Enhanced nitrogen fixation in a rhizobium etli ntrC mutant that overproduces the bradyrhizobium japonicum symbiotic terminal oxidase cbb3

Molecular Biology in the Improvement of Biological Nitrogen Fixation by Rhizobia and Extending the Scope to Cereals

The contribution of biological nitrogen fixation to the total N requirement of food and feed crops diminished in importance with the advent of synthetic N fertilizers, which fueled the “green revolution”. Despite being environmentally unfriendly, the synthetic versions gained prominence primarily due to their low cost, and the fact that most important staple crops never evolved symbiotic associations with bacteria. In the recent past, advances in our knowledge of symbiosis and nitrogen fixation and the development and application of recombinant DNA technology have created opportunities that could help increase the share of symbiotically-driven nitrogen in global consumption. With the availability of molecular biology tools, rapid improvements in symbiotic characteristics of rhizobial strains became possible. Further, the technology allowed probing the possibility of establishing a symbiotic dialogue between rhizobia and cereals. Because the evolutionary process did not forge a symbiotic relationship with the latter, the potential of molecular manipulations has been tested to incorporate a functional mechanism of nitrogen reduction independent of microbes. In this review, we discuss various strategies applied to improve rhizobial strains for higher nitrogen fixation efficiency, more competitiveness and enhanced fitness under unfavorable environments. The challenges and progress made towards nitrogen self-sufficiency of cereals are also reviewed. An approach to integrate the genetically modified elite rhizobia strains in crop production systems is highlighted.

Rhizobium etli Produces Nitrous Oxide by Coupling the Assimilatory and Denitrification Pathways

More than two-thirds of the powerful greenhouse gas nitrous oxide (N₂O) emissions from soils can be attributed to microbial denitrification and nitrification processes. Bacterial denitrification reactions are catalyzed by the periplasmic (Nap) or membrane-bound (Nar) nitrate reductases, nitrite reductases (NirK/cd ₁Nir), nitric oxide reductases (cNor, qNor/ Cu_ANor), and nitrous oxide reductase (Nos) encoded by nap/nar, nir, nor and nos genes, respectively. Rhizobium etli CFN42, the microsymbiont of common bean, is unable to respire nitrate under anoxic conditions and to perform a complete denitrification pathway. This bacterium lacks the nap, nar and nos genes but contains genes encoding NirK and cNor. In this work, we demonstrated that R. etli is able to grow with nitrate as the sole nitrogen source under aerobic and microoxic conditions. Genetic and functional characterization of a gene located in the R. etli chromosome and annotated as narB demonstrated that growth under aerobic or microoxic conditions with nitrate as nitrogen source as well as nitrate reductase activity requires NarB. In addition to be involved in nitrate assimilation, NarB is also required for NO and N₂O production by NirK and cNor, respectively, in cells grown microoxically with nitrate as the only N source. Furthermore, β-glucuronidase activity from nirK::uidA and norC::uidA fusions, as well as NorC expression and Nir and Nor activities revealed that expression of nor genes under microoxic conditions also depends on nitrate reduction by NarB. Our results suggest that nitrite produced by NarB from assimilatory nitrate reduction is detoxified by NirK and cNor denitrifying enzymes that convert nitrite into NO which in turn is reduced to N₂O, respectively.

Can stress response genes be used to improve the symbiotic performance of rhizobia?

Rhizobia are soil bacteria able to form symbioses with legumes and fix atmospheric nitrogen, converting it into a form that can be assimilated by the plant. The biological nitrogen fixation is a possible strategy to reduce the environmental pollution caused by the use of chemical N-fertilizers in agricultural fields. Successful colonization of the host root by free-living rhizobia requires that these bacteria are able to deal with adverse conditions in the soil, in addition to stresses that may occur in their endosymbiotic life inside the root nodules. Stress response genes, such as otsAB, groEL, clpB, rpoH play an important role in tolerance of free-living rhizobia to different environmental conditions and some of these genes have been shown to be involved in the symbiosis. This review will focus on stress response genes that have been reported to improve the symbiotic performance of rhizobia with their host plants. For example, chickpea plants inoculated with a Mesorhizobium strain modified with extra copies of the groEL gene showed a symbiotic effectiveness approximately 1.5 fold higher than plants inoculated with the wild-type strain. Despite these promising results, more studies are required to obtain highly efficient and tolerant rhizobia strains, suitable for different edaphoclimatic conditions, to be used as field inoculants.

