Global control of bacterial nitrogen and carbon metabolism by a PTSNtr-regulated switch

The nitrogen-related phosphotransferase system (PTSNtr) of Rhizobium leguminosarum bv. viciae 3841 transfers phosphate from PEP via PtsP and NPr to two output regulators, ManX and PtsN. ManX controls central carbon metabolism via the tricarboxylic acid (TCA) cycle, while PtsN controls nitrogen uptake, exopolysaccharide production, and potassium homeostasis, each of which is critical for cellular adaptation and survival. Cellular nitrogen status modulates phosphorylation when glutamine, an abundant amino acid when nitrogen is available, binds to the GAF sensory domain of PtsP, preventing PtsP phosphorylation and subsequent modification of ManX and PtsN. Under nitrogen-rich, carbon-limiting conditions, unphosphorylated ManX stimulates the TCA cycle and carbon oxidation, while unphosphorylated PtsN stimulates potassium uptake. The effects are reversed with the phosphorylation of ManX and PtsN, occurring under nitrogen-limiting, carbon-rich conditions; phosphorylated PtsN triggers uptake and nitrogen metabolism, the TCA cycle and carbon oxidation are decreased, while carbon-storage polymers such as surface polysaccharide are increased. Deleting the GAF domain from PtsP makes cells “blind” to the cellular nitrogen status. PTSNtr constitutes a switch through which carbon and nitrogen metabolism are rapidly, and reversibly, regulated by protein:protein interactions. PTSNtr is widely conserved in proteobacteria, highlighting its global importance.

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Regulation of acetate metabolism and coordination with the TCA cycle via a processed small RNA

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1815288116 ◽

2018 ◽

Vol 116 (3) ◽

pp. 1043-1052 ◽

Cited By ~ 16

Author(s):

François De Mets ◽

Laurence Van Melderen ◽

Susan Gottesman

Keyword(s):

Small Rna ◽

Posttranscriptional Regulation ◽

Tca Cycle ◽

Central Carbon Metabolism ◽

Growth Defect ◽

Acetate Metabolism ◽

Overflow Metabolism ◽

Acetyl Phosphate ◽

Rnase E ◽

The Tca Cycle

Bacterial regulatory small RNAs act as crucial regulators in central carbon metabolism by modulating translation initiation and degradation of target mRNAs in metabolic pathways. Here, we demonstrate that a noncoding small RNA, SdhX, is produced by RNase E-dependent processing from the 3′UTR of thesdhCDAB-sucABCDoperon, encoding enzymes of the tricarboxylic acid (TCA) cycle. InEscherichia coli, SdhX negatively regulatesackA, which encodes an enzyme critical for degradation of the signaling molecule acetyl phosphate, while the downstreamptagene, encoding the enzyme critical for acetyl phosphate synthesis, is not significantly affected. This discoordinate regulation ofptaandackAincreases the accumulation of acetyl phosphate when SdhX is expressed. Mutations insdhXthat abolish regulation ofackAlead to more acetate in the medium (more overflow metabolism), as well as a strong growth defect in the presence of acetate as sole carbon source, when the AckA-Pta pathway runs in reverse. SdhX overproduction confers resistance to hydroxyurea, via regulation ofackA. SdhX abundance is tightly coupled to the transcription signals of TCA cycle genes but escapes all known posttranscriptional regulation. Therefore, SdhX expression directly correlates with transcriptional input to the TCA cycle, providing an effective mechanism for the cell to link the TCA cycle with acetate metabolism pathways.

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Comparative metabolomics of Phialemonium curvatum as an omnipotent fungus cultivated on crude palm oil versus glucose

Microbial Cell Factories ◽

10.1186/s12934-020-01434-w ◽

2020 ◽

Vol 19 (1) ◽

Author(s):

Arief Izzairy Zamani ◽

Susann Barig ◽

Sarah Ibrahim ◽

Hirzun Mohd. Yusof ◽

Julia Ibrahim ◽

...

