A glutamine-amidotransferase-like protein modulates FixT anti-kinase activity in Sinorhizobium meliloti

Feedback Control of a Two-Component Signaling System by an Fe-S-Binding Receiver Domain

Two-component signaling systems (TCSs) function to detect environmental cues and transduce this information into a change in transcription. In its simplest form, TCS-dependent regulation of transcription entails phosphoryl-transfer from a sensory histidine kinase to its cognate DNA-binding receiver protein. However, in certain cases, auxiliary proteins may modulate TCSs in response to secondary environmental cues. Caulobacter crescentus FixT is one such auxiliary regulator. FixT is composed of a single receiver domain and functions as a feedback inhibitor of the FixL-FixJ (FixLJ) TCS, which regulates the transcription of genes involved in adaptation to microaerobiosis. We sought to define the impact of fixT on Caulobacter cell physiology and to understand the molecular mechanism by which FixT represses FixLJ signaling. fixT deletion results in excess production of porphyrins and premature entry into stationary phase, demonstrating the importance of feedback inhibition of the FixLJ signaling system. Although FixT is a receiver domain, it does not affect dephosphorylation of the oxygen sensor kinase FixL or phosphoryl-transfer from FixL to its cognate receiver FixJ. Rather, FixT represses FixLJ signaling by inhibiting the FixL autophosphorylation reaction. We have further identified a 4-cysteine motif in Caulobacter FixT that binds an Fe-S cluster and protects the protein from degradation by the Lon protease. Our data support a model in which the oxidation of this Fe-S cluster promotes the degradation of FixT in vivo This proteolytic mechanism facilitates clearance of the FixT feedback inhibitor from the cell under normoxia and resets the FixLJ system for a future microaerobic signaling event.IMPORTANCE Two-component signal transduction systems (TCSs) are broadly conserved in the bacterial kingdom and generally contain two molecular components, a sensor histidine kinase and a receiver protein. Sensor histidine kinases alter their phosphorylation state in direct response to a physical or chemical cue, whereas receiver proteins "receive" the phosphoryl group from the kinase to regulate a change in cell physiology. We have discovered that a single-domain receiver protein, FixT, binds an Fe-S cluster and controls Caulobacter heme homeostasis though its function as a negative-feedback regulator of the oxygen sensor kinase FixL. We provide evidence that the Fe-S cluster protects FixT from Lon-dependent proteolysis in the cell and endows FixT with the ability to function as a second, autonomous oxygen/redox sensor in the FixL-FixJ signaling pathway. This study introduces a novel mechanism of regulated TCS feedback control by an Fe-S-binding receiver domain.

Key roles of microsymbiont amino acid metabolism in rhizobia-legume interactions

Rhizobia are bacteria in the α-proteobacterial genera Rhizobium, Sinorhizobium, Mesorhizobium, Azorhizobium and Bradyrhizobium that reduce (fix) atmospheric nitrogen in symbiotic association with a compatible host plant. In free-living and/or symbiotically associated rhizobia, amino acids may, in addition to their incorporation into proteins, serve as carbon, nitrogen or sulfur sources, signals of cellular nitrogen status and precursors of important metabolites. Depending on the rhizobia-host plant combination, microsymbiont amino acid metabolism (biosynthesis, transport and/or degradation) is often crucial to the establishment and maintenance of an effective nitrogen-fixing symbiosis and is intimately interconnected with the metabolism of the plant. This review summarizes past findings and current research directions in rhizobial amino acid metabolism and evaluates the genetic, biochemical and genome expression studies from which these are derived. Specific sections deal with the regulation of rhizobial amino acid metabolism, amino acid transport, and finally the symbiotic roles of individual amino acids in different plant-rhizobia combinations.

Identification and characterization of a NaCl-responsive genetic locus involved in survival during desiccation in Sinorhizobium meliloti

The Rhizobiaceae are a bacterial family of enormous agricultural importance due to the ability of its members to fix atmospheric nitrogen in an intimate relationship with plants. Their survival as naturally occurring soil bacteria in agricultural soils as well as popular seed inocula is affected directly by drought and salinity. Survival after desiccation in the presence of NaCl is enabled by underlying genetic mechanisms in the model organism Sinorhizobium meliloti 1021. Since salt stress parallels a loss in water activity, the identification of NaCl-responsive loci may identify loci involved in survival during desiccation. This approach enabled identification of the loci asnO and ngg by their reduced ability to grow on increased NaCl concentrations, likely due to their inability to produce the osmoprotectant N-acetylglutaminylglutamine (NAGGN). In addition, the mutant harboring ngg::Tn5luxAB was affected in its ability to survive desiccation and responded to osmotic stress. The desiccation sensitivity may have been due to secondary functions of Ngg (N-acetylglutaminylglutamine synthetase)-like cell wall metabolism as suggested by the presence of a d-alanine-d-alanine ligase (dAla-dAla) domain and by sensitivity of the mutant to β-lactam antibiotics. asnO::Tn5luxAB is expressed during the stationary phase under normal growth conditions. Amino acid sequence similarity to enzymes producing β-lactam inhibitors and increased resistance to β-lactam antibiotics may indicate that asnO is involved in the production of a β-lactam inhibitor.