Nodule carbohydrate catabolism is enhanced in the Medicago truncatula A17-Sinorhizobium medicae WSM419 symbiosis

The symbiotic association between Medicago truncatula and Sinorhizobium meliloti is a well-established model system in the legume–Rhizobium community. Despite its wide use, the symbiotic efficiency of this model has been recently questioned and an alternative microsymbiont, S. medicae, has been proposed. However, little is known about the physiological mechanisms behind the higher symbiotic efficiency of S. medicae WSM419. In the present study, we inoculated M. truncatula Jemalong A17 with either S. medicae WSM419 or S. meliloti 2011 and compared plant growth, photosynthesis, N₂-fixation rates, and plant nodule carbon and nitrogen metabolic activities in the two systems. M. truncatula plants in symbiosis with S. medicae showed increased biomass and photosynthesis rates per plant. Plants grown in symbiosis with S. medicae WSM419 also showed higher N₂-fixation rates, which were correlated with a larger nodule biomass, while nodule number was similar in both systems. In terms of plant nodule metabolism, M. truncatula–S. medicae WSM419 nodules showed increased sucrose-catabolic activity, mostly associated with sucrose synthase, accompanied by a reduced starch content, whereas nitrogen-assimilation activities were comparable to those measured in nodules infected with S. meliloti 2011. Taken together, these results suggest that S. medicae WSM419 is able to enhance plant carbon catabolism in M. truncatula nodules, which allows for the maintaining of high symbiotic N₂-fixation rates, better growth and improved general plant performance.

Enhanced expression of Rhizobium etli cbb₃ oxidase improves drought tolerance of common bean symbiotic nitrogen fixation

To investigate the involvement of Rhizobium etli cbb(3) oxidase in the response of Phaseolus vulgaris to drought, common bean plants were inoculated with the R. etli strain, CFNX713, overexpressing this oxidase in bacteroids (cbb(3)(+)) and subjected to drought conditions. The negative effect of drought on plant and nodule dryweight, nitrogen content, and nodule functionality was more pronounced in plants inoculated with the wild-type (WT) strain than in those inoculated with the cbb(3)(+) strain. Regardless of the plant treatment, bacteroids produced by the cbb(3)(+) strain showed higher respiratory capacity than those produced by the WT strain. Inoculation of plants with the cbb(3)(+) strain alleviated the negative effect of a moderate drought on the respiratory capacity of bacteroids and the energy charge of the nodules. Expression of the FixP and FixO components of the cbb(3) oxidase was higher in bacteroids of the cbb(3)(+) strain than in those of the WT strain under all experimental conditions. The decline in sucrose synthase activity and the decrease in dicarboxylic acids provoked by moderate drought stress were more pronounced in nodules from plants inoculated with the WT strain than in those inoculated with the cbb(3)(+) strain. Taken together, these results suggest that inoculation of plants with a R. etli strain having enhanced expression of cbb(3) oxidase in bacteroids reduces the sensitivity of P. vulgaris-R. etli symbiosis to drought and can modulate carbon metabolism in nodules.

Use of cultivation-dependent and -independent techniques to assess contamination of central venous catheters: a pilot study

Background

Catheters are the most common cause of nosocomial infections and are associated with increased risk of mortality, length of hospital stay and cost. Prevention of infections and fast and correct diagnosis is highly important.

Methods

In this study traditional semiquantitative culture-dependent methods for diagnosis of bacteria involved in central venous catheter-related infections as described by Maki were compared with the following culture-independent molecular biological methods: Clone libraries, denaturant gradient gel electrophoresis, phylogeny and fluorescence in situ hybridization.

