Early nodulin genes are induced in alfalfa root outgrowths elicited by auxin transport inhibitors

Expression of different calmodulin genes in bean (Phaseolus vulgaris L.): role of nod factor on calmodulin gene regulation

Three calmodulin (PvCaM-1, PvCaM-2, and PvCaM-3) clones were isolated from a Phaseolus vulgaris nodule cDNA library. All clones contain the complete coding region and are 62 to 74% homologous within this region. Compared to plant CaM consensus sequences, PvCaM-2 has a novel tyrosine118 residue, representing a putative phosphorylation site. Southern analysis suggested that calmodulin is encoded by a gene family. These three CaM clones are expressed mainly in young tissues and meristems. The expression pattern of PvCaM-2 and PvCaM-3 is almost identical but different from that of PvCaM-1, suggesting that PvCaM-1 is a well-defined CaM gene, whereas PvCaM-2 and PvCaM-3 could be alleles. PvCaM clones are expressed early in nodules, and transcript levels increase from nodule primordia to nodule-like structures induced by the Nod factor. Conversely, in roots, Nod factor lowers mRNA levels of all three PvCaM clones, but especially of PvCaM-1. Inhibition of PvCaM-1 expression also is observed when 2,3,5-triiodobenzoic acid is added and is prevented when roots are treated with indole-3-acetic acid, suggesting that PvCaM-1 regulation is related to the Nod factor inhibition of polar auxin transport. These results could suggest that CaM clones do not participate in the early signaling generated by the Nod factor but do participate in early events of nodule formation.

Co-inoculation with Bacillus sp. CECT 450 improves nodulation in Phaseolus vulgaris L

The strain Bacillus sp. CECT 450 increased nodulation on bean (Phaseolus vulgaris L.) when co-inoculated with Rhizobium tropici CIAT 899. This positive effect occured under controlled conditions on perlite-vermiculite, sand, or in a mixture of soil and sand. This increase was also observed in a field assay. Nodulation kinetic studies suggested that the synergistic effect is pronounced during the latter stages of cultivation. In contrast, the same bacteria co-inoculated with Bradyrhizobium japonicum USDA 110 reduced nodulation on soybean (Glycine max (L.) Merr.). Inoculation with Bacillus sp. CECT 450 alone had no effect on bean plants, but reduced root growth in soybean. The survival of Bacillus sp. CECT 450 on inoculated seeds was high, even when inoculated seeds were maintained for several months at room temperature.

Overlapping plant signal transduction pathways induced by a parasitic nematode and a rhizobial endosymbiont

Root-knot nematodes and rhizobia establish interactions with roots characterized by the de novo induction of host structures, termed giant cells and nodules, respectively. Two transcription regulators, PHAN and KNOX, required for the establishment of meristems were previously shown to be expressed in tomato giant cells. We isolated the orthologues of PHAN and KNOX (Mt-phan and Mt-knox-1) from the model legume Medicago truncatula, and established the spatial distribution of their expression in situ. We confirmed that Mt-phan and Mt-knox-1 are expressed in lateral root initials and in nematode-induced giant cells and showed that they are expressed in nodules induced by Sinorhizobium meliloti. Expression of both genes becomes spatially restricted as the nodules develop. We further examined nematode feeding sites for the expression of two genes involved in nodule formation, ccs52 (encodes a mitotic inhibitor) and ENOD40 (encodes an early, nodulation mitogen), and found transcripts of both genes to be present in and around giant cells induced in Medicago. Collectively, these results reveal common elements of host responses to mutualistic and parasitic plant endosymbionts and imply that overlapping regulatory pathways lead to giant cells and nodules. We discuss these pathways in the context of phytohormones and parallels between beneficial symbiosis and disease.

Effects of cytokinin on ethylene production and nodulation in pea (Pisum sativum) cv. Sparkle

In this study, we were interested in learning if cytokinins play a role in the developmental process that leads to nodulation in the pea cv. Sparkle. We demonstrate that the application of the synthetic cytokinin BAP (6-benzyl-amino-purine) results in a number of nodulation-related changes. BAP stimulates the production of ethylene, a known inhibitor of nodulation. At low levels (up to 1 &mgr;M), BAP also stimulates nodulation but as its concentration is increased (up to 25 &mgr;M), nodule number decreases. In BAP-treated roots, the infection threads are abnormal; they are twisted, very knotty, and generally grow in a direction parallel to the root surface. In addition, the centers of cell division in the inner cortex are very few. Thus, BAP-treated Sparkle appears to phenocopy the low-nodulating pea mutant R50 [Guinel FC, Sloetjes LL (2000) Ethylene is involved in the nodulation phenotype of Pisum sativum R50 (sym 16), a pleiotropic mutant that nodulates poorly and has pale green leaves. J Exp Bot 51: 885-894]. However, it appears doubtful that there is a direct correlation between the actions of cytokinin and ethylene in causing a reduction in nodule organogenesis because nodulation is not restored by treating BAP-treated Sparkle with ethylene inhibitors.