Keyword(s):

Carbon Source ◽

Organic Acids ◽

Vegetable Oil ◽

Carbon Metabolism ◽

Sole Carbon Source ◽

Carbon Sources ◽

Tca Cycle ◽

Central Carbon Metabolism ◽

Targeted Metabolomics ◽

Central Carbon

Abstract Background Sugars and triglycerides are common carbon sources for microorganisms. Nonetheless, a systematic comparative interpretation of metabolic changes upon vegetable oil or glucose as sole carbon source is still lacking. Selected fungi that can grow in acidic mineral salt media (MSM) with vegetable oil had been identified recently. Hence, this study aimed to investigate the overall metabolite changes of an omnipotent fungus and to reveal changes at central carbon metabolism corresponding to both carbon sources. Results Targeted and non-targeted metabolomics for both polar and semi-polar metabolites of Phialemonium curvatum AWO2 (DSM 23903) cultivated in MSM with palm oil (MSM-P) or glucose (MSM-G) as carbon sources were obtained. Targeted metabolomics on central carbon metabolism of tricarboxylic acid (TCA) cycle and glyoxylate cycle were analysed using LC–MS/MS-TripleQ and GC–MS, while untargeted metabolite profiling was performed using LC–MS/MS-QTOF followed by multivariate analysis. Targeted metabolomics analysis showed that glyoxylate pathway and TCA cycle were recruited at central carbon metabolism for triglyceride and glucose catabolism, respectively. Significant differences in organic acids concentration of about 4- to 8-fold were observed for citric acid, succinic acid, malic acid, and oxaloacetic acid. Correlation of organic acids concentration and key enzymes involved in the central carbon metabolism was further determined by enzymatic assays. On the other hand, the untargeted profiling revealed seven metabolites undergoing significant changes between MSM-P and MSM-G cultures. Conclusions Overall, this study has provided insights on the understanding on the effect of triglycerides and sugar as carbon source in fungi global metabolic pathway, which might become important for future optimization of carbon flux engineering in fungi to improve organic acids production when vegetable oil is applied as the sole carbon source.

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A mitochondrial GABA permease connects the GABA shunt and the TCA cycle, and is essential for normal carbon metabolism

The Plant Journal ◽

10.1111/j.1365-313x.2011.04612.x ◽

2011 ◽

Vol 67 (3) ◽

pp. 485-498 ◽

Cited By ~ 105

Author(s):

Simon Michaeli ◽

Aaron Fait ◽

Kelly Lagor ◽

Adriano Nunes-Nesi ◽

Nicole Grillich ◽

...

Keyword(s):

Carbon Metabolism ◽

Tca Cycle ◽

Gaba Shunt ◽

The Tca Cycle ◽

Normal Carbon

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Procyclic trypanosomes recycle glucose catabolites and TCA cycle intermediates to stimulate growth in the presence of physiological amounts of proline

PLoS Pathogens ◽

10.1371/journal.ppat.1009204 ◽

2021 ◽

Vol 17 (3) ◽

pp. e1009204

Author(s):

Oriana Villafraz ◽

Marc Biran ◽

Erika Pineda ◽

Nicolas Plazolles ◽

Edern Cahoreau ◽

...

Keyword(s):

Carbon Sources ◽

Tca Cycle ◽

Central Carbon Metabolism ◽

Tsetse Fly ◽

Growth Defect ◽

Insect Vector ◽

Metabolic Intermediates ◽

The Tca Cycle ◽

Production And Consumption ◽

Tca Cycle Intermediates

Trypanosoma brucei, a protist responsible for human African trypanosomiasis (sleeping sickness), is transmitted by the tsetse fly where the procyclic forms of the parasite develop in the proline-rich (1–2 mM) and glucose-depleted digestive tract. Proline is essential for the midgut colonization of the parasite in the insect vector, however other carbon sources could be available and used to feed its central metabolism. Here we show that procyclic trypanosomes can consume and metabolize metabolic intermediates, including those excreted from glucose catabolism (succinate, alanine and pyruvate), with the exception of acetate, which is the ultimate end-product excreted by the parasite. Among the tested metabolites, tricarboxylic acid (TCA) cycle intermediates (succinate, malate and α-ketoglutarate) stimulated growth of the parasite in the presence of 2 mM proline. The pathways used for their metabolism were mapped by proton-NMR metabolic profiling and phenotypic analyses of thirteen RNAi and/or null mutants affecting central carbon metabolism. We showed that (i) malate is converted to succinate by both the reducing and oxidative branches of the TCA cycle, which demonstrates that procyclic trypanosomes can use the full TCA cycle, (ii) the enormous rate of α-ketoglutarate consumption (15-times higher than glucose) is possible thanks to the balanced production and consumption of NADH at the substrate level and (iii) α-ketoglutarate is toxic for trypanosomes if not appropriately metabolized as observed for an α-ketoglutarate dehydrogenase null mutant. In addition, epimastigotes produced from procyclics upon overexpression of RBP6 showed a growth defect in the presence of 2 mM proline, which is rescued by α-ketoglutarate, suggesting that physiological amounts of proline are not sufficient per se for the development of trypanosomes in the fly. In conclusion, these data show that trypanosomes can metabolize multiple metabolites, in addition to proline, which allows them to confront challenging environments in the fly.

