Effects of flavonoids released naturally from bean (Phaseolus vulgaris) on nodD-regulated gene transcription in Rhizobium leguminosarum bv. phaseoli.

Nine flavonoid aglycones released from black bean (Phaseolus vulgaris 'PI165426CS') seeds and roots induced nodC::lacZ transcription in Rhizobium leguminosarum bv. phaseoli strains containing extra cloned copies of the regulatory genes nodD1, nodD2, or nodD3 from that biovar. Individual flavonoids generally induced highest levels of nodC::lacZ transcription (Imax) with extra copies of nodD2, and the concentration required for half-maximum induction (I50) was lowest with extra copies of nodD1 genes. One apparently unique feature of R. l. bv. phaseoli is that naturally released flavonoids with very diverse structures induce nod genes. For all three nodD genes, two compounds exuded from roots, genistein and naringenin, produced much higher levels of nodC::lacZ transcription than other flavonoids, but this fact was not explained by increased transcription of the nodD genes themselves. The remaining seven flavonoid aglycones showed reproducibly different capacities to induce nodC::lacZ transcription, but all were considerably less powerful inducers than genistein and naringenin in strains with extra copies of each of the nodD genes. Tests with glycosides of the nod-gene inducers showed that glycosides, which are normally released by bean, had lower I50 values than the corresponding aglycones with all nodD genes. Additive interactions observed between the strong nod-gene inducer genistein and the weak inducer eriodictyol remain to be explained at the molecular level.

The products of Rhizobium genes, psi and pss, which affect exopolysaccharide production, are associated with the bacterial cell surface.

Translational fusions between a mutant phoA (lacking its promoter, ribosomal binding site and signal peptide sequence) and Rhizobium 'symbiotic' genes were isolated. Since these fusions expressed alkaline phosphatase (AP), the product of phoA, the genes into which phoA was inserted apparently specify proteins located in the bacterial periplasm or cell membrane, the compartment in which AP has activity. These genes were psiA and genes upstream of psiA (psiA is required for normal nodule development and strains with multicopy psiA fail to make exopolysaccharide (EPS) and to nodulate). Fusions between phoA and pss (exo) genes, which are required for EPS production, also resulted in the expression of AP indicating that products of these pss genes were located at the cell surface. Using gus fusions to psiA and pssA, we found that the former was expressed in N2-fixing bean root nodules but the latter was not.

Regulatory functions of the three nodD genes of Rhizobium leguminosarum biovar phaseoli.

The three nodD genes of a strain of Rhizobium leguminosarum biovar phaseoli were cloned to study their effects on transcription of themselves and of the nodC genes of biovars phaseoli and viciae. Efficient transcription of nodD1 required nodD1 and was enhanced by exposure of the cells to bean exudate consistent with the presence of a nod-box preceding the noIE-nodD1 operon. Transcription of nodD2 and nodD3 was constitutive. nodC of R. leguminosarum biovar phaseoli was activated by each of the nodD genes of that biovar in the absence of inducers but expression was enhanced in cells grown with bean exudate or the flavonoids genistein or naringenin. A mutant of nodD2, lacking 60 bp at its 3' end, activated nodC in the presence of inducer, but was defective in regulating certain of the nodD genes. The nodC gene of R. leguminosarum biovar viciae responded differently to the various nodD genes of R. leguminosarum biovar phaseoli than did the nodC of the latter biovar.

A Rhizobium leguminosarum mutant defective in symbiotic iron acquisition.

