scholarly journals Revealing metabolic flexibility ofCandidatusAccumulibacter phosphatis through redox cofactor analysis and metabolic network modeling

2018 ◽  
Author(s):  
Leonor Guedes da Silva ◽  
Karel Olavarria Gamez ◽  
Joana Castro Gomes ◽  
Kasper Akkermans ◽  
Laurens Welles ◽  
...  
Keyword(s):  
Metabolic Network ◽  
Environmental Conditions ◽  
Metabolic Flux ◽  
Metabolic Flexibility ◽  
Omics Data ◽  
Metabolic Potential ◽  
Wide Range ◽  
Central Carbon ◽  
Accumulibacter Phosphatis ◽  
Metabolic Strategies

ABSTRACTEnvironmental fluctuations in the availability of nutrients lead to intricate metabolic strategies.CandidatusAccumulibacter phosphatis, a polyphosphate accumulating organism (PAO) responsible for enhanced biological phosphorus removal (EBPR) from wastewater treatment systems, is prevalent in aerobic/anaerobic environments. While the overall metabolic traits of these bacteria are well described, the inexistence of isolates has led to controversial conclusions on the metabolic pathways used.Here, we experimentally determined the redox cofactor preference of different oxidoreductases in the central carbon metabolism of a highly enrichedCa. A. phosphatis culture. Remarkably, we observed that the acetoacetyl-CoA reductase engaged in polyhydroxyalkanoates (PHA) synthesis is NADH-preferring instead of the generally assumed NADPH dependency. Based on previously published meta-omics data and the results of enzymatic assays, a reduced central carbon metabolic network was constructed and used for simulating different metabolic operating modes. In particular, scenarios with different acetate-to-glycogen consumption ratios were simulated. For a high ratio (i.e. more acetate), a polyphosphate-based metabolism arises as optimal with a metabolic flux through the glyoxylate shunt. In case of a low acetate-to-glycogen ratio, glycolysis is used in combination with reductive branch of the TCA cycle. Thus, optimal metabolic flux strategies will depend on the environment (acetate uptake) and on intracellular storage compounds availability (polyphosphate/glycogen).This metabolic flexibility is enabled by the NADH-driven PHA synthesis. It allows for maintaining metabolic activity under varying environmental substrate conditions, with high carbon conservation and lower energetic costs compared to NADPH dependent PHA synthesis. Such (flexible) metabolic redox coupling can explain PAOs’ competitiveness under oxygen-fluctuating environments.IMPORTANCEHere we demonstrate how microbial metabolism can adjust to a wide range of environmental conditions. Such flexibility generates a selective advantage under fluctuating environmental conditions. It can also explain the different observations reported in PAO literature, including the capacity ofCa. Accumulibacter phosphatis to act like glycogen accumulating organisms (GAO). These observations stem from slightly different experimental conditions and controversy only arises when one assumes metabolism can only operate in one single mode. Furthermore, we also show how the study of metabolic strategies is possible when combining-omics data with functional assays and modeling. Genomic information can only provide the potential of a microorganism. The environmental context and other complementary approaches are still needed to study and predict the functional application of such metabolic potential.

scholarly journals Revealing the Metabolic Flexibility of “Candidatus Accumulibacter phosphatis” through Redox Cofactor Analysis and Metabolic Network Modeling

2020 ◽  
Vol 86 (24) ◽  
Author(s):  
Leonor Guedes da Silva ◽  
Karel Olavarria Gamez ◽  
Joana Castro Gomes ◽  
Kasper Akkermans ◽  
Laurens Welles ◽  
...  
Keyword(s):  
Metabolic Network ◽  
Environmental Conditions ◽  
Metabolic Flux ◽  
Metabolic Flexibility ◽  
Metabolic Potential ◽  
Experimental Conditions ◽  
Wide Range ◽  
Central Carbon ◽  
Accumulibacter Phosphatis ◽  
Metabolic Strategies

