The manganese-responsive repressor Mur of Rhizobium leguminosarum is a member of the Fur-superfamily that recognizes an unusual operator sequence

Genomics and transcriptomics insights into luteolin effects on the beta-rhizobial strain Cupriavidus necator UYPR2.512

Cupriavidus necator UYPR2.512 is a rhizobial strain that belongs to the Beta-subclass of proteobacteria, able to establish successful symbiosis with Mimosoid legumes. The initial steps of rhizobium-legumes symbioses involve the reciprocal recognition by chemical signals, being luteolin one of the molecules involved. However, there is a lack of information on the effect of luteolin in beta-rhizobia. In this work, we used long-read sequencing to complete the genome of UYPR2.512 providing evidence for the existence of four closed circular replicons. We used an RNA-Seq approach to analyse the response of UYPR2.512 to luteolin. One hundred and forty-five genes were differentially expressed, with similar numbers of downregulated and upregulated genes. Most repressed genes were mapped to the main chromosome, while the upregulated genes were overrepresented among pCne512e, containing the symbiotic genes. Induced genes included the nod operon and genes implicated in exopolysaccharides and flagellar biosynthesis. We identified many genes involved in iron, copper and other heavy metals metabolism. Among repressed genes, we identified genes involved in basal carbon and nitrogen metabolism. Our results suggest that in response to luteolin, C. necator strain UYPR2.512 reshapes its metabolism in order to be prepared for the forthcoming symbiotic interaction.

Structural basis for zinc-induced activation of a zinc uptake transcriptional regulator

The zinc uptake regulator (Zur) is a member of the Fur (ferric uptake regulator) family transcriptional regulators that plays important roles in zinc homeostasis and virulence of bacteria. Upon zinc perception, Zur binds to the promoters of zinc responsive genes and controls their transcription. However, the mechanism underlying zinc-mediated Zur activation remains unclear. Here we report a 2.2-Å crystal structure of apo Zur from the phytopathogen Xanthomonas campestris pv. campestris (XcZur), which reveals the molecular mechanism that XcZur exists in a closed inactive state before regulatory zinc binding. Subsequently, we present a 1.9-Å crystal structure of holo XcZur, which, by contrast, adopts an open state that has enough capacity to bind DNA. Structural comparison and hydrogen deuterium exchange mass spectrometry (HDX-MS) analyses uncover that binding of a zinc atom in the regulatory site, formed by the hinge region, the dimerization domain and the DNA binding domain, drives a closed-to-open conformational change that is essential for XcZur activation. Moreover, key residues responsible for DNA recognition are identified by site-directed mutagenesis. This work provides important insights into zinc-induced XcZur activation and valuable discussions on the mechanism of DNA recognition.

Fur-like proteins: Beyond the ferric uptake regulator (Fur) paralog

Proteins belonging to the FUR (ferric uptake regulator) family are the cornerstone of metalloregulation in most prokaryotes. Although numerous reviews have been devoted to these proteins, these reports are mainly focused on the Fur paralog that gives name to the family. In the last years, the increasing knowledge on the other, less ubiquitous members of this family has evidenced their importance in bacterial metabolism. As the Fur paralog, the major regulator of iron homeostasis, Zur, Irr, BosR and PerR are tightly related to stress defenses and host-pathogen interaction being in many cases essential for virulence. Furthermore, the Nur and Mur paralogs largely contribute to control nickel and manganese homeostasis, which are cofactors of pivotal proteins for host colonization and bacterial redox homeostasis. The present review highlights the main features of FUR proteins that differ to the canonical Fur paralog either in the coregulatory metal, such as Zur, Nur and Mur, or in the action mechanism to control target genes, such as PerR, Irr and BosR.

