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BackgroundAlgae accumulate lipids to endure different kinds of environmental stresses including macronutrient starvation. Although this response has been extensively studied, an in depth understanding of the transcriptional regulatory network (TRN) that controls the transition into lipid accumulation remains elusive. In this study, we used a systems biology approach to elucidate the transcriptional program that coordinates the nitrogen starvation-induced metabolic readjustments that drive lipid accumulation in Chlamydomonas reinhardtii.ResultsWe demonstrate that nitrogen starvation triggered differential regulation of 2147 transcripts, which were co-regulated in 215 distinct modules and temporally ordered as 31 transcriptional waves. An early-stage response was triggered within 12 min that initiated growth arrest through activation of key signaling pathways, while simultaneously preparing the intracellular environment for later stages by modulating transport processes and ubiquitin-mediated protein degradation. Subsequently, central metabolism and carbon fixation were remodeled to trigger the accumulation of triacylglycerols. Further analysis revealed that these waves of genome-wide transcriptional events were coordinated by a regulatory program orchestrated by at least 17 transcriptional regulators, many of which had not been previously implicated in this process. We demonstrate that the TRN coordinates transcriptional downregulation of 57 metabolic enzymes across a period of nearly 4 h to drive an increase in lipid content per unit biomass. Notably, this TRN appears to also drive lipid accumulation during sulfur starvation, while phosphorus starvation induces a different regulatory program. The TRN model described here is available as a community-wide web-resource at http://networks.systemsbiology.net/chlamy-portal.ConclusionsIn this work, we have uncovered a comprehensive mechanistic model of the TRN controlling the transition from N starvation to lipid accumulation. The program coordinates sequentially ordered transcriptional waves that simultaneously arrest growth and lead to lipid accumulation. This study has generated predictive tools that will aid in devising strategies for the rational manipulation of regulatory and metabolic networks for better biofuel and biomass production.

Microalgae have reemerged as organisms of prime biotechnological interest due to their ability to synthesize a suite of valuable chemicals. To harness the capabilities of these organisms, we need a comprehensive systems-level understanding of their metabolism, which can be fundamentally achieved through large-scale mechanistic models of metabolism. In this study, we present a revised and significantly improved genome-scale metabolic model for the widely-studied microalga, Chlamydomonas reinhardtii. The model, iCre1355, represents a major advance over previous models, both in content and predictive power. iCre1355 encompasses a broad range of metabolic functions encoded across the nuclear, chloroplast and mitochondrial genomes accounting for 1355 genes (1460 transcripts), 2394 and 1133 metabolites. We found improved performance over the previous metabolic model based on comparisons of predictive accuracy across 306 phenotypes (from 81 mutants), lipid yield analysis and growth rates derived from chemostat-grown cells (under three conditions). Measurement of macronutrient uptake revealed carbon and phosphate to be good predictors of growth rate, while nitrogen consumption appeared to be in excess. We analyzed high-resolution time series transcriptomics data using iCre1355 to uncover dynamic pathway-level changes that occur in response to nitrogen starvation and changes in light intensity. This approach enabled accurate prediction of growth rates, the cessation of growth and accumulation of triacylglycerols during nitrogen starvation, and the temporal response of different growth-associated pathways to increased light intensity. Thus, iCre1355 represents an experimentally validated genome-scale reconstruction of C. reinhardtii metabolism that should serve as a useful resource for studying the metabolic processes of this and related microalgae.

Open burning of household solid waste is a large source of air pollutants worldwide, especially in developing countries. However, waste burning emissions are either missing or have large uncertainties in local, regional, or global emission inventories due to limited emission factor (EF) and activity data. Detailed particulate matter (PM) chemical speciation data is even scarcer. This paper reports source profiles and EFs for PM2.5 species as well as acidic and alkali gases measured from laboratory combustion of ten waste categories that represent open burning in South Africa. Carbonaceous materials contributed more than 70 % of PM2.5 mass. Elemental carbon (EC) was most abundant from flaming materials (e.g., plastic bags, textile, and combined materials) and its climate forcing exceeded the corresponding CO2 emissions by a factor of 2–5. Chlorine had the highest EFs among elements measured by X-ray fluorescence (XRF) for all materials; vegetation emissions showed high abundances of potassium, consistent with its use as a marker for biomass burning. Fresh PM2.5 emitted from waste burning appeared to be acidic. Moist vegetation and food discards had the highest hydrogen fluoride (HF) and PM fluoride EFs due to fluorine accumulation in plants, while burning rubber had the highest hydrogen chloride (HCl) and PM chloride EFs due to high chlorine content in the rubber. Plastic bottles and bags, rubber, and food discards had the highest EFs for polycyclic aromatic hydrocarbons (PAHs) and nitro-PAHs as well as their associated toxicities. Distinct differences between odd and even carbon preferences were found for alkanes from biological and petroleum-based materials: dry vegetation, paper, textile, and food discards show preference for the odd-numbered alkanes, while the opposite is true for plastic bottles, bags, and rubber. As phthalates are used as plasticizers, their highest EFs were found for plastic bottles and bags, rubber, and combined materials. Data from this study will be useful for health and climate impact assessments, speciated emission inventories, source-oriented dispersion models, and receptor-based source apportionment. [ABSTRACT FROM AUTHOR]

