Subcellular localization of the nodD gene product in Rhizobium leguminosarum

Rhizobium etli CE3-DsRed pMP604: a useful biological tool to study initial infection steps in Phaseolus vulgaris nodulation

Rhizobium etli CE3-DsRed pMP604 drives infection 12-24 h earlier than R. etli CE3-DsRed and it is an excellent tool in live-cell imaging studies of IT developement in P. vulgaris roots. The study of the cellular dynamics of nodulation has frequently been limited by the difficulty of performing live-cell imaging in nodule primordia and legume roots, which are constituted by multiple cell layers, such is the case of Phaseolus vulgaris. Seeking conditions to reduce the time it takes for rhizobia to infect P. vulgaris root, we decided to explore the nodulation properties of Rhizobium etli CE3 pMP604, a strain that constitutively produces Nod factors through a flavonoids-independent transcriptional activation which is often used to purify Nod factors. Even though the strain infects 12-24 h earlier than the parental R. etli CE3 strain, infection thread (IT) formation, nodule organogenesis processes and N₂-fixation activity are similar for both strains. Additionally, we have confirmed that R. etli CE3-DsRed pMP604 is an excellent tool to trace IT development in P. vulgaris roots.

Structural and functional characterization of Pseudomonas aeruginosa global regulator AmpR

Pseudomonas aeruginosa is a dreaded pathogen in many clinical settings. Its inherent and acquired antibiotic resistance thwarts therapy. In particular, derepression of the AmpC β-lactamase is a common mechanism of β-lactam resistance among clinical isolates. The inducible expression of ampC is controlled by the global LysR-type transcriptional regulator (LTTR) AmpR. In the present study, we investigated the genetic and structural elements that are important for ampC induction. Specifically, the ampC (PampC) and ampR (PampR) promoters and the AmpR protein were characterized. The transcription start sites (TSSs) of the divergent transcripts were mapped using 5' rapid amplification of cDNA ends-PCR (RACE-PCR), and strong σ(54) and σ(70) consensus sequences were identified at PampR and PampC, respectively. Sigma factor RpoN was found to negatively regulate ampR expression, possibly through promoter blocking. Deletion mapping revealed that the minimal PampC extends 98 bp upstream of the TSS. Gel shifts using membrane fractions showed that AmpR binds to PampC in vitro whereas in vivo binding was demonstrated using chromatin immunoprecipitation-quantitative PCR (ChIP-qPCR). Additionally, site-directed mutagenesis of the AmpR helix-turn-helix (HTH) motif identified residues critical for binding and function (Ser38 and Lys42) and critical for function but not binding (His39). Amino acids Gly102 and Asp135, previously implicated in the repression state of AmpR in the enterobacteria, were also shown to play a structural role in P. aeruginosa AmpR. Alkaline phosphatase fusion and shaving experiments suggest that AmpR is likely to be membrane associated. Lastly, an in vivo cross-linking study shows that AmpR dimerizes. In conclusion, a potential membrane-associated AmpR dimer regulates ampC expression by direct binding.

Quantitative analysis of the naringenin-inducible proteome in Rhizobium leguminosarum by isobaric tagging and mass spectrometry

The rhizobium-legume interaction is a critical cornerstone of crop productivity and environmental sustainability. Its potential improvement relies on elucidation of the complex molecular dialogue between its two partners. In the present study, the proteomic patterns of gnotobiotic cultures of Rhizobium leguminosarum bv. viciae 3841 grown for 6 h in presence or absence of the nod gene-inducing plant flavonoid naringenin (10 μM) were analyzed using the iTRAQ approach. A total of 1334 proteins were identified corresponding to 18.67% of the protein-coding genes annotated in the sequenced genome of bv. viciae 3841. The abundance levels of 47 proteins were increased upon naringenin treatment showing fold change ratios ranging from 1.5 to 25 in two biological replicates. Besides the nod units, naringenin enhanced the expression of a number of other genes, many of which organized in operons, including β(1-2) glucan production and secretion, succinoglycan export, the RopA outer membrane protein with homology to an oligogalacturonide-specific porin motif, other enzymes for carbohydrate and amino acid metabolism, and proteins involved in the translation machinery. Data were validated at the transcriptional and phenotypic levels by RT-PCR and an assay of secreted sugars in culture supernatants, respectively. The current approach provides not only a high-resolution analysis of the prokaryotic proteome but also unravels the rhizobium molecular dialogue with legumes by detecting the enhanced expression of several symbiosis-associated proteins, whose flavonoid-dependency had not yet been reported.