Transition metal transporters in rhizobia: tuning the inorganic micronutrient requirements to different living styles

A group of bacteria known as rhizobia are key players in symbiotic nitrogen fixation (SNF) in partnership with legumes. After a molecular exchange, the bacteria end surrounded by a plant membrane forming symbiosomes, organelle-like structures, where they differentiate to bacteroids and fix nitrogen. This symbiotic process is highly dependent on dynamic nutrient exchanges between the partners. Among these are transition metals (TM) participating as inorganic and organic cofactors of fundamental enzymes. While the understanding of how plant transporters facilitate TMs to the very near environment of the bacteroid is expanding, our knowledge on how bacteroid transporters integrate to TM homeostasis mechanisms in the plant host is still limited. This is significantly relevant considering the low solubility and scarcity of TMs in soils, and the in crescendo gradient of TM bioavailability rhizobia faces during the infection and bacteroid differentiation processes. In the present work, we review the main metal transporter families found in rhizobia, their role in free-living conditions and, when known, in symbiosis. We focus on discussing those transporters which could play a significant role in TM-dependent biochemical and physiological processes in the bacteroid, thus paving the way towards an optimized SNF.

Manganese transport is essential for N2 -fixation by Rhizobium leguminosarum in bacteroids from galegoid but not phaseoloid nodules

Rhizobium leguminosarum has two high-affinity Mn2+ transport systems encoded by sitABCD and mntH. In symbiosis, sitABCD and mntH were expressed throughout nodules and also strongly induced in Mn2+ -limited cultures of free-living cells. Growth of a sitA mntH double mutant was severely reduced under Mn2+ limitation and sitA and mntH single mutants were more sensitive to oxidative stress. The double sitA mntH mutant of R. leguminosarum was unable to fix nitrogen (Fix- ) with legumes belonging to the galegoid clade (Pisum sativum, Vicia faba and Vicia hirsuta). The presence of infection thread-like structures and sparsely-packed plant cells in nodules suggest that bacteroid development was blocked, either at a late stage of infection thread progression or during bacteroid-release. In contrast, a double sitA mntH mutant was Fix+ on common bean (Phaseoli vulgaris), a member of the phaseoloid clade of legumes, indicating a host-specific symbiotic requirement for Mn2+ transport.

Magnesium-dependent processes are targets of bacterial manganese toxicity

A Bradyrhizobium japonicum mutant defective in the gene encoding the high-affinity Mn(2+) transporter MntH has a severe growth phenotype under manganese limitation. Here, we isolated suppressor mutants of an mntH strain that grew under manganese limitation, and activities of high-affinity Mn(2+) transport and Mn(2+) -dependent enzymes were partially rescued. The suppressor strains harbour gain-of-function mutations in the gene encoding the Mg(2+) channel MgtE. The MgtE variants likely allow Mn(2+) entry via loss of a gating mechanism that normally holds the transporter in the closed state when cellular Mg(2+) levels are high. Both MgtE-dependent and MgtE-independent suppressor phenotypes were recapitulated by magnesium-limited growth of the mntH strain. Growth studies of wild-type cells suggest that manganese is toxic to cells when environmental magnesium is low. Moreover, extracellular manganese and magnesium levels were manipulated to inhibit growth without substantially altering the intracellular content of either metal, implying that manganese toxicity depends on its cellular distribution rather than the absolute concentration. Mg(2+) -dependent enzyme activities were found to be inhibited or stimulated by Mn(2+) . We conclude that Mn(2+) can occupy Mg(2+) binding sites in cells, and suggest that Mg(2+) -dependent processes are targets of manganese toxicity.

The FUR (ferric uptake regulator) superfamily: diversity and versatility of key transcriptional regulators

Control of metal homeostasis is essential for life in all kingdoms. In most prokaryotic organisms the FUR (ferric uptake regulator) family of transcriptional regulators is involved in the regulation of iron and zinc metabolism through control by Fur and Zur proteins. A third member of this family, the peroxide-stress response PerR, is present in most Gram-positives, establishing a tight functional interaction with the global regulator Fur. These proteins play a pivotal role for microbial survival under adverse conditions and in the expression of virulence in most pathogens. In this paper we present the current state of the art in the knowledge of the FUR family, including those members only present in more reduced numbers of bacteria, namely Mur, Nur and Irr. The huge amount of work done in the two last decades shows that FUR proteins present considerable diversity in their regulatory mechanisms and interesting structural differences. However, much work needs to be done to obtain a more complete picture of this family, especially in connection with the roles of some members as gas and redox sensors as well as to fully characterize their participation in bacterial adaptative responses.