Flavonoids act as negative regulators of auxin transport in vivo in arabidopsis

Polar transport of the plant hormone auxin controls many aspects of plant growth and development. A number of synthetic compounds have been shown to block the process of auxin transport by inhibition of the auxin efflux carrier complex. These synthetic auxin transport inhibitors may act by mimicking endogenous molecules. Flavonoids, a class of secondary plant metabolic compounds, have been suggested to be auxin transport inhibitors based on their in vitro activity. The hypothesis that flavonoids regulate auxin transport in vivo was tested in Arabidopsis by comparing wild-type (WT) and transparent testa (tt4) plants with a mutation in the gene encoding the first enzyme in flavonoid biosynthesis, chalcone synthase. In a comparison between tt4 and WT plants, phenotypic differences were observed, including three times as many secondary inflorescence stems, reduced plant height, decreased stem diameter, and increased secondary root development. Growth of WT Arabidopsis plants on naringenin, a biosynthetic precursor to those flavonoids with auxin transport inhibitor activity in vitro, leads to a reduction in root growth and gravitropism, similar to the effects of synthetic auxin transport inhibitors. Analyses of auxin transport in the inflorescence and hypocotyl of independent tt4 alleles indicate that auxin transport is elevated in plants with a tt4 mutation. In hypocotyls of tt4, this elevated transport is reversed when flavonoids are synthesized by growth of plants on the flavonoid precursor, naringenin. These results are consistent with a role for flavonoids as endogenous regulators of auxin transport.

Flavonoids induced in cells undergoing nodule organogenesis in white clover are regulators of auxin breakdown by peroxidase

It was tested whether flavonoids that specifically accumulate in cells undergoing early nodule organogenesis could affect auxin turnover by a peroxidase to explain local changes in auxin distribution that occur during nodule formation in white clover (Trifolium repens cv. Haifa). A fluorometric assay was developed to determine the kinetics of indoleacetic acid (IAA) breakdown rates by a horseradish peroxidase in vitro. Three flavonoid compounds, which had previously been localized and identified, were purified from root tissue and their tissue concentrations estimated. A derivative of 7,4'-dihydroxyflavone (DHF), as well as free DHF, strongly inhibited auxin breakdown by peroxidase at concentrations estimated in the root tissue. Formononetin, an isoflavonoid accumulating in nodule primordia, accelerated auxin breakdown by peroxidase at concentrations estimated to be present in the roots. These results suggest that local changes in flavonoid accumulation could regulate local auxin levels during nodule organogenesis. The results are consistent with previous observations on the localization of auxin during nodule organogenesis. A model for the interaction of flavonoids with peroxidases is proposed to explain changes auxin during nodule development. A similar mechanism could be involved in lateral root and root gall formation.

Flavonoids induced in cells undergoing nodule organogenesis in white clover are regulators of auxin breakdown by peroxidase

It was tested whether flavonoids that specifically accumulate in cells undergoing early nodule organogenesis could affect auxin turnover by a peroxidase to explain local changes in auxin distribution that occur during nodule formation in white clover (Trifolium repens cv. Haifa). A fluorometric assay was developed to determine the kinetics of indoleacetic acid (IAA) breakdown rates by a horseradish peroxidase in vitro. Three flavonoid compounds, which had previously been localized and identified, were purified from root tissue and their tissue concentrations estimated. A derivative of 7,4'-dihydroxyflavone (DHF), as well as free DHF, strongly inhibited auxin breakdown by peroxidase at concentrations estimated in the root tissue. Formononetin, an isoflavonoid accumulating in nodule primordia, accelerated auxin breakdown by peroxidase at concentrations estimated to be present in the roots. These results suggest that local changes in flavonoid accumulation could regulate local auxin levels during nodule organogenesis. The results are consistent with previous observations on the localization of auxin during nodule organogenesis. A model for the interaction of flavonoids with peroxidases is proposed to explain changes auxin during nodule development. A similar mechanism could be involved in lateral root and root gall formation.

Accumulation of ENOD2-like transcripts in non-nodulating woody papilionoid legumes

Japanese pagodatree (Styphnolobium japonicum [L.] Schott) and American yellowwood (Cladrastis kentukea Dum.-Cours.) Rudd are the first woody, non-nodulating papilionoid legumes shown to possess putative early nodulin 2 (ENOD2) genes. ENOD2 cDNAs from Japanese pagodatree (807 bp) and American yellowwood (735 bp) have 75% to 79% sequence identity to ENOD2 sequences and encode deduced proteins that possess conserved ENOD2 pentapeptides (PPHEK and PPEYQ). Lower percentages of glucose and higher percentages of histidine and valine suggest that SjENOD2 and CkENOD2 are different from other ENOD2s. Hybridization analyses indicate the clones represent ENOD2 gene families of two to four genes in Japanese pagodatree and American yellowwood genomes, and ENOD2-like transcripts were detected in stems and flowers, as well as roots. Only roots of control species that nodulate, Maackia amurensis Rupr. & Maxim. and alfalfa (Medicago sativa), produced pseudonodules after treatment with zeatin or 2,3,5-triiodobenzoic acid, an auxin transport inhibitor. Accumulation of MaENOD2 transcripts was enhanced during the first 10 d of treatment, but 2,3,5-triiodobenzoic acid and zeatin enhanced transcript accumulation after 30 d in roots of Japanese pagodatree and American yellowwood. Characteristics that distinguish ENOD2 gene families in basal, non-nodulating woody legumes from other ENOD2 genes may provide new information about the function of these genes during symbiotic and non-symbiotic organ development.

