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Jianping Yu - One of the best experts on this subject based on the ideXlab platform.
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The plasticity of cyanobacterial Carbon Metabolism.
Current Opinion in Chemical Biology, 2017Co-Authors: Wei Xiong, Damien Douchi, Melissa Cano, Bo Wang, Jianping YuAbstract:This opinion article aims to raise awareness of a fundamental issue which governs sustainable production of biofuels and bio-chemicals from photosynthetic cyanobacteria. Discussed is the plasticity of Carbon Metabolism, by which the cyanobacterial cells flexibly distribute intracellular Carbon fluxes towards target products and adapt to environmental/genetic alterations. This intrinsic feature in cyanobacterial Metabolism is being understood through recent identification of new biochemical reactions and engineering on low-throughput pathways. We focus our discussion on new insights into the nature of metabolic plasticity in cyanobacteria and its impact on hydroCarbons (e.g. ethylene and isoprene) production. We discuss approaches that need to be developed to rationally rewire photosynthetic Carbon fluxes throughout primary Metabolism. We outline open questions about the regulatory mechanisms of the metabolic network that remain to be answered, which might shed light on photosynthetic Carbon Metabolism and help optimize design principles in order to improve the production of fuels and chemicals in cyanobacteria.
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Phosphoketolase pathway contributes to Carbon Metabolism in cyanobacteria
Nature Plants, 2015Co-Authors: Wei Xiong, Sarah Rommelfanger, Maria Ghirardi, Melissa Cano, Pin-ching Maness, Erica Gjersing, Jianping YuAbstract:Central Carbon Metabolism in cyanobacteria consists of the CBB cycle, glycolysis, the pentose phosphate pathway and the TCA cycle. Metabolic analyses of mutant and wild-type Synechocystis reveal the presence of a functional phosphoketolase pathway, previously uncharacterized in photosynthetic organisms. Central Carbon Metabolism in cyanobacteria comprises the Calvin–Benson–Bassham (CBB) cycle, glycolysis, the pentose phosphate (PP) pathway and the tricarboxylic acid (TCA) cycle. Redundancy in this complex metabolic network renders the rational engineering of cyanobacterial Metabolism for the generation of biomass, biofuels and chemicals a challenge. Here we report the presence of a functional phosphoketolase pathway, which splits xylulose-5-phosphate (or fructose-6-phosphate) to acetate precursor acetyl phosphate, in an engineered strain of the model cyanobacterium Synechocystis ( Δ glgC/xylAB ), in which glycogen synthesis is blocked, and xylose catabolism enabled through the introduction of xylose isomerase and xylulokinase. We show that this mutant strain is able to metabolise xylose to acetate on nitrogen starvation. To see whether acetate production in the mutant is linked to the activity of phosphoketolase, we disrupted a putative phosphoketolase gene ( slr0453 ) in the Δ glgC/xylAB strain, and monitored metabolic flux using ^13C labelling; acetate and 2-oxoglutarate production was reduced in the light. A metabolic flux analysis, based on isotopic data, suggests that the phosphoketolase pathway metabolises over 30% of the Carbon consumed by Δ glgC/xylAB during photomixotrophic growth on xylose and CO_2. Disruption of the putative phosphoketolase gene in wild-type Synechocystis also led to a deficiency in acetate production in the dark, indicative of a contribution of the phosphoketolase pathway to heterotrophic Metabolism. We suggest that the phosphoketolase pathway, previously uncharacterized in photosynthetic organisms, confers flexibility in energy and Carbon Metabolism in cyanobacteria, and could be exploited to increase the efficiency of cyanobacterial Carbon Metabolism and photosynthetic productivity.
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Phosphoketolase pathway contributes to Carbon Metabolism in cyanobacteria
Nature plants, 2015Co-Authors: Wei Xiong, Sarah Rommelfanger, Maria Ghirardi, Melissa Cano, Pin-ching Maness, Erica Gjersing, Jianping YuAbstract:Central Carbon Metabolism in cyanobacteria consists of the CBB cycle, glycolysis, the pentose phosphate pathway and the TCA cycle. Metabolic analyses of mutant and wild-type Synechocystis reveal the presence of a functional phosphoketolase pathway, previously uncharacterized in photosynthetic organisms.
Eshchar Mizrachi - One of the best experts on this subject based on the ideXlab platform.