Results

In accordance with previous studies, the cultivation of central venous catheters from 18 patients revealed that S. epidermidis and other coagulase-negative staphylococci were most abundant and that a few other microorganisms such as P. aeruginosa and K. pneumoniae occasionally were found on the catheters. The molecular analysis using clone libraries and sequencing, denaturant gradient gel electrophoresis and sequencing provided several important results. The species found by cultivation were confirmed by molecular methods. However, many other bacteria belonging to the phyla Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes were also found, stressing that only a minor portion of the species present were found by cultivation. Some of these bacteria are known to be pathogens, some have not before been described in relation to human health, and some were not closely related to known pathogens and may represent new pathogenic species. Furthermore, there was a clear difference between the bacterial species found in biofilm on the external (exluminal) and internal (luminal) side of the central venous catheter, which can not be detected by Maki's method. Polymicrobial biofilms were observed on most of the catheters and were much more common than the cultivation-dependent methods indicated.

Conclusion

The results show that diagnosis based on molecular methods improves the detection of microorganisms involved in central catheter-related infections. The importance of these microorganisms needs to be investigated further, also in relation to contamination risk from improper catheter handling, as only in vivo contaminants are of interest. This information can be used for development of fast and more reliable diagnostic tools, which can be used in combination with traditional methods.

Novel reiterated Fnr-type proteins control the production of the symbiotic terminal oxidase cbb3 in Rhizobium etli CFN42

Symbiotic nitrogen-fixing bacteria express a terminal oxidase with a high oxygen affinity, the cbb3-type oxidase encoded by the fixNOQP operon. Previously, we have shown that, in Rhizobium etli CFN42, the repeatedfixNOQP operons (fixNOQPd and fixNOQPf) have a differential role in nitrogen fixation. Only the fixNOQPd operon is required for the establishment of an effective symbiosis; microaerobic induction of this operon is under the control of at least three transcriptional regulators, FixKf, FnrNd, and FnrNchr, belonging to the Crp/Fnr family. In this work, we describe two novel Crp/Fnr-type transcriptional regulators (StoRd and StoRf, symbiotic terminal oxidase regulators) that play differential roles in the control of key genes for nitrogen fixation. Mutations either in stoRd or stoRf enhance the microaerobic expression of both fixNOQP reiterations, increasing also the synthesis of the cbb3-type oxidase in nodules. Despite their structural similarity, a differential role of these genes was also revealed, since a mutation in stoRd but not in stoRf enhanced both the expression of fixKf and the nitrogen-fixing capacity of R. etli CFN42.

Metabolic reconstruction and modeling of nitrogen fixation in Rhizobium etli

Rhizobiaceas are bacteria that fix nitrogen during symbiosis with plants. This symbiotic relationship is crucial for the nitrogen cycle, and understanding symbiotic mechanisms is a scientific challenge with direct applications in agronomy and plant development. Rhizobium etli is a bacteria which provides legumes with ammonia (among other chemical compounds), thereby stimulating plant growth. A genome-scale approach, integrating the biochemical information available for R. etli, constitutes an important step toward understanding the symbiotic relationship and its possible improvement. In this work we present a genome-scale metabolic reconstruction (iOR363) for R. etli CFN42, which includes 387 metabolic and transport reactions across 26 metabolic pathways. This model was used to analyze the physiological capabilities of R. etli during stages of nitrogen fixation. To study the physiological capacities in silico, an objective function was formulated to simulate symbiotic nitrogen fixation. Flux balance analysis (FBA) was performed, and the predicted active metabolic pathways agreed qualitatively with experimental observations. In addition, predictions for the effects of gene deletions during nitrogen fixation in Rhizobia in silico also agreed with reported experimental data. Overall, we present some evidence supporting that FBA of the reconstructed metabolic network for R. etli provides results that are in agreement with physiological observations. Thus, as for other organisms, the reconstructed genome-scale metabolic network provides an important framework which allows us to compare model predictions with experimental measurements and eventually generate hypotheses on ways to improve nitrogen fixation.