Expression profiles of 22 novel molecular markers for organogenetic pathways acting in alfalfa nodule development

During symbiotic nodule development, a variety of molecular signals of rhizobia and plant origin are likely to be involved in the control of the expression of specific genes in the legume Medicago sativa (alfalfa). Twenty-two new, nodule-associated Expressed Sequence Tags (ESTs, MsNod clones) as well as 16 clones for previously reported alfalfa nodulins were identified by cold-plaque screening. Protein homologs were found for 10 of the 22 MsNod-encoded polypeptides, revealing putative novel functions associated with this symbiosis. Expression of these MsNod genes was investigated in spontaneous nodules (generated in the absence of bacteria), in nodules induced by a Sinorhizobium meliloti wild-type strain and Eps- and Bac- mutant derivatives, as well as in roots inoculated with a Nod- mutant strain. This analysis enabled us to correlate plant gene expression with the different stages of nodule ontogeny and invasion. The effect of phytohormones on MsNod gene expression was analyzed in cytokinin- and auxin-treated alfalfa roots. Cytokinin induced the accumulation of seven MsNod transcripts, four of them were also regulated by the synthetic auxin 2,4-D (2,4-dichlorophenoxyacetic acid). Comparison of MsNod expression profiles in wild-type and transgenic M. truncatula roots overexpressing the early nodulin Enod40 suggested that one clone, the M. sativa L3 ribosomal protein homolog (MsNod377), is a putative component of an Enod40-dependent pathway acting during nodule development. These novel molecular markers may help in the investigation of gene networks and regulatory circuits controlling nodule organogenesis.

Flavan-containing cells delimit Frankia-infected compartments in Casuarina glauca nodules

We investigated the involvement of polyphenols in the Casuarina glauca-Frankia symbiosis. Histological analysis revealed a cell-specific accumulation of phenolics in C. glauca nodule lobes, creating a compartmentation in the cortex. Histochemical and biochemical analyses indicated that these phenolic compounds belong to the flavan class of flavonoids. We show that the same compounds were synthesized in nodules and uninfected roots. However, the amount of each flavan was dramatically increased in nodules compared with uninfected roots. The use of in situ hybridization established that chalcone synthase transcripts accumulate in flavan-containing cells at the apex of the nodule lobe. Our findings are discussed in view of the possible role of flavans in plant-microbe interactions.

Regulation of symbiotic root nodule development

Symbiosis between rhizobia and leguminous plants leads to the formation of N2-fixing root nodules. The interaction of rhizobia and plants shows a high degree of host specificity based on the exchange of chemical signals between the symbiotic partners. The plant signals, flavonoids exuded by the roots, activate the expression of nodulation genes, resulting in the production of the rhizobial lipochitooligosaccharide signals (Nod factors). Nod factors act as morphogens that, under conditions of nitrogen limitation, induce cells within the root cortex to divide and to develop into nodule primordia. This review focuses on how the production of Nod factors is regulated, how these signals are perceived and transduced by the plant root, and the physiological conditions and plant factors that control the early events leading to root nodule development.

Nodule parenchyma-specific expression of the sesbania rostrata early nodulin gene SrEnod2 is mediated by its 3' untranslated region

The early nodulin Enod2 gene encodes a putative hydroxyproline-rich cell wall protein and is expressed exclusively in the nodule parenchyma cell layer. The latter finding suggests that the Enod2 protein may contribute to the special morphological features of the nodule parenchyma and to the creation of an oxygen diffusion barrier. The Enod2 gene of the stem-nodulating legume Sesbania rostrata (SrEnod2) is induced specifically in roots by the plant hormone cytokinin, and this induction occurs at a post-transcriptional level. Here, we characterize the cis determinant(s) in the SrEnod2 locus responsible for nodule parenchyma-specific expression and show that the 3' untranslated region (UTR) of the SrEnod2 gene is both required and sufficient for directing chimeric reporter gene expression in the nodule parenchyma of transgenic Lotus corniculatus plants. Moreover, we show that the SrEnod2 3' UTR does not act as a tissue-specific enhancer element. By conducting a detailed deletion analysis of the 5' and 3' SrEnod2 regions, we delimited the minimal promoter of the SrEnod2 gene, and it appears that the 5' flanking sequences are not essential for nodule parenchyma-specific expression. This finding is in contrast with the report that the 5' upstream region of the soybean Enod2 gene directs nodule parenchyma-specific expression, indicating that different mechanisms may be involved in regulating the expression of these two genes. We definitively demonstrate that the cis element(s) for tissue-specific expression is located within the 3' UTR of a plant nuclear gene.

Auxin transport inhibition precedes root nodule formation in white clover roots and is regulated by flavonoids and derivatives of chitin oligosaccharides

The expression of the auxin responsive reporter construct, GH3:gusA, was examined in transgenic white clover plants to assess changes in the auxin balance during the earliest stages of root nodule formation. Reporter gene expression was monitored at marked locations after the application of bacteria or signal molecules using two precise inoculation techniques: spot-inoculation and a novel method for ballistic microtargeting. Changes in GH3:gusA expression were monitored after the inoculation of Rhizobium leguminosarum biovar trifolii, non-host rhizobia, lipo-chitin oligosaccharides (LCOs), chitin oligosaccharides, a synthetic auxin transport inhibitor (naphthylphthalamic acid; NPA), auxin, the ENOD40-1 peptide or different flavonoids. The results show that clover-nodulating rhizobia induce a rapid, transient and local downregulation of GH3:gusA expression during nodule initiation followed by an upregulation of reporter gene expression at the site of nodule initiation. Microtargeting of auxin caused a local and acropetal upregulation of GH3:gusA expression, whereas NPA caused local and acropetal downregulation of expression. Both spot-inoculation and microtargeting of R. l. bv. trifolii LCOs or flavonoid aglycones induced similar changes to GH3:gusA expression as NPA. O-acetylated chitin oligosaccharides caused similar changes to GH3:gusA expression as R. l. bv. trifolii spot-inoculation, but only after delivery by microtargeting. Non-O-acetylated chitin oligosaccharides, flavonoid glucosides or the ENOD40-1 peptide failed to induce any detectable changes in GH3:gusA expression. GH3:gusA expression patterns during the later stages of nodule and lateral root development were similar. These results support the hypothesis that LCOs and chitin oligosaccharides act by perturbing the auxin flow in the root during the earliest stages of nodule formation, and that endogenous flavonoids could mediate this response.

