedly, aconitase inactivation enhanced stationary-phase survival relative to the wild-type strain. Aconitase is an iron-sulfur cluster-containing enzyme that is highly susceptible to oxidative inactivation. We speculate that reversible loss of the iron-sulfur cluster in wild-type organisms is a survival strategy used to circumvent oxidative stress induced during host-pathogen interactions. Taken together, these data demonstrate the importance of the TCA cycle in the life cycle of this medically important pathogen.

Global analysis of the Bacillus subtilis Fur regulon and the iron starvation stimulon

The Bacillus subtilis ferric uptake repressor (Fur) protein coordinates a global transcriptional response to iron starvation. We have used DNA microarrays to define the Fur regulon and the iron starvation stimulon. We identify 20 operons (containing 39 genes) that are derepressed both by mutation of fur and by treatment of cells with the iron chelator 2,2'-dipyridyl. These operons are direct targets of Fur regulation as judged by DNase I footprinting. Analyses of lacZ reporter fusions to six Fur-regulated promoter regions reveal that repression is highly selective for iron. In addition to the Fur regulon, iron starvation induces members of the PerR regulon and leads to reduced expression of cytochromes. However, we did not find any evidence for genes that are directly activated by Fur or repressed by Fur under iron-limiting conditions. Although genome searches using the 19 bp Fur box consensus are useful in identifying candidate Fur-regulated genes, some genes associated with Fur boxes are not demonstrably regulated by Fur, whereas other genes are regulated from sites with little apparent similarity to the conventional Fur consensus.

Escherichia coli genes involved in resistance to pyrazinoic acid, the active component of the tuberculosis drug pyrazinamide

The natural resistance of Escherichia coli to pyrazinoic acid (POA), the active derivative of pyrazinamide, was investigated. The TolC mutant was found to be more susceptible to POA and other weak acids than the wild-type strain. Mutation in EmrB but not AcrB efflux protein slightly increased POA susceptibility. Two transposon mutants with increased susceptibility to POA were found to harbor mutations in acnA encoding aconitase-1 and ygiY encoding a putative two-component sensor protein. Complementation of the AcnA and YgiY mutants conferred resistance to POA, whereas the complemented TolC mutant became resistant to POA and other weak acids.

Iron deficiency decreases mitochondrial aconitase abundance and citrate concentration without affecting tricarboxylic acid cycle capacity in rat liver

Mitochondrial aconitase (m-acon) is the tricarboxylic acid (TCA) cycle enzyme that converts citrate to isocitrate. m-Acon mRNA is a potential target for regulation by iron regulatory proteins (IRPs), suggesting a link between dietary iron intake, m-acon synthesis, and energy metabolism. Our previous studies indicate that m-acon is one of a limited number of proteins that is down-regulated in iron-deficient liver. Here we use isolated hepatocytes to study the relationships among decreased m-acon abundance, TCA cycle function and cellular citrate concentration in iron deficiency. Rats were fed an iron-deficient (ID) (2 mg Fe/kg diet) diet, or they were pair-fed (PF) or freely fed (C) a control diet (50 mg Fe/kg diet) for up to 21 d. Hepatocyte total IRP activity was greater by d 2 in the ID group than in the C and PF groups and by d 10, the difference was maximal. Liver IRP activity was inversely correlated with m-acon abundance (r = -0.93, P < 0.0001). However, the decrease in m-acon abundance did not affect the ability of hepatocytes to oxidize 2-[(14)C]pyruvate or 1-[(14)C]acetate, indicating that TCA cycle capacity was not affected. Interestingly, by d 21, total liver citrate concentration was 40% lower in ID than in PF rats, suggesting enhanced utilization of citrate. However, the decrease in citrate concentration was not reflected in a change in liver total lipid concentration. Taken together, our results indicate that the iron-dependent regulation of m-acon in liver does not alter TCA cycle capacity but suggest that IRP-mediated changes in m-acon expression may modulate citrate use in other aspects of intermediary or iron metabolism.

