Dynamic metabolic profiling of cyanobacterial glycogen biosynthesis under conditions of nitrate depletion

Integrated pathway mining and selection of an artificial CYP79-mediated bypass to improve benzylisoquinoline alkaloid biosynthesis

BACKGROUND

Computational mining of useful enzymes and biosynthesis pathways is a powerful strategy for metabolic engineering. Through systematic exploration of all conceivable combinations of enzyme reactions, including both known compounds and those inferred from the chemical structures of established reactions, we can uncover previously undiscovered enzymatic processes. The application of the novel alternative pathways enables us to improve microbial bioproduction by bypassing or reinforcing metabolic bottlenecks. Benzylisoquinoline alkaloids (BIAs) are a diverse group of plant-derived compounds with important pharmaceutical properties. BIA biosynthesis has developed into a prime example of metabolic engineering and microbial bioproduction. The early bottleneck of BIA production in Escherichia coli consists of 3,4-dihydroxyphenylacetaldehyde (DHPAA) production and conversion to tetrahydropapaveroline (THP). Previous studies have selected monoamine oxidase (MAO) and DHPAA synthase (DHPAAS) to produce DHPAA from dopamine and oxygen; however, both of these enzymes produce toxic hydrogen peroxide as a byproduct.

RESULTS

In the current study, in silico pathway design is applied to relieve the bottleneck of DHPAA production in the synthetic BIA pathway. Specifically, the cytochrome P450 enzyme, tyrosine N-monooxygenase (CYP79), is identified to bypass the established MAO- and DHPAAS-mediated pathways in an alternative arylacetaldoxime route to DHPAA with a peroxide-independent mechanism. The application of this pathway is proposed to result in less formation of toxic byproducts, leading to improved production of reticuline (up to 60 mg/L at the flask scale) when compared with that from the conventional MAO pathway.

CONCLUSIONS

This study showed improved reticuline production using the bypass pathway predicted by the M-path computational platform. Reticuline production in E. coli exceeded that of the conventional MAO-mediated pathway. The study provides a clear example of the integration of pathway mining and enzyme design in creating artificial metabolic pathways and suggests further potential applications of this strategy in metabolic engineering.

Comparison of Amine-Modified Polymeric Stationary Phases for Polar Metabolomic Analysis Based on Unified-Hydrophilic Interaction/Anion Exchange Liquid Chromatography/High-Resolution Mass Spectrometry (Unified-HILIC/AEX/HRMS)

In metabolomic analysis, one of the most commonly used techniques to support the detection sensitivity and quantitation of mass spectrometry is combining it with liquid chromatography. Recently, we developed a method that enables comprehensive single-run measurement of hydrophilic metabolites using unified-hydrophilic interaction/anion exchange liquid chromatography/high-resolution mass spectrometry (unified-HILIC/AEX/HRMS) with a polymer-based mixed amines column (Gelpack GL-HilicAex). However, the importance of stationary phase functional groups and mobile phase conditions for the separation mechanisms and sensitive detection in unified-HILIC/AEX/HRMS is not yet fully understood. This study aimed to understand the importance of the mobile and stationary phases in unified-HILIC/AEX/HRMS. Two different alkali-resistant polymer-based amines-modified columns (Gelpack GL-HilicAex, primary, secondary, tertiary, and quaternary amine-modified polyglycerol dimethacrylate gel; Asahipak NH2P-50 2D, secondary amine-modified polyvinyl alcohol gel) and two eluents (acetonitrile and ammonium bicarbonate solution, pH 9.8) were used for comparative validation. A comparison of mobile phase conditions using both columns confirmed that the two-step separation from HILIC to AEX characteristic of unified-HILIC/AEX requires a linear gradient condition from acetonitrile to nearly 50% water and AEX with up to 40 mM bicarbonate ions. We found that when alkali-resistant hydrophilic polymer packing materials are modified with amines, unified-HILIC/AEX separation can be reproduced if at least one secondary amine associated with the amine series is present in the stationary phase. Furthermore, the difference in sensitivity in the HILIC and AEX modes owing to the different columns indicates the need for further improvements in the mobile phase composition and stationary phase.

Exogenous Trehalose Improves Growth, Glycogen and Poly-3-Hydroxybutyrate (PHB) Contents in Photoautotrophically Grown Arthrospira platensis under Nitrogen Deprivation

Glycogen and poly-3-hydroxybutyrate (PHB) are excellent biopolymer products from cyanobacteria. In this study, we demonstrate that nitrogen metabolism is positively influenced by the exogenous application of trehalose (Tre) in Arthrospira platensis under nitrogen-deprived (-N) conditions. Cells were cultivated photoautotrophically for 5 days under -N conditions, with or without the addition of exogenous Tre. The results revealed that biomass and chlorophyll-a content of A. platensis experienced enhancement with the addition of 0.003 M and 0.03 M Tre in the -N medium after one day, indicating relief from growth inhibition caused by nitrogen deprivation. The highest glycogen content (54.09 ± 1.6% (w/w) DW) was observed in cells grown for 2 days under the -N + 0.003 M Tre condition (p < 0.05), while the highest PHB content (15.2 ± 0.2% (w/w) DW) was observed in cells grown for 3 days under the -N + 0.03 M Tre condition (p < 0.05). The RT-PCR analysis showed a significant increase in glgA and phaC transcript levels, representing approximately 1.2- and 1.3-fold increases, respectively, in A. platensis grown under -N + 0.003 M Tre and -N + 0.03 M Tre conditions. This was accompanied by the induction of enzyme activities, including glycogen synthase and PHA synthase with maximal values of 89.15 and 0.68 µmol min-1 mg-1 protein, respectively. The chemical structure identification of glycogen and PHB from A. platensis was confirmed by FTIR and NMR analysis. This research represents the first study examining the performance of trehalose in promoting glycogen and PHB production in cyanobacteria under nitrogen-deprived conditions.