Detection of and response to signals involved in host-microbe interactions by plant-associated bacteria

Diverse interactions between hosts and microbes are initiated by the detection of host-released chemical signals. Detection of these signals leads to altered patterns of gene expression that culminate in specific and adaptive changes in bacterial physiology that are required for these associations. This concept was first demonstrated for the members of the family Rhizobiaceae and was later found to apply to many other plant-associated bacteria as well as to microbes that colonize human and animal hosts. The family Rhizobiaceae includes various genera of rhizobia as well as species of Agrobacterium. Rhizobia are symbionts of legumes, which fix nitrogen within root nodules, while Agrobacterium tumefaciens is a pathogen that causes crown gall tumors on a wide variety of plants. The plant-released signals that are recognized by these bacteria are low-molecular-weight, diffusible molecules and are detected by the bacteria through specific receptor proteins. Similar phenomena are observed with other plant pathogens, including Pseudomonas syringae, Ralstonia solanacearum, and Erwinia spp., although here the signals and signal receptors are not as well defined. In some cases, nutritional conditions such as iron limitation or the lack of nitrogen sources seem to provide a significant cue. While much has been learned about the process of host detection over the past 20 years, our knowledge is far from being complete. The complex nature of the plant-microbe interactions makes it extremely challenging to gain a comprehensive picture of host detection in natural environments, and thus many signals and signal recognition systems remain to be described.

Membrane localization of the ToxR winged-helix domain is required for TcpP-mediated virulence gene activation in Vibrio cholerae

ToxR is a bitopic membrane protein that controls virulence gene expression in Vibrio cholerae. Its cytoplasmic domain is homologous to the winged helix-turn-helix ('winged helix') DNA-binding/transcription activation domain found in a variety of prokaryotic and eukaryotic regulators, whereas its periplasmic domain is of ill-defined function. Several genes in V. cholerae are regulated by ToxR, but by apparently different mechanisms. Whereas ToxR directly controls the transcription of genes encoding two outer membrane proteins, OmpU and OmpT, it co-operates with a second membrane-localized transcription factor called TcpP to activate transcription of the gene encoding ToxT, which regulates transcription of cholera toxin (ctxAB) and the toxin-co-regulated pilus (tcp). To determine the requirements for gene activation by ToxR, different domains of the protein were analysed for their ability to control expression of toxT, ompU and ompT. Soluble forms of the cytoplasmic winged-helix domain regulated ompU and ompT gene expression properly but did not activate toxT transcription. Membrane localization of the winged helix was sufficient for both omp gene regulation and TcpP-dependent toxT transcription, irrespective of the type of periplasmic domain or even the presence of a periplasmic domain. These results suggest that (i) the major function for membrane localization of ToxR is for its winged-helix domain to co-operate with TcpP to activate transcription; (ii) the periplasmic domain of ToxR is not required for TcpP-dependent activation of toxT transcription; and (iii) membrane localization is not a strict requirement for DNA binding and transcription activation by ToxR.

Regulation of gene expression by cell-to-cell communication: acyl-homoserine lactone quorum sensing

Quorum sensing is an example of community behavior prevalent among diverse bacterial species. The term "quorum sensing" describes the ability of a microorganism to perceive and respond to microbial population density, usually relying on the production and subsequent response to diffusible signal molecules. A significant number of gram-negative bacteria produce acylated homoserine lactones (acyl-HSLs) as signal molecules that function in quorum sensing. Bacteria that produce acyl-HSLs can respond to the local concentration of the signaling molecules, and high population densities foster the accumulation of inducing levels of acyl-HSLs. Depending upon the bacterial species, the physiological processes regulated by quorum sensing are extremely diverse, ranging from bioluminescence to swarming motility. Acyl-HSL quorum sensing has become a paradigm for intercellular signaling mechanisms. A flurry of research over the past decade has led to significant understanding of many aspects of quorum sensing including the synthesis of acyl-HSLs, the receptors that recognize the acyl-HSL signal and transduce this information to the level of gene expression, and the interaction of these receptors with the transcriptional machinery. Recent studies have begun to integrate acyl-HSL quorum sensing into global regulatory networks and establish its role in developing and maintaining the structure of bacterial communities.

