Modeling the Calvin-Benson cycle

<p>Abstract</p> <p>Background</p> <p>Modeling the Calvin-Benson cycle has a history in the field of theoretical biology. Anyone who intends to model this system will look at existing models to adapt, refine and improve them. With the goal to study the regulation of carbon metabolism, we investigated a broad range of relevant models for their suitability to provide the basis for further modeling efforts. Beyond a critical analysis of existing models, we furthermore investigated the question how adjacent metabolic pathways, for instance photorespiration, can be integrated in such models.</p> <p>Results</p> <p>Our analysis reveals serious problems with a range of models that are publicly available and widely used. The problems include the irreproducibility of the published results or significant differences between the equations in the published description of the model and model itself in the supplementary material. In addition to and based on the discussion of existing models, we furthermore analyzed approaches in PGA sink implementation and confirmed a weak relationship between the level of its regulation and efficiency of PGA export, in contrast to significant changes in the content of metabolic pool within the Calvin-Benson cycle.</p> <p>Conclusions</p> <p>In our study we show that the existing models that have been investigated are not suitable for reuse without substantial modifications. We furthermore show that the minor adjacent pathways of the carbon metabolism, neglected in all kinetic models of Calvin-Benson cycle, cannot be substituted without consequences in the mass production dynamics. We further show that photorespiration or at least its first step (O₂fixation) has to be implemented in the model if this model is aimed for analyses out of the steady state.</p

Recent developments in photorespiration research.

Abstract Photorespiration is the light-dependent release of CO 2 initiated by Rubisco (ribulose-1,5-bisphosphate carboxylase/oxygenase) during oxygenic photosynthesis. It occurs during the biochemical reactions of the photorespiratory C 2 cycle, which is an ancillary metabolic process that allows photosynthesis to occur in oxygen-containing environments. Recent research has identified the genes for many plant photorespiratory enzymes, allowing precise functional analyses by reverse genetics. Similar studies with cyanobacteria disclosed the evolutionary origin of photorespiratory metabolism in these ancestors of plastids

High-to-low CO2 acclimation reveals plasticity of the photorespiratory pathway and indicates regulatory links to cellular metabolism of Arabidopsis

Background: Photorespiratory carbon metabolism was long considered as an essentially closed and nonregulated pathway with little interaction to other metabolic routes except nitrogen metabolism and respiration. Most mutants of this pathway cannot survive in ambient air and require CO 2-enriched air for normal growth. Several studies indicate that this CO 2 requirement is very different for individual mutants, suggesting a higher plasticity and more interaction of photorespiratory metabolism as generally thought. To understand this better, we examined a variety of high- and low-level parameters at 1% CO 2 and their alteration during acclimation of wild-type plants and selected photorespiratory mutants to ambient air. Methodology and Principal Findings: The wild type and four photorespiratory mutants of Arabidopsis thaliana (Arabidopsis) were grown to a defined stadium at 1% CO 2 and then transferred to normal air (0.038% CO 2). All other conditions remained unchanged. This approach allowed unbiased side-by-side monitoring of acclimation processes on several levels. For all lines, diel (24 h) leaf growth, photosynthetic gas exchange, and PSII fluorescence were monitored. Metabolite profiling was performed for the wild type and two mutants. During acclimation, considerable variation between the individual genotypes was detected in many of the examined parameters, which correlated with the position of the impaired reaction in the photorespiratory pathway. Conclusions: Photorespiratory carbon metabolism does not operate as a fully closed pathway. Acclimation from high to low CO 2 was typically steady and consistent for a number of features over several days, but we also found unexpected short-term events, such as an intermittent very massive rise of glycine levels after transition of one particular mutant to ambient air. We conclude that photorespiration is possibly exposed to redox regulation beyond known substrate-level effects. Additionally, our data support the view that 2-phosphoglycolate could be a key regulator of photosynthetic-photorespiratory metabolism as a whole. © 2012 Timm et al

Modulation of the Major Paths of Carbon in Photorespiratory Mutants of Synechocystis