Transcriptional regulation by Ferric Uptake Regulator (Fur) in pathogenic bacteria

In the ancient anaerobic environment, ferrous iron (Fe²⁺) was one of the first metal cofactors. Oxygenation of the ancient world challenged bacteria to acquire the insoluble ferric iron (Fe³⁺) and later to defend against reactive oxygen species (ROS) generated by the Fenton chemistry. To acquire Fe³⁺, bacteria produce low-molecular weight compounds, known as siderophores, which have extremely high affinity for Fe³⁺. However, during infection the host restricts iron from pathogens by producing iron- and siderophore-chelating proteins, by exporting iron from intracellular pathogen-containing compartments, and by limiting absorption of dietary iron. Ferric Uptake Regulator (Fur) is a transcription factor which utilizes Fe²⁺ as a corepressor and represses siderophore synthesis in pathogens. Fur, directly or indirectly, controls expression of enzymes that protect against ROS damage. Thus, the challenges of iron homeostasis and defense against ROS are addressed via Fur. Although the role of Fur as a repressor is well-documented, emerging evidence demonstrates that Fur can function as an activator. Fur activation can occur through three distinct mechanisms (1) indirectly via small RNAs, (2) binding at cis regulatory elements that enhance recruitment of the RNA polymerase holoenzyme (RNAP), and (3) functioning as an antirepressor by removing or blocking DNA binding of a repressor of transcription. In addition, Fur homologs control defense against peroxide stress (PerR) and control uptake of other metals such as zinc (Zur) and manganese (Mur) in pathogenic bacteria. Fur family members are important for virulence within bacterial pathogens since mutants of fur, perR, or zur exhibit reduced virulence within numerous animal and plant models of infection. This review focuses on the breadth of Fur regulation in pathogenic bacteria.

A new approach to studying ion uptake by actinomycetes

A streptomycete that had the ability to avidly sequester iron via siderophores was previously isolated from environmental soil samples. The chelating agent expressed by this organism is confirmed by HPLC as desferrioxamine E. Although the traditional chromo azuerol sulphate (CAS) assay for detection of siderophores is based upon the chelation of iron we were interested to examine the relationship of these iron-capturing molecules with other ions. Consequently, a new approach was employed that enabled the assessment of the affinity of the siderophore moieties for other ions by adapting the CAS assay. The present study reveals that the isolate produced a siderophore that was capable of sequestering a range of ions including Mn, Co, Cd, Ni, Al, Li, Cu, Zn and Mg. On the basis of the assay described it would appear that the organism sequesters copper more readily than iron. This raises an age-old debate surrounding the replacement of copper as a fundamentally essential element with iron as a consequence of the evolution of the di-oxygen environment.

Manganese uptake in marine bacteria; the novel MntX transporter is widespread in Roseobacters, Vibrios, Alteromonadales and the SAR11 and SAR116 clades

We showed that two very different manganese transporters occur in various important genera of marine bacteria. The ABC transporter encoded by sitABCD of the model Roseobacter-clade bacterium Ruegeria pomeroyi DSS-3 is required for Mn(2+) import and was repressed by the Mur (Manganese uptake regulator) transcriptional regulator in Mn-replete media. Most genome-sequenced Roseobacter strains contain SitABCD, which are in at least two sub-groups, judged by their amino-acid sequences. However, a few Roseobacters, for example, Roseovarius nubinhibens, lack sitABCD, but these contain another gene, mntX, which encodes a predicted inner membrane polypeptide and is preceded by cis-acting Mur-responsive MRS sequences. It was confirmed directly that mntX of Roseovarius nubinhibens encodes a manganese transporter that was required for growth in Mn-depleted media and that its expression was repressed by Mur in Mn-replete conditions. MntX homologues occur in the deduced proteomes of several bacterial species. Strikingly, all of these live in marine habitats, but are in distantly related taxonomic groups, in the γ- and α-proteobacteria. Notably, MntX was prevalent in nearly all strains of Vibrionales, including the important pathogen, Vibrio cholerae. It also occurs in a strain of the hugely abundant Candidatus Pelagibacter (SAR11), and in another populous marine bacterium, Candidatus Puniceispirillum marinum (SAR116). Consistent with this, MntX was abundant in marine bacterial metagenomes, with one sub-type occurring in an as-yet unknown bacterial clade.