A quorum sensing-associated virulence gene of Pseudomonas aeruginosa encodes a LysR-like transcription regulator with a unique self-regulatory mechanism

The human opportunistic pathogen Pseudomonas aeruginosa strain PA14 infects both plants and animals. Previously, using plants to screen directly for P. aeruginosa virulence-attenuated mutants, we identified a locus, pho34B12, relevant in mammalian pathogenesis. Here, nonsense point mutations in the two opposing ORFs identified in the pho34B12 locus revealed that one of them, mvfR (multiple virulence factor Regulator), is able to control all of the phenotypes that mutant phoA34B12 displays. Both genetic and biochemical evidence demonstrate that the mvfR gene encodes a LysR-like transcriptional factor that positively regulates the production of elastase, phospholipase, and of the autoinducers, 3oxo-dodecanoyl homoserine lactone (PAI I) and 2-heptyl-3-hydroxy-4-quinolone (PQS), as well as the expression of the phnAB operon, involved in phenazine biosynthesis. We demonstrate that the MvfR protein is membrane-associated and acts as a transcriptional activator until cells reach stationary phase, when a unique negative feedback mechanism is activated to signal the down-regulation of the MvfR protein. This work reveals an unprecedented virulence mechanism of P. aeruginosa and identifies a unique indispensable player in the P. aeruginosa quorum-sensing cascade.

In Rhizobium leguminosarum, NodD represses its own transcription by competing with RNA polymerase for binding sites

We isolated RNA polymerase (RNAP) from Rhizobium leguminosarum, the nitrogen-fixing symbiont of peas and VICIA: Its 91 kDa subunit, which is homologous to sigma(70) of Escherichia coli RNAP, is necessary for transcription of the regulatory nodD gene, which in the presence of certain flavonoids induces transcription of other nod genes that are needed for the early steps of infection. We also show that negative autoregulation of nodD was achieved through competition between RNAP and NodD for their respective binding sites, which largely overlap. Combined with the result that high concentrations of the flavonoid inducer naringenin relieved the binding affinity of NodD for its target DNA, the way in which the nod genes are activated is discussed.

Molecular basis of symbiotic promiscuity

Eukaryotes often form symbioses with microorganisms. Among these, associations between plants and nitrogen-fixing bacteria are responsible for the nitrogen input into various ecological niches. Plants of many different families have evolved the capacity to develop root or stem nodules with diverse genera of soil bacteria. Of these, symbioses between legumes and rhizobia (Azorhizobium, Bradyrhizobium, Mesorhizobium, and Rhizobium) are the most important from an agricultural perspective. Nitrogen-fixing nodules arise when symbiotic rhizobia penetrate their hosts in a strictly controlled and coordinated manner. Molecular codes are exchanged between the symbionts in the rhizosphere to select compatible rhizobia from pathogens. Entry into the plant is restricted to bacteria that have the "keys" to a succession of legume "doors". Some symbionts intimately associate with many different partners (and are thus promiscuous), while others are more selective and have a narrow host range. For historical reasons, narrow host range has been more intensively investigated than promiscuity. In our view, this has given a false impression of specificity in legume-Rhizobium associations. Rather, we suggest that restricted host ranges are limited to specific niches and represent specialization of widespread and more ancestral promiscuous symbioses. Here we analyze the molecular mechanisms governing symbiotic promiscuity in rhizobia and show that it is controlled by a number of molecular keys.

New Rhizobium leguminosarum flavonoid-induced proteins revealed by proteome analysis of differentially displayed proteins

Proteome analysis was used to establish the first two-dimensional protein map of Rhizobium. R. leguminosarum bv. trifolii strain ANU843 was grown in defined medium in the presence and absence of the flavonoid 7,4'-dihydroxyflavone. Over 1,700 constitutive proteins were resolved, representing about 30% of the estimated genomic output. Proteome analysis of flavonoid-treated cells was done to reveal differentially displayed proteins. The results showed that while the global expression pattern of proteins was largely unaltered by the treatment, four inducible proteins were observed. The four inducible proteins and 20 constitutively expressed proteins were subjected to sequence analysis to provide internal standards for the construction of a two-dimensional Rhizobium protein data base. The identity of 12 proteins, including NodE and NodB, was established. NodE was present throughout the growth of the cells but was diminished in amount in stationary phase cells whereas NodB was not detected in the later stages of growth. Two of the induced proteins sequenced did not match any known nodulation gene product, with one of these being present in mid-late log and stationary phase cells and possessing four consecutive His residues at the N-terminal sequencing was successful with 100 to 200 fmol of protein. Proteome analysis provides a sensitive new tool to examine plant-microbe interactions.