ppGpp accumulation reduces the expression of the global nitrogen homeostasis-modulating NtcA regulon by affecting 2-oxoglutarate levels

The cyanobacterium Synechococcus elongatus PCC 7942 accumulates alarmone guanosine tetraphosphate (ppGpp) under stress conditions, such as darkness. A previous study observed that artificial ppGpp accumulation under photosynthetic conditions led to the downregulation of genes involved in the nitrogen assimilation system, which is activated by the global nitrogen regulator NtcA, suggesting that ppGpp regulates NtcA activity. However, the details of this mechanism have not been elucidated. Here, we investigate the metabolic responses associated with ppGpp accumulation by heterologous expression of the ppGpp synthetase RelQ. The pool size of 2-oxoglutarate (2-OG), which activates NtcA, is significantly decreased upon ppGpp accumulation. De novo 13C-labeled CO2 assimilation into the Calvin-Benson-Bassham cycle and glycolytic intermediates continues irrespective of ppGpp accumulation, whereas the labeling of 2-OG is significantly decreased under ppGpp accumulation. The low 2-OG levels in the RelQ overexpression cells could be because of the inhibition of metabolic enzymes, including aconitase, which are responsible for 2-OG biosynthesis. We propose a metabolic rearrangement by ppGpp accumulation, which negatively regulates 2-OG levels to maintain carbon and nitrogen balance.

The Carbon Flow Shifts from Primary to Secondary Metabolism during Xylem Vessel Cell Differentiation in Arabidopsis thaliana

Xylem vessel cell differentiation is characterized by the deposition of a secondary cell wall (SCW) containing cellulose, hemicellulose and lignin. VASCULAR-RELATED NAC-DOMAIN7 (VND7), a plant-specific NAC (NAM, ATAF1/2, and CUC2) transcription factor, is a master regulator of xylem vessel cell differentiation in Arabidopsis (Arabidopsis thaliana). Previous metabolome analysis using the VND7-inducible system in tobacco BY-2 cells successfully revealed significant quantitative changes in primary metabolites during xylem vessel cell differentiation. However, the flow of primary metabolites is not yet well understood. Here, we performed a metabolomic analysis of VND7-inducible Arabidopsis T87 suspension cells. Capillary electrophoresis-time-of-flight mass spectrometry quantified 57 metabolites, and subsequent data analysis highlighted active changes in the levels of UDP-glucose and phenylalanine, which are building blocks of cellulose and lignin, respectively. In a metabolic flow analysis using stable carbon 13 (13C) isotope, the 13C-labeling ratio specifically increased in 3-phosphoglycerate after 12 h of VND7 induction, followed by an increase in shikimate after 24 h of induction, while the inflow of 13C into lactate from pyruvate was significantly inhibited, indicating an active shift of carbon flow from glycolysis to the shikimate pathway during xylem vessel cell differentiation. In support of this notion, most glycolytic genes involved in the downstream of glyceraldehyde 3-phosphate were downregulated following the induction of xylem vessel cell differentiation, whereas genes for the shikimate pathway and phenylalanine biosynthesis were upregulated. These findings provide evidence for the active shift of carbon flow from primary metabolic pathways to the SCW polymer biosynthetic pathway at specific points during xylem vessel cell differentiation.

FOXK1 promotes nonalcoholic fatty liver disease by mediating mTORC1-dependent inhibition of hepatic fatty acid oxidation

Nonalcoholic fatty liver disease (NAFLD) is a chronic metabolic disorder caused by overnutrition and can lead to nonalcoholic steatohepatitis (NASH) and hepatocellular carcinoma (HCC). The transcription factor Forkhead box K1 (FOXK1) is implicated in regulation of lipid metabolism downstream of mechanistic target of rapamycin complex 1 (mTORC1), but its role in NAFLD-NASH pathogenesis is understudied. Here, we show that FOXK1 mediates nutrient-dependent suppression of lipid catabolism in the liver. Hepatocyte-specific deletion of Foxk1 in mice fed a NASH-inducing diet ameliorates not only hepatic steatosis but also associated inflammation, fibrosis, and tumorigenesis, resulting in improved survival. Genome-wide transcriptomic and chromatin immunoprecipitation analyses identify several lipid metabolism-related genes, including Ppara, as direct targets of FOXK1 in the liver. Our results suggest that FOXK1 plays a key role in the regulation of hepatic lipid metabolism and that its inhibition is a promising therapeutic strategy for NAFLD-NASH, as well as for HCC.

L-Lactate treatment by photosynthetic cyanobacteria expressing heterogeneous L-lactate dehydrogenase

L-Lactate is a major waste compound in cultured animal cells. To develop a sustainable animal cell culture system, we aimed to study the consumption of L-lactate using a photosynthetic microorganism. As genes involved in L-lactate utilization were not found in most cyanobacteria and microalgae, we introduced the NAD-independent L-lactate dehydrogenase gene from Escherichia coli (lldD) into Synechococcus sp. PCC 7002. The lldD-expressing strain consumed L-lactate added to basal medium. This consumption was accelerated by expression of a lactate permease gene from E. coli (lldP) and an increase in culture temperature. Intracellular levels of acetyl-CoA, citrate, 2-oxoglutarate, succinate, and malate, and extracellular levels of 2-oxoglutarate, succinate, and malate, increased during L-lactate utilization, suggesting that the metabolic flux from L-lactate was distributed toward the tricarboxylic acid cycle. This study provides a perspective on L-lactate treatment by photosynthetic microorganisms, which would increase the feasibility of animal cell culture industries.

