The composite genome of the legume symbiont Sinorhizobium meliloti

The scarcity of usable nitrogen frequently limits plant growth. A tight metabolic association with rhizobial bacteria allows legumes to obtain nitrogen compounds by bacterial reduction of dinitrogen (N2) to ammonium (NH4+). We present here the annotated DNA sequence of the alpha-proteobacterium Sinorhizobium meliloti, the symbiont of alfalfa. The tripartite 6.7-megabase (Mb) genome comprises a 3.65-Mb chromosome, and 1.35-Mb pSymA and 1.68-Mb pSymB megaplasmids. Genome sequence analysis indicates that all three elements contribute, in varying degrees, to symbiosis and reveals how this genome may have emerged during evolution. The genome sequence will be useful in understanding the dynamics of interkingdom associations and of life in soil environments.

The temporal and spatial transcription pattern in root nodules of Vicia faba nodulin genes encoding glycine-rich proteins

Four different transcript sequences encoding gene products with an unusually high glycine content were identified in Vicia faba root nodules. Northern blot analysis revealed a strong nodule specific expression of the corresponding genes. Time course experiments showed that two of these genes were transcribed before the onset of leghemoglobin expression and hence were designated VfENOD-GRP2 and VfENOD-GRP5, whereas the first detection of VfNOD-GRP1 and VfNOD-GRP4 transcripts coincided with the appearance of leghemoglobin transcripts in V. faba root nodules. A characteristic feature of all encoded nodulins was a hydrophobic N-terminus, which in the case of the nodulins ENOD-GRP2 and ENOD-GRP5 has the characteristics of a signal peptide. Such a structure is comparable to other plant glycine-rich proteins decribed as components of the plant cell wall. Based on tissue print hybridizations, we found that VfNOD-GRP1, VfENOD-GRP2 and VfNOD-GRP4 were expressed in the interzone II-III and in the whole nitrogen-fixing zone III. In contrast to VfENOD-GRP2 and VfNOD-GRP4, the signal intensity of hybridizing VfNOD-GRP1 transcripts was slightly reduced in the more proximal part of broad bean root nodules. Apart from the interzone II-III and the nitrogen fixing zone III, VfENOD-GRP5 RNA was also detected in large areas of the prefixing zone II.

Diversity of uncultured microorganisms associated with the seagrass Halophila stipulacea estimated by restriction fragment length polymorphism analysis of PCR-amplified 16S rRNA genes

The diversity of microorganisms associated with the leaves of the seagrass Halophila stipulacea in the northern Gulf of Elat was examined by culture-independent analysis. Microorganisms were harvested by a sonication treatment for total-community genomic DNA isolation. Oligonucleotides complementary to conserved regions in the 16S rRNA-encoding DNA (rDNA) of bacteria were used for PCR amplification. The 16S rDNA PCR products were subcloned and further characterized by a restriction fragment length analysis termed ARDRA (amplified rDNA restriction analysis). These analyses were carried out after reamplifying the cloned fragments with two primers binding symmetrically to the plasmid immediately on both sides of the cloned insert. Computer-aided clustering was performed after separate restriction analysis with enzymes HinfI and HpaII. By this method, 103 cloned 16S rDNA fragments were clustered into a total of 58 different groups. Sequence analysis of clones with an identical ARDRA pattern confirmed that members of an ARDRA group were closely related to each other. The sequenced clones were found to be affiliated with a marine snow-associated plastid-like rRNA clone and with a marine Hyphomonas strain, respectively. The method applied in this study could be useful for the routine study of other microbial communities of interest.

The Metabolites of the Herbicide L-Phosphinothricin (Glufosinate) (Identification, Stability, and Mobility in Transgenic, Herbicide-Resistant, and Untransformed Plants)

The metabolism of the herbicide L-phosphinothricin (L-Pt) was analyzed in tobacco (Nicotiana tabacum), alfalfa (Medicago sativa), and carrot (Daucus carota). In transgenic, Pt-resistant plants expressing the Pt-N-acetyltransferase gene (pat), L-Pt was acetylated, resulting in two forms of N-acetyl-Pt (ac-Pt). In transgenic plants expressing only low pat-encoded acetylating activity as well as in genetically unmodified plants, three metabolic compounds 4-methylphosphinico-2-oxo-butanoic acid, 3-methylphosphinico-propanoic acid (MPP), and 4-methylphosphinico-2-hydroxy-butanoic acid (MHB) were identified. Hence, the transgene-encoded acetylation of L-Pt competes with a plant-specific degradation. The compounds MPP, MHB, and ac-Pt were found to be the final, stable products of the plant's metabolic pathways. The mobility of these stable compounds in the plant was investigated: L-Pt as well as the derived metabolites were found to be preferentially transported to the upper regions of the plant.

Cooperative Action of Rhizobium meliloti Nodulation and Infection Mutants during the Process of Forming Mixed Infected Alfalfa Nodules

Alfalfa plants co-inoculated with Rhizobium meliloti nodulation (Nod-) and infection mutants deficient in exopolysaccharide production (Inf-EPS-) formed mixed infected nodules that were capable of fixing atmospheric nitrogen. The formation of infected nodules was dependent on close contact between the inoculation partners. When the partners were separated by a filter, empty Fix- nodules were formed, suggesting that infection thread formation in alfalfa is dependent on signals from the nodulation and infection genes. In mixed infected nodules, both nodulation and infection mutants colonized the plant cells and differentiated into bacteroids. The formation of bacteroids was not dependent on cell-to-cell contact between the mutants. Immunogold/silver staining revealed that the ratio of the two mutants varied considerably in colonized plant cells following mixed inoculation. The introduction of an additional nif/fix mutation into one of the inoculation partners did not abolish nitrogen fixation in mixed infected nodules. The expression of nif D::lacZ fusions additionally demonstrated that mutations in the nodulation and infection genes did not prevent the nif genes from being expressed in the mutant bacteroids.