The genetic and biochemical basis for nodulation of legumes by rhizobia

Soil bacteria of the genera Azorhizobium, Bradyrhizobium, and Rhizobium are collectively termed rhizobia. They share the ability to penetrate legume roots and elicit morphological responses that lead to the appearance of nodules. Bacteria within these symbiotic structures fix atmosphere nitrogen and thus are of immense ecological and agricultural significance. Although modern genetic analysis of rhizobia began less than 20 years ago, dozens of nodulation genes have now been identified, some in multiple species of rhizobia. These genetic advances have led to the discovery of a host surveillance system encoded by nodD and to the identification of Nod factor signals. These derivatives of oligochitin are synthesized by the protein products of nodABC, nodFE, NodPQ, and other nodulation genes; they provoke symbiotic responses on the part of the host and have generated immense interest in recent years. The symbiotic functions of other nodulation genes are nonetheless uncertain, and there remain significant gaps in our knowledge of several large groups of rhizobia with interesting biological properties. This review focuses on the nodulation genes of rhizobia, with particular emphasis on the concept of biological specificity of symbiosis with legume host plants.

The Rhizobium-plant symbiosis

Rhizobium, Bradyrhizobium, and Azorhizobium species are able to elicit the formation of unique structures, called nodules, on the roots or stems of the leguminous host. In these nodules, the rhizobia convert atmospheric N2 into ammonia for the plant. To establish this symbiosis, signals are produced early in the interaction between plant and rhizobia and they elicit discrete responses by the two symbiotic partners. First, transcription of the bacterial nodulation (nod) genes is under control of the NodD regulatory protein, which is activated by specific plant signals, flavonoids, present in the root exudates. In return, the nod-encoded enzymes are involved in the synthesis and excretion of specific lipooligosaccharides, which are able to trigger on the host plant the organogenic program leading to the formation of nodules. An overview of the organization, regulation, and function of the nod genes and their participation in the determination of the host specificity is presented.

Analysis of Vibrio cholerae ToxR function by construction of novel fusion proteins

The ToxR protein is a transmembrane protein that regulates the expression of several virulence factors of Vibrio cholerae. Previous analysis of fusion proteins between ToxR and alkaline phosphatase (ToxR-PhoA) suggested that ToxR was active as a dimer. In order to determine whether dimerization of the ToxR periplasmic domain was essential for activity, this domain was replaced by monomeric and dimeric protein domains. Surprisingly, PhoA (dimeric), beta-lactamase (monomeric, ToxR-Bla), or the leucine zipper of GCN4 (dimeric, ToxR-GCN4-M) could substitute functionally for the ToxR periplasmic domain. ToxR-GCN4 fusion proteins, in which the ToxR transmembrane domain was eliminated (ToxR-GCN4-C), were inactive, but an additional fusion protein that contained a heterologous membrane-spanning domain retained activity. Strains containing each of these ToxR fusion proteins were analysed for in vivo colonization properties and response to in vitro growth conditions that are known to affect expression of the ToxR regulon. Strains containing ToxR-GCN4-M and ToxR-Bla responded like wild-type strains to in vitro growth conditions. In the infant-mouse colonization model, strains containing ToxR fusion proteins were all deficient in colonization relative to strains containing wild-type ToxR, and strains containing monomeric ToxR-Bla were most severely outcompeted. These results suggest that, under in vitro conditions, ToxR does not require a dimerized periplasmic domain, but that, under in vivo conditions, the correct conformation of the ToxR periplasmic domain may be more important for function.