Enhanced supply of acetyl-CoA by exogenous pantothenate kinase promotes synthesis of poly(3-hydroxybutyrate)

BACKGROUND

Coenzyme A (CoA) is a carrier of acyl groups. This cofactor is synthesized from pantothenic acid in five steps. The phosphorylation of pantothenate is catalyzed by pantothenate kinase (CoaA), which is a key step in the CoA biosynthetic pathway. To determine whether the enhancement of the CoA biosynthetic pathway is effective for producing useful substances, the effect of elevated acetyl-CoA levels resulting from the introduction of the exogenous coaA gene on poly(3-hydroxybutyrate) [P(3HB)] synthesis was determined in Escherichia coli, which express the genes necessary for cyanobacterial polyhydroxyalkanoate synthesis (phaABEC).

RESULTS

E. coli containing the coaA gene in addition to the pha genes accumulated more P(3HB) compared with the transformant containing the pha genes alone. P(3HB) production was enhanced by precursor addition, with P(3HB) content increasing from 18.4% (w/w) to 29.0% in the presence of 0.5 mM pantothenate and 16.3%-28.2% by adding 0.5 mM β-alanine. Strains expressing the exogenous coaA in the presence of precursors contained acetyl-CoA in excess of 1 nmol/mg of dry cell wt, which promoted the reaction toward P(3HB) formation. The amount of acetate exported into the medium was three times lower in the cells carrying exogenous coaA and pha genes than in the cells carrying pha genes alone. This was attributed to significantly enlarging the intracellular pool size of CoA, which is the recipient of acetic acid and is advantageous for microbial production of value-added materials.

CONCLUSIONS

Enhancing the CoA biosynthetic pathway with exogenous CoaA was effective at increasing P(3HB) production. Supplementing the medium with pantothenate facilitated the accumulation of P(3HB). β-Alanine was able to replace the efficacy of adding pantothenate.

Dark accumulation of downstream glycolytic intermediates initiates robust photosynthesis in cyanobacteria

Photosynthesis must maintain stability and robustness throughout fluctuating natural environments. In cyanobacteria, dark-to-light transition leads to drastic metabolic changes from dark respiratory metabolism to CO2 fixation through the Calvin-Benson-Bassham (CBB) cycle using energy and redox equivalents provided by photosynthetic electron transfer. Previous studies have shown that catabolic metabolism supports the smooth transition into CBB cycle metabolism. However, metabolic mechanisms for robust initiation of photosynthesis are poorly understood due to lack of dynamic metabolic characterizations of dark-to-light transitions. Here, we show rapid dynamic changes (on a time scale of seconds) in absolute metabolite concentrations and 13C tracer incorporation after strong or weak light irradiation in the cyanobacterium Synechocystis sp. PCC 6803. Integration of this data enabled estimation of time-resolved nonstationary metabolic flux underlying CBB cycle activation. This dynamic metabolic analysis indicated that downstream glycolytic intermediates, including phosphoglycerate and phosphoenolpyruvate, accumulate under dark conditions as major substrates for initial CO2 fixation. Compared with wild-type Synechocystis, significant decreases in the initial oxygen evolution rate were observed in 12 h dark preincubated mutants deficient in glycogen degradation or oxidative pentose phosphate pathways. Accordingly, the degree of decrease in the initial oxygen evolution rate was proportional to the accumulated pool size of glycolytic intermediates. These observations indicate that the accumulation of glycolytic intermediates is essential for efficient metabolism switching under fluctuating light environments.

Enhanced production of 3,4-dihydroxybutyrate from xylose by engineered yeast via xylonate re-assimilation under alkaline condition

To realize lignocellulose-based bioeconomy, efficient conversion of xylose into valuable chemicals by microbes is necessary. Xylose oxidative pathways that oxidize xylose into xylonate can be more advantageous than conventional xylose assimilation pathways because of fewer reaction steps without loss of carbon and ATP. Moreover, commodity chemicals like 3,4-dihydroxybutyrate and 3-hydroxybutyrolactone can be produced from the intermediates of xylose oxidative pathway. However, successful implementations of xylose oxidative pathway in yeast have been hindered because of the secretion and accumulation of xylonate which is a key intermediate of the pathway, leading to low yield of target product. Here, high-yield production of 3,4-dihydroxybutyrate from xylose by engineered yeast was achieved through genetic and environmental perturbations. Specifically, 3,4-dihydroxybutyrate biosynthetic pathway was established in yeast through deletion of ADH6 and overexpression of yneI. Also, inspired by the mismatch of pH between host strain and key enzyme of XylD, alkaline fermentations (pH ≥ 7.0) were performed to minimize xylonate accumulation. Under the alkaline conditions, xylonate was re-assimilated by engineered yeast and combined product yields of 3,4-dihydroxybutyrate and 3-hydroxybutyrolactone resulted in 0.791 mol/mol-xylose, which is highest compared with previous study. These results shed light on the utility of the xylose oxidative pathway in yeast.

Chemical Triggering Cyanobacterial Glycogen Accumulation: Methyl Viologen Treatment Increases Synechocystis sp. PCC 6803 Glycogen Storage by Enhancing Levels of Gene Transcript and Substrates in Glycogen Synthesis

