Reimport of carbon from cytosolic and vacuolar sugar pools into the Calvin–Benson cycle explains photosynthesis labeling anomalies

Xu, Yuanmei; Wieloch, Thomas; Kaste, Joshua A. M.; Shachar‐Hill, Yair; Sharkey, Thomas D.

doi:10.1073/pnas.2121531119

Cited by 55 publications

(121 citation statements)

References 51 publications

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“…However, according to recent analyses of metabolic fluxes in leaves of Arabidopsis thaliana and Camelina sativa, mitochondrial respiration is relatively low (1 to 1.6% relative to net carbon assimilation) (Ma et al, 2014;Xu et al, 2022). By contrast, respiration by the cytosolic OPPP is 5% relative to net carbon assimilation in Camelina sativa leaves (Xu et al, 2022). Similarly, in sunflower leaves, respiration by the OPPP in chloroplasts is relatively high under both high (see above) and low Ca (Wieloch et al, 2021a(Wieloch et al, , 2022a.…”

Section: A Paradigm Shift In the Field Of Leaf Respirationmentioning

confidence: 99%

“…In the past, research of leaf respiration had a strong focus on mitochondrial processes. However, according to recent analyses of metabolic fluxes in leaves of Arabidopsis thaliana and Camelina sativa, mitochondrial respiration is relatively low (1 to 1.6% relative to net carbon assimilation) (Ma et al, 2014;Xu et al, 2022). By contrast, respiration by the cytosolic OPPP is 5% relative to net carbon assimilation in Camelina sativa leaves (Xu et al, 2022).…”

Section: A Paradigm Shift In the Field Of Leaf Respirationmentioning

confidence: 99%

“…State-of-the-art isotope techniques enable analyses of specific metabolic fluxes (Ehlers et al, 2015;Wieloch et al, 2021bWieloch et al, , 2022cXu et al, 2022). Recently, we reported two deuterium (D) fractionation signals (i.e., systematic D variability) in starch glucose of sunflower leaves (Wieloch et al, 2022a).…”

Section: Introductionmentioning

confidence: 99%

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Respiration by the Oxidative Pentose Phosphate Pathway in Chloroplasts Responds to Atmospheric CO<sub>2</sub> Concentration

Wieloch¹

2022

Preprint

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Despite significant research efforts, the question of whether rising atmospheric CO2 concentrations (Ca) affect leaf respiration remains unanswered. Here, I reanalyse published hydrogen isotope abundances in starch glucose of sunflower leaves. I report that, as Ca increases from 450 to 1500 ppm, respiration by the oxidative pentose phosphate pathway in chloroplasts increases from 0 to ≈ 5% relative to net carbon assimilation. This is consistent with known regulatory properties of the pathway. Summarising recent reports of metabolic fluxes in plant leaves, a picture emerges in which mitochondrial processes are distinctly less important for overall respiration than the oxidative pentose phosphate pathways in chloroplasts and the cytosol. Regulatory properties of these pathways are consistent with observations of lower-than-expected stimulations of photosynthesis by increasing Ca. Reported advances in understanding leaf respiratory mechanisms may enable modelling and prediction of respiration effects (inter alia) on biosphere-atmosphere CO2 exchange and plant performance under climate change.

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Section: A Paradigm Shift In the Field Of Leaf Respirationmentioning

confidence: 99%

Section: A Paradigm Shift In the Field Of Leaf Respirationmentioning

confidence: 99%

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Respiration by the Oxidative Pentose Phosphate Pathway in Chloroplasts Responds to Atmospheric CO<sub>2</sub> Concentration

Wieloch¹

2022

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“…Sites of cofactor consumption and production in central carbon metabolism. Previously, we estimated carbon fluxes in 4-week-old photosynthesising Camelina sativa leaves (Xu et al 2022). According to this analysis, pathways in black carry significant flux.…”

Section: Introductionmentioning

confidence: 99%

“…In a recently published study, we estimated carbon fluxes across central metabolism in illuminated Camelina sativa leaves, including flux through the CBC, photorespiration, glycolysis, the tricarboxylic acid cycle, and starch, sucrose, fatty acid, and amino acid biosynthesis (Xu et al 2022). Importantly, our analyses explained the 13 C labelling lag of CBC metabolites (a longstanding conundrum in plant biochemistry) by reinjection of weakly labelled carbon from vacuolar and cytosolic sugar pools into the CBC.…”