What determines the efficiency of N(2)-fixing Rhizobium-legume symbioses?

Biological nitrogen fixation is vital to nutrient cycling in the biosphere and is the major route by which atmospheric dinitrogen (N(2)) is reduced to ammonia. The largest single contribution to biological N(2) fixation is carried out by rhizobia, which include a large group of both alpha and beta-proteobacteria, almost exclusively in association with legumes. Rhizobia must compete to infect roots of legumes and initiate a signaling dialog with host plants that leads to nodule formation. The most common form of infection involves the growth of rhizobia down infection threads which are laid down by the host plant. Legumes form either indeterminate or determinate types of nodules, with these groups differing widely in nodule morphology and often in the developmental program by which rhizobia form N(2) fixing bacteroids. In particular, indeterminate legumes from the inverted repeat-lacking clade (IRLC) (e.g., peas, vetch, alfalfa, medics) produce a cocktail of antimicrobial peptides which cause endoreduplication of the bacterial genome and force rhizobia into a nongrowing state. Bacteroids often become dependent on the plant for provision of key cofactors, such as homocitrate needed for nitrogenase activity or for branched chain amino acids. This has led to the suggestion that bacteroids at least from the IRLC can be considered as ammoniaplasts, where they are effectively facultative plant organelles. A low O(2) tension is critical both to induction of genes needed for N(2) fixation and to the subsequent exchange of nutrient between plants and bacteroids. To achieve high rates of N(2) fixation, the legume host and Rhizobium must be closely matched not only for infection, but for optimum development, nutrient exchange, and N(2) fixation. In this review, we consider the multiple steps of selection and bacteroid development and how these alter the overall efficiency of N(2) fixation.

Osmotically induced synthesis of the dipeptide N-acetylglutaminylglutamine amide is mediated by a new pathway conserved among bacteria

The dipeptide N-acetylglutaminylglutamine amide (NAGGN) was discovered in the bacterium Sinorhizobium meliloti grown at high osmolarity, and subsequently shown to be synthesized and accumulated by a few osmotically challenged bacteria. However, its biosynthetic pathway remained unknown. Recently, two genes, which putatively encode a glutamine amidotransferase and an acetyltransferase and are up-regulated by osmotic stress, were identified in Pseudomonas aeruginosa. In this work, a locus carrying the orthologous genes in S. meliloti, asnO and ngg, was identified, and the genetic and molecular characterization of the NAGGN biosynthetic pathway is reported. By using NMR experiments, it was found that strains inactivated in asnO and ngg were unable to produce the dipeptide. Such inability has a deleterious effect on S. meliloti growth at high osmolarity, demonstrating the key role of NAGGN biosynthesis in cell osmoprotection. beta-Glucuronidase activity from transcriptional fusion revealed strong induction of asnO expression in cells grown in increased NaCl concentration, in good agreement with the NAGGN accumulation. The asnO-ngg cluster encodes a unique enzymatic machinery mediating nonribosomal peptide synthesis. This pathway first involves Ngg, a bifunctional enzyme that catalyzes the formation of the intermediate N-acetylglutaminylglutamine, and second AsnO, required for subsequent addition of an amide group and the conversion of N-acetylglutaminylglutamine into NAGGN. Interestingly, a strong conservation of the asnO-ngg cluster is observed in a large number of bacteria with different lifestyles, such as marine, symbiotic, and pathogenic bacteria, highlighting the ecological importance of NAGGN synthesis capability in osmoprotection and also potentially in bacteria host-cell interactions.

Isolation and characterization of pcsB, the gene for a polyene carboxamide synthase that tailors pimaricin into AB-400

From cell-free extracts of Streptomyces RGU5.3, a tailoring activity of pimaricin, leading to the biosynthesis of its natural carboxamide derivative AB-400, was recently identified. The two polyene macrolides, pimaricin and AB-400, were produced in almost equal quantities and can be detected in the fermentation broth of the producer strain. This report concerns the isolation and partial characterization of the gene, polyene carboxamide synthase (pcsB), responsible for the bioconversion. The gene encoded an asparagine synthase-like protein, belonging to the type II glutamine amidotransferase family, and was named pcsB. The fermentation broth of a recombinant strain carrying the engineered pcsB gene under the control of the inducible tipA promoter within an integrative vector produces the carboxamide AB-400 as the main polyene macrolide.