Two-stage cultivation is effective for glycogen production by cyanobacteria. Cells were first grown under adequate nitrate supply (BG11) to increase biomass and subsequently transferred to nitrogen deprivation (-N) to stimulate glycogen accumulation. However, the two-stage method is time-consuming and requires extensive energy. Thus, one-stage cultivation that enables both cell growth and glycogen accumulation is advantageous. Such one-stage method could be achieved using a chemical triggering glycogen storage. However, there is a limited study on such chemicals. Here, nine compounds previously reported to affect cyanobacterial cellular functions were examined in Synechocystis sp. PCC 6803. 2-Phenylethanol, phenoxyethanol, 3-(3,4-dichlorophenyl)-1,1-dimethylurea and methyl viologen can stimulate glycogen accumulation. The oxidative stress agent, methyl viologen significantly increased glycogen levels up to 57% and 69% [w/w dry weight (DW)] under BG11 and -N cultivation, respectively. One-stage cultivation where methyl viologen was directly added to the pre-grown culture enhanced glycogen storage to 53% (w/w DW), compared to the 10% (w/w DW) glycogen level of the control cells without methyl viologen. Methyl viologen treatment reduced the contents of total proteins (including phycobiliproteins) but caused increased transcript levels of glycogen synthetic genes and elevated levels of metabolite substrates for glycogen synthesis. Metabolomic results suggested that upon methyl viologen treatment, proteins degraded to amino acids, some of which could be used as a carbon source for glycogen synthesis. Results of oxygen evolution and metabolomic analysis suggested that photosynthesis and carbon fixation were not completely inhibited upon methyl viologen treatment, and these two processes may partially generate upstream metabolites required for glycogen synthesis.

Manipulation of topoisomerase expression inhibits cell division but not growth and reveals a distinctive promoter structure in Synechocystis

In cyanobacteria DNA supercoiling varies over the diurnal cycle and is integrated with temporal programs of transcription and replication. We manipulated DNA supercoiling in Synechocystis sp. PCC 6803 by CRISPRi-based knockdown of gyrase subunits and overexpression of topoisomerase I (TopoI). Cell division was blocked but cell growth continued in all strains. The small endogenous plasmids were only transiently relaxed, then became strongly supercoiled in the TopoI overexpression strain. Transcript abundances showed a pronounced 5'/3' gradient along transcription units, incl. the rRNA genes, in the gyrase knockdown strains. These observations are consistent with the basic tenets of the homeostasis and twin-domain models of supercoiling in bacteria. TopoI induction initially led to downregulation of G+C-rich and upregulation of A+T-rich genes. The transcriptional response quickly bifurcated into six groups which overlap with diurnally co-expressed gene groups. Each group shows distinct deviations from a common core promoter structure, where helically phased A-tracts are in phase with the transcription start site. Together, our data show that major co-expression groups (regulons) in Synechocystis all respond differentially to DNA supercoiling, and suggest to re-evaluate the long-standing question of the role of A-tracts in bacterial promoters.

Enhanced polyglucan contents in divergent cyanobacteria under nutrient-deprived photoautotrophy: transcriptional and metabolic changes in response to increased glycogen accumulation in nitrogen-deprived Synechocystis sp. PCC 6803

Cyanobacteria accumulate polyglucan as main carbohydrate storage. Here, the cellular polyglucan content was determined in 27 cyanobacterial strains from 25 genera. The polyglucan contents were significantly enhanced in 20 and 23 strains under nitrogen (-N) and phosphate (-P) deprivation, respectively. High polyglucan accumulation was not associated with particular evolutionary groups but was strain specific. The highest polyglucan accumulations of 46.2% and 52.5% (w/w dry weight; DW) were obtained under -N in Synechocystis sp. PCC 6803 (hereafter Synechocystis) and Chroococcus limneticus, respectively. In Synechocystis, 80-97% (w/w) of the polyglucan was glycogen. Transcriptome and metabolome analyses during glycogen accumulation under -N were determined in Synechocystis. The genes responsible for the supply of the substrates for glycogen synthesis: glycerate-1,3-phosphate and fructose-1,6-phosphate, were significantly up-regulated. The genes encoding the enzymes converting succinate to malate in TCA cycle, were significantly down-regulated. The genes encoding the regulator proteins which inhibits metabolism at lower part of glycolysis pathway, were also significantly up-regulated. The transcript levels of PII protein and the level of 2-oxoglutarate, which form a complex that inhibits lower part of glycolysis pathway, were significantly increased. Thus, the increased Synechocystis glycogen accumulation under -N was likely to be mediated by the increased supply of glycogen synthesis substrates and metabolic inhibitions at lower part of glycolysis pathway and TCA cycle.

Revalorization of Microalgae Biomass for Synergistic Interaction and Sustainable Applications: Bioplastic Generation

Microalgae and cyanobacteria are photosynthetic microorganisms’ sources of renewable biomass that can be used for bioplastic production. These microorganisms have high growth rates, and contrary to other feedstocks, such as land crops, they do not require arable land. In addition, they can be used as feedstock for bioplastic production while not competing with food sources (e.g., corn, wheat, and soy protein). In this study, we review the macromolecules from microalgae and cyanobacteria that can serve for the production of bioplastics, including starch and glycogen, polyhydroxyalkanoates (PHAs), cellulose, polylactic acid (PLA), and triacylglycerols (TAGs). In addition, we focus on the cultivation of microalgae and cyanobacteria for wastewater treatment. This approach would allow reducing nutrient supply for biomass production while treating wastewater. Thus, the combination of wastewater treatment and the production of biomass that can serve as feedstock for bioplastic production is discussed. The comprehensive information provided in this communication would expand the scope of interdisciplinary and translational research.