Open burning of household solid waste is a large source of air pollutants worldwide, especially in developing countries. However, waste burning emissions are either missing or have large uncertainties in local, regional, or global emission inventories due to limited emission factor (EF) and activity data. Detailed particulate matter (PM) chemical speciation data is even scarcer. This paper reports source profiles and EFs for PM2.5 species as well as acidic and alkali gases measured from laboratory combustion of ten waste categories that represent open burning in South Africa. Carbonaceous materials contributed more than 70 % of PM2.5 mass. Elemental carbon (EC) was most abundant from flaming materials (e.g., plastic bags, textile, and combined materials) and its climate forcing exceeded the corresponding CO2 emissions by a factor of 2–5. Chlorine had the highest EFs among elements measured by X-ray fluorescence (XRF) for all materials; vegetation emissions showed high abundances of potassium, consistent with its use as a marker for biomass burning. Fresh PM2.5 emitted from waste burning appeared to be acidic. Moist vegetation and food discards had the highest hydrogen fluoride (HF) and PM fluoride EFs due to fluorine accumulation in plants, while burning rubber had the highest hydrogen chloride (HCl) and PM chloride EFs due to high chlorine content in the rubber. Plastic bottles and bags, rubber, and food discards had the highest EFs for polycyclic aromatic hydrocarbons (PAHs) and nitro-PAHs as well as their associated toxicities. Distinct differences between odd and even carbon preferences were found for alkanes from biological and petroleum-based materials: dry vegetation, paper, textile, and food discards show preference for the odd-numbered alkanes, while the opposite is true for plastic bottles, bags, and rubber. As phthalates are used as plasticizers, their highest EFs were found for plastic bottles and bags, rubber, and combined materials. Data from this study will be useful for health and climate impact assessments, speciated emission inventories, source-oriented dispersion models, and receptor-based source apportionment. [ABSTRACT FROM AUTHOR]

Open burning of household and municipal solid waste is a common practice in many developing countries. Due to limited resources for collection and proper disposal, solid waste is often disposed of in neighborhoods and open burned in piles to reduce odors and create space for incoming waste. Emissions from these ground-level and low-temperature burns cause air pollution, leading to adverse health effects among community residents. This study conducted laboratory combustion experiments to characterize gas and particle emissions from ten waste categories representative of those burned in South Africa: paper, leather/rubber, textiles, plastic bottles, plastic bags, vegetation (with three different moisture content levels), food discards, and combined materials. Carbon dioxide (CO2) and carbon monoxide (CO) were measured in real-time to calculate modified combustion efficiencies (MCE). MCE is used along with video observations to determine fuel-based emission factors (EFs) during flaming and smoldering phases as well as the entire combustion process. Fuel elemental composition and moisture content have strong influences on emissions. Plastic bags have the highest carbon content and the highest combustion efficiency, leading to the highest EFs for CO2. Textiles have the highest nitrogen and sulfur contents, resulting in the highest EFs for nitrogen oxides (NOx) and sulfur dioxide (SO2). Emissions are similar for vegetation with 0 % and 20 % moisture contents; however, EFs for CO and particulate matter (PM) from the vegetation with 50 % moisture content are 3 and 30 times, respectively, emissions from 0 % and 20 % moisture contents. This study also shows that neglecting carbon in the ash and PM can lead to significant overestimation of EFs. Results from this study are applicable to emission inventory improvements as well as air quality management to assess the health and climate effects of household waste open burning. [ABSTRACT FROM AUTHOR]