Early symbiotic responses induced by Sinorhizobium meliloti iIvC mutants in alfalfa

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

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

Biosynthesis of branched-chain amino acids is essential for effective symbioses between betarhizobia and Mimosa pudica

Burkholderia phymatum STM815 and Cupriavidus taiwanensis LMG19424 are betaproteobacterial strains that can effectively nodulate several species of the large legume genus Mimosa. A Tn5 mutant, derived from B. phymatum STM815 (KM60), and another derived from C. taiwanensis LMG19424 (KM184-55) induced Fix(-) nodules on Mimosa pudica. The Tn5-interrupted genes of the mutants showed strong homologies to ilvE, which encodes a branched-chain amino acid aminotransferase, and leuC, which encodes the large subunit of isopropylmalate isomerase. Both enzymes are known to be involved in the biosynthetic pathways for branched-chain amino acids (BCAAs) (leucine, valine and isoleucine). The B. phymatum ilvE mutant, KM60, was not auxotrophic for BCAAs and could grow well on minimal medium with pyruvate as a carbon source and ammonia as a nitrogen source. However, it grew less efficiently than the wild-type (WT) strain when ammonia was substituted with valine or isoleucine as a nitrogen source. The BCAA aminotransferase activity of KM60 was significantly reduced relative to the WT strain, especially with isoleucine and valine as amino group donors. The C. taiwanensis leuC mutant, KM184-55, could not grow on a minimal medium with pyruvate as a carbon source and ammonia as a nitrogen source, but its growth was restored when leucine was added to the medium. The isopropylmalate isomerase activity of KM184-55 was completely lost compared with the WT strain. Both mutants recovered their respective enzyme activities after complementation with the WT ilvE or leuC genes and were subsequently able to grow as well as their parental strains on minimal medium. They were also able to form nitrogen-fixing nodules on M. pudica. We conclude that the biosynthesis of BCAAs is essential for the free-living growth of betarhizobia, as well as for their ability to form effective symbioses with their host plant.

Genetic differences between Bradyrhizobium japonicum variant strains contrasting in N(2)-fixation efficiency revealed by representational difference analysis

Two variant strains of Bradyrhizobium japonicum, derived from SEMIA 566, adapted to the stressful environmental conditions of the Brazilian Cerrados and characterized by contrasting capacities for N(2) fixation, were compared by representational difference analysis (RDA). Twenty-four gene sequences that are unique to the highly effective strain S 370 were identified, eight showing high similarity to known genes, nine encoding putative proteins and seven representing conserved hypothetical or hypothetical proteins; they were classified in eight functional categories. Among those genes, some were highlighted for their known or potential functions in plant-microbe interactions. The nodulation outer protein P (nopP), related to the type-III secretion system (TTSS) and a major determinant of nodulation of some tropical legumes, was detected in the genome of strain S 370. Three coding sequences (CDS) identified by RDA were expressed in proteomics experiments with B. japonicum strain USDA 110 (ChvE and NopP). The use of the sequences identified by RDA in the highly effective strain S 370 might represent an important tool to speed up strain selection programs, accelerating pre-screening procedures. Additionally, the conserved hypothetical and hypothetical proteins identified in strain S 370 might encode important but still unknown proteins related to the symbiosis that deserve further study.

Auxotrophy accounts for nodulation defect of most Sinorhizobium meliloti mutants in the branched-chain amino acid biosynthesis pathway

Some Sinorhizobium meliloti mutants in genes involved in isoleucine, valine, and leucine biosynthesis were previously described as being unable to induce nodule formation on host plants. Here, we present a reappraisal of the interconnection between the branched-chain amino acid biosynthesis pathway and the nodulation process in S. meliloti. We characterized the symbiotic phenotype of seven mutants that are auxotrophic for isoleucine, valine, or leucine in two closely related S. meliloti strains, 1021 and 2011. We showed that all mutants were similarly impaired for nodulation and infection of the Medicago sativa host plant. In most cases, the nodulation phenotype was fully restored by the addition of the missing amino acids to the plant growth medium. This strongly suggests that auxotrophy is the cause of the nodulation defect of these mutants. However, we confirmed previous findings that ilvC and ilvD2 mutants in the S. meliloti 1021 genetic background could not be restored to nodulation by supplementation with exogenous amino acids even though their Nod factor production appeared to be normal.