Combining metabolite doping and metabolic engineering to improve 2-phenylethanol production by engineered cyanobacteria

2-Phenylethanol (2-PE) is a rose-scented aromatic compound, with broad application in cosmetic, pharmaceutical, food and beverage industries. Many plants naturally synthesize 2-PE via Shikimate Pathway, but its extraction is expensive and low-yielding. Consequently, most 2-PE derives from chemical synthesis, which employs petroleum as feedstock and generates unwanted by products and health issues. The need for “green” processes and the increasing public demand for natural products are pushing biotechnological production systems as promising alternatives. So far, several microorganisms have been investigated and engineered for 2-PE biosynthesis, but a few studies have focused on autotrophic microorganisms. Among them, the prokaryotic cyanobacteria can represent ideal microbial factories thanks to their ability to photosynthetically convert CO2 into valuable compounds, their minimal nutritional requirements, high photosynthetic rate and the availability of genetic and bioinformatics tools. An engineered strain of Synechococcus elongatus PCC 7942 for 2-PE production, i.e., p120, was previously published elsewhere. The strain p120 expresses four heterologous genes for the complete 2-PE synthesis pathway. Here, we developed a combined approach of metabolite doping and metabolic engineering to improve the 2-PE production kinetics of the Synechococcus elongatus PCC 7942 p120 strain. Firstly, the growth and 2-PE productivity performances of the p120 recombinant strain were analyzed to highlight potential metabolic constraints. By implementing a BG11 medium doped with L-phenylalanine, we covered the metabolic burden to which the p120 strain is strongly subjected, when the 2-PE pathway expression is induced. Additionally, we further boosted the carbon flow into the Shikimate Pathway by overexpressing the native Shikimate Kinase in the Synechococcus elongatus PCC 7942 p120 strain (i.e., 2PE_aroK). The combination of these different approaches led to a 2-PE yield of 300 mg/gDW and a maximum 2-PE titer of 285 mg/L, 2.4-fold higher than that reported in literature for the p120 recombinant strain and, to our knowledge, the highest recorded for photosynthetic microorganisms, in photoautotrophic growth condition. Finally, this work provides the basis for further optimization of the process aimed at increasing 2-PE productivity and concentration, and could offer new insights about the use of cyanobacteria as appealing microbial cell factories for the synthesis of aromatic compounds.

Development of a stable semi-continuous lipid production system of an oleaginous Chlamydomonas sp. mutant using multi-omics profiling

Background

Microalgal lipid production has attracted global attention in next-generation biofuel research. Nitrogen starvation, which drastically suppresses cell growth, is a common and strong trigger for lipid accumulation in microalgae. We previously developed a mutant Chlamydomonas sp. KAC1801, which can accumulate lipids irrespective of the presence or absence of nitrates. This study aimed to develop a feasible strategy for stable and continuous lipid production through semi-continuous culture of KAC1801.

Results

KAC1801 continuously accumulated > 20% lipid throughout the subculture (five generations) when inoculated with a dry cell weight of 0.8–0.9 g L⁻¹ and cultured in a medium containing 18.7 mM nitrate, whereas the parent strain KOR1 accumulated only 9% lipid. Under these conditions, KAC1801 continuously produced biomass and consumed nitrates. Lipid productivity of 116.9 mg L⁻¹ day⁻¹ was achieved by semi-continuous cultivation of KAC1801, which was 2.3-fold higher than that of KOR1 (50.5 mg L⁻¹ day⁻¹). Metabolome and transcriptome analyses revealed a depression in photosynthesis and activation of nitrogen assimilation in KAC1801, which are the typical phenotypes of microalgae under nitrogen starvation.

Conclusions

By optimizing nitrate supply and cell density, a one-step cultivation system for Chlamydomonas sp. KAC1801 under nitrate-replete conditions was successfully developed. KAC1801 achieved a lipid productivity comparable to previously reported levels under nitrogen-limiting conditions. In the culture system of this study, metabolome and transcriptome analyses revealed a nitrogen starvation-like response in KAC1801.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13068-022-02196-w.

Effects of Light and Temperature on the Metabolic Profiling of Two Habitat-Dependent Bloom-Forming Cyanobacteria

Rapid proliferation of cyanobacteria in both benthic and suspended (planktonic) habitats is a major threat to environmental safety, as they produce nuisance compounds such as cytotoxins and off-flavors, which degrade the safety and quality of water supplies. Temperature and light irradiance are two of the key factors in regulating the occurrence of algal blooms and production of major off-flavors. However, the role of these factors in regulating the growth and metabolism is poorly explored for both benthic and planktonic cyanobacteria. To fill this gap, we studied the effects of light and temperature on the growth and metabolic profiling of both benthic (Hapalosiphon sp. MRB220) and planktonic (Planktothricoides sp. SR001) environmental species collected from a freshwater reservoir in Singapore. Moreover, this study is the first report on the metabolic profiling of cyanobacteria belonging to two different habitats in response to altered environmental conditions. The highest growth rate of both species was observed at the highest light intensity (100 μmol photons/m²/s) and at a temperature of 33 °C. Systematic metabolite profiling analysis suggested that temperature had a more profound effect on metabolome of the Hapalosiphon, whereas light had a greater effect in the case of Planktothricoides. Interestingly, Planktothricoides sp. SR001 showed a specialized adaptation mechanism via biosynthesis of arginine, and metabolism of cysteine and methionine to survive and withstand higher temperatures of 38 °C and higher. Hence, the mode of strategies for coping with different light and temperature conditions was correlated with the growth and alteration in metabolic activities for physiological and ecological adaptations in both species. In addition, we putatively identified a number of unique metabolites with a broad range of antimicrobial activities in both species in response to both light and temperature. These metabolites could play a role in the dominant behavior of these species in suppressing competition during bloom formation. Overall, this study elucidated novel insights into the effects of environmental factors on the growth, metabolism, and adaptation strategies of cyanobacteria from two different habitats, and could be useful in controlling their harmful effects on human health and environmental concerns.

Machine learning discovery of missing links that mediate alternative branches to plant alkaloids

Engineering the microbial production of secondary metabolites is limited by the known reactions of correctly annotated enzymes. Therefore, the machine learning discovery of specialized enzymes offers great potential to expand the range of biosynthesis pathways. Benzylisoquinoline alkaloid production is a model example of metabolic engineering with potential to revolutionize the paradigm of sustainable biomanufacturing. Existing bacterial studies utilize a norlaudanosoline pathway, whereas plants contain a more stable norcoclaurine pathway, which is exploited in yeast. However, committed aromatic precursors are still produced using microbial enzymes that remain elusive in plants, and additional downstream missing links remain hidden within highly duplicated plant gene families. In the current study, machine learning is applied to predict and select plant missing link enzymes from homologous candidate sequences. Metabolomics-based characterization of the selected sequences reveals potential aromatic acetaldehyde synthases and phenylpyruvate decarboxylases in reconstructed plant gene-only benzylisoquinoline alkaloid pathways from tyrosine. Synergistic application of the aryl acetaldehyde producing enzymes results in enhanced benzylisoquinoline alkaloid production through hybrid norcoclaurine and norlaudanosoline pathways.

