The Disruption of a Gene Encoding a Putative Arylesterase Impairs Pyruvate Dehydrogenase Complex Activity and Nitrogen Fixation in <i>Sinorhizobium meliloti</i>

Soto, Marı́a José; Sanjuán, Juan; Olivares, José

doi:10.1094/mpmi.2001.14.6.811

Cited by 4 publications

(4 citation statements)

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“…This result is qualitatively in agreement with the fact that icd mutants on S. meliloti are symbiotically ineffective [28]. Similarly, constraint-based modeling concludes that a reduction of enzymatic activity in pyruvate dehydrogenase (PDH) induces a significant reduction in symbiotic nitrogen fixation but does not impair it as occurs in the case of S. meliloti bacteroids [29], see Figure 3 (B). This finding suggests that the role of PDH in the production of acetyl-coenzyme A can be replaced by alternative pathways in R. etli bacteroids [5].…”

Section: Discussionsupporting

confidence: 80%

Systems biology of bacterial nitrogen fixation: High-throughput technology and its integrative description with constraint-based modeling

Resendis‐Antonio¹,

Hernández²,

Salazar³

et al. 2011

BMC Syst Biol

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BackgroundBacterial nitrogen fixation is the biological process by which atmospheric nitrogen is uptaken by bacteroids located in plant root nodules and converted into ammonium through the enzymatic activity of nitrogenase. In practice, this biological process serves as a natural form of fertilization and its optimization has significant implications in sustainable agricultural programs. Currently, the advent of high-throughput technology supplies with valuable data that contribute to understanding the metabolic activity during bacterial nitrogen fixation. This undertaking is not trivial, and the development of computational methods useful in accomplishing an integrative, descriptive and predictive framework is a crucial issue to decoding the principles that regulated the metabolic activity of this biological process.ResultsIn this work we present a systems biology description of the metabolic activity in bacterial nitrogen fixation. This was accomplished by an integrative analysis involving high-throughput data and constraint-based modeling to characterize the metabolic activity in Rhizobium etli bacteroids located at the root nodules of Phaseolus vulgaris (bean plant). Proteome and transcriptome technologies led us to identify 415 proteins and 689 up-regulated genes that orchestrate this biological process. Taking into account these data, we: 1) extended the metabolic reconstruction reported for R. etli; 2) simulated the metabolic activity during symbiotic nitrogen fixation; and 3) evaluated the in silico results in terms of bacteria phenotype. Notably, constraint-based modeling simulated nitrogen fixation activity in such a way that 76.83% of the enzymes and 69.48% of the genes were experimentally justified. Finally, to further assess the predictive scope of the computational model, gene deletion analysis was carried out on nine metabolic enzymes. Our model concluded that an altered metabolic activity on these enzymes induced different effects in nitrogen fixation, all of these in qualitative agreement with observations made in R. etli and other Rhizobiaceas.ConclusionsIn this work we present a genome scale study of the metabolic activity in bacterial nitrogen fixation. This approach leads us to construct a computational model that serves as a guide for 1) integrating high-throughput data, 2) describing and predicting metabolic activity, and 3) designing experiments to explore the genotype-phenotype relationship in bacterial nitrogen fixation.

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Section: Discussionsupporting

confidence: 80%

Systems biology of bacterial nitrogen fixation: High-throughput technology and its integrative description with constraint-based modeling

Resendis‐Antonio¹,

Hernández²,

Salazar³

et al. 2011

BMC Syst Biol

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“…The genes encoding the pyruvate dehydrogenase complex (pdhABC) are cotranscribed elsewhere on the chromosome (Cabanes et al 2000). Although dihydrolipoyl dehydrogenase can be shared between the pyruvate dehydrogenase and ␣-ketoglutarate dehydrogenase complexes (Mattevi et al 1992), a second dihydrolipoyl dehydrogenase (lpdA1) is encoded near pdhABC, and a mutation that was polar on its transcription abolished pyruvate dehydrogenase activity (Soto et al 2001).…”

Section: Tricarboxylic Acid Cyclementioning

confidence: 99%

Physiology, genetics, and biochemistry of carbon metabolism in the alphaproteobacteriumSinorhizobium meliloti

Geddes

Oresnik

2014

Can. J. Microbiol.