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Organellar Carbon Metabolism is coordinated with distinct developmental phases of secondary xylem
New Phytologist, 2019Co-Authors: Desre Pinard, Alexander Andrew Myburg, Ana Carolina Fierro, Kathleen Marchal, Eshchar MizrachiAbstract:: Subcellular compartmentation of plant biosynthetic pathways in the mitochondria and plastids requires coordinated regulation of nuclear encoded genes, and the role of these genes has been largely ignored by wood researchers. In this study, we constructed a targeted systems genetics coexpression network of xylogenesis in Eucalyptus using plastid and mitochondrial Carbon metabolic genes and compared the resulting clusters to the aspen xylem developmental series. The constructed network clusters reveal the organization of transcriptional modules regulating subcellular metabolic functions in plastids and mitochondria. Overlapping genes between the plastid and mitochondrial networks implicate the common transcriptional regulation of Carbon Metabolism during xylem secondary growth. We show that the central processes of organellar Carbon Metabolism are distinctly coordinated across the developmental stages of wood formation and are specifically associated with primary growth and secondary cell wall deposition. We also demonstrate that, during xylogenesis, plastid-targeted Carbon Metabolism is partially regulated by the central clock for Carbon allocation towards primary and secondary xylem growth, and we discuss these networks in the context of previously established associations with wood-related complex traits. This study provides a new resolution into the integration and transcriptional regulation of plastid- and mitochondrial-localized Carbon Metabolism during xylogenesis.
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Organellar Carbon Metabolism is coordinated with distinct developmental phases of secondary xylem
New Phytologist, 2019Co-Authors: Desre Pinard, Alexander Andrew Myburg, Ana Carolina Fierro, Kathleen Marchal, Eshchar MizrachiAbstract:: Subcellular compartmentation of plant biosynthetic pathways in the mitochondria and plastids requires coordinated regulation of nuclear encoded genes, and the role of these genes has been largely ignored by wood researchers. In this study, we constructed a targeted systems genetics coexpression network of xylogenesis in Eucalyptus using plastid and mitochondrial Carbon metabolic genes and compared the resulting clusters to the aspen xylem developmental series. The constructed network clusters reveal the organization of transcriptional modules regulating subcellular metabolic functions in plastids and mitochondria. Overlapping genes between the plastid and mitochondrial networks implicate the common transcriptional regulation of Carbon Metabolism during xylem secondary growth. We show that the central processes of organellar Carbon Metabolism are distinctly coordinated across the developmental stages of wood formation and are specifically associated with primary growth and secondary cell wall deposition. We also demonstrate that, during xylogenesis, plastid-targeted Carbon Metabolism is partially regulated by the central clock for Carbon allocation towards primary and secondary xylem growth, and we discuss these networks in the context of previously established associations with wood-related complex traits. This study provides a new resolution into the integration and transcriptional regulation of plastid- and mitochondrial-localized Carbon Metabolism during xylogenesis.
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organellar Carbon Metabolism is co ordinated with distinct developmental phases of secondary xylem
ISSN: 0028-646X, 2019Co-Authors: Desre Pinard, Alexander Andrew Myburg, Kathleen Marchal, Ana Carolina Elisa Fierro Gutierrez, Eshchar MizrachiAbstract:Subcellular compartmentation of plant biosynthetic pathways in the mitochondria and plastids requires coordinated regulation of nuclear encoded genes, and the role of these genes has been largely ignored by wood researchers. In this study, we constructed a targeted systems genetics coexpression network of xylogenesis in Eucalyptus using plastid and mitochondrial Carbon metabolic genes and compared the resulting clusters to the aspen xylem developmental series. The constructed network clusters reveal the organization of transcriptional modules regulating subcellular metabolic functions in plastids and mitochondria. Overlapping genes between the plastid and mitochondrial networks implicate the common transcriptional regulation of Carbon Metabolism during xylem secondary growth. We show that the central processes of organellar Carbon Metabolism are distinctly coordinated across the developmental stages of wood formation, and are specifically associated with primary growth and secondary cell wall deposition. We also demonstrate that during xylogenesis, plastid targeted Carbon Metabolism is partially regulated by the central clock for Carbon allocation towards primary and secondary xylem growth, and discuss these networks in the context of previously established associations with wood-related complex traits. This study provides a new resolution into the integration and transcriptional regulation of plastid and mitochondrial localized Carbon Metabolism during xylogenesis.
Yan Zhang - One of the best experts on this subject based on the ideXlab platform.