Producing plant secondary metabolites by microbes is limited by the known enzymatic reactions. Here, the authors apply machine learning to predict missing link enzymes of benzylisoquinoline alkaloid (BIA) biosynthesis in Papaver somniferum, and validate the specialized activities through heterologous production.

Metabolomics-based engineering for biofuel and bio-based chemical production in microalgae and cyanobacteria: A review

Metabolomics, an essential tool in modern synthetic biology based on the design-build-test-learn platform, is useful for obtaining a detailed understanding of cellular metabolic mechanisms through comprehensive analyses of the metabolite pool size and its dynamic changes. Metabolomics is critical to the design of a rational metabolic engineering strategy by determining the rate-limiting reaction and assimilated carbon distribution in a biosynthetic pathway of interest. Microalgae and cyanobacteria are promising photosynthetic producers of biofuels and bio-based chemicals, with high potential for developing a bioeconomic society through bio-based carbon neutral manufacturing. Metabolomics technologies optimized for photosynthetic organisms have been developed and utilized in various microalgal and cyanobacterial species. This review provides a concise overview of recent achievements in photosynthetic metabolomics, emphasizing the importance of microalgal and cyanobacterial cell factories that satisfy industrial requirements.

Nitrogen Availability Affects the Metabolic Profile in Cyanobacteria

Nitrogen is essential for the biosynthesis of various molecules in cells, such as amino acids and nucleotides, as well as several types of lipids and sugars. Cyanobacteria can assimilate several forms of nitrogen, including nitrate, ammonium, and urea, and the physiological and genetic responses to these nitrogen sources have been studied previously. However, the metabolic changes in cyanobacteria caused by different nitrogen sources have not yet been characterized. This study aimed to elucidate the influence of nitrate and ammonium on the metabolic profiles of the cyanobacterium Synechocystis sp. strain PCC 6803. When supplemented with NaNO₃ or NH₄Cl as the nitrogen source, Synechocystis sp. PCC 6803 grew faster in NH₄Cl medium than in NaNO₃ medium. Metabolome analysis indicated that some metabolites in the CBB cycle, glycolysis, and TCA cycle, and amino acids were more abundant when grown in NH₄Cl medium than NaNO₃ medium. ¹⁵N turnover rate analysis revealed that the nitrogen assimilation rate in NH₄Cl medium was higher than in NaNO₃ medium. These results indicate that the mechanism of nitrogen assimilation in the GS-GOGAT cycle differs between NaNO₃ and NH₄Cl. We conclude that the amounts and biosynthetic rate of cyanobacterial metabolites varies depending on the type of nitrogen.

Resveratrol production from several types of saccharide sources by a recombinant Scheffersomyces stipitis strain

Resveratrol is a plant-derived aromatic compound with a wide range of beneficial properties including antioxidant and anti-aging effects. The resveratrol currently available on the market is predominantly extracted from certain plants such as grape and the Japanese knotweed Polygonum cuspidatum. Due to the unstable harvest of these plants and the low resveratrol purity obtained, it is necessary to develop a stable production process of high-purity resveratrol from inexpensive feedstocks. Here, we attempted to produce resveratrol from a wide range of sugars as carbon sources by a using the genetically-engineered yeast Scheffersomyces stipitis (formerly known as Pichia stipitis), which possesses a broad sugar utilization capacity. First, we constructed the resveratrol producing strain by introducing genes coding the essential enzymes for resveratrol biosynthesis [tyrosine ammonia-lyase 1 derived from Herpetosiphon aurantiacus (HaTAL1), 4-coumarate: CoA ligase 2 derived from Arabidopsis thaliana (At4CL2), and stilbene synthase 1 derived from Vitis vinifera (VvVST1)]. Subsequently, a feedback-insensitive allele of chorismate mutase was overexpressed in the constructed strain to improve resveratrol production. The constructed strain successfully produced resveratrol from a broad range of biomass-derived sugars [glucose, fructose, xylose, N-acetyl glucosamine (GlcNAc), galactose, cellobiose, maltose, and sucrose] in shake flask cultivation. Significant resveratrol titers were detected in cellobiose and sucrose fermentation (529.8 and 668.6 mg/L after 120 h fermentation, respectively), twice above the amount obtained with glucose (237.6 mg/L). Metabolomic analysis revealed an altered profile of the metabolites involved in the glycolysis and shikimate pathways, and also of cofactors and metabolites of energy metabolisms, depending on the substrate used. The levels of resveratrol precursors such as L-tyrosine increased in cellobiose and sucrose-grown cells. The results indicate that S. stipitis is an attractive microbial platform for resveratrol production from broad types of biomass-derived sugars and the selection of suitable substrates is crucial for improving resveratrol productivity of this yeast.

Probing Individual Particles in Aquatic Suspensions by Simultaneously Measuring Polarized Light Scattering and Fluorescence

Suspended particles play a significant role in aquatic systems. However, existing methods to probe suspended particles have several limitations. In this paper, we present a portable prototype to in situ probe individual particles in aquatic suspensions by simultaneously measuring polarized light scattering and fluorescence, aiming to obtain an effective classification of microplastics and microalgae. Results show that the obtained classification accuracy is significantly higher than that for either of these two methods. The setup also successfully measures submicron particles and discriminates two species of Synechococcus. Our study demonstrates the feasibility of simultaneously measuring polarized light scattering and fluorescence, and the promising capability of our method for further aquatic environmental monitoring.

