Transcriptomic Analysis of
 Rhizobium leguminosarum
 Biovar viciae in Symbiosis with Host Plants
 Pisum sativum
 and
 Vicia cracca

Karunakaran, Ramakrishnan; Ramachandran, Vinoy K.; Seaman, Jonathan C.; East, Alison K.; Mouhsine, Bouchra; Mauchline, Tim H.; Prell, Jürgen; Skeffington, Alastair; Poole, Philip S.

doi:10.1128/jb.00165-09

Cited by 112 publications

(125 citation statements)

References 66 publications

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“…Pyruvate is then converted to acetyl coenzyme A (acetylCoA) by pyruvate dehydrogenase, subsequently condensed with oxaloacetate to citrate by citrate synthase, and further metabolized by the tricarboxylic acid (TCA) cycle. In agreement with this, pea bacteroids have a strong transcriptional upregulation of the decarboxylating arm of the TCA cycle (citrate synthase, aconitase, and 2-ketoglutarate dehydrogenase), which agrees with the measured activities of these enzymes (11,16 …”

supporting

confidence: 71%

Pyruvate Is Synthesized by Two Pathways in Pea Bacteroids with Different Efficiencies for Nitrogen Fixation

et al. 2010

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Nitrogen fixation in legume bacteroids is energized by the metabolism of dicarboxylic acids, which requires their oxidation to both oxaloacetate and pyruvate. In alfalfa bacteroids, production of pyruvate requires NAD ؉ malic enzyme (Dme) but not NADP ؉ malic enzyme (Tme). However, we show that Rhizobium leguminosarum has two pathways for pyruvate formation from dicarboxylates catalyzed by Dme and by the combined activities of phosphoenolpyruvate (PEP) carboxykinase (PckA) and pyruvate kinase (PykA). Both pathways enable N 2 fixation, but the PckA/PykA pathway supports N 2 fixation at only 60% of that for Dme. Double mutants of dme and pckA/pykA did not fix N 2 . Furthermore, dme pykA double mutants did not grow on dicarboxylates, showing that they are the only pathways for the production of pyruvate from dicarboxylates normally expressed. PckA is not expressed in alfalfa bacteroids, resulting in an obligate requirement for Dme for pyruvate formation and N 2 fixation. When PckA was expressed from a constitutive nptII promoter in alfalfa dme bacteroids, acetylene was reduced at 30% of the wild-type rate, although this level was insufficient to prevent nitrogen starvation. Dme has N-terminal, malic enzyme (Me), and C-terminal phosphotransacetylase (Pta) domains. Deleting the Pta domain increased the peak acetylene reduction rate in 4-week-old pea plants to 140 to 150% of the wild-type rate, and this was accompanied by increased nodule mass. Plants infected with Pta deletion mutants did not have increased dry weight, demonstrating that there is not a sustained change in nitrogen fixation throughout growth. This indicates a complex relationship between pyruvate synthesis in bacteroids, nitrogen fixation, and plant growth.The largest input of available nitrogen in the biosphere comes from the biological reduction of atmospheric N 2 to ammonium (20). Most of this comes from legume-Rhizobium symbioses, which arise from infection of host plants and result in root nodules (21). Signaling between the plant and bacterium is initiated by plant-released flavonoids and related compounds, which elicit the synthesis of lipochitooligosaccharide Nod factors by rhizobia (21). Bacteria are trapped by curling root hairs that they enter via infection threads. These grow into a zone of newly induced meristematic cells in the cortex that form the origin of the nodule. Bacteria are released from infection threads by endocytosis and surrounded by a plantderived symbiosome membrane. Plants provide differentiated bacteria (bacteroids) with dicarboxylic acids which energize N 2 reduction to ammonium for secretion back to the plant (24, 37). A simple exchange of dicarboxylates and ammonium is the classical model of nutrient exchange in nodules, but amino acid transport by pea bacteroids has also been shown to be essential (13). This is because bacteroids reduce the synthesis of branched-chain amino acids and become symbiotic auxotrophs that depend on their provision by the plant (25). Thus, when the two broad-specificity amino acid ABC trans...

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supporting

confidence: 71%

Pyruvate Is Synthesized by Two Pathways in Pea Bacteroids with Different Efficiencies for Nitrogen Fixation

et al. 2010

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“…RNA preparations, microarrays, and qRT-PCR were performed as described previously (28). A full description of the microarray results can be found elsewhere (13). R. leguminosarum uptake assays were performed with 25 M (4.625 kBq of 14 C) solute (7) and using cultures grown in acid minimal salts (AMS) with 10 mM glucose and 10 mM NH4Cl to an OD600 of Ϸ0.4.…”

Section: Methodsmentioning

confidence: 99%

Legumes regulate Rhizobium bacteroid development and persistence by the supply of branched-chain amino acids

Prell

White

Bourdès

et al. 2009

Proc. Natl. Acad. Sci. U.S.A.