Escherichia coli aconitases and oxidative stress: post-transcriptional regulation of sodA expression

Escherichia coli possesses two aconitases, a stationary-phase enzyme (AcnA), which is induced by iron and oxidative stress, and a major but less stable enzyme (AcnB), synthesized during exponential growth. In addition to the catalytic activities of the holo-proteins, the apo-proteins function as post-transcriptional regulators by site-specific binding to acn mRNAs. Thus, it has been suggested that inactivation of the enzymes could mediate a rapidly reacting post-transcriptional component of the bacterial oxidative stress response. Here it is shown that E. coli acn mutants are hypersensitive to the redox-stress reagents H(2)O(2) and methyl viologen. Proteomic analyses further revealed that the level of superoxide dismutase (SodA) is enhanced in acnB and acnAB mutants, and by exposure to methyl viologen. The amounts of other proteins, including thioredoxin reductase, 2-oxoglutarate dehydrogenase, succinyl-CoA synthetase and chaperone proteins, were also affected in the acn mutants. The altered patterns of sodA expression were confirmed in studies with sodA-lacZ reporter strains. Quantitative Northern blotting indicated that AcnA enhances the stability of the sodA transcript, whereas AcnB lowers its stability. Direct evidence that the apo-proteins have positive (AcnA) and negative (AcnB) effects on SodA synthesis was obtained from in vitro transcription-translation experiments. It is suggested that the aconitase proteins of E. coli serve as a protective buffer against the basal level of oxidative stress that accompanies aerobic growth by acting as a sink for reactive oxygen species and by modulating translation of the sodA transcript.

In vitro serial passage of Staphylococcus aureus: changes in physiology, virulence factor production, and agr nucleotide sequence

Recently, we observed that Staphylococcus aureus strains newly isolated from patients had twofold-higher aconitase activity than a strain passaged extensively in vitro, leading us to hypothesize that aconitase specific activity decreases over time during in vitro passage. To test this hypothesis, a strain recovered from a patient with toxic shock syndrome was serially passaged for 6 weeks, and the aconitase activity was measured. Aconitase specific activity decreased 38% (P < 0.001) by the sixth week in culture. During serial passage, S. aureus existed as a heterogeneous population with two colony types that had pronounced (wild type) or negligible zones of beta-hemolytic activity. The cell density-sensing accessory gene regulatory (agr) system regulates beta-hemolytic activity. Surprisingly, the percentage of colonies with a wild-type beta-hemolytic phenotype correlated strongly with aconitase specific activity (rho = 0.96), suggesting a common cause of the decreased aconitase specific activity and the variation in percentage of beta-hemolytic colonies. The loss of the beta-hemolytic phenotype also coincided with the occurrence of mutations in the agrC coding region or the intergenic region between agrC and agrA in the derivative strains. Our results demonstrate that in vitro growth is sufficient to result in mutations within the agr operon. Additionally, our results demonstrate that S. aureus undergoes significant phenotypic and genotypic changes during serial passage and suggest that vigilance should be used when extrapolating data obtained from the study of high-passage strains.

Fur-mediated transcriptional and post-transcriptional regulation of FeSOD expression in Escherichia coli

Fur (ferric uptake regulation protein) activates sodB expression, increasing expression levels by a factor of seven and sodB transcript stability by a factor of three. Post-transcriptional regulation of sodB was investigated by searching for endoribonucleases that might be involved in sodB mRNA degradation. The activation of sodB expression was significantly reduced if both the RNaseE and RNaseIII genes were mutated. This correlated with cleavage at a palindromic sequence located in the 5' untranslated region of the sodB transcript. An RNA-binding assay showed that Fur did not directly protect the sodB transcript. It was hypothesized that the persistence of Fur-mediated activation of sodB expression in the RNase double mutant was probably due to an effect at the transcriptional level. Therefore, it was investigated whether Fur had a direct transcriptional effect in vitro. Fur bound the sodB promoter region with low affinity, but it was not able to increase sodB transcription. H-NS-mediated repression of sodB expression, which has been shown to be Fur-dependent, was characterized. No DNA-bending region was identified in the sodB promoter region. H-NS did not interfere with the post-transcriptional effect of Fur. Fur-dependent H-NS and the Fur post-transcriptional effect were not additive. This suggests that Fur and H-NS effects are indirect and may be mediated by a common intermediate.

AcnC of Escherichia coli is a 2-methylcitrate dehydratase (PrpD) that can use citrate and isocitrate as substrates

Escherichia coli possesses two well-characterized aconitases (AcnA and AcnB) and a minor activity (designated AcnC) that is retained by acnAB double mutants and represents no more than 5% of total wild-type aconitase activity. Here it is shown that a 2-methylcitrate dehydratase (PrpD) encoded by the prpD gene of the propionate catabolic operon (prpRBCDE) is identical to AcnC. Inactivation of prpD abolished the residual aconitase activity of an AcnAB-null strain, whereas inactivation of ybhJ, an unidentified acnA paralogue, had no significant effect on AcnC activity. Purified PrpD catalysed the dehydration of citrate and isocitrate but was most active with 2-methylcitrate. PrpD also catalysed the dehydration of several other hydroxy acids but failed to hydrate cis-aconitate and related substrates containing double bonds, indicating that PrpD is not a typical aconitase but a dehydratase. Purified PrpD was shown to be a monomeric iron-sulphur protein (M(r) 54000) having one unstable [2Fe-2S] cluster per monomer, which is needed for maximum catalytic activity and can be reconstituted by treatment with Fe(2+) under reducing conditions.