Signal integration in bacterial two-component regulatory systems

Two-component systems (TCSs) and phosphorelays are key mediators of bacterial signal transduction. The signals activating these systems promote the phosphorylated state of a response regulator, which is generally the form that carries out specific functions such as binding to DNA and catalysis of biochemical reactions. An emerging class of proteins-termed TCS connectors-modulate the output of TCSs by affecting the phosphorylation state of response regulators. TCS connectors use different mechanisms of action for signal integration, as well as in the coordination and fine-tuning of cellular processes. Present in both Gram-positive and Gram-negative bacteria, TCS connectors are critical for a variety of physiological functions including sporulation, competence, antibiotic resistance, and the transition to stationary phase.

Identification of genes relevant to symbiosis and competitiveness in Sinorhizobium meliloti using signature-tagged mutants

Sinorhizobium meliloti enters an endosymbiosis with alfalfa plants through the formation of nitrogen-fixing nodules. In order to identify S. meliloti genes required for symbiosis and competitiveness, a method of signature-tagged mutagenesis was used. Two sets, each consisting of 378 signature-tagged mutants with a known transposon insertion site, were used in an experiment in planta. As a result, 67 mutants showing attenuated symbiotic phenotypes were identified, including most of the exo, fix, and nif mutants in the sets. For 38 mutants in genes previously not described to be involved in competitiveness or symbiosis in S. meliloti, attenuated competitiveness phenotypes were tested individually. A large part of these phenotypes was confirmed. Moreover, additional symbiotic defects were observed for mutants in several novel genes such as infection deficiency phenotypes (ilvI and ilvD2 mutants) or delayed nodulation (pyrE, metA, thiC, thiO, and thiD mutants).

FixJ: a major regulator of the oxygen limitation response and late symbiotic functions of Sinorhizobium meliloti

Sinorhizobium meliloti exists either in a free-living state in the soil or in symbiosis within legume nodules, where the bacteria differentiate into nitrogen-fixing bacteroids. Expression of genes involved in nitrogen fixation and associated respiration is governed by two intermediate regulators, NifA and FixK, respectively, which are controlled by a two-component regulatory system FixLJ in response to low-oxygen conditions. In order to identify the FixLJ regulon, gene expression profiles were determined in microaerobic free-living cells as well as during the symbiotic life of the bacterium for the wild type and a fixJ null-mutant strain. We identified 122 genes activated by FixJ in either state, including 87 novel targets. FixJ controls 74% of the genes induced in microaerobiosis (2% oxygen) and the majority of genes expressed in mature bacteroids. Ninety-seven percent of FixJ-activated genes are located on the symbiotic plasmid pSymA. Transcriptome profiles of a nifA and a fixK mutant showed that NifA activates a limited number of genes, all specific to the symbiotic state, whereas FixK controls more than 90 genes, involved in free-living and/or symbiotic life. This study also revealed that FixJ has no other direct targets besides those already known. FixJ is involved in the regulation of functions such as denitrification or amino acid/polyamine metabolism and transport. Mutations in selected novel FixJ targets did not affect the ability of the bacteria to form nitrogen-fixing nodules on Medicago sativa roots. From these results, we propose an updated model of the FixJ regulon.

A highly conserved Sinorhizobium meliloti operon is induced microaerobically via the FixLJ system and by nitric oxide (NO) via NnrR

A previously generated collection of 11 Tn5-luxAB insertion mutants of Sinorhizobium meliloti harbouring lux reporter gene fusions induced under microaerobic (1% O2) conditions was further characterized and mapped on the sequenced S. meliloti genome. One highly induced gene fusion from this collection (loe-7) was found to be located in the intergenic region between sma1292, encoding a putative protease/collagenase, and a gene of unknown function (sma1294). The loe-7 fusion had been shown previously to be partially controlled by the oxygen sensor/regulator FixLJ system, but significant ( approximately 40%) Lux activity remained in a fixLJ mutant background. Therefore, a secondary Tn1721 mutagenesis of the loe-7 strain was carried out. Nine Tn1721 ('dark') insertions completely abolishing the Lux activity of the loe-7 fusion under microaerobic conditions were isolated. Surprisingly, five dark insertions mapped in denitrification genes [napA, napC, nirK--two insertions--and sma1245 encoding a NnrR-like transcriptional regulator controlling denitrification in response to nitric oxide (NO)]; Tn1721 insertions in the respiration genes fixG and fixP resulted in a reduced expression of the loe-7-lux fusion, and insertions in the regulatory genes fixJ and fixK1 resulted in low, but still detectable Lux activity. On the contrary, insertions in the norD or norQ genes resulted in constitutive Lux activity. In these mutant strains, NO would be expected to accumulate under microaerobic conditions. NO was found to be able to strongly induce the loe-7-luxAB fusion under microaerobic and aerobic conditions, but only in the presence of the functional nnrR-like gene (sma1245). These results suggest that NO, via the NnrR regulator, can serve as a signal molecule to induce the loe-7-luxAB fusion in concert with the FixLJ system.