Iron acquisition by symbiotic Rhizobium spp. is essential for nitrogen fixation in the legume root nodule symbiosis. Rhizobium leguminosarum 116, an ineffective mutant strain with a defect in iron acquisition, was isolated after nitrosoguanidine mutagenesis of the effective strain 1062. The pop-1 mutation in strain 116 imparted to it a complex phenotype, characteristic of iron deficiency: the accumulation of porphyrins (precursors of hemes) so that colonies emitted a characteristic pinkish-red fluorescence when excited by UV light, reduced levels of cytochromes b and c, and wild-type growth on high-iron media but low or no growth in low-iron broth and on solid media supplemented with the iron scavenger dipyridyl. Several iron(III)-solubilizing agents, such as citrate, hydroxyquinoline, and dihydroxybenzoate, stimulated growth of 116 on low-iron solid medium; anthranilic acid, the R. leguminosarum siderophore, inhibited low-iron growth of 116. The initial rate of 55Fe uptake by suspensions of iron-starved 116 cells was 10-fold less than that of iron-starved wild-type cells. Electron microscopic observations revealed no morphological abnormalities in the small, white nodules induced by 116. Nodule cortical cells were filled with vesicles containing apparently normal bacteroids. No premature degeneration of bacteroids or of plant cell organelles was evident. We mapped pop-1 by R plasmid-mediated conjugation and recombination to the ade-27-rib-2 region of the R. leguminosarum chromosome. No segregation of pop-1 and the symbiotic defect was observed among the recombinants from these crosses. Cosmid pKN1, a pLAFR1 derivative containing a 24-kilobase-pair fragment of R. leguminosarum DNA, conferred on 116 the ability to grow on dipyridyl medium and to fix nitrogen symbiotically. These results indicate that the insert cloned in pKN1 encodes an element of the iron acquisition system of R. leguminosarum that is essential for symbiotic nitrogen fixation.

Transcription of rhiA, a gene on a Rhizobium leguminosarum bv. viciae Sym plasmid, requires rhiR and is repressed by flavanoids that induce nod genes.

Strains of Rhizobium leguminosarum biovar viciae specifically make an abundant protein (Rhi) in free-living culture but not in bacteroids. Genes needed for Rhi synthesis are on a Sym plasmid and here we show that one of these genes, rhiA, is the structural gene that specifies this polypeptide. Transcription of rhiA requires a regulatory gene, rhiR, located close to rhiA and to nod genes involved in nodulation. Mutations in rhiA or rhiR do not appear to affect symbiotic nitrogen fixation. Transcription of rhiA is repressed in cells grown in the presence of the flavanone hesperetin or the flavone apigenin, both of which are potent inducers of transcription of nod genes. This was deduced from the use of rhiA-lacZ fusions; however, when the Rhi polypeptide was detected in SDS gels, there was no apparent difference in the intensity of its staining in extracts obtained from cells grown with or without these flavanoid nod gene inducer molecules. However, a mutation in a nodulation gene, nolR, also closely linked to the nod and rhi genes, caused a severe depression in the amount of Rhi (as seen on gels) that was made in cells grown in the presence of inducer flavanoids.

Analysis of pss genes of Rhizobium leguminosarum required for exopolysaccharide synthesis and nodulation of peas: their primary structure and their interaction with psi and other nodulation genes.

Strains of Rhizobium leguminosarum (R.l.) biovar viciae containing pss mutations fail to make the acidic exopolysaccharides (EPS) and are unable to nodulate peas. It was found that they also failed to nodulate Vicia hirsuta, another host of this biovar. When peas were co-inoculated with pss mutant derivatives of a strain of R.l. by viciae containing a sym plasmid plus a cured strain lacking a sym plasmid (and which is thus Nod-, but for different reasons) but which makes the acidic EPS, normal numbers of nodules were formed, the majority of which failed to fix nitrogen (the occasional Fix+ nodules were presumably induced by strains that arose as a result of genetic exchange between cells of the two inoculants in the rhizosphere). Bacteria from the Fix- nodules contained, exclusively, the strain lacking its sym plasmid. When pss mutant strains were co-inoculated with a Nod- strain with a mutation in the regulatory gene nodD (which is on the sym plasmid pRL1JI), normal numbers of Fix+ nodules were formed, all of which were occupied solely by the nodD mutant strain. Since a mutation in nodD abolishes activation of other nod genes required for early stages of infection, these nod genes appear to be dispensable for subsequent stages in nodule development. Recombinant plasmids, containing cloned pss genes, overcame the inhibitory effects of psi, a gene which when cloned in the plasmid vector pKT230, inhibits both EPS production and nodulation ability. Determination of the sequence of the pss DNA showed that one, or perhaps two, genes are required for correcting strains that either carry pss mutations or contain multi-copy psi.(ABSTRACT TRUNCATED AT 250 WORDS)

Identification of nodX, a gene that allows Rhizobium leguminosarum biovar viciae strain TOM to nodulate Afghanistan peas.