Effects of Low Temperature, Nitrogen Starvation and Their Combination on the Photosynthesis and Metabolites of Thermosynechococcus E542: A Comparison Study

Both low temperature and nitrogen starvation caused chlorosis of cyanobacteria. Here, in this study, for the first time, we compared the effects of low temperature, nitrogen starvation, and their combination on the photosynthesis and metabolites of a thermophilic cyanobacterium strain, Thermosynechococcus E542. Under various culture conditions, the growth rates, pigment contents, and chlorophyll fluorescence were monitored, and the composition of alkanes, lipidomes, and carbohydrates were determined. It was found that low temperature (35 °C) significantly suppressed the growth of Thermosynechococcus E542. Nitrogen starvation at 45 °C and 55 °C did not affect the growth; however, combined treatment of low temperature and nitrogen starvation led to the lowest growth rate and biomass productivity. Both low temperature and nitrogen starvation caused significantly declined contents of pigments, but they resulted in a different effect on the OJIP curves, and their combination led to the lowest pigment contents. The composition of fatty acids and alkanes was altered upon low-temperature cultivation, while nitrogen starvation caused reduced contents of all lipids. The low temperature did not affect carbohydrate contents, while nitrogen starvation greatly enhanced carbohydrate content, and their combination did not enhance carbohydrate content, but led to reduced productivity. These results revealed the influence of low temperature, nitrogen starvation, and their combined treatment for the accumulation of phycobiliproteins, lipids, and carbohydrates of a thermophilic cyanobacterium strain, Thermosynechococcus E542.

Targeting leukemia-specific dependence on the de novo purine synthesis pathway

Acute myeloid leukemia (AML) is a devastating disease, and clinical outcomes are still far from satisfactory. Here, to identify novel targets for AML therapy, we performed a genome-wide CRISPR/Cas9 screen using AML cell lines, followed by a second screen in vivo. We show that PAICS, an enzyme involved in de novo purine biosynthesis, is a potential target for AML therapy. AML cells expressing shRNA-PAICS exhibited a proliferative disadvantage, indicating a toxic effect of shRNA-PAICS. Treatment of human AML cells with a PAICS inhibitor suppressed their proliferation by inhibiting DNA synthesis and promoting apoptosis and had anti-leukemic effects in AML PDX models. Furthermore, CRISPR/Cas9 screens using AML cells in the presence of the inhibitor revealed genes mediating resistance or synthetic lethal to PAICS inhibition. Our findings identify PAICS as a novel therapeutic target for AML and further define components of de novo purine synthesis pathway and its downstream effectors essential for AML cell survival.

Lutein production with Chlorella sorokiniana MB-1-M12 using novel two-stage cultivation strategies - metabolic analysis and process improvement

Microalgae-derived carotenoids have increasingly been considered as feasible green alternatives for synthetic antioxidants. In this study, the lutein high-yielding strain (Chlorella sorokiniana MB-1; henceforth MB-1) and its mutant derivative (C. sorokiniana MB-1-M12; henceforth M12) were evaluated for their growth, biomass production, and lutein accumulation in three different cultivation modes - photoautotrophy, mixotrophy, and heterotrophy. M12 could grow effectively under heterotrophic conditions, but the lutein content was lower, indicating the necessity of photo-induction for lutein accumulation. Metabolic analysis of MB-1 and M12 in autotrophic growth in the presence of carbon dioxide indicated that carbon assimilation and channeling of the fixed metabolites towards carotenoid accumulation was elevated in M12 compared to MB-1. Novel two-stage alternative cultivation strategies (Autotrophic/Heterotrophic and Mixotrophic/Heterotrophic cultures) were applied for enhancing lutein production in M12. Maximum lutein quantity (6.17 mg/g) and production (33.64 mg/L) were obtained with the TSHM strategy that is considered the best two-stage operation.

Arthrospira platensis as a Feasible Feedstock for Bioethanol Production

In recent decades and to deal with the scarcity of fossil fuels, many studies have been developed in order to set up a sustainable biofuel production sector. This new sector must be efficient (high productivity), economically profitable (low production costs and therefore acceptable fuel prices), and ethical (low carbon balance, no competition with food resources). The production of bioethanol is based on the fermentation of reserve sugars, accumulated in the form of starch in microalgae and glycogen in cyanobacteria. The advantage of this bioenergy production route lies in the fact that the post-crop fermentation process is at the industrial stage since it has already been tested for many years for the production of bioethanol from agricultural resources. One of the most cultivated cyanobacteria is Arthrospira (“Spirulina”) and its production is also already at industrial scale. Depending on the cultivation conditions, this cyanobacteria is able to accumulate up to 65% DW (dry weight) of glycogen, making it a feasible feedstock for bioethanol production. The aim of this review is to provide a clear overview of these operating conditions for glycogen accumulation.