Manganese is required for oxidative metabolism in unstressed Bradyrhizobium japonicum cells

Recent studies of Mn(2+) transport mutants indicate that manganese is essential for unstressed growth in some bacterial species, but is required primarily for induced stress responses in others. A Bradyrhizobium japonicum mutant defective in the high-affinity Mn(2+) transporter gene mntH has a severe growth phenotype under manganese limitation, suggesting a requirement for the metal under unstressed growth. Here, we found that activities of superoxide dismutase and the glycolytic enzyme pyruvate kinase were deficient in an mntH strain grown under manganese limitation. We identified pykM as the only pyruvate kinase-encoding gene based on deficiency in activity of a pykM mutant, rescue of the growth phenotype with pyruvate, and pyruvate kinase activity of purified recombinant PykM. PykM is unusual in that it required Mn(2+) rather than Mg(2+) for high activity, and that neither fructose-1,6-bisphosphate nor AMP was a positive allosteric effector. The mntH-dependent superoxide dismutase is encoded by sodM, the only expressed superoxide dismutase-encoding gene under unstressed growth conditions. An mntH mutant grew more slowly on pyruvate under manganese-limited conditions than did a pykM sodM double mutant, implying additional manganese-dependent processes. The findings implicate roles for manganese in key steps in unstressed oxidative metabolism in B. japonicum.

Mur regulates the gene encoding the manganese transporter MntH in Brucella abortus 2308

MntH is the only high-affinity manganese transporter identified in Brucella. A previous study showed that MntH is required for the wild-type virulence of Brucella abortus 2308 in mice (Anderson ES, et al., Infect. Immun. 77:3466-3474, 2009) and indicated that the mntH gene is regulated in a manganese-responsive manner in this strain by a Mur homolog. In the study presented here, the transcriptional start site for mntH in B. abortus 2308 was determined by primer extension analysis. Specific interactions between Mur and the mntH promoter region were demonstrated in an electrophoretic mobility shift assay (EMSA), and a Mur binding site was identified in the -55 to -24 region of the mntH promoter by DNase I footprint analysis. The specificity of the interaction of Mur with the putative Mur box was further evaluated by EMSA employing oligonucleotides in which the consensus nucleotides in this region were substituted. These studies not only confirm a direct role for Mur in the Mn-responsive regulation of mntH expression in Brucella abortus 2308 but also identify the cis-acting elements upstream of mntH that are responsible for this regulation.

Bacterial outer membrane channel for divalent metal ion acquisition

The prevailing model of bacterial membrane function predicts that the outer membrane is permeable to most small solutes because of pores with limited selectivity based primarily on size. Here, we identified mnoP in the Gram-negative bacterium Bradyrhizobium japonicum as a gene coregulated with the inner membrane Mn(2+) transporter gene mntH. MnoP is an outer membrane protein expressed specifically under manganese limitation. MnoP acts as a channel to facilitate the tranlocation of Mn(2+), but not Co(2+) or Cu(2+), into reconstituted proteoliposomes. An mnoP mutant is defective in high-affinity Mn(2+) transport into cells and has a severe growth phenotype under manganese limitation. We suggest that the outer membrane is a barrier to divalent metal ions that requires a selective channel to meet the nutritional needs of the cell.