Rhizobia catabolize nod gene-inducing flavonoids via C-ring fission mechanisms

Gas chromatographic and mass spectrometric analyses of derivatized culture medium extracts were used to identify the products of flavonoid metabolism by rhizobia. A number of Rhizobium species and biovars degraded their nod gene-inducing flavonoids by mechanisms which originated in a cleavage of the C-ring of the molecule and which yielded conserved A- and B-ring products among the metabolites. In contrast, Pseudomonas putida degraded quercetin via an initial fission in its A-ring, and Agrobacterium tumefaciens displayed a nonspecific mode of flavonoid degradation which yielded no conserved A- or B-ring products. When incubated with rhizobia, flavonoids with OH substitutions at the 5 and 7 positions yielded phloroglucinol as the conserved A-ring product, and those with a single OH substitution at the 7 position yielded resorcinol. A wider range of structures was found among the B-ring derivatives, including p-coumaric, p-hydroxybenzoic, protocatechuic, phenylacetic, and caffeic acids. The isoflavonoids genistein and daidzein were also degraded via C-ring fission by Rhizobium fredii and Rhizobium sp. strain NGR234, respectively. Partially characterized aromatic metabolites with potential nod gene-inducing activity were detected among the products of naringenin degradation by Rhizobium leguminosarum bv. viciae. The initial structural modification of nod gene-inducing flavonoids by rhizobia can generate chalcones, whose open C-ring system may have implications for the binding of inducers to the nodD gene product.

The molecular basis of the host specificity of the Rhizobium bacteria

The interaction between soil bacteria belonging to the genera Rhizobium, Bradyrhizobium and Azorhizobium and leguminous plants results in the induction of a new plant organ, the root nodule. After invading these root nodules via infection threads the bacteria start to fix atmospheric nitrogen into ammonia which is beneficial for the host plant. This symbiotic interaction is highly host-specific in that each rhizobial strain is able to associate with only a limited number of host plant species. The subject of this presentation is the molecular mechanism by which the bacterium determines its host-specific characteristics. This mechanism appears to be based on at least two stages of molecular signaling between the bacterium and the plant host. In the first stage, flavonoids secreted by the plant root induce, in a host specific way, the transcription of bacterial genes which are involved in nodulation, the so-called nod genes. This leads to the second step of the signaling system: the production and secretion of lipo-oligosaccharide molecules by the Rhizobium bacteria. These signal molecules, which are acylated forms of small fragments of chitin, have various discernable effects on the roots of the host plants. One of these effects is the dedifferentiation of groups of cells located in the cortex which leads to the formation of nodule meristems. In their mitogenic activity the bacterial signals resemble several well-known plant hormones like auxins and cytokinins. However, there are two major differences: (i) the bacterial signals lead to the induction of a specific organ and (ii) they are host-specific in that only the signals produced by compatible bacteria are able to induce meristems. The nod genes determine this stage of host specificity by their essential role in the biosynthesis of the signal molecules. They appear to encode enzymes which are involved in the processes of fatty acid biosynthesis, fatty acid transfer, chitin synthesis and chitin modification. I will illustrate the statement that the nod gene products are ideal model enzymes for the study of these important processes because they are not needed in the free-living state of the bacteria.

The Vibrio fischeri luminescence gene activator LuxR is a membrane-associated protein

The Vibrio fischeri luminescence (lux) genes are activated at sufficiently high culture densities by the transcriptional activator LuxR in combination with a diffusible signal compound termed autoinducer. We have used antibodies directed against LuxR in immunoprecipitation experiments to study the subcellular location of this transcription factor. The LuxR polypeptide was detected in membranes and not in the soluble pool of cytoplasmic proteins from V. fischeri. LuxR was not released from the membranes by 0.6 M KCl or by the nonionic detergents Nonidet P-40, N-octyl-beta-D-glucopyranoside, and Triton X-100. LuxR and a number of other V. fischeri proteins were released from the membranes by EDTA. The autoinducer had no detectable influence on the subcellular location of LuxR. In spheroplasts, neither the abundance nor the molecular mass of the LuxR antigen was influenced by treatment with proteinase K. Together with other information, these results indicate that LuxR is an amphipathic protein that is associated with the cytoplasmic membrane of V. fischeri.

Regulation and function of rhizobial nodulation genes

This review focuses on the functions of nodulation (nod) genes in the interaction between rhizobia and legumes. The nod genes are the key bacterial determinants of the signal exchange between the two symbiotic partners. The product of the nodD gene is a transcriptional activator protein that functions as receptor for a flavonoid plant compound. This signaling induces the expression of a set of nod genes that produces several related Nod factors, substituted lipooligosaccharides. The Nod factors are then excreted and serve as signals sent from the bacterium to the plant. The plant responds with the development of a root nodule. The plant-derived flavonoid, as well as the rhizobial signal, must have distinct chemical structures which guarantee that only matching partners are brought together.