Background: Recent studies using transcript and metabolite profiles of wild-type and gene deletion mutants revealed that photorespiratory pathways are essential for the growth of Synechocystis sp. PCC 6803 under atmospheric conditions. Pool size changes of primary metabolites, such as glycine and glycolate, indicated a link to photorespiration. Methodology/Principal Findings: The C-13 labelling kinetics of primary metabolites were analysed in photoautotrophically grown cultures of Synechocystis sp. PCC 6803 by gas chromatography-mass spectrometry (GC-MS) to demonstrate the link with photorespiration. Cells pre-acclimated to high CO2 (5%, HC) or limited CO2 (0.035%, LC) conditions were pulse-labelled under very high (2% w/w) C-13-NaHCO3 (VHC) conditions followed by treatment with ambient C-12 at HC and LC conditions, respectively. The C-13 enrichment, relative changes in pool size, and C-13 flux of selected metabolites were evaluated. We demonstrate two major paths of CO2 assimilation via Rubisco in Synechocystis, i.e., from 3PGA via PEP to aspartate, malate and citrate or, to a lesser extent, from 3PGA via glucose-6-phosphate to sucrose. The results reveal evidence of carbon channelling from 3PGA to the PEP pool. Furthermore, C-13 labelling of glycolate was observed under conditions thought to suppress photorespiration. Using the glycolate-accumulating Delta glcD1 mutant, we demonstrate enhanced C-13 partitioning into the glycolate pool under conditions favouring photorespiration and enhanced C-13 partitioning into the glycine pool of the glycine-accumulating Delta gcvT mutant. Under LC conditions, the photorespiratory mutants Delta glcD1 and Delta gcvT showed enhanced activity of the additional carbon-fixing PEP carboxylase pathway. Conclusions/Significance: With our approach of non-steady-state C-13 labelling and analysis of metabolite pool sizes with respective C-13 enrichments, we identify the use and modulation of major pathways of carbon assimilation in Synechocystis in the presence of high and low inorganic carbon supplies

Evaluating the SWAT model to predict streamflow, nitrate loadings and crop yields in a small agricultural catchment

This study aimed to evaluate the applicability of the Soil and Water Assessment Tool (SWAT) to predict streamflow, nitrate loadings and crop yields for a small agricultural catchment in northeastern Germany. To this end, a 167&thinsp;ha catchment was delineated consisting of 10 hydrological response units. Daily data for streamflow and nitrate loadings from 2004 to 2015 were used to calibrate and validate the model, while annual values for crop yields (winter wheat, winter barley, rapeseed, maize silage) were available. In addition, the detailed field maps provided by the local farmer were used to implement exact crop rotations and nitrogen fertilization into the model. Nash-Sutcliffe-Efficiencies for streamflow were 0.54 during the calibration and 0.57 for the validation period. The modeling performance for nitrate loadings were lower with 0.31 for the calibration and 0.42 for the validation period. The average crop yields were reproduced well, while SWAT failed to reproduce the inter-annual crop yield variations. A scenario analysis revealed that a slight decrease of nitrogen fertilization leads to significant reductions in nitrate loadings, while crop yields remained on a high level. The outcome of the study may help practitioners to operate according to an economic and environmental optimal N management. Nevertheless, experimental studies with varying fertilization intensities at catchment scale are needed to underpin the modeling results.</p

Räumliche Variabilität und zeitliche Trends des Trockenstressrisikos von Kiefernstandorten in Mecklenburg-Vorpommern

Die Bodenwasserverfügbarkeit bestimmt zu einem hohen Maße die Vitalität von Bäumen und Waldstandorten. In einigen Teilen Euro-pas wurde in den letzten Jahrzehnten eine häufigere Anzahl von Trockenperioden beobachtet, die bereits das Baumwachstum negativ beeinflusst haben. Es wurden langfristige Trends von Bodentrockenheit unter Kiefernstandorten entlang des klimatischen Gradienten in Mecklenburg-Vorpommern mit dem physikalisch basierten Modell LWF-BROOK90 untersucht. Die Ergebnisse zeigen eine zunehmende Anzahl von Trockenstresstagen ostwärts mit abnehmenden Niederschlagssummen. Die klimatischen Unterschiede innerhalb des Landes werden teilweise von den spezifischen Standortbedingungen und Bodeneigenschaften überprägt. Bodentrockenheit hat in den letzten Jahrzehnten deutlich zugenommen, wobei die östlichen Standorte stärker als die westlichen betroffen sind. Die zunehmende Bodentrockenheit konnte auf einen erhöhten Verdunstungsanspruch der Atmosphäre zurückgeführt werden aufgrund höherer Temperaturen in Kombination mit leicht abnehmenden Niederschlägen während der Sommermonate. Um die negativen Auswirkungen künftiger klimatischer Änderungen zu minimieren, sollten Anpassungsmaßnahmen vorzugsweise im Osten des Landes durchgeführt werden