Heme binding to the second, lower-affinity site of the global iron regulator Irr from Rhizobium leguminosarum promotes oligomerization

The iron responsive regulator Irr is found in a wide range of α-proteobacteria, where it regulates many genes in response to the essential but toxic metal iron. Unlike Fur, the transcriptional regulator that is used for iron homeostasis by almost all other bacterial lineages, Irr does not sense Fe(2+) directly, but, rather, interacts with a physiologically important form of iron, namely heme. Recent studies of Irr from the N(2)-fixing symbiont Rhizobium leguminosarum (Irr(Rl)) showed that it binds heme with submicromolar affinity at a His-Xxx-His (HxH) motif. This caused the protein to dissociate from its cognate DNA regulatory iron control element box sequences, thus allowing expression of its target genes under iron-replete conditions. In the present study, we report new insights into the mechanisms and consequences of heme binding to Irr. In addition to the HxH motif, Irr binds heme at a second, lower-affinity site. Spectroscopic studies of wild-type Irr and His variants show that His46 and probably His66 are involved in coordinating heme in a low-spin state at this second site. By contrast to the well-studied Irr from Bradyrhizobium japonicum, neither heme site of Irr(Rl) stabilizes ferrous heme. Furthermore, we show that heme-free Irr(Rl) exists as a mixture of dimeric and larger, likely hexameric, forms and that heme binding promotes Irr(Rl) oligomerization. Bioanalytical studies of Irr(Rl) variants showed that this property is not dependent on the HxH motif but is associated with heme binding at the second site.

STRUCTURED DIGITAL ABSTRACT

• Irr binds to irr by molecular sieving (View Interaction 1, 2) • Irr binds to irr by cosedimentation in solution (View interaction).

Transcriptional control of the Bradyrhizobium japonicum irr gene requires repression by fur and Antirepression by Irr

Bradyrhizobium japonicum Fur mediates manganese-responsive transcriptional control of the mntH gene independently of iron, but it also has been implicated in iron-dependent regulation of the irr gene. Thus, we sought to address the apparent discrepancy in Fur responsiveness to metals. Irr is a transcriptional regulator found in iron-limited cells. Here, we show that irr gene mRNA was regulated by both iron and manganese, and repression occurred only in the presence of both metals. Under these conditions, Fur occupied the irr promoter in vivo in the parent strain, and irr mRNA expression was derepressed in a fur mutant. Under low iron conditions, the irr promoter was occupied by Irr, but not by Fur, and control by manganese was lost. Fur occupancy of the irr promoter was dependent on manganese, but not iron, in an irr mutant, suggesting that Irr normally interferes with Fur binding. Correspondingly, regulation of irr mRNA was dependent only on manganese in the irr strain. The Irr binding site within the irr promoter partially overlaps the Fur binding site. DNase I footprinting analysis showed that Irr interfered with Fur binding in vitro. In addition, Fur repression of transcription from the irr promoter in vitro was relieved by Irr. We conclude that Fur mediates manganese-dependent repression of irr transcription and that Irr acts as an antirepressor under iron limitation by preventing Fur binding to the promoter.

Roles of Agrobacterium tumefaciens RirA in iron regulation, oxidative stress response, and virulence

The analysis of genetics and physiological functions of Agrobacterium tumefaciens RirA (rhizobial iron regulator) has shown that it is a transcription regulator and a repressor of iron uptake systems. The rirA mutant strain (NTLrirA) overproduced siderophores and exhibited a highly constitutive expression of genes involved in iron uptake (fhuA, irp6A, and fbpA) compared to that of the wild-type strain (NTL4). The deregulation in the iron control of iron uptake in NTLrirA led to iron overload in the cell, which was supported by the observation that the NTLrirA mutant was more sensitive than wild-type NTL4 to an iron-activated antibiotic, streptonigrin. The NTLrirA mutant was more sensitive than the parental strain to oxidants, including hydrogen peroxide, organic hydroperoxide, and a superoxide generator, menadione. However, the addition of an iron chelator, 2,2'-dipyridyl, reversed the mutant hypersensitivity to H(2)O(2) and organic hydroperoxide, indicating the role of iron in peroxide toxicity. Meanwhile, the reduced level of superoxide dismutase (SodBIII) was partly responsible for the menadione-sensitive phenotype of the NTLrirA mutant. The NTLrirA mutant showed a defect in tumorigenesis on tobacco leaves, which likely resulted from the increased sensitivity of NTLrirA to oxidants and the decreased ability of NTLrirA to induce virulence genes (virB and virE). These data demonstrated that RirA is important for A. tumefaciens during plant-pathogen interactions.