Molecular mechanism of host specificity in legume-rhizobium symbiosis

Rhizobium - legume symbiosis is a highly specific interaction between the two partners. Host specificity is evident at early stages of infection and results from multiple interactions involving signalling among bacteria and host plants. Host specific plant signals (flavanoids) convert the NodD protein to an active form and its binding with nod box initiates the transcription of inducible nod operons. Common nod genes (nodABC) code for an extracellular mitogenic Nod factor which is required for nodule organogenesis. Host specific genes (hsn) modify the Nod factor to induce root hair deformation on specific hosts. The structure of Nod factor controls host range distinction between species and biovars of rhizobia. Interactions of lectins and Exopolysaccharide/Lipopolysaccharide result in host specific attachment of Rhizobium and its subsequent invasion. Change in Expopolysaccharide structure by the transfer of hsn genes enables the Rhizobium to bind with heterologous host lectins. Conversely, changes in root lectins via gene manipulation enables the heterologous rhizobia to bind and initiate nodulation on heterologous hosts. Finally, host specific signals are required to initiate nitrogen fixation in nodules that are formed.

The NodD protein does not bind to the promoters of inducible nodulation genes in extracts of bacteroids of Rhizobium leguminosarum biovar viciae

In a previous study, we showed that in bacteroids, transcription of the inducible nod genes does not occur and expression of nodD is decreased by 65% (H. R. M. Schlaman, B. Horvath, E. Vijgenboom, R.J.H. Okker, and B. J. J. Lugtenberg, J. Bacteriol. 173:4277-4287, 1991). In the present study, we show, using gel retardation, that in crude extracts of bacteroids of Rhizobium leguminosarum biovar (bv.) viciae, NodD protein does not bind to the nodF, nodM, and nodO box and that it binds only weakly to the nodA box. Binding of NodD from bacteroids to nod box DNA could be restored by mild proteinase K treatment, indicating that NodD is present in bacteroids in an altered form or complex which prevents its binding to nod box DNA. In addition, a novel nodA box DNA-protein complex was found which is specific for the nodA promoter region. This novel complex was formed neither with material from cultured bacterial cells nor with an extract from uninfected roots, and it did not contain NodD but another protein. These results are consistent with the hypothesis that the protein present in the novel retardation complex acts as a transcriptional repressor causing the decreased nodD expression in bacteroids. Such a repressor also explains the lack of nodABCIJ transcription despite the weak NodD binding to the nodA box.

Isoliquiritigenin, a strong nod gene- and glyceollin resistance-inducing flavonoid from soybean root exudate

Isoflavonoid signal molecules from soybean (Glycine max (L.) Merr.) seed and root exudate induce the transcription of nodulation (nod) genes in Bradyrhizobium japonicum. In this study, a new compound with symbiotic activity was isolated from soybean root exudate. The isolated 2',4',4-trihydroxychalcone (isoliquiritigenin) is characterized by its strong inducing activity for the nod genes of B. japonicum. These genes are already induced at concentrations 1 order of magnitude below those required of the previously described isoflavonoid inducers genistein and daidzein. Isoliquiritigenin is also a potent inducer of glyceollin resistance in B. japonicum, which renders this bacterium insensitive to potentially bactericidal concentrations of glyceollin, the phytoalexin of G. max. No chemotactic effect of isoliquiritigenin was observed. The highly efficient induction of nod genes and glyceollin resistance by isoliquiritigenin suggests the ecological significance of this compound, although it is not a major flavonoid constituent of the soybean root exudate in quantitative terms.

Evolution of regulation of steroid-mediated intercellular communication in vertebrates: insights from flavonoids, signals that mediate plant-rhizobia symbiosis

Various flavonoids, such as genistein, luteolin, and coumestrol, have actions in mammals that are mediated by binding either to classical estrogen receptors or to type II receptors, which also bind estrogen. These actions are of intense interest because they may be the basis for the protective actions of plants against certain cancers, such as breast cancer. The biological activity of flavonoids in mammals raises some questions. Is the hormonal action of flavonoids "an accident" derived from their phenolic groups and general hydrophobicity, which gives them some properties in common with estrogens? Or do flavonoids regulate gene transcription in other organisms? And, if so, is there a connection between their actions in these organisms and in mammals? Some answers to these questions are provided by the actions of plant-derived flavonoids in regulating gene transcription in rhizobia, bacteria that form nitrogen-fixing nodules in the roots of legumes, which has several interesting similarities with steroid-mediated actions in vertebrates. First, there is specificity in the actions of flavonoids in rhizobia; oxidation or reduction of the flavonoid or removal of a hydroxyl group can alter its biological activity. Moreover, some flavonoids are anti-inducers functioning like steroid antagonists to negate the actions of inducers. Also there are sequence similarities between various steroid metabolizing enzymes and proteins found in rhizobia, which indicates that these proteins are derived from a common ancestor. For example, 17 beta-hydroxysteroid dehydrogenase, which catalyzes the interconversion of the alcohol and ketone a C17 on estrogens and androgens, 11 beta-hydroxysteroid dehydrogenase, which catalyzes the interconversion of the alcohol and ketone at C11 of glucocorticoids, and 3 alpha,20 beta-hydroxysteroid dehydrogenase, which catalyzes the interconversion of the alcohol and ketone at C20 of corticosteroids, are homologs of proteins found in rhizobia. Thus, the binding of flavonoids to vertebrate proteins may represent an evolutionary linkage between the actions of steroids in mammals and communication between plants and rhizobia.