Desiccation tolerance: a simple process?

Water is essential for life, and thus the removal of water from a cell is a severe, often lethal stress. This is not a remarkable observation but it is one that is often taken for granted. Desiccation-tolerant cells implement structural, physiological and molecular mechanisms to survive severe water deficit. These mechanisms, and the components and pathways which facilitate them, are poorly understood. Here, recent developments are considered to illustrate the importance of desiccation, longevity and cell stasis in basic microbiology, and the relevance of the topic to the metabolic engineering of sensitive cells, including those of humans.

Characterizations of highly expressed genes of four fast-growing bacteria

Predicted highly expressed (PHX) genes are characterized for the completely sequenced genomes of the four fast-growing bacteria Escherichia coli, Haemophilus influenzae, Vibrio cholerae, and Bacillus subtilis. Our approach to ascertaining gene expression levels relates to codon usage differences among certain gene classes: the collection of all genes (average gene), the ensemble of ribosomal protein genes, major translation/transcription processing factors, and genes for polypeptides of chaperone/degradation complexes. A gene is predicted highly expressed (PHX) if its codon frequencies are close to those of the ribosomal proteins, major translation/transcription processing factor, and chaperone/degradation standards but strongly deviant from the average gene codon frequencies. PHX genes identified by their codon usage frequencies among prokaryotic genomes commonly include those for ribosomal proteins, major transcription/translation processing factors (several occurring in multiple copies), and major chaperone/degradation proteins. Also PHX genes generally include those encoding enzymes of essential energy metabolism pathways of glycolysis, pyruvate oxidation, and respiration (aerobic and anaerobic), genes of fatty acid biosynthesis, and the principal genes of amino acid and nucleotide biosyntheses. Gene classes generally not PHX include most repair protein genes, virtually all vitamin biosynthesis genes, genes of two-component sensor systems, most regulatory genes, and most genes expressed in stationary phase or during starvation. Members of the set of PHX aminoacyl-tRNA synthetase genes contrast sharply between genomes. There are also subtle differences among the PHX energy metabolism genes between E. coli and B. subtilis, particularly with respect to genes of the tricarboxylic acid cycle. The good agreement of PHX genes of E. coli and B. subtilis with high protein abundances, as assessed by two-dimensional gel determination, is verified. Relationships of PHX genes with stoichiometry, multifunctionality, and operon structures are also examined. The spatial distribution of PHX genes within each genome reveals clusters and significantly long regions without PHX genes.

The hairpin loop but not the bulged C of the iron responsive element is essential for high affinity binding to iron regulatory protein-1

Vertebrates control intracellular iron concentration principally through the interaction of iron regulatory proteins with mRNAs that contain an iron responsive element, a small hairpin with a bulged C. The hairpin loop and bulged C have previously been assumed to be critical for binding and have been proposed to make direct contact with the iron regulatory proteins. However, we show here that a U or G can be substituted for the bulged C provided that specific nucleotides are also present within internal loops. The K(d), IC(50) and chemical modifications of the iron responsive element variants are similar to the wild-type. Results are more consistent with a role in which the C-bulge functions to orient the hairpin for optimal protein binding rather than to directly contact the protein. Characterization of these novel iron responsive element variants may facilitate the identification of additional mRNAs whose expression is controlled by iron regulatory proteins, as well as provide insight into the nature of a critical RNA-protein interaction.