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A large proportion of genes within a genome encode proteins that play a role in metabolism. The Alphaproteobacteria are a ubiquitous group of bacteria that play a major role in a number of environments. For well over 50 years, carbon metabolism in Rhizobium has been studied at biochemical and genetic levels. Here, we review the pre- and post-genomics literature of the metabolism of the alphaproteobacterium Sinorhizobium meliloti. This review provides an overview of carbon metabolism that is useful to readers interested in this organism and to those working on other organisms that do not follow other model system paradigms.

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“…Pyruvate dehydrogenase is a multienzyme complex encoded by two genes, pdhAa and pdhAb, in S. meliloti (Cabanes et al, 2000). Mutation of a putative arylesterase (ada), that clusters with the genes for pyruvate dehydrogenase, reduced the activity of pyruvate dehydrogenase in S. meliloti 16-fold and resulted in a Fix 2 phenotype (Soto et al, 2001). In rhizobia there are two forms of malic enzyme: an NADP 1 -dependant malic enzyme with high affinity that is stimulated by ammonium, and an NAD 1 -dependant malic enzyme with a lower affinity that is stimulated by potassium and ammonium salts (Finan et al, 1991;Driscoll and Finan, 1993;Driscoll and Finan, 1996).…”

Section: Nitrogen Fixation and Bacteroid Metabolism Of Dicarboxylatesmentioning

confidence: 99%

Nutrient Sharing between Symbionts

White

Prell²,

James³

et al. 2007

Plant Physiology

210

158

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In this review, we consider the exchange of nutrients between the host plant and the bacterial microsymbiont in nitrogen-fixing legume root nodules. During nodule formation, the host tissues and the bacterial microsymbiont develop in response to each other to form a specialized tissue that maintains an environment where nitrogen fixation can occur (Brewin, 2004;Mergaert et al., 2006;Prell and Poole, 2006). This complex development will not be considered here but, at the end of the process, specialized, nitrogen-fixing forms of the bacteria, known as bacteroids, reside in the plant cytosol, enclosed within plant-derived membranes. These organelle-like structures are known as symbiosomes; the plant-derived membrane that surrounds the bacteroid is the symbiosome (or peribacteroid) membrane and the space between the two is the symbiosome (or peribacteroid) space. An infected plant cell may be packed with thousands of symbiosomes. The exchange of nutrients that is fundamental to N 2 fixation therefore involves metabolism in the plant to provide carbon and nitrogen compounds to the bacteroids and to assimilate the metabolites that bacteroids release. Nutrients transferred between the symbionts must traverse both the symbiosome and the bacteroid membranes. It is clear that there is more than one pattern whereby successful nutrient exchange can take place: There are two basic types of legume nodules, determinate and indeterminate, and there are fundamental differences between the two in how they develop and in their carbon and nitrogen metabolism. This review focuses on the metabolism of carbon and nitrogen compounds in the symbionts and on the exchange of nutrients across the bacteroid and symbiosome membranes. Particular attention is paid to the movement of primary carbon and nitrogen sources and how they are utilized by both bacteroids and the plant.

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The Disruption of a Gene Encoding a Putative Arylesterase Impairs Pyruvate Dehydrogenase Complex Activity and Nitrogen Fixation in Sinorhizobium meliloti

Cited by 4 publications

References 20 publications

Systems biology of bacterial nitrogen fixation: High-throughput technology and its integrative description with constraint-based modeling

Systems biology of bacterial nitrogen fixation: High-throughput technology and its integrative description with constraint-based modeling

Physiology, genetics, and biochemistry of carbon metabolism in the alphaproteobacteriumSinorhizobium meliloti

Nutrient Sharing between Symbionts

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