Evolution of enzymatic regulation of prostaglandin action: novel connections to regulation of human sex and adrenal function, antibiotic synthesis and nitrogen fixation

The recent determination of the amino acid sequences of enzymes that metabolize prostaglandins and steroids has revealed interesting connections between some of these enzymes. Human placental 15-hydroxyprostaglandin dehydrogenase, which catalyzes the oxidation of the C15 alcohol on prostaglandins E2 and F2 alpha, is homologous to 11 beta-hydroxysteroid, 17 beta-hydroxysteroid, and 3 alpha, 20 beta-hydroxysteroid dehydrogenases. That is, these four enzymes are derived from a common ancestor. Moreover, enzymes important in synthesis of antibiotics and proteins synthesized by soil bacteria that form nitrogen-fixing nodules in alfalfa and soybeans are homologous to 15-hydroxyprostaglandin dehydrogenase. These homologies provide important insights into the origins of intercellular communication that is mediated by prostaglandins, steroids, and fatty acids.

Transduction of plant signal molecules by the Rhizobium NodD proteins

The regulatory NodD proteins of Rhizobium bacteria mediate the activation of a gene set responsible for symbiotic nodule formation by plant signal molecules. Here we discuss the signal recognition and gene activation properties of NodD and present a model summarizing the current knowledge on NodD action.

Suppression of nodulation gene expression in bacteroids of Rhizobium leguminosarum biovar viciae

The expression of nod genes of Rhizobium leguminosarum bv. viciae in nodules of Pisum sativum was investigated at both the translational and transcriptional levels. By using immunoblots, it was found that the levels of NodA, NodI, NodE, and NodO proteins were reduced at least 14-fold in bacteriods compared with cultured cells, whereas NodD protein was reduced only 3-fold. Northern (RNA) blot hybridization, RNase protection assays, and in situ RNA hybridization together showed that, except for the nodD transcript, none of the other nod gene transcripts were present in bacteroids. The amount of nodD transcript in bacteroids was reduced only two- to threefold compared with that in cultured cells. Identical results were found with a Rhizobium strain harboring multicopies of nodD and with a strain containing a NodD protein (NodD604) which is activated independently of flavonoids. Furthermore, it was found that mature pea nodules contain inhibitors of induced nod gene transcription but that NodD604 was insensitive to these compounds. In situ RNA hybridization on sections from P. sativum and Vicia hirsuta nodules showed that transcription of inducible nod genes is switched off before the bacteria differentiate into bacteroids. This is unlikely to be due to limiting amounts of NodD, the absence of inducing compounds, or the presence of anti-inducers. The observed switch off of transcription during the development of symbiosis is a general phenomenon and is apparently caused by a yet unknown, negative regulation mechanism.

Isoflavonoid-inducible resistance to the phytoalexin glyceollin in soybean rhizobia