Studying early nodulin gene ENOD40 expression and induction by nodulation factor and cytokinin in transgenic alfalfa

ENOD40, an early nodulin gene, is expressed following inoculation with Rhizobium meliloti or by adding R. meliloti-produced nodulation (Nod) factors or the plant hormone cytokinin to uninoculated roots. We isolated two MsENOD40 clones, designated MsENOD40-1 and MsENOD40-2, with distinct promoters from an alfalfa (Medicago sativa cv Chief) genomic library. The promoters were fused to the reporter gene uidA (gus), and the constructs were introduced into alfalfa. We observed that the MsENOD40-1 construct was expressed almost exclusively under symbiotic conditions. The MsENOD40-2 construct was transcribed under both symbiotic and nonsymbiotic conditions and in nonnodular and nodular tissues. Both MsENOD40 promoter-gus constructs were similarly expressed as nodules developed, and both were expressed in roots treated with 6-benzylaminopurine or purified Nod factor. However, no blue color was detected in nodule-like structures induced by the auxin transport inhibitor N-1-(naphthyl)phthalamic acid on roots of plants containing the MsENOD40-1 promoter construct, whereas pseudonodules from plants containing the MsENOD40-2 promoter construct stained blue. A 616-bp region at the distal 5' end of the promoter is important for proper spatial expression of MsENOD40 in nodules and also for Nod-factor and cytokinin-induced expression.

Chitin oligosaccharides can induce cortical cell division in roots of Vicia sativa when delivered by ballistic microtargeting

Rhizobia, bacterial symbionts of leguminous plants, produce lipo-chitin oligosaccharide (LCO) signal molecules that can induce nodule organogenesis in the cortex of legume roots in a host-specific way. The multi-unsaturated fatty acyl and the O-acetyl moieties of the LCOs of Rhizobium leguminosarum biovar viciae were shown to be essential for obtaining root nodule induction in Vicia sativa plants. We have used ballistic microtargeting as a novel approach to deliver derivatives of the nodulation signal molecules inside the roots of V. sativa. This method offers the unique ability to introduce soluble compounds into the tissue at a small area. The mitogenic effect of microtargeting of chitin oligosaccharides, including an analysis of the influence of the chain length and modifications, was tested in a qualitative assay. The role of a cell division factor from the root stele, uridine, has also been examined in these experiments. The results show that O-acetylated chitin oligosaccharides can induce root cortical cell divisions when delivered by microtargeting. For this effect it is essential that uridine is co-targeted. The foci of cortical cell division were often similar to root nodule primordia. Anatomical examination also revealed chimeric structures that share characteristics with lateral root and nodule primordia. Our data favour a model in which the oligosaccharide moiety of the rhizobial LCO induces cortical cell division and the fatty acyl moiety plays a role in transport of the LCO into the plant tissue.

Cloning of a WD-repeat-containing gene from alfalfa (Medicago sativa): a role in hormone-mediated cell division?

Rhizobium meliloti can interact symbiotically with Medicago plants thereby inducing the formation of root nodules. Screening of a young nodule cDNA library led to the isolation of a cDNA from Medicago sativa, Msgbl, that comprises a new member of the RACK1 (Receptor of Activated C Kinase) subfamily of WD-repeat proteins. This subfamily shows homology to the beta-subunit of heterotrimeric G proteins. Besides RACK1, this subfamily contains several plant genes including the well characterized auxin-inducible ArcA of tobacco. The Msgbl gene is strongly expressed in young embryos and in leaves, and is induced upon cytokinin treatment of roots. Whereas northern analysis failed to reveal differences in expression between total RNA from roots and nodules, in situ hybridization demonstrated that the transcript was most abundant in dividing cells of nodule primordia and in the nodule meristem. Msgbl may be related to the signal transduction acting in response to hormone-mediated cell division.

Evolutionary diversity of symbiotically induced nodule MADS box genes: characterization of nmhC5, a member of a novel subfamily

Unique organs called nodules form on legume roots in response to intracellular infection by soil bacteria in the genus Rhizobium. This study describes a new MADS box gene, nmhC5, which along with nmh7 (J. Heard and K. Dunn, Proc. Natl. Acad. Sci. USA 92:5273-5277, 1995), is expressed in alfalfa (Medicago sativa) root nodules. Together, these genes represent the first putative transcription factors identified in nodules. Expression in a root-derived structure supports the growing sentiment that MADS box proteins have diverse roles in plant development. Comparison of the putative translation product of nmhC5 with those of other reported members of the MADS box family suggests that the overall structure of nmhC5 is conserved. Evolutionary analysis among the MADS box family showed that nmhC5 is orthologous to a root-expressed clone in Arabidopsis thaliana, agl17, and that nmh7 is similar to the floral subfamily with AP3 (DefA)/PI (Glo). Consistent with a prediction of homodimer formation, NMHC5 was shown to bind a CArG consensus sequence in vitro. In contrast, NMH7, which shows structural similarity to MADS box proteins that form heterodimers, did not bind the CArG element in an in vitro DNA-binding assay, suggesting the existence of an unknown dimer partner. The root-derived MADS box genes constitute a novel subfamily of vegetatively expressed MADS box genes. The evolutionary diversity between nmh7 and nmhC5 could represent an overall mechanistic conservation between plant developmental processes or could mean that nmh7 and nmhC5 make fundamentally different contributions to the development of the nodule.