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Review of spatial analysis of urban Carbon Metabolism
Ecological Modelling, 2018Co-Authors: Yan Zhang, Qiong Wu, Brian D FathAbstract:Urban areas have contributed 75% of the global CO2 emissions. Therefore, seeking global Carbon reduction solutions from the perspective of city has become a focus of decision-makers in charge of environmental protection. The Carbon emission reduction potential in land management and spatial adjustment has become an important mean for achieving regional and global sustainable development. In this paper, we systematically review and synthesize four main aspects of urban Carbon Metabolism spatial analysis, namely: (1) advances in urban Carbon Metabolism, (2) Carbon accounting based on land use and cover change, (3) spatial distribution of urban Carbon Metabolism and influencing factors, and (4) forecasting based on land use change (Land Use and Cover Change – LUCC). In addition, we point out current deficiencies in the study of urban Carbon Metabolism, such as incomplete process analysis and lack of spatial display. Based on previous research, we propose a spatial-analysis-centric outlook on urban Carbon Metabolism, including the following key approaches: (1) future researchers should simultaneously consider natural and socioeconomic components, as well as vertical (flows from land to atmosphere) and horizontal (flows among different land use types) Carbon flows, to obtain a more complete picture of the entire urban Carbon Metabolism system; (2) Carbon metabolic spatial mapping can be implemented in patches to better serve government’s goals for optimal regulation and spatial planning; (3) researchers should refine current urban-scale research, also expanding it to the metropolitan (i.e., urban agglomeration) scale, to establish multi-scale, multi-level, and organic network structures, and study the spatial distribution pattern of Carbon Metabolism within and among cities and metropolitan areas, which will lay a scientific foundation for urban, regional, and national sustainable development.
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Analyzing spatial patterns of urban Carbon Metabolism: A case study in Beijing, China
Landscape and Urban Planning, 2014Co-Authors: Yan Zhang, Xia Linlin, Xiang WeiningAbstract:Analyzing the spatial pattern of a city's Carbon Metabolism can provide insights into the spatial adjustments required to mitigate the greenhouse effect. Using GIS software and empirical coefficients, we analyzed the spatial distribution of Beijing's Carbon Metabolism in 5 years (1990, 1995, 2000, 2005, and 2008), and analyzed both temporal and spatial changes in this pattern. Our results highlight the importance of the expansion of built-up areas in defining the patterns of Beijing's Carbon Metabolism, and let us explore options for changing these patterns. Carbon emission was high in the highly urbanized southeastern parts of the city and low in the less-urbanized northwestern parts, whereas Carbon sequestration showed the opposite pattern (low in southeastern parts and high in northwestern parts). During the study period, Carbon sequestration only offset 2.4% of Carbon emission, indicating a serious imbalance of the city's Carbon Metabolism. The city's core built-up area expanded along eight axes, and its form fluctuated between simpler and more complex. From a small-scale perspective, the spatial pattern mainly showed expansion and aggregation of patches with high Carbon emission and shrinkage and fragmentation of patches with high Carbon sequestration. These results provide insights that will guide the development of more effective management of the spatial patterns of Carbon emission and sequestration.
Wei Xiong - One of the best experts on this subject based on the ideXlab platform.
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The plasticity of cyanobacterial Carbon Metabolism.
Current Opinion in Chemical Biology, 2017Co-Authors: Wei Xiong, Damien Douchi, Melissa Cano, Bo Wang, Jianping YuAbstract:This opinion article aims to raise awareness of a fundamental issue which governs sustainable production of biofuels and bio-chemicals from photosynthetic cyanobacteria. Discussed is the plasticity of Carbon Metabolism, by which the cyanobacterial cells flexibly distribute intracellular Carbon fluxes towards target products and adapt to environmental/genetic alterations. This intrinsic feature in cyanobacterial Metabolism is being understood through recent identification of new biochemical reactions and engineering on low-throughput pathways. We focus our discussion on new insights into the nature of metabolic plasticity in cyanobacteria and its impact on hydroCarbons (e.g. ethylene and isoprene) production. We discuss approaches that need to be developed to rationally rewire photosynthetic Carbon fluxes throughout primary Metabolism. We outline open questions about the regulatory mechanisms of the metabolic network that remain to be answered, which might shed light on photosynthetic Carbon Metabolism and help optimize design principles in order to improve the production of fuels and chemicals in cyanobacteria.