Roles of aconitase in growth, metabolism, and morphological differentiation of Streptomyces coelicolor

The studies of aconitase presented here, along with those of citrate synthase (P. H. Viollier, W. Minas, G. E. Dale, M. Folcher, and C. J. Thompson, J. Bacteriol. 183:3184-3192, 2001), were undertaken to investigate the role of the tricarboxylic acid (TCA) cycle in Streptomyces coelicolor development. A single aconitase activity (AcoA) was detected in protein extracts of cultures during column purification. The deduced amino acid sequence of the cloned acoA gene constituted the N-terminal sequence of semipurified AcoA and was homologous to bacterial A-type aconitases and bifunctional eukaryotic aconitases (iron regulatory proteins). The fact that an acoA disruption mutant (BZ4) did not grow on minimal glucose media in the absence of glutamate confirmed that this gene encoded the primary vegetative aconitase catalyzing flux through the TCA cycle. On glucose-based complete medium, BZ4 had defects in growth, antibiotic biosynthesis, and aerial hypha formation, partially due to medium acidification and accumulation of citrate. The inhibitory effects of acids and citrate on BZ4 were partly suppressed by buffer or by introducing a citrate synthase mutation. However, the fact that growth of an acoA citA mutant remained impaired, even on a nonacidogenic carbon source, suggested alternative functions of AcoA. Immunoblots revealed that AcoA was present primarily during substrate mycelial growth on solid medium. Transcription of acoA was limited to the early growth phase in liquid cultures from a start site mapped in vitro and in vivo.

Iron and metal regulation in bacteria

In Escherichia coli, the iron regulator Fur is regulated by two oxidative-stress response regulators. The generation of dangerous radicals by oxygen and iron is the basis for this dual regulation, which is also found in eukaryotes. The binding of iron-regulated transcripts to apo-aconitase and results of mRNA half-life studies indicate that there is post-transcriptional iron regulation in bacteria, as in eukaryotes. Fur contains two metal-binding sites, one for Zn2+ and one for Fe2+. Zinc uptake systems are regulated by members of the Fur protein family, and zinc is a cofactor. DtxR and related proteins constitute another family of iron regulators, first found in Gram-positive organisms with a high GC content. In organisms with Fur-dependent iron regulation, members of the DtxR family regulate manganese transport.

Iron regulatory proteins and the molecular control of mammalian iron metabolism

Mammalian iron homeostasis is maintained through the concerted action of sensory and regulatory networks that modulate the expression of proteins of iron metabolism at the transcriptional and/or post-transcriptional levels. Regulation of gene transcription provides critical developmental, cell cycle, and cell-type-specific controls on iron metabolism. Post-transcriptional control through the action of iron regulatory protein 1 (IRP1) and IRP2 coordinate the use of messenger RNA-encoding proteins that are involved in the uptake, storage, and use of iron in all cells of the body. IRPs may also provide a link between iron availability and cellular citrate use. Multiple factors, including iron, nitric oxide, oxidative stress, phosphorylation, and hypoxia/reoxygenation, influence IRP function. Recent evidence indicates that there is diversity in the function of the IRP system with respect to the response of specific IRPs to the same effector, as well as the selectivity with which IRPs modulate the use of specific messenger RNA.

The CitST two-component system regulates the expression of the Mg-citrate transporter in Bacillus subtilis

citS and citT genes encoding a new two-component system were identified in the 71 degrees region between the pel and citM loci on the Bacillus subtilis chromosome. citS- and citT-deficient strains were unable to grow on minimal plates including citrate as a sole carbon source. In addition, a strain deficient in citM, which encodes the secondary transporter of the Mg-citrate complex, exhibited the same phenotype on this medium. Northern blot analysis revealed that citM was polycistronically transcribed with the downstream yflN gene, and that CitS and CitT were necessary for transcription of the citM-yflN operon. Upon addition of 2 mM citrate to DSM, this operon was strongly induced after the middle of the exponential growth phase in the wild type, but not in the citST double null mutant. Moreover, the transcription of this operon was completely repressed in the presence of 1% glucose. We found a sequence exhibiting homology to a catabolite-responsive element (cre) in the citM promoter region. Glucose repression was lost in ccpA and citM-cre mutants. From the result of a citM-promoter deletion experiment, putative CitT target sequences were found to be located around two regions, from -62 to -74 and from -149 to -189, relative to the citM start point. Furthermore, DNase I footprinting assays revealed that these two CitT target regions extended maximally from -36 to -84 and from -168 to -194. From these findings, we concluded that the expression of citM is positively regulated by the CitST system and negatively regulated by CcpA.