Gene(s) conferring the ability of Rhizobium leguminosarum biovar viciae strain TOM to nodulate primitive peas (cultivar Afghanistan) had been located in a 2.0 kb region of its sym plasmid, pRL5JI. In this DNA, a single open reading frame of 1101 bp, corresponding to a gene, nodX was found. nodX is downstream of nodJ which is present in strain TOM and also in the sym plasmid of a typical strain of this biovar. nodX specifies a hydrophobic protein (of Mr 41,036) with no clear similarity to other proteins in data bases. Mutations in nodX abolished nodulation of Afghanistan peas but not nodulation of commercial peas. nodX-lacZ fusions were used to show that transcription of nodX was activated by root exudates from both commercial and Afghanistan peas and by defined flavonoids. Exudate from Afghanistan peas activated nod genes of typical strains of R. leguminosarum biovar viciae which fail to nodulate these peas; thus, their failure to nodulate these primitive peas is not due to a lack of activation of their nod genes by exudate from Afghanistan peas. A homologue of nodX exists in R. leguminosarum biovar trifolii (which nodulates clover) but not in typical strains of R. leguminosarum biovar viciae.

Transcription of a Rhizobium leguminosarum biovar phaseoli gene needed for melanin synthesis is activated by nifA of Rhizobium and Klebsiella pneumoniae.

The Rhizobium leguminosarum biovar phaseoli symbiotic plasmid pRP2JI carries a gene, melA, specifying the enzyme tyrosinase, which is responsible for the production of the pigment melanin in these bacteria. Transcription of melA is activated by the nifA gene of Rhizobium and, when the cloned melA gene is transferred to Escherichia coli, melA is expressed if the recipients contain nifA gene of Klebsiella pneumoniae. This nifA-dependent activation was temperature sensitive and required the ntrA gene. The cloned nifA gene of K. pneumoniae, when transferred to a nifA mutant of Rhizobium phaseoli biovar phaseoli, corrected the Mel- but not the Fix- phenotype. nifA of R. leguminosarum biovar phaseoli activated melA at higher levels in cells grown in low concentrations of oxygen. Also, nifA of R. leguminosarum biovar phaseoli activated nifH of K. pneumoniae in Escherichia coli cells grown in low-oxygen concentrations.

Identification of two classes of Rhizobium phaseoli genes required for melanin synthesis, one of which is required for nitrogen fixation and activates the transcription of the other.

The symbiotic plasmid pRP2JI of Rhizobium phaseoli strain 8002 was shown to contain two separate regions of DNA which are required and sufficient for the synthesis of the pigment melanin. One of these regions containing the class II mel gene(s) was located to other genes involved in nodulation and in nitrogen fixation. Mutations in this region abolished both the ability to synthesize melanin and to fix nitrogen in Phaseolus bean root nodules. Mutations in the other, unlinked region, containing class I mel gene(s), also abolished melanin synthesis but did not affect symbiotic nitrogen fixation. Transcriptional fusions between the class I mel gene and the Escherichia coli lacZ gene were constructed and it was demonstrated that the class II mel gene(s) activated their transcription in free-living culture. Further, strains containing the cloned regulatory class II gene(s) synthesized melanin when growing in minimal medium, in contrast to wild-type strains which became pigmented only in complete medium containing yeast extract and tryptone. It was shown by hybridization experiments that the regulatory mel gene was closely linked to or may correspond to the regulatory nifA gene; a fragment of R. phaseoli DNA which included the class II gene(s) of R. phaseoli hybridized to a previously identified nifA-like gene of R. leguminosarum, the species that nodulates peas.

Rhizobium leguminosarum genes involved in early stages of nodulation.

Nodulation genes from Rhizobium leguminosarum have been subcloned and transferred to a strain of R. phaseoli with its symbiotic plasmid deleted (and therefore its nodulation and nitrogen fixation genes). Normal infection and nodule development occurred when these strains were added to the roots of Pisum sativum (peas) and Vicia hirsuta. The pea nodules were examined by electron microscopy; bacteroid forms were seen surrounded by peribacteroid membranes and using immuno-gold labelling it was shown that the nodule cells contained leghaemoglobin within the cytoplasm. By subcloning and analysing the nodulation region it was found that a small (3.2 X 10(3) bases) fragment of DNA contained three genes involved in root hair curling, the first observed step in the interaction between R. leguminosarum and the root hair cells of these legumes.