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

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

Disruption of sitA compromises Sinorhizobium meliloti for manganese uptake required for protection against oxidative stress

During the initial stages of symbiosis with the host plant Medicago sativa, Sinorhizobium meliloti must overcome an oxidative burst produced by the plant in order for proper symbiotic development to continue. While identifying mutants defective in symbiosis and oxidative stress defense, we isolated a mutant with a transposon insertion mutation of sitA, which encodes the periplasmic binding protein of the putative iron/manganese ABC transporter SitABCD. Disruption of sitA causes elevated sensitivity to the reactive oxygen species hydrogen peroxide and superoxide. Disruption of sitA leads to elevated catalase activity and a severe decrease in superoxide dismutase B (SodB) activity and protein level. The decrease in SodB level strongly correlates with the superoxide sensitivity of the sitA mutant. We demonstrate that all free-living phenotypes of the sitA mutant can be rescued by the addition of exogenous manganese but not iron, a result that strongly implies that SitABCD plays an important role in manganese uptake in S. meliloti.

Organogenesis of legume root nodules

The N(2)-fixing nodules elicited by rhizobia on legume roots represent a useful model for studying plant development. Nodule formation implies a complex progression of temporally and spatially regulated events of cell differentiation/dedifferentiation involving several root tissues. In this review we describe the morphogenetic events leading to the development of these histologically well-structured organs. These events include (1) root hair deformation, (2) development and growth of infection threads, (3) induction of the nodule primordium, and (4) induction, activity, and persistence of the nodular meristem and/or of foci of meristematic activities. Particular attention is given to specific aspects of the symbiosis, such as the early stages of intracellular invasion and to differentiation of the intracellular form of rhizobia, called symbiosomes. These developmental aspects were correlated with (1) the regulatory signals exchanged, (2) the plant genes expressed in specific cell types, and (3) the staining procedures that allow the recognition of some cell types. When strictly linked with morphogenesis, the nodulation phenotypes of plant and bacterial mutants such as the developmental consequence of the treatment with metabolic inhibitors, metabolic intermediates, or the variation of physical parameters are described. Finally, some aspects of nodule senescence and of regulation of nodulation are discussed.

A global analysis of protein expression profiles in Sinorhizobium meliloti: discovery of new genes for nodule occupancy and stress adaptation

A proteomic examination of Sinorhizobium meliloti strain 1021 was undertaken using a combination of 2-D gel electrophoresis, peptide mass fingerprinting, and bioinformatics. Our goal was to identify (i) putative symbiosis- or nutrient-stress-specific proteins, (ii) the biochemical pathways active under different conditions, (iii) potential new genes, and (iv) the extent of posttranslational modifications of S. meliloti proteins. In total, we identified the protein products of 810 genes (13.1% of the genome's coding capacity). The 810 genes generated 1,180 gene products, with chromosomal genes accounting for 78% of the gene products identified (18.8% of the chromosome's coding capacity). The activity of 53 metabolic pathways was inferred from bioinformatic analysis of proteins with assigned Enzyme Commission numbers. Of the remaining proteins that did not encode enzymes, ABC-type transporters composed 12.7% and regulatory proteins 3.4% of the total. Proteins with up to seven transmembrane domains were identified in membrane preparations. A total of 27 putative nodule-specific proteins and 35 nutrient-stress-specific proteins were identified and used as a basis to define genes and describe processes occurring in S. meliloti cells in nodules and under stress. Several nodule proteins from the plant host were present in the nodule bacteria preparations. We also identified seven potentially novel proteins not predicted from the DNA sequence. Post-translational modifications such as N-terminal processing could be inferred from the data. The posttranslational addition of UMP to the key regulator of nitrogen metabolism, PII, was demonstrated. This work demonstrates the utility of combining mass spectrometry with protein arraying or separation techniques to identify candidate genes involved in important biological processes and niche occupations that may be intransigent to other methods of gene expression profiling.