ABSTRACT Environmental fluctuations in the availability of nutrients lead to intricate metabolic strategies. “Candidatus Accumulibacter phosphatis,” a polyphosphate-accumulating organism (PAO) responsible for enhanced biological phosphorus removal (EBPR) from wastewater treatment systems, is prevalent in aerobic/anaerobic environments. While the overall metabolic traits of these bacteria are well described, the nonavailability of isolates has led to controversial conclusions on the metabolic pathways used. In this study, we experimentally determined the redox cofactor preferences of different oxidoreductases in the central carbon metabolism of a highly enriched “Ca. Accumulibacter phosphatis” culture. Remarkably, we observed that the acetoacetyl coenzyme A reductase engaged in polyhydroxyalkanoate (PHA) synthesis is NADH preferring instead of showing the generally assumed NADPH dependency. This allows rethinking of the ecological role of PHA accumulation as a fermentation product under anaerobic conditions and not just a stress response. Based on previously published metaomics data and the results of enzymatic assays, a reduced central carbon metabolic network was constructed and used for simulating different metabolic operating modes. In particular, scenarios with different acetate-to-glycogen consumption ratios were simulated, which demonstrated optima using different combinations of glycolysis, glyoxylate shunt, or branches of the tricarboxylic acid (TCA) cycle. Thus, optimal metabolic flux strategies will depend on the environment (acetate uptake) and on intracellular storage compound availability (polyphosphate/glycogen). This NADH-related metabolic flexibility is enabled by the NADH-driven PHA synthesis. It allows for maintaining metabolic activity under various environmental substrate conditions, with high carbon conservation and lower energetic costs than for NADPH-dependent PHA synthesis. Such (flexible) metabolic redox coupling can explain the competitiveness of PAOs under oxygen-fluctuating environments. IMPORTANCE Here, we demonstrate how microbial storage metabolism can adjust to a wide range of environmental conditions. Such flexibility generates a selective advantage under fluctuating environmental conditions. It can also explain the different observations reported in PAO literature, including the capacity of “Ca. Accumulibacter phosphatis” to act like glycogen-accumulating organisms (GAOs). These observations stem from slightly different experimental conditions, and controversy arises only when one assumes that metabolism can operate only in a single mode. Furthermore, we also show how the study of metabolic strategies is possible when combining omics data with functional cofactor assays and modeling. Genomic information can only provide the potential of a microorganism. The environmental context and other complementary approaches are still needed to study and predict the functional expression of such metabolic potential.

scholarly journals Entner–Doudoroff pathway and Non-OxPPP bypasses glycolysis and OxPPP in Ralstonia solanacearum

2020 ◽  
Author(s):  
Poonam Jyoti ◽  
Manu Shree ◽  
Chandrakant Joshi ◽  
Tulika Prakash ◽  
Suvendra Kumar Ray ◽  
...  
Keyword(s):  
Network Analysis ◽  
Metabolic Network ◽  
Ralstonia Solanacearum ◽  
Metabolic Flux ◽  
Pentose Phosphate ◽  
Flux Analysis ◽  
Flux Balance ◽  
Metabolic Network Analysis ◽  
Central Carbon ◽  
Balance Analysis