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Hierarchical routing in carbon metabolism favors iron-scavenging strategy in iron-deficient soilPseudomonasspecies

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.2016380117 ◽

2020 ◽

Vol 117 (51) ◽

pp. 32358-32369 ◽

Cited By ~ 1

Author(s):

Caroll M. Mendonca ◽

Sho Yoshitake ◽

Hua Wei ◽

Anne Werner ◽

Samantha S. Sasnow ◽

...

Keyword(s):

Pseudomonas Putida ◽

Carbon Metabolism ◽

Nutrient Deficiency ◽

Tca Cycle ◽

Substrate Uptake ◽

Siderophore Biosynthesis ◽

Energy Demands ◽

The Tca Cycle ◽

Iron Deficient ◽

Gluconeogenic Substrates

High-affinity iron (Fe) scavenging compounds, or siderophores, are widely employed by soil bacteria to survive scarcity in bioavailable Fe. Siderophore biosynthesis relies on cellular carbon metabolism, despite reported decrease in both carbon uptake and Fe-containing metabolic proteins in Fe-deficient cells. Given this paradox, the metabolic network required to sustain the Fe-scavenging strategy is poorly understood. Here, through multiple13C-metabolomics experiments with Fe-replete and Fe-limited cells, we uncover how soilPseudomonasspecies reprogram their metabolic pathways to prioritize siderophore biosynthesis. Across the three species investigated (Pseudomonas putidaKT2440,Pseudomonas protegensPf-5, andPseudomonas putidaS12), siderophore secretion is higher during growth on gluconeogenic substrates than during growth on glycolytic substrates. In response to Fe limitation, we capture decreased flux toward the tricarboxylic acid (TCA) cycle during the metabolism of glycolytic substrates but, due to carbon recycling to the TCA cycle via enhanced anaplerosis, the metabolism of gluconeogenic substrates results in an increase in both siderophore secretion (up to threefold) and Fe extraction (up to sixfold) from soil minerals. During simultaneous feeding on the different substrate types, Fe deficiency triggers a hierarchy in substrate utilization, which is facilitated by changes in protein abundances for substrate uptake and initial catabolism. Rerouted metabolism further promotes favorable fluxes in the TCA cycle and the gluconeogenesis–anaplerosis nodes, despite decrease in several proteins in these pathways, to meet carbon and energy demands for siderophore precursors in accordance with increased proteins for siderophore biosynthesis. Hierarchical carbon metabolism thus serves as a critical survival strategy during the metal nutrient deficiency.

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Quantitative analysis of the physiological contributions of glucose to the TCA cycle

10.1101/840538 ◽

2019 ◽

Cited By ~ 1

Author(s):

Shiyu Liu ◽

Ziwei Dai ◽

Daniel E. Cooper ◽

David G. Kirsch ◽

Jason W. Locasale

Keyword(s):

Quantitative Analysis ◽

Metabolic Flux ◽

Isotope Labeling ◽

Tca Cycle ◽

Central Carbon Metabolism ◽

Flux Analysis ◽

Experimental Conditions ◽

The Tca Cycle ◽

Metabolic Physiology

ABSTRACTThe carbon source for catabolism in vivo is a fundamental question in metabolic physiology. Limited by data and rigorous mathematical analysis, controversy exists over the nutritional sources for carbon in the tricarboxylic acid (TCA) cycle under physiological settings. Using isotope-labeling data in vivo across several experimental conditions, we construct multiple models of central carbon metabolism and develop methods based on metabolic flux analysis (MFA) to solve for the preferences of glucose, lactate, and other nutrients used in the TCA cycle across many tissues. We show that in nearly all circumstances, glucose contributes more than lactate as a nutrient source for the TCA cycle. This conclusion is verified in different animal strains from different studies, different administrations of 13C glucose, and is extended to multiple tissue types. Thus, this quantitative analysis of organismal metabolism defines the relative contributions of nutrient fluxes in physiology, provides a resource for analysis of in vivo isotope tracing data, and concludes that glucose is the major nutrient used for catabolism in mammals.