Tyrosinase from Rhizobium etli Is Involved in Nodulation Efficiency and Symbiosis-Associated Stress Resistance

Tyrosinase (EC 1.14.18.1) is a monophenol oxidase responsible for the synthesis of the black pigment known as melanin. The tyrosinase gene (melA) is plasmid-encoded in many rhizobial species. In Rhizobium etli CFN42, the genetic location of melA in the symbiotic plasmid (p42d) and its RpoN-NifA regulation suggest an involvement in symbiosis. In this work, we analyzed the symbiotic phenotype of a streptomycin-resistant derivative of CFN42 (CE3), a melA mutant (SP2) and a complemented strain (SP66), demonstrating that melA inactivation reduced nodule formation rate and diminished total nodule number by 27% when compared to the CE3 strain. The nitrogen fixation capacity of the mutant strain was not affected. Also, in vitro assays were performed where the resistance of CE3, SP2 and SP66 strains to H(2)O(2) was evaluated; the melA mutant strain was consistently less resistant to peroxide. In another series of experiments, Escherichia coli W3110 strain expressing R. etli melA displayed enhanced resistance to p-hydroxybenzoic, vanillinic and syringic acids, which are phenolic compounds frequently found in the soil. Our results are the first to demonstrate a specific role for tyrosinase in R. etli: this enzyme is required during early symbiosis, apparently providing resistance against reactive oxygen species and phenolic compounds generated as part of the plant protective responses.

Pleiotropic effects of mutations that alter the Sinorhizobium meliloti cytochrome c respiratory system

Using transposon mutagenesis, mutations have been isolated in several genes (ccdA, cycM, ccmC, ccmB and senC) that play a role in Sinorhizobium meliloti cytochrome metabolism. As in other bacteria, mutations in the S. meliloti ccdA, ccmB and ccmC genes resulted in the absence of all c-type cytochromes. However, the S. meliloti ccdA mutant also lacked cytochrome oxidase aa(3), a defect that does not appear to have been reported for other bacteria. The aa(3)-type cytochromes were also missing from a mutant strain with an insertion into the gene encoding the haem-containing subunit (SU)I of aa(3) cytochrome c oxidase, but not in mutants unable to make SUII or SUIII, indicating that CcdA probably plays a role in assembling SUI. The cytochrome-deficient mutants also had other free-living phenotypes, including a significant decrease in growth rate on rich media and increased motility on minimal media. A senC mutant also had significantly decreased motility, but the motility and growth properties of the cycM mutant were unchanged. Unlike similar mutants in Bradyrhizobium japonicum and Rhizobium leguminosarum, an S. meliloti Rm1021 cycM mutant contained cytochrome oxidase aa(3). Cytochrome maturation in strain Rm1021 appeared to be similar to maturation in other rhizobia, but there were some differences in the cytochrome composition of the strain, and respiration chain function and assembly.

Regulatory role of Rhizobium etli CNPAF512 fnrN during symbiosis

The Rhizobium etli CNPAF512 fnrN gene was identified in the fixABCX rpoN(2) region. The corresponding protein contains the hallmark residues characteristic of proteins belonging to the class IB group of Fnr-related proteins. The expression of R. etli fnrN is highly induced under free-living microaerobic conditions and during symbiosis. This microaerobic and symbiotic induction of fnrN is not controlled by the sigma factor RpoN and the symbiotic regulator nifA or fixLJ, but it is due to positive autoregulation. Inoculation of Phaseolus vulgaris with an R. etli fnrN mutant strain resulted in a severe reduction in the bacteroid nitrogen fixation capacity compared to the wild-type capacity, confirming the importance of FnrN during symbiosis. The expression of the R. etli fixN, fixG, and arcA genes is strictly controlled by fnrN under free-living microaerobic conditions and in bacteroids during symbiosis with the host. However, there is an additional level of regulation of fixN and fixG under symbiotic conditions. A phylogenetic analysis of the available rhizobial FnrN and FixK proteins grouped the proteins in three different clusters.

Key role of bacterial NH(4)(+) metabolism in Rhizobium-plant symbiosis

Symbiotic nitrogen fixation is carried out in specialized organs, the nodules, whose formation is induced on leguminous host plants by bacteria belonging to the family Rhizobiaceae: Nodule development is a complex multistep process, which requires continued interaction between the two partners and thus the exchange of different signals and metabolites. NH(4)(+) is not only the primary product but also the main regulator of the symbiosis: either as ammonium and after conversion into organic compounds, it regulates most stages of the interaction, from the production of nodule inducers to the growth, function, and maintenance of nodules. This review examines the adaptation of bacterial NH(4)(+) metabolism to the variable environment generated by the plant, which actively controls and restricts bacterial growth by affecting oxygen and nutrient availability, thereby allowing a proficient interaction and at the same time preventing parasitic invasion. We describe the regulatory circuitry responsible for the downregulation of bacterial genes involved in NH(4)(+) assimilation occurring early during nodule invasion. This is a key and necessary step for the differentiation of N(2)-fixing bacteroids (the endocellular symbiotic form of rhizobia) and for the development of efficient nodules.