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Phosphoketolase pathway contributes to Carbon Metabolism in cyanobacteria
Nature Plants, 2015Co-Authors: Wei Xiong, Sarah Rommelfanger, Maria Ghirardi, Melissa Cano, Pin-ching Maness, Erica Gjersing, Jianping YuAbstract:Central Carbon Metabolism in cyanobacteria consists of the CBB cycle, glycolysis, the pentose phosphate pathway and the TCA cycle. Metabolic analyses of mutant and wild-type Synechocystis reveal the presence of a functional phosphoketolase pathway, previously uncharacterized in photosynthetic organisms. Central Carbon Metabolism in cyanobacteria comprises the Calvin–Benson–Bassham (CBB) cycle, glycolysis, the pentose phosphate (PP) pathway and the tricarboxylic acid (TCA) cycle. Redundancy in this complex metabolic network renders the rational engineering of cyanobacterial Metabolism for the generation of biomass, biofuels and chemicals a challenge. Here we report the presence of a functional phosphoketolase pathway, which splits xylulose-5-phosphate (or fructose-6-phosphate) to acetate precursor acetyl phosphate, in an engineered strain of the model cyanobacterium Synechocystis ( Δ glgC/xylAB ), in which glycogen synthesis is blocked, and xylose catabolism enabled through the introduction of xylose isomerase and xylulokinase. We show that this mutant strain is able to metabolise xylose to acetate on nitrogen starvation. To see whether acetate production in the mutant is linked to the activity of phosphoketolase, we disrupted a putative phosphoketolase gene ( slr0453 ) in the Δ glgC/xylAB strain, and monitored metabolic flux using ^13C labelling; acetate and 2-oxoglutarate production was reduced in the light. A metabolic flux analysis, based on isotopic data, suggests that the phosphoketolase pathway metabolises over 30% of the Carbon consumed by Δ glgC/xylAB during photomixotrophic growth on xylose and CO_2. Disruption of the putative phosphoketolase gene in wild-type Synechocystis also led to a deficiency in acetate production in the dark, indicative of a contribution of the phosphoketolase pathway to heterotrophic Metabolism. We suggest that the phosphoketolase pathway, previously uncharacterized in photosynthetic organisms, confers flexibility in energy and Carbon Metabolism in cyanobacteria, and could be exploited to increase the efficiency of cyanobacterial Carbon Metabolism and photosynthetic productivity.
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Phosphoketolase pathway contributes to Carbon Metabolism in cyanobacteria
Nature plants, 2015Co-Authors: Wei Xiong, Sarah Rommelfanger, Maria Ghirardi, Melissa Cano, Pin-ching Maness, Erica Gjersing, Jianping YuAbstract:Central Carbon Metabolism in cyanobacteria consists of the CBB cycle, glycolysis, the pentose phosphate pathway and the TCA cycle. Metabolic analyses of mutant and wild-type Synechocystis reveal the presence of a functional phosphoketolase pathway, previously uncharacterized in photosynthetic organisms.
Brian D Fath - One of the best experts on this subject based on the ideXlab platform.
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Review of spatial analysis of urban Carbon Metabolism
Ecological Modelling, 2018Co-Authors: Yan Zhang, Qiong Wu, Brian D FathAbstract:Urban areas have contributed 75% of the global CO2 emissions. Therefore, seeking global Carbon reduction solutions from the perspective of city has become a focus of decision-makers in charge of environmental protection. The Carbon emission reduction potential in land management and spatial adjustment has become an important mean for achieving regional and global sustainable development. In this paper, we systematically review and synthesize four main aspects of urban Carbon Metabolism spatial analysis, namely: (1) advances in urban Carbon Metabolism, (2) Carbon accounting based on land use and cover change, (3) spatial distribution of urban Carbon Metabolism and influencing factors, and (4) forecasting based on land use change (Land Use and Cover Change – LUCC). In addition, we point out current deficiencies in the study of urban Carbon Metabolism, such as incomplete process analysis and lack of spatial display. Based on previous research, we propose a spatial-analysis-centric outlook on urban Carbon Metabolism, including the following key approaches: (1) future researchers should simultaneously consider natural and socioeconomic components, as well as vertical (flows from land to atmosphere) and horizontal (flows among different land use types) Carbon flows, to obtain a more complete picture of the entire urban Carbon Metabolism system; (2) Carbon metabolic spatial mapping can be implemented in patches to better serve government’s goals for optimal regulation and spatial planning; (3) researchers should refine current urban-scale research, also expanding it to the metropolitan (i.e., urban agglomeration) scale, to establish multi-scale, multi-level, and organic network structures, and study the spatial distribution pattern of Carbon Metabolism within and among cities and metropolitan areas, which will lay a scientific foundation for urban, regional, and national sustainable development.