AbstractIn Ralstonia solanacearum, a devastating phytopathogen whose metabolism is poorly understood, we observed that Entner-Doudoroff (ED) pathway and NonOxidative pentose phosphate pathway (OxPPP) bypasses glycolysis and OxPPP under glucose oxidation. Evidences derived from 13C stable isotopes feeding and genome annotation based comparative metabolic network analysis supported the observations. Comparative metabolic network analysis derived from the currently available 53 annotated R. solanacearum strains also including the recently reported strain (F1C1), representing the four phylotypes confirmed the lack of key genes coding for phosphofructokinase (pfk-1) and phosphogluconate dehydrogenase (gnd) enzymes that are relevant for glycolysis and OxPPP respectively. R. solanacearum F1C1 cells fed with 13C Glucose (99%[1-13C]- or 99%[1,2-13C]- or 40%[13C6]-glucose) followed by GC-MS based labelling analysis of fragments from amino acids, glycerol and ribose provided clear evidence that rather than Glycolysis and OxPPP, ED pathway and NonOxPPP are the main routes sustaining metabolism in R. solanacearum. The 13C incorporation in the mass ions of alanine (m/z 260, m/z 232); valine (m/z 288, m/z 260), glycine (m/z 218), serine (m/z 390, m/z 362), histidine (m/z 440, m/z 412), tyrosine (m/z 466, m/z 438), phenylalanine (m/z 336, m/z 308), glycerol (m/z 377) and ribose (m/z 160) mapped the pathways supporting the observations. The outcomes help better defining the central carbon metabolic network of R. solanacearum that can be integrated with 13C metabolic flux analysis as well as flux balance analysis studies for defining the metabolic phenotypes.ImportanceUnderstanding the metabolic versatility of Ralstonia solanacearum is important as it regulates the tradeoff between virulence and metabolism (1, 2) in a wide range of plant hosts. Due to a lack of clear evidence until this work, several published research papers reported on potential roles of Glycolysis and Oxidative pentose phosphate pathways (OxPPP) in R. solanacearum (3, 4). This work provided evidence from 13C stable isotopes feeding and genome annotation based comparative metabolic network analysis that Entner-Doudoroff pathway and Non-OxPPP bypasses glycolysis and OxPPP during the oxidation of Glucose, one of the host xylem pool that serves as a potential carbon source (5). The outcomes help better defining the central carbon metabolic network of R. solanacearum that can be integrated with 13C metabolic flux analysis as well as flux balance analysis studies for defining the metabolic phenotypes. The study highlights the need to critically examine phytopathogens whose metabolism is poorly understood.

A metabolic network of a phosphate-accumulating organism provides new insights into enhanced biological phosphorous removal

2011 ◽  
Vol 64 (12) ◽  
pp. 2410-2416
Author(s):  
Sergio Bordel
Keyword(s):  
Metabolic Network ◽  
Process Design ◽  
Carbon Metabolism ◽  
Central Carbon Metabolism ◽  
Phosphorous Removal ◽  
Flux Balance ◽  
Central Carbon ◽  
Balance Analysis ◽  
Polyphosphate Accumulation ◽  
Accumulibacter Phosphatis

Here we present a metabolic network representing the central carbon metabolism as well as the synthesis of polyhydroxyalcanohates and the polyphosphate accumulation mechanisms of the bacterium Candidatus Accumulibacter phosphatis, which was previously identified from metagenomic studies in enhanced biological phosphorous removal sludges. The reconstructed metabolic network, together with flux balance analysis can be used to provide new insights into controversial aspects of the metabolism of phosphate-accumulating organisms and is also a tool that can be used in to help enhanced biological phosphorous removal (EBPR) process design and operation.

scholarly journals Benchmarking kinetic models of Escherichia coli metabolism

2020 ◽  
Author(s):  
Denis Shepelin ◽  
Daniel Machado ◽  
Lars K. Nielsen ◽  
Markus J. Herrgård
Keyword(s):  
Escherichia Coli ◽  
Kinetic Models ◽  
Metabolic Flux ◽  
Reaction Rates ◽  
Ease Of Use ◽  
Omics Data ◽  
Data Types ◽  
Cell Factories ◽  
Cellular Environment ◽  
Central Carbon