Identification and characterization of the iron regulatory element in the ferritin gene of a plant (soybean)

Iron increases ferritin synthesis, targeting plant DNA and animal mRNA. The ferritin promoter in plants has not been identified, in contrast to the ferritin promoter and mRNA iron-responsive element (IRE) in animals. The soybean leaf, a natural tissue for ferritin expression, and DNA, with promoter deletions and luciferase or glucuronidase reporters, delivered with particle bombardment, were used to show that an 86-base pair fragment (iron regulatory element (FRE)) controlled iron-mediated derepression of the ferritin gene. Mutagenesis with linkers of random sequence detected two subdomains separated by 21 base pairs. FRE has no detectable homology to the animal IRE or to known promoters in DNA and bound a trans-acting factor in leaf cell extracts. FRE/factor binding was abrogated by increased tissue iron, in analogy to mRNA (IRE)/iron regulatory protein in animals. Maximum ferritin derepression was obtained with 50 microm iron citrate (1:10) or 500 microm iron citrate (1:1) but Fe-EDTA was ineffective, although the leaf iron concentration was increased; manganese, zinc, and copper had no effect. The basis for different responses in ferritin expression to different iron complexes, as well as the significance of using DNA but not mRNA as an iron regulatory target in plants, remain unknown.

Effects of aluminum on activity of krebs cycle enzymes and glutamate dehydrogenase in rat brain homogenate

Aluminum is a neurotoxic agent for animals and humans that has been implicated as an etiological factor in several neurodegenerative diseases and as a destabilizer of cell membranes. Due to its high reactivity, Al3+ is able to interfere with several biological functions, including enzymatic activities in key metabolic pathways. In this paper we report that, among the enzymes that constitute the Krebs cycle, only two are activated by aluminum: alpha-ketoglutarate dehydrogenase and succinate dehydrogenase. In contrast, aconitase, shows decreased activity in the presence of the metal ion. Al3+ also inhibits glutamate dehydrogenase, an allosteric enzyme that is closely linked to the Krebs cycle. A possible correlation between aluminum, the Krebs cycle and aging processes is discussed.

Nitric oxide modulates the activity of tobacco aconitase

Recent evidence suggests an important role for nitric oxide (NO) signaling in plant-pathogen interactions. Additional elucidation of the role of NO in plants will require identification of NO targets. Since aconitases are major NO targets in animals, we examined the effect of NO on tobacco (Nicotiana tabacum) aconitase. The tobacco aconitases, like their animal counterparts, were inhibited by NO donors. The cytosolic aconitase in animals, in addition to being a key redox and NO sensor, is converted by NO into an mRNA binding protein (IRP, or iron-regulatory protein) that regulates iron homeostasis. A tobacco cytosolic aconitase gene (NtACO1) whose deduced amino acid sequence shared 61% identity and 76% similarity with the human IRP-1 was cloned. Furthermore, residues involved in mRNA binding by IRP-1 were conserved in NtACO1. These results reveal additional similarities between the NO signaling mechanisms used by plants and animals.

A developmentally regulated aconitase related to iron-regulatory protein-1 is localized in the cytoplasm and in the mitochondrion of Trypanosoma brucei

Mitochondrial energy metabolism and Krebs cycle activities are developmentally regulated in the life cycle of the protozoan parasite Trypanosoma brucei. Here we report cloning of a T. brucei aconitase gene that is closely related to mammalian iron-regulatory protein 1 (IRP-1) and plant aconitases. Kinetic analysis of purified recombinant TbACO expressed in Escherichia coli resulted in a K(m) (isocitrate) of 3 +/- 0.4 mM, similar to aconitases of other organisms. This was unexpected since an arginine conserved in the aconitase protein family and crucial for substrate positioning in the catalytic center and for activity of pig mitochondrial aconitase (Zheng, L., Kennedy, M. C., Beinert, H., and Zalkin, H. (1992) J. Biol. Chem. 267, 7895-7903) is substituted by leucine in the TbACO sequence. Expression of the 98-kDa TbACO was shown to be lowest in the slender bloodstream stage of the parasite, 8-fold elevated in the stumpy stage, and increased a further 4-fold in the procyclic stage. The differential expression of TbACO protein contrasted with only minor changes in TbACO mRNA, indicating translational or post-translational mechanisms of regulation. Whereas animal cells express two distinct compartmentalized aconitases, mitochondrial aconitase and cytoplasmic aconitase/IRP-1, TbACO accounts for total aconitase activity in trypanosomes. By cell fractionation and immunofluorescence microscopy, we show that native as well as a transfected epitope-tagged TbACO localizes in both the mitochondrion (30%) and in the cytoplasm (70%). Together with phylogenetic reconstructions of the aconitase family, this suggests that animal IRPs have evolved from a multicompartmentalized ancestral aconitase. The possible functions of a cytoplasmic aconitase in trypanosomes are discussed.