Regulation of Gene Expression in Response to Oxygen in
            <i>Rhizobium etli</i>
            : Role of FnrN in
            <i>fixNOQP</i>
            Expression and in Symbiotic Nitrogen Fixation

López, Oswaldo; Morera, Claudia; Miranda-Ríos, Juan; Girard, Lourdes; Romero, David; Soberón, Mário

doi:10.1128/jb.183.24.6999-7006.2001

Cited by 43 publications

(39 citation statements)

References 35 publications

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“…As in M. loti, duplicated fixNOPQ operons occur in R. leguminosarum (41), R. etli (24), and S. meliloti (14); this is probably a result of the evolution of symbiosis and oxygen respiration (13,38). The array of fixNOPQ operons in M. loti MAFF303099 is unique in that both operons are located on a single chromosome (18).…”

Section: Discussionmentioning

confidence: 99%

“…fixNOQP encodes a symbiotic cytochrome c oxidase complex that is specifically required for bacteroid respiration in the presence of very low O 2 concentrations (13,34). Like Rhizobium leguminosarum (41), Rhizobium etli (24), and S. meliloti (14), M. loti MAFF303099 possesses two sets of fixNOQP genes, one inside the symbiosis island and the other outside the symbiosis island. Interestingly, the DNA region around the copy of fixNOQP outside the symbiosis island is an EI even in bacteroids (Fig.…”

Section: Vol 186 2004mentioning

confidence: 99%

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Expression Islands Clustered on the Symbiosis Island of the Mesorhizobium loti Genome

et al. 2004

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Rhizobia are symbiotic nitrogen-fixing soil bacteria that are associated with host legumes. The establishment of rhizobial symbiosis requires signal exchanges between partners in microaerobic environments that result in mutualism for the two partners. We developed a macroarray for Mesorhizobium loti MAFF303099, a microsymbiont of the model legume Lotus japonicus, and monitored the transcriptional dynamics of the bacterium during symbiosis, microaerobiosis, and starvation. Global transcriptional profiling demonstrated that the clusters of genes within the symbiosis island (611 kb), a transmissible region distinct from other chromosomal regions, are collectively expressed during symbiosis, whereas genes outside the island are downregulated. This finding implies that the huge symbiosis island functions as clustered expression islands to support symbiotic nitrogen fixation. Interestingly, most transposase genes on the symbiosis island were highly upregulated in bacteroids, as were nif, fix, fdx, and rpoN. The genome region containing the fixNOPQ genes outside the symbiosis island was markedly upregulated as another expression island under both microaerobic and symbiotic conditions. The symbiosis profiling data suggested that there was activation of amino acid metabolism, as well as nif-fix gene expression. In contrast, genes for cell wall synthesis, cell division, DNA replication, and flagella were strongly repressed in differentiated bacteroids. A highly upregulated gene in bacteroids, mlr5932 (encoding 1-aminocyclopropane-1-carboxylate deaminase), was disrupted and was confirmed to be involved in nodulation enhancement, indicating that disruption of highly expressed genes is a useful strategy for exploring novel gene functions in symbiosis.Through the symbiotic nitrogen fixation process, bacteria belonging to the family Rhizobiaceae convert atmospheric dinitrogen (N 2 ) to ammonia (NH 3 ), which can be effectively used by host legume plants. The establishment of a rhizobiumlegume symbiosis requires induction of new developmental programs in the partners. The symbiotic interaction begins with signal exchanges of flavonoids and Nod factors (lipochitooligosaccharides) between the two partners (6). In legume nodules, microaerobic environments trigger the rhizobial expression of nitrogen-fixing genes, such as nif and fix, via an oxygen-sensing system (13). However, the establishment of nitrogen-fixing symbiosis probably requires more complex steps triggered by reciprocal signal exchanges that lead to the organogenesis of nodules, differentiation of microsymbionts, and efficacy of nodulation (27). In addition to this symbiotic lifestyle, rhizobia survive in soils with many environment stresses, such as nutrient starvation.Lotus japonicus is a promising model legume for studying molecular interactions between symbiosis partners (20). Schauser et al. (40) first identified the plant regulatory gene nin, which is responsible for the nodule organogenesis program, in this legume. Recently, the receptor-like kinase genes have...