Zinc-handling in cyanobacteria: an update

Zinc is a constituent of all six classes of enzymes, plays important roles in gene regulation, and is thought to be essential for most organisms. Despite initial discoveries of cyanobacterial metallothioneins, zinc efflux pumps and uptake systems, and zinc sensors, our knowledge of the zinc requirements, uptake, and detoxification mechanisms of cyanobacteria is still limited. Although cyanobacteria occupy extremely diverse habitats, most available data pertains to freshwater species, and almost no studies of zinc-handling mechanisms have been conducted in marine species. The current report highlights what is known about zinc homeostasis in cyanobacteria, and presents an analysis of the 40 sequenced cyanobacterial genomes.

Genomic insights into Mn(II) oxidation by the marine alphaproteobacterium Aurantimonas sp. strain SI85-9A1

Microbial Mn(II) oxidation has important biogeochemical consequences in marine, freshwater, and terrestrial environments, but many aspects of the physiology and biochemistry of this process remain obscure. Here, we report genomic insights into Mn(II) oxidation by the marine alphaproteobacterium Aurantimonas sp. strain SI85-9A1, isolated from the oxic/anoxic interface of a stratified fjord. The SI85-9A1 genome harbors the genetic potential for metabolic versatility, with genes for organoheterotrophy, methylotrophy, oxidation of sulfur and carbon monoxide, the ability to grow over a wide range of O(2) concentrations (including microaerobic conditions), and the complete Calvin cycle for carbon fixation. Although no growth could be detected under autotrophic conditions with Mn(II) as the sole electron donor, cultures of SI85-9A1 grown on glycerol are dramatically stimulated by addition of Mn(II), suggesting an energetic benefit from Mn(II) oxidation. A putative Mn(II) oxidase is encoded by duplicated multicopper oxidase genes that have a complex evolutionary history including multiple gene duplication, loss, and ancient horizontal transfer events. The Mn(II) oxidase was most abundant in the extracellular fraction, where it cooccurs with a putative hemolysin-type Ca(2+)-binding peroxidase. Regulatory elements governing the cellular response to Fe and Mn concentration were identified, and 39 targets of these regulators were detected. The putative Mn(II) oxidase genes were not among the predicted targets, indicating that regulation of Mn(II) oxidation is controlled by other factors yet to be identified. Overall, our results provide novel insights into the physiology and biochemistry of Mn(II) oxidation and reveal a genome specialized for life at the oxic/anoxic interface.

Agrobacterium tumefaciens fur has important physiological roles in iron and manganese homeostasis, the oxidative stress response, and full virulence

In Agrobacterium tumefaciens, the balance between acquiring enough iron and avoiding iron-induced toxicity is regulated in part by Fur (ferric uptake regulator). A fur mutant was constructed to address the physiological role of the regulator. Atypically, the mutant did not show alterations in the levels of siderophore biosynthesis and the expression of iron transport genes. However, the fur mutant was more sensitive than the wild type to an iron chelator, 2,2'-dipyridyl, and was also more resistant to an iron-activated antibiotic, streptonigrin, suggesting that Fur has a role in regulating iron concentrations. A. tumefaciens sitA, the periplasmic binding protein of a putative ABC-type iron and manganese transport system (sitABCD), was strongly repressed by Mn(2+) and, to a lesser extent, by Fe(2+), and this regulation was Fur dependent. Moreover, the fur mutant was more sensitive to manganese than the wild type. This was consistent with the fact that the fur mutant showed constitutive up-expression of the manganese uptake sit operon. Fur(At) showed a regulatory role under iron-limiting conditions. Furthermore, Fur has a role in determining oxidative resistance levels. The fur mutant was hypersensitive to hydrogen peroxide and had reduced catalase activity. The virulence assay showed that the fur mutant had a reduced ability to cause tumors on tobacco leaves compared to wild-type NTL4.