Regulation of gene expression in response to oxygen in Rhizobium etli: role of FnrN in fixNOQP expression and in symbiotic nitrogen fixation

Previously, we reported finding duplicated fixNOQP operons in Rhizobium etli CFN42. One of these duplicated operons is located in the symbiotic plasmid (fixNOQPd), while the other is located in a cryptic plasmid (fixNOQPf). Although a novel FixL-FixKf regulatory cascade participates in microaerobic expression of both fixNOQP duplicated operons, we found that a mutation in fixL eliminates fixNOQPf expression but has only a moderate effect on expression of fixNOQPd. This suggests that there are differential regulatory controls. Interestingly, only the fixNOQPd operon was essential for symbiotic nitrogen fixation (L. Girard, S. Brom, A. Dávalos, O. Lopez, M. Soberón, and D. Romero, Mol. Plant-Microbe Interact. 13:1283-1292, 2000). Searching for potential candidates responsible for the differential expression, we characterized two fnrN homologs (encoding transcriptional activators of the cyclic AMP receptor protein [CRP]-Fnr family) in R. etli CFN42. One of these genes (fnrNd) is located on the symbiotic plasmid, while the other (fnrNchr) is located on the chromosome. Analysis of the expression of the fnrN genes using transcriptional fusions with lacZ showed that the two fnrN genes are differentially regulated, since only fnrNd is expressed in microaerobic cultures of the wild-type strain while fnrNchr is negatively controlled by FixL. Mutagenesis of the two fnrN genes showed that both genes participate, in conjunction with FixL-FixKf, in the microaerobic induction of the fixNOQPd operon. Participation of these genes is also seen during the symbiotic process, in which mutations in fnrNd and fnrNchr, either singly or in combination, lead to reductions in nitrogen fixation. Therefore, R. etli employs a regulatory circuit for induction of the fixNOQPd operon that involves at least three transcriptional regulators of the CRP-Fnr family. This regulatory circuit may be important for ensuring optimal production of the cbb(3), terminal oxidase during symbiosis.

Differential regulation of fixN-reiterated genes in Rhizobium etli by a novel fixL-fixK cascade

Among the complexities in the regulation of nitrogen fixation in the Rhizobiaceae are reiteration of regulatory components as well as variant roles for each component between species. For Rhizobium etli CFN42, we reported that the symbiotic plasmid (pCFN42d) contains a key regulatory gene (fixKd) and genes for a symbiotic cytochrome oxidase (fixNOQPd). Here we discuss the occurrence of reiteration of these genes (fixKf and fixNOQPf) and the finding of an unusual fixL homolog on a plasmid previously considered cryptic (pCFN42f). The structure of the deduced FixL polypeptide is suggestive of a fusion of the receiver and transmitter modules of a two-component regulatory system as described in R. leguminosarum bv. viciae VF39. Gene fusion analysis, coupled with mutation of each regulatory element, revealed that free-living expression of FixKf was dependent fully on FixL. In contrast, synthesis of FixKd was not detected under the conditions tested. The FixKf protein is needed for microaerobic expression of both fixN reiterations, whereas the FixKd protein appears to be dispensable. Interestingly, expression of the fixN reiterations exhibits a differential dependence for FixL, where transcription of fixNf was suppressed in the absence of FixL but expression of fixNd still showed significant levels. This suggests the existence of a FixL-independent mechanism for expression of the fixNd reiteration. Surprisingly, mutations in fixL, fixKd, or fixKf (either singly or in combination) did not alter symbiotic effectiveness. A mutation in fixNd (but not in fixNf) was, however, severely affected, indicating a differential role for these reiterations in nitrogen fixation.