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Section: Discussionmentioning

confidence: 99%

Section: Vol 186 2004mentioning

confidence: 99%

Expression Islands Clustered on the Symbiosis Island of the Mesorhizobium loti Genome

et al. 2004

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“…Previous studies on several bacterial species suggest that Crp/Fnr regulators are involved in responses to a variety of intracellular or extracellular signals, such as anoxia, carbon monoxide, temperature, nitric oxide, and oxidative and nitrosative stress (1,13,35,42) and control metabolic pathways such as photosynthesis, nitrogen fixation, aromatic compound degradation, and respiration (11,25,31,39).…”

mentioning

confidence: 99%

Functional Characterization of Crp/Fnr-Type Global Transcriptional Regulators in Desulfovibrio vulgaris Hildenborough

Zhou

Chen

Zane

et al. 2012

Appl Environ Microbiol

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Crp/Fnr-type global transcriptional regulators regulate various metabolic pathways in bacteria and typically function in response to environmental changes. However, little is known about the function of four annotated Crp/Fnr homologs (DVU0379, DVU2097, DVU2547, and DVU3111) in Desulfovibrio vulgaris Hildenborough. A systematic study using bioinformatic, transcriptomic, genetic, and physiological approaches was conducted to characterize their roles in stress responses. Similar growth phenotypes were observed for the crp/fnr deletion mutants under multiple stress conditions. Nevertheless, the idea of distinct functions of Crp/Fnr-type regulators in stress responses was supported by phylogeny, gene transcription changes, fitness changes, and physiological differences. The four D. vulgaris Crp/Fnr homologs are localized in three subfamilies (HcpR, CooA, and cc). The crp/fnr knockout mutants were well separated by transcriptional profiling using detrended correspondence analysis (DCA), and more genes significantly changed in expression in a ⌬DVU3111 mutant (JW9013) than in the other three paralogs. In fitness studies, strain JW9013 showed the lowest fitness under standard growth conditions (i.e., sulfate reduction) and the highest fitness under NaCl or chromate stress conditions; better fitness was observed for a ⌬DVU2547 mutant (JW9011) under nitrite stress conditions and a ⌬DVU2097 mutant (JW9009) under air stress conditions. A higher Cr(VI) reduction rate was observed for strain JW9013 in experiments with washed cells. These results suggested that the four Crp/Fnr-type global regulators play distinct roles in stress responses of D. vulgaris. DVU3111 is implicated in responses to NaCl and chromate stresses, DVU2547 in nitrite stress responses, and DVU2097 in air stress responses.T ranscription factors, promoter sequences, and regulatory circuit architecture are often referred as "the regulatory genome" (27, 33), and transcription factors are central to the function of regulatory networks (5). Organisms rely on regulatory networks to orchestrate the transcription of genes in response to internal or external environmental changes in order to optimize metabolism and enhance survival. Crp/Fnr regulators are global transcriptional regulators widely distributed in bacteria. The characteristic structure of Crp/Fnr is a C-terminal helix-turn-helix (HTH) motif that fits the DNA major groove and an N-terminal nucleotide binding domain (34). This class of transcriptional factors is named after the first two representatives discovered in Escherichia coli, i.e., the Crp (cyclic AMP [cAMP] receptor protein) and Fnr (fumarate and nitrate reductase regulator protein) (4, 21, 24, 27). Crp/Fnr regulators are generally classified into different subfamilies (e.g., CooA, Crp, Dnr, FixK, Fnr, HbaR, NnrR, etc.) according to phylogenetic affiliations (50). The increasing number of sequenced whole genomes has added to a growing list of Crp/Fnr family regulators identified in bacteria (9, 26); however, functions for most are not well defin...

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“…Bacterial respiration is important for nitrogen fixation for two reasons: it (1) reduces oxidative damage to nitrogenase by consuming oxygen, and (2) simultaneously generates ATP molecules needed for nitrogen fixation. R. etli is characterized by a branched respiratory chain which involves at least four terminal cytochrome oxidases [26,27] and whose activity is regulated by the oxygen concentration in the environment. Nonzero fluxes through oxidative phosphorylation were observed in the simulation results, indicating oxidative phosphorylation is needed to maximize symbiotic nitrogen fixation.…”

Section: Utilization Of Central Metabolismmentioning

confidence: 99%

Metabolic Reconstruction and Modeling of Nitrogen Fixation in Rhizobium etli

Resendis‐Antonio¹,

Reed²,

Encarnación³

et al. 2005

PLoS Comput Biol

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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.

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Regulation of Gene Expression in Response to Oxygen in Rhizobium etli : Role of FnrN in fixNOQP Expression and in Symbiotic Nitrogen Fixation

Cited by 43 publications

References 35 publications

Expression Islands Clustered on the Symbiosis Island of the Mesorhizobium loti Genome

Expression Islands Clustered on the Symbiosis Island of the Mesorhizobium loti Genome

Functional Characterization of Crp/Fnr-Type Global Transcriptional Regulators in Desulfovibrio vulgaris Hildenborough

Metabolic Reconstruction and Modeling of Nitrogen Fixation in Rhizobium etli

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