Transcriptome Analysis of Polyhydroxybutyrate Cycle Mutants Reveals Discrete Loci Connecting Nitrogen Utilization and Carbon Storage in
            <i>Sinorhizobium meliloti</i>

D’Alessio, Maya; Nordeste, Ricardo; Doxey, Andrew C.; Charles, Trevor C.

doi:10.1128/msystems.00035-17

Cited by 17 publications

(10 citation statements)

References 95 publications

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“…Single cross-over plasmid integration was used to construct knockouts of seven of these eight genes in a wild type background containing a smc03121 :: lacZ fusion ( Figure 5A ), and it was observed that disrupting just the bdhA gene, encoding a 3-hydroxybutyrate dehydrogenase ( Aneja and Charles 1999 ), resulted in transcriptional up-regulation of smc03121 ( Figure 5B ). This result was also seen in a recent RNA-seq study of S. meliloti poly-3-hydroxybutyrate (PHB) cycle mutants ( D’Alessio et al 2017 ). However, smc03121 was induced and expressed equally in all eight gene mutants when the medium was supplemented with 10 mM 3-hydroxybutyrate ( Figure 5B ).…”

Section: Resultssupporting

confidence: 67%

Inter-replicon Gene Flow Contributes to Transcriptional Integration in the Sinorhizobium meliloti Multipartite Genome

diCenzo

Wellappili

Golding

et al. 2018

G3 Genes|Genomes|Genetics

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Integration of newly acquired genes into existing regulatory networks is necessary for successful horizontal gene transfer (HGT). Ten percent of bacterial species contain at least two DNA replicons over 300 kilobases in size, with the secondary replicons derived predominately through HGT. The Sinorhizobium meliloti genome is split between a 3.7 Mb chromosome, a 1.7 Mb chromid consisting largely of genes acquired through ancient HGT, and a 1.4 Mb megaplasmid consisting primarily of recently acquired genes. Here, RNA-sequencing is used to examine the transcriptional consequences of massive, synthetic genome reduction produced through the removal of the megaplasmid and/or the chromid. Removal of the pSymA megaplasmid influenced the transcription of only six genes. In contrast, removal of the chromid influenced expression of ∼8% of chromosomal genes and ∼4% of megaplasmid genes. This was mediated in part by the loss of the ETR DNA region whose presence on pSymB is due to a translocation from the chromosome. No obvious functional bias among the up-regulated genes was detected, although genes with putative homologs on the chromid were enriched. Down-regulated genes were enriched in motility and sensory transduction pathways. Four transcripts were examined further, and in each case the transcriptional change could be traced to loss of specific pSymB regions. In particularly, a chromosomal transporter was induced due to deletion of bdhA likely mediated through 3-hydroxybutyrate accumulation. These data provide new insights into the evolution of the multipartite bacterial genome, and more generally into the integration of horizontally acquired genes into the transcriptome.

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Section: Resultssupporting

confidence: 67%

Inter-replicon Gene Flow Contributes to Transcriptional Integration in the Sinorhizobium meliloti Multipartite Genome

diCenzo

Wellappili

Golding

et al. 2018

G3 Genes|Genomes|Genetics

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“…Despite rhizobia requiring oxygen for ATP synthesis, oxygen levels in nodules are only 10 to 40 nM ( 9 ), which is a requirement for highly oxygen-sensitive nitrogenase enzyme activity ( 10 ). The challenge of balancing carbon allocation under these conditions is evidenced by the synthesis of lipids and carbon polymers, such as polyhydroxybutyrate (PHB), which indicate imbalances in nutrient supply ( 8 , 11 ). PHB and lipids have been suggested to play a role as carbon and redox sinks for bacteroids, although their accumulation is variable between rhizobial strains and their role remains to be elucidated ( 8 , 12 , 13 ).…”

Section: Introductionmentioning

confidence: 99%

Metabolic control of nitrogen fixation in rhizobium-legume symbioses

et al. 2021

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Rhizobia induce nodule formation on legume roots and differentiate into bacteroids, which catabolize plant-derived dicarboxylates to reduce atmospheric N2 into ammonia. Despite the agricultural importance of this symbiosis, the mechanisms that govern carbon and nitrogen allocation in bacteroids and promote ammonia secretion to the plant are largely unknown. Using a metabolic model derived from genome-scale datasets, we show that carbon polymer synthesis and alanine secretion by bacteroids facilitate redox balance in microaerobic nodules. Catabolism of dicarboxylates induces not only a higher oxygen demand but also a higher NADH/NAD+ ratio than sugars. Modeling and 13C metabolic flux analysis indicate that oxygen limitation restricts the decarboxylating arm of the tricarboxylic acid cycle, which limits ammonia assimilation into glutamate. By tightly controlling oxygen supply and providing dicarboxylates as the energy and electron source donors for N2 fixation, legumes promote ammonia secretion by bacteroids. This is a defining feature of rhizobium-legume symbioses.

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“…Despite rhizobia requiring oxygen for ATP synthesis, oxygen levels in nodules are only 10 -40 nM 9 , which is a requirement for highly oxygen-sensitive nitrogenase enzyme activity 10 . The challenge of balancing carbon allocation under these conditions is evidenced by the synthesis of lipids and carbon polymers, such as polyhydroxybutyrate (PHB), which indicate imbalances in nutrient supply 8,11 . PHB and lipids have been suggested to play a role as carbon and redox sinks for bacteroids, although their accumulation is variable between rhizobial strains and their role remains to be elucidated 8,12,13 .…”

Section: Introductionmentioning

confidence: 99%

Metabolic constraints on nitrogen fixation by rhizobia in legume nodules

Schulte

Borah

Wheatley

et al. 2021

Preprint

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Rhizobia induce nodule formation on legume roots and differentiate into bacteroids, which use plant-derived dicarboxylates as energy and electron sources for reduction of atmospheric N2 into ammonia for secretion to plants. Using heterogeneous genome-scale datasets, we reconstructed a model of bacteroid metabolism to investigate the effects of varying dicarboxylate and oxygen supply on carbon and nitrogen allocation. Modelling and 13C metabolic flux analysis in bacteroids indicate that microaerobiosis restricts the decarboxylating arm of the TCA cycle and limits ammonia assimilation into glutamate. Catabolism of dicarboxylates induces a higher oxygen demand but also a higher NADH/NAD+ ratio compared to sugars. Carbon polymer synthesis and alanine secretion by bacteroids facilitate redox balance in microaerobic nodules with alanine secretion increasing as oxygen tension decreases. Our results provide a framework for understanding fundamental constraints on rhizobial metabolism during symbiotic nitrogen fixation.

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Transcriptome Analysis of Polyhydroxybutyrate Cycle Mutants Reveals Discrete Loci Connecting Nitrogen Utilization and Carbon Storage in Sinorhizobium meliloti

Cited by 17 publications

References 95 publications

Inter-replicon Gene Flow Contributes to Transcriptional Integration in the Sinorhizobium meliloti Multipartite Genome

Inter-replicon Gene Flow Contributes to Transcriptional Integration in the Sinorhizobium meliloti Multipartite Genome

Metabolic control of nitrogen fixation in rhizobium-legume symbioses

Metabolic constraints on nitrogen fixation by rhizobia in legume nodules

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