The antibacterial effect of the soybean phytoalexin glyceollin was assayed using a liquid microculture technique. Log-phase cells of Bradyrhizobium japonicum and Sinorhizobium fredii were sensitive to glyceollin. As revealed by growth rates and survival tests, these species were able to tolerate glyceollin after adaptation. Incubation in low concentrations of the isoflavones genistein and daidzein induced resistance to potentially bactericidal concentrations of glyceollin. This inducible resistance is not due to degradation or detoxification of the phytoalexin. The inducible resistance could be detected in B. japonicum 110spc4 and 61A101, representing the two taxonomically divergent groups of this species, as well as in S. fredii HH103, suggesting that this trait is a feature of all soybean-nodulating rhizobia. Glyceollin resistance was also inducible in a nodD1D2YABC deletion mutant of B. japonicum 110spc4, suggesting that there exists another recognition site for flavonoids besides the nodD genes identified so far. Exudate preparations from roots infected with Phytophthora megasperma f. sp. glycinea exhibited a strong bactericidal effect toward glyceollin-sensitive cells of B. japonicum. This killing effect was not solely due to glyceollin since purified glyceollin at concentrations similar to those present in exudate preparations had a much lower toxicity. However, glyceollin-resistant cells were also more resistant to exudate preparations than glyceollin-sensitive cells. Isoflavonoid-inducible resistance must therefore be ascribed an important role for survival of rhizobia in the rhizosphere of soybean roots.

Homology of the ligand-binding regions of Rhizobium symbiotic regulatory protein NodD and vertebrate nuclear receptors

The signal specificity and structure of sensor-activator proteins from different species (NodD of Rhizobium bacteria and vertebrate nuclear receptors) were compared. Several compounds (including flavonoids, coumestrol and estradiol) that bind to mammalian receptors also interact with NodD proteins. NodD-dependent synergism of the signal compounds luteolin and catechin was observed suggesting that these compounds bind directly to NodD. Two regions comprising 63 and 37 amino acids in NodD showed 45% and 36% homology, respectively, with the estrogen receptor. These regions, designated as modules M1 and M2, coincide with conserved parts of the ligand-binding domains of the nuclear receptors. A part of NodD overlapping with the M1 module was predicted to be membrane associated and was 46% homologous to a membrane-spanning sensory segment of the Agrobacterium VirA protein. We suggest that the homologous polypeptide modules detected in NodD and the nuclear receptors originate from a common ancestor protein and may be directly involved in ligand binding.

Novel organization of the common nodulation genes in Rhizobium leguminosarum bv. phaseoli strains

Nodulation by Rhizobium, Bradyrhizobium, and Azorhizobium species in the roots of legumes and nonlegumes requires the proper expression of plant genes and of both common and specific bacterial nodulation genes. The common nodABC genes form an operon or are physically mapped together in all species studied thus far. Rhizobium leguminosarum bv. phaseoli strains are classified in two groups. The type I group has reiterated nifHDK genes and a narrow host range of nodulation. The type II group has a single copy of the nifHDK genes and a wide host range of nodulation. We have found by genetic and nucleotide sequence analysis that in type I strain CE-3, the functional common nodA gene is separated from the nodBC genes by 20 kb and thus is transcriptionally separated from the latter genes. This novel organization could be the result of a complex rearrangement, as we found zones of identity between the two separated nodA and nodBC regions. Moreover, this novel organization of the common nodABC genes seems to be a general characteristic of R. leguminosarum bv. phaseoli type I strains. Despite the separation, the coordination of the expression of these genes seems not to be altered.

Subcellular localization of the Rhizobium leguminosarum nodI gene product

By the use of antibodies raised against a fusion protein of lacZ'-nodI (produced in Escherichia coli) which specifically react with NodI protein, it was shown that in wild-type Rhizobium leguminosarum biovar viciae NodI protein (i) is recovered with the cytoplasmic membrane fraction and (ii) is translated as part of the nodABCIJ operon. In addition, it was found that the bacterial chromosomal background strongly influences the expression of several nod genes.

Strain-Specific Inhibition of nod Gene Induction in Bradyrhizobium japonicum by Flavonoid Compounds

A broad-host-range plasmid, pEA2-21, containing a Bradyrhizobium japonicum nodABC'-'lacZ translational fusion was used to identify strain-specific inhibitors of the genes required for soybean nodulation, the common nod genes. The responses of type strains of B. japonicum serogroups USDA 110, USDA 123, USDA 127, USDA 129, USDA 122, and USDA 138 to nod gene inhibitors were compared. Few compounds inhibited nod gene expression in B. japonicum USDA 110. In contrast, nod gene expression in strains belonging to several other serogroups was inhibited by most of the flavonoids tested. However, the application of two of these strain-specific compounds, chrysin and naringenin, had little effect on the pattern of competition between indigenous and inoculum strains of B. japonicum in greenhouse and field trials. Preliminary studies with radiolabeled chrysin and naringenin suggest that the different responses to nod gene inhibitors may be partly due to the degree to which plant flavonoids can be metabolized by each strain.