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169

157

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One of the largest contributions to biologically available nitrogen comes from the reduction of N 2 to ammonia by rhizobia in symbiosis with legumes. Plants supply dicarboxylic acids as a carbon source to bacteroids, and in return they receive ammonia. However, metabolic exchange must be more complex, because effective N 2 fixation by Rhizobium leguminosarum bv viciae bacteroids requires either one of two broad-specificity amino acid ABC transporters (Aap and Bra). It was proposed that amino acids cycle between plant and bacteroids, but the model was unconstrained because of the broad solute specificity of Aap and Bra. Here, we constrain the specificity of Bra and ectopically express heterologous transporters to demonstrate that branched-chain amino acid (LIV) transport is essential for effective N 2 fixation. This dependence of bacteroids on the plant for LIV is not due to their known down-regulation of glutamate synthesis, because ectopic expression of glutamate dehydrogenase did not rescue effective N 2 fixation. Instead, the effect is specific to LIV and is accompanied by a major reduction in transcription and activity of LIV biosynthetic enzymes. Bacteroids become symbiotic auxotrophs for LIV and depend on the plant for their supply. Bacteroids with aap bra null mutations are reduced in number, smaller, and have a lower DNA content than wild type. Plants control LIV supply to bacteroids, regulating their development and persistence. This makes it a critical control point for regulation of symbiosis.mutualism ͉ nitrogen fixation ͉ peas ͉ symbiosis T he largest input of available nitrogen in the biosphere comes from biological reduction of atmospheric N 2 to ammonium (1). Most of this comes from legume-Rhizobium symbioses, arising from infection of host plants and resulting in root structures called nodules (2). These symbioses are initiated by plant-released flavonoids and related compounds, which elicit synthesis of lipochitooligosaccharide Nod factors by rhizobia. Bacteria are trapped by curling root hairs that they enter via infection threads. These grow into the root cortex, into a zone of newly induced meristematic cells forming the origin of the nodule. Bacteria are released from infection threads by endocytosis and are surrounded by a plant-derived symbiosome membrane. In nodules of galegoid legumes (a clade in the subfamily Papilionoideae, such as Medicago, Pisum, or Vicia), bacteria undergo dramatic increases in size, shape, and DNA content (3) before they start to reduce N 2 . Plants provide differentiated bacteria (bacteroids) with dicarboxylic acids, which energize N 2 reduction to ammonium for secretion back to the plant (4).A simple exchange of dicarboxylates and ammonium is the classical model of nutrient exchange in nodules, but amino acid transport by bacteroids has also been shown to be essential (5). Rhizobium leguminosarum mutated in 2 broad-specificity amino acid ABC transporters (Aap and Bra) formed N 2 -fixing pea bacteroids that appeared morphologically normal in electron micrographs,...

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“…Genes involved in root exudate usage, root attachment, and survival are induced in bacteria colonizing roots (120,121). In vitro expression technology (IVET) (122), proteomic analysis, microarray and RNA Seq transcriptomics, and genetic analysis have revealed rhizobial (120,121,123), Pseudomonas (124,125), Streptomyces (126), and other bacterial genes expressed on roots or rhizospheres. Similarly, bacteria may differentially express genes when in guts.…”

Section: Similar Bacterium-host Interactions In Guts and Rootsmentioning

confidence: 99%

Gut and Root Microbiota Commonalities

Ramírez-Puebla¹,

Servín-Garcidueñas²,

Jiménez-Marín³

et al. 2013

Appl Environ Microbiol

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Animal guts and plant roots have absorption roles for nutrient uptake and converge in harboring large, complex, and dynamic groups of microbes that participate in degradation or modification of nutrients and other substances. Gut and root bacteria regulate host gene expression, provide metabolic capabilities, essential nutrients, and protection against pathogens, and seem to share evolutionary trends.

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Transcriptomic Analysis of Rhizobium leguminosarum Biovar viciae in Symbiosis with Host Plants Pisum sativum and Vicia cracca

Cited by 112 publications

References 66 publications

Pyruvate Is Synthesized by Two Pathways in Pea Bacteroids with Different Efficiencies for Nitrogen Fixation

Pyruvate Is Synthesized by Two Pathways in Pea Bacteroids with Different Efficiencies for Nitrogen Fixation

Legumes regulate Rhizobium bacteroid development and persistence by the supply of branched-chain amino acids

Gut and Root Microbiota Commonalities

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