Section: Introductionmentioning

confidence: 99%

Compartment-specific energy requirements of photosynthetic carbon metabolism in Camelina sativa leaves

Wieloch

Sharkey

2022

Preprint

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Detailed knowledge about plant energy metabolism may aid crop improvements. Using published estimates of flux through central carbon metabolism, we phenotype energy metabolism in illuminated Camelina sativa leaves (grown at 22 °C, 500 μmol photons m-2 s-1) and report several findings. First, the oxidative pentose phosphate pathway (OPPP) transfers 3.3% of the NADPH consumed in the Calvin-Benson cycle to the cytosol. However, concomitantly respired CO2 accounts for 4.8% of total rubisco activity. Hence, 4.8% of the flux through the Calvin-Benson cycle and photorespiration is spent on supplying cytosolic NADPH, a significant investment. Associated energy requirements exceed the energy output of the OPPP. Thus, autotrophic carbon metabolism is not simply optimised for flux into carbon sinks but sacrifices carbon and energy use efficiency to support cytosolic energy metabolism. To reduce these costs, we suggest bioengineering plants with a repressed cytosolic OPPP, and an inserted cytosolic NADPH-dependent malate dehydrogenase tuned to compensate for the loss in OPPP activity (if required). Second, sucrose cycling is a minor investment in overall leaf energy metabolism but a significant investment in cytosolic energy metabolism. Third, energy balancing strictly requires oxidative phosphorylation, cofactor export from chloroplasts, and peroxisomal NADH import. Fourth, mitochondria are energetically self-sufficient. Fifth, carbon metabolism has an ATP/NADPH demand ratio of 1.52 which is met if 21.7% of whole electron flux is cyclic. Sixth, electron transport has a photon use efficiency of 62%. Lastly, we discuss interactions between the OPPP and the cytosolic oxidation-reduction cycle in supplying leaf cytosolic NADPH.

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Model validation and selection in metabolic flux analysis and flux balance analysis

Kaste,

Shachar‐Hill

2023

Biotechnology Progress

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Abstract13C‐Metabolic Flux Analysis (13C‐MFA) and Flux Balance Analysis (FBA) are widely used to investigate the operation of biochemical networks in both biological and biotechnological research. Both methods use metabolic reaction network models of metabolism operating at steady state so that reaction rates (fluxes) and the levels of metabolic intermediates are constrained to be invariant. They provide estimated (MFA) or predicted (FBA) values of the fluxes through the network in vivo, which cannot be measured directly. These fluxes can shed light on basic biology and have been successfully used to inform metabolic engineering strategies. Several approaches have been taken to test the reliability of estimates and predictions from constraint‐based methods and to compare alternative model architectures. Despite advances in other areas of the statistical evaluation of metabolic models, such as the quantification of flux estimate uncertainty, validation and model selection methods have been underappreciated and underexplored. We review the history and state‐of‐the‐art in constraint‐based metabolic model validation and model selection. Applications and limitations of the χ2‐test of goodness‐of‐fit, the most widely used quantitative validation and selection approach in 13C‐MFA, are discussed, and complementary and alternative forms of validation and selection are proposed. A combined model validation and selection framework for 13C‐MFA incorporating metabolite pool size information that leverages new developments in the field is presented and advocated for. Finally, we discuss how adopting robust validation and selection procedures can enhance confidence in constraint‐based modeling as a whole and ultimately facilitate more widespread use of FBA in biotechnology.

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Reimport of carbon from cytosolic and vacuolar sugar pools into the Calvin–Benson cycle explains photosynthesis labeling anomalies

Cited by 55 publications

References 51 publications

Respiration by the Oxidative Pentose Phosphate Pathway in Chloroplasts Responds to Atmospheric CO<sub>2</sub> Concentration

Respiration by the Oxidative Pentose Phosphate Pathway in Chloroplasts Responds to Atmospheric CO<sub>2</sub> Concentration

Compartment-specific energy requirements of photosynthetic carbon metabolism in Camelina sativa leaves

Model validation and selection in metabolic flux analysis and flux balance analysis

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