AbstractPredicting phenotype from genotype is the holy grail of quantitative systems biology. Kinetic models of metabolism are among the most mechanistically detailed tools for phenotype prediction. Kinetic models describe changes in metabolite concentrations as a function of enzyme concentration, reaction rates, and concentrations of metabolic effectors uniquely enabling integration of multiple omics data types in a unifying mechanistic framework. While development of such models for Escherichia coli has been going on for almost twenty years, multiple separate models have been established and systematic independent benchmarking studies have not been performed on the full set of models available. In this study we compared systematically all recently published kinetic models of the central carbon metabolism of Escherichia coli. We assess the ease of use of the models, their ability to include omics data as input, and the accuracy of prediction of central carbon metabolic flux phenotypes. We conclude that there is no clear winner among the models when considering the resulting tradeoffs in performance and applicability to various scenarios. This study can help to guide further development of kinetic models, and to demonstrate how to apply such models in real-world setting, ultimately enabling the design of efficient cell factories.Author summaryKinetic modeling is a promising method to predict cell metabolism. Such models provide mechanistic description of how concentrations of metabolites change in the cell as a function of time, cellular environment and the genotype of the cell. In the past years there have been several kinetic models published for various organisms. We want to assess how reliably models of Escherichia coli metabolism could predict cellular metabolic state upon genetic or environmental perturbations. We test selected models in the ways that represent common metabolic engineering practices including deletion and overexpression of genes. Our results suggest that all published models have tradeoffs and the model to use should be chosen depending on the specific application. We show in which cases users could expect the best performance from published models. Our benchmarking study should help users to make a better informed choice and also provides systematic training and testing dataset for model developers.

Systematic Investigation of Mouse Models of Parkinson’s Disease by Transcriptome Mapping on a Brain-Specific Genome-Scale Metabolic Network

2021 ◽  
Author(s):  
Ecehan Abdik ◽  
Tunahan Cakir
Keyword(s):  
Parkinson’S Disease ◽  
Parkinson's Disease ◽  
Metabolic Network ◽  
Mouse Models ◽  
Mus Musculus ◽  
Metabolic Networks ◽  
Systematic Investigation ◽  
Omics Data ◽  
Metabolic Alterations ◽  
Genome Scale

Genome-scale metabolic networks enable systemic investigation of metabolic alterations caused by diseases by providing interpretation of omics data. Although Mus musculus (mouse) is one of the most commonly used model...

scholarly journals Genome analysis of Pseudomonas sp. OF001 and Rubrivivax sp. A210 suggests multicopper oxidases catalyze manganese oxidation required for cylindrospermopsin transformation

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Erika Berenice Martínez-Ruiz ◽  
Myriel Cooper ◽  
Jimena Barrero-Canosa ◽  
Mindia A. S. Haryono ◽  
Irina Bessarab ◽  
...  
Keyword(s):  
Calvin Cycle ◽  
Multicopper Oxidase ◽  
Genomic Islands ◽  
Biotechnological Applications ◽  
High Similarity ◽  
Multicopper Oxidases ◽  
Metabolic Potential ◽  
Natural Habitats ◽  
Manganese Oxidation ◽  
Wide Range

Abstract Background Cylindrospermopsin is a highly persistent cyanobacterial secondary metabolite toxic to humans and other living organisms. Strain OF001 and A210 are manganese-oxidizing bacteria (MOB) able to transform cylindrospermopsin during the oxidation of Mn2+. So far, the enzymes involved in manganese oxidation in strain OF001 and A210 are unknown. Therefore, we analyze the genomes of two cylindrospermopsin-transforming MOB, Pseudomonas sp. OF001 and Rubrivivax sp. A210, to identify enzymes that could catalyze the oxidation of Mn2+. We also investigated specific metabolic features related to pollutant degradation and explored the metabolic potential of these two MOB with respect to the role they may play in biotechnological applications and/or in the environment. Results Strain OF001 encodes two multicopper oxidases and one haem peroxidase potentially involved in Mn2+ oxidation, with a high similarity to manganese-oxidizing enzymes described for Pseudomonas putida GB-1 (80, 83 and 42% respectively). Strain A210 encodes one multicopper oxidase potentially involved in Mn2+ oxidation, with a high similarity (59%) to the manganese-oxidizing multicopper oxidase in Leptothrix discophora SS-1. Strain OF001 and A210 have genes that might confer them the ability to remove aromatic compounds via the catechol meta- and ortho-cleavage pathway, respectively. Based on the genomic content, both strains may grow over a wide range of O2 concentrations, including microaerophilic conditions, fix nitrogen, and reduce nitrate and sulfate in an assimilatory fashion. Moreover, the strain A210 encodes genes which may convey the ability to reduce nitrate in a dissimilatory manner, and fix carbon via the Calvin cycle. Both MOB encode CRISPR-Cas systems, several predicted genomic islands, and phage proteins, which likely contribute to their genome plasticity. Conclusions The genomes of Pseudomonas sp. OF001 and Rubrivivax sp. A210 encode sequences with high similarity to already described MCOs which may catalyze manganese oxidation required for cylindrospermopsin transformation. Furthermore, the analysis of the general metabolism of two MOB strains may contribute to a better understanding of the niches of cylindrospermopsin-removing MOB in natural habitats and their implementation in biotechnological applications to treat water.