Sinorhizobium meliloti fur-like (Mur) protein binds a fur box-like sequence present in the mntA promoter in a manganese-responsive manner

In Sinorhizobium meliloti, the Mur(Sm) protein, a homologue of the ferric uptake regulator (Fur), mediates manganese-dependent regulation of the MntABCD manganese uptake system. In this study, we analyzed Mur(Sm) binding to the promoter region of the S. meliloti mntA gene. We demonstrated that Mur(Sm) protein binds with high affinity to the promoter region of mntA gene in a manganese-responsive manner. Moreover, the results presented here indicate that two monomers, or one dimer, of Mur(Sm) binds the DNA. The binding region was identified by DNase I footprinting analysis and covers a region of about 30 bp long that contains a palindromic sequence. The Mur(Sm) binding site, present in the mntA promoter region, is similar to a Fur box; however, manganese-activated Mur(Sm) binds a canonical Fur box with very low affinity. Furthermore, the data obtained indicate that Mur(Sm) responds to physiological concentrations of manganese.

Living without Fur: the subtlety and complexity of iron-responsive gene regulation in the symbiotic bacterium Rhizobium and other alpha-proteobacteria

The alpha-proteobacteria include several important genera, including the symbiotic N(2)-fixing "rhizobia", the plant pathogen Agrobacterium, the mammalian pathogens Brucella, Bartonella as well as many others that are of environmental or other interest--including Rhodobacter, Caulobacter and the hugely abundant marine genus Pelagibacter. Only a few species--mainly different members of the rhizobia--have been analyzed directly for their ability to use and to respond to iron. These studies, however, have shown that at least some of the "alphas" differ fundamentally in the ways in which they regulate their genes in response to Fe availability. In this paper, we build on our own work on Rhizobium leguminosarum (the symbiont of peas, beans and clovers) and on Bradyrhizobium japonicum, which nodulates soybeans and which has been studied in Buffalo and Zürich. In the former species, the predominant Fe-responsive regulator is not Fur, but RirA, a member of the Rrf2 protein family and which likely has an FeS cluster cofactor. In addition, there are several R. leguminosarum genes that are expressed at higher levels in Fe-replete conditions and at least some of these are regulated by Irr, a member of the Fur superfamily and which has the unusual property of being degraded by the presence of heme. In silico analyses of the genome sequences of other bacteria indicate that Irr occurs in all members of the Rhizobiales and the Rhodobacterales and that RirA is found in all but one branch of these two lineages, the exception being the clade that includes B. japonicum. Nearly all the Rhizobiales and the Rhodobacterales contain a gene whose product resembles bona fide Fur. However, direct genetic studies show that in most of the Rhizobiales and in the Rhodobacterales it is a "Mur" (a manganese responsive repressor of a small number of genes involved in Mn uptake) or, in Bradyrhizobium, it recognizes the operator sequences of only a few genes that are involved in Fe metabolism. We propose that the Rhizobiales and the Rhodobacterales have relegated Fur to a far more minor role than in (say) E. coli and that they employ Irr and, in the Rhizobiales, RirA as their global Fe-responsive transcriptional regulators. In contrast to the direct interaction between Fe2+ and conventional Fur, we suggest that these bacteria sense Fe more indirectly as functions of the intracellular concentrations of FeS clusters and of heme. Thus, their "iron-omes" may be more accurately linked to the real-time needs for the metal and not just to its absolute concentration in the environment.

Functional specialization within the Fur family of metalloregulators

The ferric uptake regulator (Fur) protein, as originally described in Escherichia coli, is an iron-sensing repressor that controls the expression of genes for siderophore biosynthesis and iron transport. Although Fur is commonly thought of as a metal-dependent repressor, Fur also activates the expression of many genes by either indirect or direct mechanisms. In the best studied model systems, Fur functions as a global regulator of iron homeostasis controlling both the induction of iron uptake functions (under iron limitation) and the expression of iron storage proteins and iron-utilizing enzymes (under iron sufficiency). We now appreciate that there is a tremendous diversity in metal selectivity and biological function within the Fur family which includes sensors of iron (Fur), zinc (Zur), manganese (Mur), and nickel (Nur). Despite numerous studies, the mechanism of metal ion sensing by Fur family proteins is still controversial. Other family members use metal catalyzed oxidation reactions to sense peroxide-stress (PerR) or the availability of heme (Irr).