Expression of early nodulin genes in alfalfa mycorrhizae indicates that signal transduction pathways used in forming arbuscular mycorrhizae and Rhizobium-induced nodules may be conserved

Transcripts for two genes expressed early in alfalfa nodule development (MsENOD40 and MsENOD2) are found in mycorrhizal roots, but not in noncolonized roots or in roots infected with the fungal pathogen Rhizoctonia solani. These same two early nodulin genes are expressed in uninoculated roots upon application of the cytokinin 6-benzylaminopurine. Correlated with the expression of the two early nodulin genes, we found that mycorrhizal roots contain higher levels of trans-zeatin riboside than nonmycorrhizal roots. These data suggest that there may be conservation of signal transduction pathways between the two symbioses-nitrogen-fixing nodules and phosphate-acquiring mycorrhizae.

Plant genes involved in root-nodule development on legumes

Rhizobium is able to induce the formation of a new organ on roots of leguminous plants, the root nodule, in which the penetrated bacteria fix atmospheric nitrogen. This process is initiated by specific lipo-oligosaccharides, called Nod factors, secreted by the bacterium. Nodule formation proceeds through distinct steps like infection thread formation and activation of mitotic activity in cortical cells. During these steps specific plant genes, nodulin genes, are induced and several of these have been identified and characterized. Nodulin genes are used now as markers to study Nod factor perception and signal transduction.

Influence of indoleacetic-acid-producing Bacillus isolates on the nodulation of Phaseolus vulgaris by Rhizobium etli under gnotobiotic conditions

Twenty-two Bacillus spp. isolates from the rhizosphere of Phaseolus vulgaris 'Contender' were identified using Biolog™, gas chromatographic fatty acid methyl ester, and 23S rDNA analyses. Some of the Bacillus isolates produced significant amounts of the phytohormone indoleacetic acid (IAA) when grown in a liquid culture medium supplemented with 100 μg L-tryptophan/L; less IAA was produced in culture medium not supplemented with L-tryptophan. Thin-layer chromatography, high-performance liquid chromatography, gas chromatography – mass spectrometry, and the avena coleoptile bioassay were used to identify and quantify IAA produced by Bacillus isolates. Significant differences were observed in the amounts of IAA produced by different strains of Bacillus, with amounts varying from 0.40 to 4.88 μg/mL. α-Methyltryptophan-resistant mutants of Bacillus exhibited altered IAA production and excreted tryptophan into the growing medium. The IAA-producing Bacillus isolates promoted root growth and (or) nodulation when coinoculated with Rhizobium etli (TAL 182) on Phaseolus vulgaris 'Contender' under gnotobiotic conditions in growth chambers. Coinoculation resulted in increased nodule number, nodule fresh weight, nitrogenase activity, leghemoglobin content, and total soluble protein content in the root nodules of Phaseolus vulgaris. In contrast, coinoculation with α-methyltryptophan mutants resulted in decreased nodulation, indicating that Bacillus isolates have a direct effect on either the Rhizobium or the plant and the effect may not be singularly attributed to their ability to produce IAA in vitro.Key words: Bacillus, indoleacetic acid production, nodulation enhancement.

Modification of phytohormone response by a peptide encoded by ENOD40 of legumes and a nonlegume

The gene ENOD40 is expressed during early stages of legume nodule development. A homolog was isolated from tobacco, which, as does ENOD40 from legumes, encodes an oligopeptide of about 10 amino acids. In tobacco protoplasts, these peptides change the response to auxin at concentrations as low as 10(-12) to 10(-16)M. The peptides encoded by ENOD40 appear to act as plant growth regulators.

Plant genes induced in the Rhizobium-legume symbiosis

Rhizobium, Bradyrhizobium and Azorhizobium can elicit the formation of N2-fixing nodules on the roots or stems of their leguminous host plants. The nodule formation involves several developmental steps determined by different sets of genes from both partners, the gene expression being temporally and spatially coordinated. The plant proteins that are specifically synthesised during the formation and function of the nodule are called nodulins. The nodulins that are expressed before the onset of N2 fixation are termed early nodulins. These proteins are probably involved in the infection process as well as in nodule morphogenesis rather than in nodule function. The nodulins expressed just before or during N2 fixation are termed late nodulins and they participate in the function of the nodule by creating the physiological conditions required for nitrogen fixation, ammonium assimilation and transport. In this review we will describe nodulins, nodulin genes and the relationship between nodulin gene expression and nodule development. The study of nodulin gene expression may provide insight into root-nodule development and the mechanism of communication between bacteria and host plant.

Uridine, a cell division factor in pea roots

Nodulation (root nodule formation) in legume roots is initiated by the induction of cell divisions and formation of root nodule primordia in the plant root cortex, usually in front of the protoxylem ridges of the central root cylinder. We isolated a factor from the central cylinder (stele) of pea roots which enhances hormone-induced cell proliferation in root cortex explants at positions similar to those of nodule primordia. The factor was identified as uridine. Uridine may act as a morphogen in plant roots at picomolar concentrations.