Analysis of high yielding maize production - a study based on a commercial crop

2008 ◽  
Vol 48 (3) ◽  
pp. 296 ◽  
Author(s):  
C. J. Birch ◽  
G. McLean ◽  
A. Sawers
Keyword(s):  
Retrospective Analysis ◽  
Environmental Conditions ◽  
Sowing Date ◽  
Plant Population ◽  
Higher Plant ◽  
Maize Crop ◽  
Wide Range ◽  
Commercial Crop ◽  
Reduced Temperature

This paper reports on the use of APSIM – Maize for retrospective analysis of performance of a high input, high yielding maize crop and analysis of predicted performance of maize grown with high inputs over the long-term (>100 years) for specified scenarios of environmental conditions (temperature and radiation) and agronomic inputs (sowing date, plant population, nitrogen fertiliser and irrigation) at Boort, Victoria, Australia. It uses a high yielding (17 400 kg/ha dry grain, 20 500 kg/ha at 15% water) commercial crop grown in 2004–05 as the basis of the study. Yield for the agronomic and environmental conditions of 2004–05 was predicted accurately, giving confidence that the model could be used for the detailed analyses undertaken. The analysis showed that the yield achieved was close to that possible with the conditions and agronomic inputs of 2004–05. Sowing dates during 21 September to 26 October had little effect on predicted yield, except when combined with reduced temperature. Single year and long-term analyses concluded that a higher plant population (11 plants/m2) is needed to optimise yield, but that slightly lower N and irrigation inputs are appropriate for the plant population used commercially (8.4 plants/m2). Also, compared with changes in agronomic inputs increases in temperature and/or radiation had relatively minor effects, except that reduced temperature reduces predicted yield substantially. This study provides an approach for the use of models for both retrospective analysis of crop performance and assessment of long-term variability of crop yield under a wide range of agronomic and environmental conditions.

ASSESSING ENVIRONMENTAL IMPACTS DURING NATURAL DISASTER: THE DEVELOPMENT OF A RAPID ENVIRONMENTAL ASSESSMENT METHODOLOGY

2002 ◽  
Vol 04 (04) ◽  
pp. 475-492 ◽  
Author(s):  
CHARLES KELLY
Keyword(s):  
Environmental Impact ◽  
Impact Assessment ◽  
Environmental Impact Assessment ◽  
Environmental Conditions ◽  
Environmental Damage ◽  
Assessment Procedure ◽  
Disaster Victims ◽  
Wide Range ◽  
Negative Impacts ◽  
The Impact

The linkages between disaster and environmental damage are recognized as important to predicting, preventing and mitigating the impact of disasters. Environmental Impact Assessment (EIA) procedures are well developed for non-ndisaster situations. However, they are conceptually and operationally inappropriate for use in disaster conditions, particularly in the first 120 days after the disaster has begun. The paper provides a conceptual overview of the requirements for an environmental impact assessment procedure appropriate for disaster conditions. These requirements are captured in guidelines for a Rapid Environmental Impact Assessment (REA) for use in disasters. The REA guides the collection and assessment of a wide range of factors which can indicate: (1) the negative impacts of a disaster on the environment, (2) the impacts of environmental conditions on the magnitude of a disaster and, (3) the positive or negative impacts of relief efforts on environmental conditions. The REA also provides a foundation for recovery program EIAs, thus improving the overall post disaster recovery process. The REA is designed primarily for relief cadres, but is also expected to be usable as an assessment tool with disaster victims. The paper discusses the field testing of the REA under actual disaster conditions.

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