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Dynamic Genome Evolution and Blueprint of Complex Virocell Metabolism in Globally-Distributed Giant Viruses

10.1101/836445 ◽

2019 ◽

Cited By ~ 1

Author(s):

Mohammad Moniruzzaman ◽

Carolina A. Martinez-Gutierrez ◽

Alaina R. Weinheimer ◽

Frank O. Aylward

Keyword(s):

Phylogenetic Trees ◽

Tca Cycle ◽

Biogeochemical Cycles ◽

Central Carbon Metabolism ◽

Host Cells ◽

Metabolic Genes ◽

The Tca Cycle ◽

Dynamic Genome ◽

Giant Viruses ◽

Global Biogeochemical Cycles

AbstractThe discovery of giant viruses with large genomes has transformed our understanding of the limits of viral complexity in the biosphere, and subsequent research in model virus-host systems has advanced our knowledge of intricate mechanisms used by these viruses to take over host cells during infection. The extent of the metabolic diversity encoded by these viruses in the environment is less well-understood, however, and their potential impact on global biogeochemical cycles remains unclear. To address this, we generated 501 metagenome-assembled genomes (MAGs) of NCLDVs from diverse environments around the globe and analyzed their encoded functional diversity and potential for reprogramming host physiology. We found that 476 (95%) of the MAGs belonged to the Mimiviridae and Phycodnaviridae families, and of these we recovered 96% from aquatic environments, highlighting the diversity of these viral families in global freshwater and marine systems. MAGs encoded diverse genes predicted to be involved in nutrient uptake and processing, light harvesting, central nitrogen metabolism, and the manipulation of cell death, underscoring the complex interplay between these viruses and their hosts. Surprisingly, numerous genomes encoded genes involved in glycolysis, gluconeogenesis, and the TCA cycle, including one genome with a 70%-complete glycolytic pathway, suggesting that many of these viruses can even reprogram fundamental aspects of their host’s central carbon metabolism. Phylogenetic trees of NCLDV metabolic genes together with their cellular homologs revealed distinct clustering of viral sequences into divergent clades, indicating these metabolic genes are virus-specific and were acquired in the distant past. Our findings reveal that diverse NCLDV genomes encode complex, cell-like metabolic capabilities with evolutionary histories that are largely independent of cellular life, strongly implicating them as distinct drivers of biogeochemical cycles in their own right.

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Dissection of Central Carbon Metabolism of Hemoglobin-ExpressingEscherichia coli by 13C Nuclear Magnetic Resonance Flux Distribution Analysis in Microaerobic Bioprocesses

Applied and Environmental Microbiology ◽

10.1128/aem.67.2.680-687.2001 ◽

2001 ◽

Vol 67 (2) ◽

pp. 680-687 ◽

Cited By ~ 27

Author(s):

Alexander D. Frey ◽

Jocelyne Fiaux ◽

Thomas Szyperski ◽

Kurt Wüthrich ◽

James E. Bailey ◽

...

Keyword(s):

Nuclear Magnetic Resonance ◽

Magnetic Resonance ◽

Carbon Metabolism ◽

Tca Cycle ◽

Central Carbon Metabolism ◽

Distribution Analysis ◽

E Coli ◽

13C Nuclear Magnetic Resonance ◽

Central Carbon ◽

Nuclear Magnetic

ABSTRACT Escherichia coli MG1655 cells expressingVitreoscilla hemoglobin (VHb), Alcaligenes eutrophus flavohemoprotein (FHP), the N-terminal hemoglobin domain of FHP (FHPg), and a fusion protein which comprises VHb and theA. eutrophus C-terminal reductase domain (VHb-Red) were grown in a microaerobic bioreactor to study the effects of low oxygen concentrations on the central carbon metabolism, using fractional13C-labeling of the proteinogenic amino acids and two-dimensional [13C, 1H]-correlation nuclear magnetic resonance (NMR) spectroscopy. The NMR data revealed differences in the intracellular carbon fluxes between E. coli cells expressing either VHb or VHb-Red and cells expressingA. eutrophus FHP or the truncated heme domain (FHPg).E. coli MG1655 cells expressing either VHb or VHb-Red were found to function with a branched tricarboxylic acid (TCA) cycle. Furthermore, cellular demands for ATP and reduction equivalents in VHb- and VHb-Red-expressing cells were met by an increased flux through glycolysis. In contrast, in E. coli cells expressingA. eutrophus hemeproteins, the TCA cycle is running cyclically, indicating a shift towards a more aerobic regulation. Consistently, E. coli cells displaying FHP and FHPg activity showed lower production of the typical anaerobic by-products formate, acetate, and d-lactate. The implications of these observations for biotechnological applications are discussed.

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