Morphological and Molecular Characteristics of Host-Conditioned Ineffective Root Nodules in Cowpea

In cowpea (Vigna unguiculata [L.] Walp.) a recessive allele, designated cpi, elicits the formation of non-N2-fixing nodules with all bacterial isolates tested. Comparisons of mutant and wild-type nodules demonstrated that the ineffective nodules were anatomically similar to the wild type and contained both infection threads and bacteroids. Ineffective nodules were smaller, however, largely because of the reduced size of the infected cells. Additionally, the number of bacteroids was reduced and senescence occurred prematurely in the infected cells. Grafting studies demonstrated that the defect in nodule development was controlled by the root rather than the shoot. Northern analysis of four nodulin genes indicated that in the ineffective nodules transcript levels of the early nodulin VuENOD2 were initially reduced but were equivalent to wild-type nodules by 21 d. In contrast, transcript levels of the early nodulin VuB were initially similar in both genotypes but as the nodules matured the mRNA levels declined more slowly in the ineffective nodules. The late nodulins leghemoglobin and uricase were expressed in the ineffective nodules but at greatly reduced levels. Thus, the cpi-conditioned defect in nodulation is associated with impaired bacteroid maturation and maintenance, altered nodulin expression, and accelerated senescence.

Symbiotic induction of a MADS-box gene during development of alfalfa root nodules

In response to infection by Rhizobium, highly differentiated organs called nodules form on legume roots. Within these organs, the symbiotic association between the host plant and bacteria is established. A putative plant transcription factor, NMH7, has been identified in alfalfa root nodules. nmh7 contains a MADS-box DNA-binding region and shows homology to flower homeotic genes. This gene is a member of a multigene family in alfalfa and was identified on the basis of nucleic acid homology to plant regulatory protein genes (MADS-box-containing genes) from Antirrhinum and Arabidopsis. RNA analysis and in situ hybridization showed that expression of this class of regulatory genes is limited to the infected cells of alfalfa root nodules and is likely to be involved in the signal transduction pathway initiated by the bacterial symbiont, Rhizobium meliloti. The expression of nmh7 in a root-derived organ is unusual for this class of regulatory genes.

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.

Synthesis of phytohormones by plant-associated bacteria

The plant hormones, auxins and cytokinins, are involved in several stages of plant growth and development such as cell elongation, cell division, tissue differentiation, and apical dominance. The biosynthesis and the underlying mechanism of auxins and cytokinins action are subjects of intense investigation. Not only plants but also microorganisms can synthesize auxins and cytokinins. The role of phytohormone biosynthesis by microorganisms is not fully elucidated: in several cases of pathogenic fungi and bacteria these compounds are involved in pathogenesis on plants; auxin and cytokinin production may also be involved in root growth stimulation by beneficial bacteria and associative symbiosis. The genetic mechanism of auxin biosynthesis and regulation by Pseudomonas, Agrobacterium, Rhizobium, Bradyrhizobium, and Azospirillum, are well studied; in these bacteria several physiological effects have been correlated to the bacterial phytohormones biosynthesis. The pathogenic bacteria Pseudomonas and Agrobacterium produce indole-3-acetic acid via the indole-3-acetamide pathway, for which the genes are plasmid borne. However, they do possess also the indole-3-pyruvic acid pathway, which is chromosomally encoded. In addition, they have genes that can conjugate free auxins or hydrolyze conjugated forms of auxins and cytokinins. In Agrobacterium there are also several genes, located near the auxin and cytokinin biosynthetic genes, that are involved in the regulation of auxins and cytokinins sensibility of the transformed plant tissue. Symbiotic bacteria Rhizobium and Bradyrhizobium synthesize indole-3-acetic acid via indole-3-pyruvic acid; also the genetic determinants for the indole-3-acetamide pathway have been detected, but their activity has not been demonstrated. In the plant growth-promoting bacterium Azospirillum, as in Agrobacterium and Pseudomonas, both the indole-3-pyruvic acid and the indole-3-acetamide pathways are present, although in Azospirillum the indole-3-pyruvic acid pathway is of major significance. In addition, biochemical evidence for a tryptophan-independent indole-3-acetic acid pathway in Azospirillum has been presented.

Signal molecules involved in plant embryogenesis

In plant embryogenesis, inductive interactions mediated by diffusable signal molecules are most likely of great importance. Evidence has been presented that at late globular stages in plant embryogenesis, perturbation of the polar auxin transport results in abberrant embryo morphology. Rhizobium lipooligosaccharides or Nod factors are a newly discovered class of bacterial molecules that are able to trigger initial steps in root nodule development in legumes. Part of the activity of Nod factors may be directed towards alteration of endogenous plant growth regulator balance. The same bacterial Nod factors promoted the formation of globular embryos in the carrot cell line ts11. Whether there exist plant analogues of the Nod factors and whether these molecules are active as a more universal control system perhaps designed to initiate and or mediate gradients in auxin and cytokinin remains to be determined.

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.

Site-specific mutagenesis of the nodule-infected cell expression (NICE) element and the AT-rich element ATRE-BS2* of the Sesbania rostrata leghemoglobin glb3 promoter