Computational reconstruction of iron- and manganese-responsive transcriptional networks in alpha-proteobacteria

We used comparative genomics to investigate the distribution of conserved DNA-binding motifs in the regulatory regions of genes involved in iron and manganese homeostasis in alpha-proteobacteria. Combined with other computational approaches, this allowed us to reconstruct the metal regulatory network in more than three dozen species with available genome sequences. We identified several classes of cis-acting regulatory DNA motifs (Irr-boxes or ICEs, RirA-boxes, Iron-Rhodo-boxes, Fur-alpha-boxes, Mur-box or MRS, MntR-box, and IscR-boxes) in regulatory regions of various genes involved in iron and manganese uptake, Fe-S and heme biosynthesis, iron storage, and usage. Despite the different nature of the iron regulons in selected lineages of alpha-proteobacteria, the overall regulatory network is consistent with, and confirmed by, many experimental observations. This study expands the range of genes involved in iron homeostasis and demonstrates considerable interconnection between iron-responsive regulatory systems. The detailed comparative and phylogenetic analyses of the regulatory systems allowed us to propose a theory about the possible evolution of Fe and Mn regulons in alpha-proteobacteria. The main evolutionary event likely occurred in the common ancestor of the Rhizobiales and Rhodobacterales, where the Fur protein switched to regulating manganese transporters (and hence Fur had become Mur). In these lineages, the role of global iron homeostasis was taken by RirA and Irr, two transcriptional regulators that act by sensing the physiological consequence of the metal availability rather than its concentration per se, and thus provide for more flexible regulation.

Beyond the Fur paradigm: iron-controlled gene expression in rhizobia

Iron is critical for bacterial growth, but problems arise from the toxicity of excess iron; thus, iron uptake is subject to tight control. The most widely found and best-studied iron-responsive regulator in Gram-negative bacteria is the ferric uptake regulator Fur. In recent years, however, it has become apparent that iron regulation in rhizobia differs from that in many other bacteria. New regulators (RirA, Irr, Mur) were identified which appear to mediate functions that in other bacteria are accomplished by Fur. Even though some of them belong to the Fur family, they exhibit properties that clearly separate them from genuine Fur proteins. This article surveys the principal mechanisms of iron acquisition and uptake in rhizobia, and puts particular emphasis on recent findings on transcriptional regulators and their means to sense the cellular iron status and to regulate gene expression. In this context, we point out differences and similarities with regard to the operators, regulons and structure of the discussed iron regulatory proteins.

The Rhizobium leguminosarum regulator IrrA affects the transcription of a wide range of genes in response to Fe availability

We show that an unusual transcriptional regulator, called IrrA, regulates many genes in the symbiotic N2-fixing bacterium Rhizobium leguminosarum in response to iron availability. Several operons in R. leguminosarum are expressed at lower levels in cells grown in Fe-depleted compared to Fe-replete medium. These include hemA1, which encodes the haem biosynthesis enzyme amino-levulinic acid synthase; sufS2BCDS1XA, which specify enzymes for FeS cluster synthesis; rirA, a global, Fe-responsive transcriptional repressor; RL0400, which likely encodes an unusual FeS cluster scaffold; and the possible ferri-siderophore ABC transporter rrp1. Reduced expression in Fe-depleted medium was effected by IrrA, a member of the Fur super-family, which in Bradyrhizobium, the symbiont of soybeans, and in the mammalian pathogen Brucella, is unstable in Fe-replete conditions, due to an interaction with haem. The R. leguminosarum IrrA likely interacts with ICE (iron-control element) motifs, conserved sequences near the promoters of its target genes. The rirA, sufS2BCDS1XA and rrp1 genes are also known to be regulated by RirA, which represses their expression in Fe-replete medium. We present a possible model for iron-responsive gene regulation in Rhizobium, in which the IrrA and RirA regulators, working in parallel, respond to the intracellular availability of haem and, possibly, of FeS clusters respectively. Thus, these regulators may sense the physiological consequences of extraneous Fe concentrations, rather than the concentration of Fe per se, as happens in those bacteria (e.g. Escherichia coli) in which the ferric uptake regulator Fur is the global Fe-responsive gene regulator.