FixJ-regulated genes evolved through promoter duplication in Sinorhizobium meliloti

The FixLJ two-component system ofSinorhizobium melilotiis a global regulator, turning on nitrogen-fixation genes in microaerobiosis. Up to now,nifAandfixKwere the only genes known to be directly regulated by FixJ. We used a genomic SELEX approach in order to isolate new FixJ targets in the genome. This led to the identification of 22 FixJ binding sites, including the known sites in thefixK1andfixK2promoters. FixJ binding sites are unevenly distributed among the three replicons constituting theS. melilotigenome: a majority are carried either by pSymA or by a short chromosomal region of non-chromosomal origin. Thus FixJ binding sites appear to be preferentially associated with the pSymA replicon, which carries thefixJgene. Functional analysis of FixJ targets led to the discovery of two new FixJ-regulated genes,smc03253andproB2. This FixJ-dependent regulation appears to be mediated by a duplication of the wholefixKpromoter region, including the beginning of thefixKgene. Similar duplications were previously reported for thenifHpromoter. By systematic comparison of all promoter regions we found 17 such duplications throughout the genome, indicating that promoter duplication is a common mechanism for the evolution of regulatory pathways inS. meliloti.

Identification and analysis of Escherichia coli proteins that interact with the histidine kinase NtrB in a yeast two-hybrid system

In this work we used the yeast two-hybrid (Y2H) system to deepen our understanding of protein-protein interactions that are involved in the nitrogen regulatory network in Escherichia coli. Three different genes, encoding GlnB, GlnK and AspA, respectively, were found among 64 positive clones identified from E. coli Sau3AI Y2H libraries using the nitrogen regulator NtrB as bait. Structural and functional analysis of the prey clones provided information on library features and the degree of saturation achieved in the screens. Further analysis revealed that the C-terminal kinase domain of NtrB is required for the interaction with GlnK, while AspA(91-312) interacts specifically with the conserved histidine phosphotransfer domain of NtrB, thus providing additional evidence for the involvement of the conserved transmitter module of the histidine kinase NtrB in input sensory functions.

The fixM flavoprotein modulates inhibition by AICAR or 5'AMP of respiratory and nitrogen fixation gene expression in Sinorhizobium meliloti

AICAR, a purine-related metabolite, was recently shown to inhibit respiratory and nifA gene expression in Sino-rhizobium meliloti. Here, we demonstrate that AICAR has essentially no or little effect in a wild-type S. meliloti strain and inhibits respiratory and nitrogen fixation gene expression only in specific mutant backgrounds. We have analyzed in detail a mutant in which addition of AICAR inhibited fixK,fixN,fixT and nifA expression. The corresponding gene,fixM, is located just downstream of fixK1 on pSymA megaplasmid and encodes a flavoprotein oxidoreductase. 5'AMP, a structural analogue of AICAR, mimicked AICAR effect as well as the nucleoside precursors AICAriboside and adenosine. The mode of action of AICAR and 5'AMP in vivo was investigated. We demonstrate that AICAR does not affect FixK transcriptional activity and instead regulates fixK and nifA gene expression. We hypothesize that AICAR and 5'AMP may modulate, possibly indirectly, the activity of the FixLJ two-component regulatory system. The possible physiological roles of AICAR, 5'AMP, and fixM in the context of symbiosis are discussed.

Rhizobial acyl carrier proteins and their roles in the formation of bacterial cell-surface components that are required for the development of nitrogen-fixing root nodules on legume hosts

Acyl carrier protein (ACP) of Escherichia coli is a small acidic protein which functions as carrier of growing acyl chains during their biosynthesis and as donor of acyl chains during transfer to target molecules. This unique ACP of E. coli is expressed constitutively. In more complex bacteria, multiple ACPs are present, indicating a channeling of pools of multi-carbon units into different biosynthetic routes. In rhizobia, for example, besides the constitutive ACP (AcpP) involved in the biosynthesis and transfer of common fatty acids, three specialized ACPs have been reported: (1) the flavonoid-inducible nodulation protein NodF, (2) AcpXL that transfers 27-hydroxyoctacosanoic acid to a sugar backbone during lipid A biosynthesis, and (3) the RkpF protein which is required for the biosynthesis of rhizobial capsular polysaccharides. All three of those specialized rhizobial ACPs are required for the biosynthesis of cell-surface molecules that play a role in establishing the symbiotic relationship between rhizobia and their legume hosts. Surprisingly, the recently sequenced genomes from Mesorhizobium loti and Sinorhizobium meliloti suggest even more candidates for ACPs in rhizobia.