Sesbania rostrata leghemoglobin glb3 (Srglb3) promoter sequences responsible for expression in infected cells of transgenic Lotus corniculatus nodules were delimited to a 78-bp Dral-Hinfl fragment. This region, which is located between coordinates -194 to -116 relative to the start codon of the Srglb3 gene, was named the nodule-infected cell expression (NICE) element. Insertion of the NICE element into the truncated nopaline synthase promoter was found to confer a nodule-specific expression pattern on this normally root-enhanced promoter. Within the NICE element, three distinct motifs ([A]AAAGAT, TTGTCTCTT, and CACCC[T]) were identified; they are highly conserved in the promoter regions of a variety of plant (leg)hemoglobin genes. The NICE element and the adjacent AT-rich element (ATRE-BS2*) were subjected to site-directed mutagenesis. The expression patterns of nine selected Srglb3 promoter fragments carrying mutations in ATRE-BS2* and 19 with mutations in the NICE element were examined. Mutations in ATRE-BS2* had varying effects on Srglb3 promoter activity, ranging from a two- to threefold reduction to a slight stimulation of activity. Mutations in the highly conserved (A)AAAGAT motif of the NICE element reduced Srglb3 promoter activity two- to fourfold, whereas mutations in the TCTT portion of the TTGTCTCTT motif virtually abolished promoter activity, demonstrating the essential nature of these motifs for Srglb3 gene expression. An A-to-T substitution in the CACCC(T) motif of the NICE element also abolished Srglb3 promoter activity, while a C-to-T mutation at position 4 resulted in a threefold reduction of promoter strength. The latter phenotypes resemble the effect of similar mutations in the conserved CACCC motif located in the promoter region of mammalian beta-globin genes. The possible analogies between these two systems will be discussed.

Isolation of chalcone synthase and chalcone isomerase cDNAs from alfalfa (Medicago sativa L.): highest transcript levels occur in young roots and root tips

Flavonoids are involved in several different interactions between plants and microorganisms. In the Rhizobium-legume symbiosis, they play an important role as inducers of rhizobial nodulation (nod) genes. We have identified from an alfalfa cDNA library four clones for chalcone synthase (CHS) and two clones for chalcone isomerase (CHI); CHS and CHI are key enzymes in flavonoid biosynthesis. In Medicago sp., CHS is encoded by 8-12 genes, and CHI is encoded by 1-2 genes. Here we report the DNA sequence of these clones as well as their relatedness to other legume CHS and CHI clones. In addition, we report on the expression patterns of two CHS gene family members as well as the CHI gene in M. sativa cv. Iroquois. While CHS and CHI transcript levels are high in root tips and entire young roots, they are low in effective nodules elicited by wild-type strains of Rhizobium meliloti and very low in aerial portions of the plant (stems, leaves, flowers). However, wounding the cotyledons results in a rapid increase in transcript levels of both chalcone synthase and chalcone isomerase genes in these organs.

Five Nodulation Mutants of White Sweetclover (Melilotus alba Desr.) Exhibit Distinct Phenotypes Blocked at Root Hair Curling, Infection Thread Development, and Nodule Organogenesis

In an effort to obtain a developmental sequence of mutations in the Rhizobium-legume interaction within a single legume species, we have characterized the early events of nodule development in 10 nodulation mutants of sweetclover, Melilotus alba Desr. cv U389, representing five genetic loci. Both seed and root exudates from all of the sweetclover mutants induced expression of the nod genes of Rhizobium meliloti. Mutants in three loci were blocked in the early stages of root hair curling. Of these, a mutant in the sym-3 locus exhibited root hair deformations in response to inoculation with R. meliloti but produced no nodules or emerging nodule primordia, suggesting a blockage in the signal transduction events leading to nodule organogenesis. In contrast, mutants in both the sym-1 and sym-5 loci formed ineffective nodules in response to inoculation but differed slightly in the type of root hair response observed. None of these three early mutants formed infection threads. Infection threads were observed in mutant sym-2 as well as in ineffective nodules. Mutant sym-4 also formed infection threads but lacked nodules. The phenotypes observed for mutants from these five loci suggest that a secondary receptor or signal produced by the plant is required for nodule development.

A gene that encodes a proline-rich nodulin with limited homology to PsENOD12 is expressed in the invasion zone of Rhizobium meliloti-induced alfalfa root nodules

To define the early stages of the interaction between Rhizobium and host legumes, we have cloned and characterized three early nodulin-encoding sequences from an alfalfa (Medicago sativa L.) cDNA library by probing with a fragment of a cDNA clone for PsENOD12, an infection-related nodulin from pea (Pisum sativum L.). Although the coding regions of the three clones are 95 to 98% homologous to each other, they are only 43% homologous to the pea clone. However, the putative signal peptide encoded by the alfalfa cDNA clones is 100% homologous to the PsENDO12 signal peptide. The spatial and temporal expression patterns of PsENOD12 and the alfalfa clones were compared. In situ hybridization experiments detected RNA transcripts in the invasion zone of mature nitrogen-fixing nodules, the same site where PsENOD12 mRNAs are found. Transcripts were also found by in situ hybridization in cells of Rhizobium meliloti exoH mutant-induced nodules penetrated by infection threads, but northern analysis did not detect transcripts in inf- (infection thread minus) nodules elicited by R. meliloti exoB nodules or in pseudonodules elicited by treatment with the auxin transport inhibitor N-1-(naphthyl)phthalamic acid. In addition, the alfalfa gene represented by these cDNA clones exhibited a temporal expression pattern that differed from that of PsENOD12, which is transiently expressed. These data, plus information derived from Southern blot analysis, indicate that we have isolated cDNA clones for a novel early nodulin, which we have designated MsENOD10 (Medicago sativa Early Nodulin 10).

Stress responses in alfalfa (Medicago sativa L.). 15. Characterization and expression patterns of members of a subset of the chalcone synthase multigene family

We have identified five different full length chalcone synthase (CHS) cDNA clones from a cDNA library produced from transcripts isolated from an elicitor-treated alfalfa cell suspension culture. Nucleotide sequence similarity between the clones varied from 88-93%. Oligonucleotides based on divergent sequences in the 5'-untranslated regions of the clones could distinguish individual genes, or groups of genes, and their corresponding transcripts. Developmentally regulated expression of the CHS transcripts was predominantly in roots and root nodules; other unidentified members of the CHS gene family are expressed in stems, leaves and nodules. One of the CHS transcripts was strongly expressed in floral tissue. All the CHS transcripts studied were induced in elicitor-treated cell suspension cultures. Transcripts were also induced in roots in response to wounding or spraying with various elicitors, and in leaves infected with Phoma medicaginis (but not in wounded leaves). The induction kinetics of CHS2 transcripts were more rapid and/or transient than those of other members of the CHS family in CuCl2-treated roots and Phoma-infected leaves. The results are discussed in terms of the evolution and functions of the CHS gene family in legumes.

Isolation and characterization of novel nodulin cDNAs representing genes expressed at early stages of soybean nodule development

We took advantage of a subtractive hybridization procedure to isolate a set of cDNA clones of nodule-specific genes (nodulin genes) from developing soybean root nodules. Single-stranded 32P-labelled cDNA synthesized from nodule poly(A)+ RNA was hybridized with a large excess of uninfected root poly(A)+ RNA. Unhybridized cDNA was selected and used to screen nodule cDNA libraries. By this procedure we isolated several novel nodulin cDNA clones together with most of the nodulin cDNAs previously described. Four novel nodulin genes, which were expressed long before the onset of nitrogen fixation, were further characterized. GmN#36 and GmN#93 transcripts appeared in the roots less than 3 days after sowing and inoculation with Bradyrhizobium, but GmN#36 transcripts were also detected at very low levels in the stems of uninfected plants. Transcripts of GmN#315 and GmN#70 first appeared at 6-7 days, just before nodule emergence. Amino acid sequences of the predicted products of GmN#36, GmN#93 and GmN#70 exhibited no significant homology to proteins identified so far. The GmN#315 encoded protein has a limited but significant homology to some plant cyanins, suggesting that it is a metal-binding glycoprotein. In situ hybridization studies revealed that GmN#36 transcripts first appeared in the pericycle cells of the root stele near the infected site. During nodule emergence they were found in a few cell layers surrounding the vascular strands connecting the nodule meristem with the root stele, and in mature nodules they were present specifically in the pericycle cells in vascular bundles. These observations led us to hypothesize that GmN#36 gene products play a role in the transport and/or degradation of photosynthate. On the other hand, GmN#93 transcripts first appeared in the primary nodule meristem just below the root epidermis. In mature nodules they were only present in the infected cells.

Conserved regulation of the soybean early nodulin ENOD2 gene promoter in determine and indeterminate transgenic root nodules

The beta-glucuronidase (GUS) activity expressed from the soybean early nodulin ENOD2(B) gene promoter was localized histochemically in nodules of Lotus corniculatus and Trifolium repens. In both the determinate Lotus nodules and the indeterminate Trifolium nodules, activity was found in the parenchyma cells and especially in cells close to the vascular tissue of nodules. The characteristic cell-specific expression of the soybean ENOD2 gene was therefore maintained by the ENOD2(B) promoter in the two developmentally different nodule types. Important DNA elements recognized in transgenic nodules were identified by deletion and hybrid promoter analysis in Lotus corniculatus. An indispensable positive element (PE) and a possible tissue specific element was defined between positions -1792 and -1582 from the transcription start site. Another qualitative control element located between -380 and -53 conferred the ENOD2 characteristic cell type expression on hybrid promoters. This element contains the conserved nodulin gene sequences CTCTT and AAAGAT. In contrast to the ENOD2(B) promoter a chimeric leghemoglobin Ibc3-GUS gene was expressed in the infected cells of both types of nodules. In the indeterminate nodules expression was restricted to the interzone II-III and the active nitrogen-fixing zone III. Interchange of the distal strong positive element (SPE) of Ibc3 and the ENOD2 positive element resulted in an expression pattern different from that observed for the Ibc3 and ENOD2 genes, indicating that different interactions of trans-acting factors are required for regulation of early as well as late nodulin genes.

Two functional soybean genes encoding p34cdc2 protein kinases are regulated by different plant developmental pathways

We have isolated two cDNA clones (cdc2-S5 and cdc2-S6) encoding p34cdc2 protein kinases, homologs of yeast cdc2/CDC28 genes, from a soybean nodule cDNA library. The two sequences share 90% sequence homology in the coding regions. The 5' and 3' noncoding regions are distinct from each other, however, indicating that at least two genes encode p34cdc2 protein kinases in soybean. Both sequences can rescue the cdc28 mutation in Saccharomyces cerevisiae but rescue it with different efficiency. Genomic Southern analysis showed the existence of two copies for each of these genes, which are not closely linked and are nonallelic. The relative expression level of the two soybean p34cdc2 genes varies in different tissues. Expression of cdc2-S5 is higher in roots and root nodules, whereas cdc2-S6 is more actively expressed in aerial tissues, indicating that regulation of these two p34cdc2 genes is coupled with plant developmental pathways. Expression of cdc2-S5 is, furthermore, enhanced after Rhizobium infection, whereas cdc2-S6 fails to respond, suggesting that cdc2-S5 plays a role in nodule initiation and organogenesis. This latter gene preferentially responds to auxin (alpha-naphthaleneacetic acid) treatment, indicating that phytohormones may be involved in the control of cell division mediated by Rhizobium infection. Thus, different p34cdc2 protein kinases may control cell division in different tissues in a multicellular organism and respond to different signals--e.g., phytohormones.