The Effect of Promoter and RBS Combination on the Growth and Glycogen Productivity of Sodium-Dependent Bicarbonate Transporter (SbtA) Overexpressing Synechococcus sp. PCC 7002 Cells

Sodium dependent bicarbonate transporter, SbtA is a high-affinity, inducible bicarbonate transporter in cyanobacterial cells. Our previous work has shown that overexpression of this transporter can significantly increase growth and glycogen accumulation in Synechococcus sp. PCC 7002 cells. In this work, we have tested the effect of two different RBS sequences (RBS1: GGAGGA and RBS2: AGGAGA) and three different promoters (P_cpcB, P_cpcB560, and P_rbcL2) on the growth and glycogen production in SbtA-overexpressing Synechococcus sp. PCC 7002 cells. Our results show that P_cpcB or P_cpcB560 were more effective than P_rbcL2 in increasing the growth and glycogen content. The choice of RBS sequence had relatively minor effect, though RBS2 was more effective than RBS1. The transformant E, with P_cpcB560 and RBS2, showed the highest growth. The biomass after 5 days of growth on air or 1% CO₂ was increased by about 90% in the strain E compared to PCC 7002 cells. All transformants overexpressing SbtA had higher glycogen content. However, growing the cells with bubbling of 1% CO₂ did not increase cellular glycogen content any further. The strain E had about 80% higher glycogen content compared to WT PCC 7002 cells. Therefore, the glycogen productivity of the strain E grown with air-bubbling was about 2.5-fold that of the WT PCC 7002 cells grown similarly. Additionally, some of the transformants had higher chlorophyll content while all the transformants had higher carotenoid content compared to the PCC 7002 cells, suggesting interaction between carbon transport and pigment levels. Thus, this work shows that the choice of photosynthetic promoters and RBSs sequences can impact growth and glycogen accumulation in SbtA-overexpressing cells.

Enhanced Production of Photosynthetic Pigments and Various Metabolites and Lipids in the Cyanobacteria Synechocystis sp. PCC 7338 Culture in the Presence of Exogenous Glucose

Synechocystis strains are cyanobacteria that can produce useful biomaterials for biofuel and pharmaceutical resources. In this study, the effects of exogenous glucose (5-mM) on cell growth, photosynthetic pigments, metabolites, and lipids in Synechocystis sp. PCC 7338 (referred to as Synechocystis 7338) were investigated. Exogenous glucose increased cell growth on days 9 and 18. The highest production (mg/L) of chlorophyll a (34.66), phycocyanin (84.94), allophycocyanin (34.28), and phycoerythrin (6.90) was observed on day 18 in Synechocystis 7338 culture under 5-mM glucose. Alterations in metabolic and lipidomic profiles under 5-mM glucose were investigated using gas chromatography-mass spectrometry (MS) and nanoelectrospray ionization-MS. The highest production (relative intensity/L) of aspartic acid, glutamic acid, glycerol-3-phosphate, linolenic acid, monogalactosyldiacylglycerol (MGDG) 16:0/18:1, MGDG 16:0/20:2, MGDG 18:1/18:2, neophytadiene, oleic acid, phosphatidylglycerol (PG) 16:0/16:0, and PG 16:0/17:2 was achieved on day 9. The highest production of pyroglutamic acid and sucrose was observed on day 18. We suggest that the addition of exogenous glucose to Synechocystis 7338 culture could be an efficient strategy for improving growth of cells and production of photosynthetic pigments, metabolites, and intact lipid species for industrial applications.

Metabolic Engineering for Carotenoid Production Using Eukaryotic Microalgae and Prokaryotic Cyanobacteria

Eukaryotic microalgae and prokaryotic cyanobacteria are diverse photosynthetic organisms that produce various useful compounds. Due to their rapid growth and efficient biomass production from carbon dioxide and solar energy, microalgae and cyanobacteria are expected to become cost-effective, sustainable bioresources in the future. These organisms also abundantly produce various carotenoids, but further improvement in carotenoid productivity is needed for a successful commercialization. Metabolic engineering via genetic manipulation and mutational breeding is a powerful tool for generating carotenoid-rich strains. This chapter focuses on carotenoid production in microalgae and cyanobacteria, as well as strategies and potential target genes for metabolic engineering. Recent achievements in metabolic engineering that improved carotenoid production in microalgae and cyanobacteria are also reviewed.

CfrA, a Novel Carbon Flow Regulator, Adapts Carbon Metabolism to Nitrogen Deficiency in Cyanobacteria

Cyanobacteria unable to fix atmospheric nitrogen have evolved sophisticated adaptations to survive to long periods of nitrogen starvation. These genetic programs are still largely unknown-as evidenced by the many proteins whose expression is regulated in response to nitrogen availability, but which belong to unknown or hypothetical categories. In Synechocystis sp. PCC 6803, the global nitrogen regulator NtcA activates the expression of the sll0944 gene upon nitrogen deprivation. This gene encodes a protein that is highly conserved in cyanobacteria, but of unknown function. Based on the results described herein, we named the product of sll0944 carbon flow regulator A (CfrA). We analyzed the phenotypes of strains containing different levels of CfrA, including a knock-out strain (ΔcfrA), and two strains overexpressing CfrA from either the constitutive P _trc promoter (Ptrc-cfrA) or the arsenite-inducible promoter P _arsB (Pars-cfrA). Our results show that the amount of CfrA determines the accumulation of glycogen, and affects the synthesis of protein and photosynthetic pigments as well as amino acid pools. Strains with high levels of CfrA present high levels of glycogen and a decrease in photosynthetic pigments and protein content when nitrogen is available. Possible interactions between CfrA and the pyruvate dehydrogenase complex or PII protein have been revealed. The phenotype associated with CfrA overexpression is also observed in PII-deficient strains; however, it is lethal in this genetic background. Taken together, our results indicate a role for CfrA in the adaptation of carbon flux during acclimation to nitrogen deficiency.

Dynamic Metabolome Analysis Reveals the Metabolic Fate of Medium-Chain Fatty Acids in AML12 Cells

Several studies in hepatocyte cell lines reported that medium-chain fatty acids (MCFAs) with 6-12 carbons showed different metabolic properties from long-chain fatty acids (LCFAs). However, these studies reported unclear effects of different fatty acid molecules on hepatocyte metabolism. This study is aimed to capture the metabolic kinetics of MCFA assimilation in AML12 cells treated with octanoic acid (FA 8:0), decanoic acid (FA 10:0), or lauric acid (FA12:0) [LCFA; oleic acid (FA 18:1)] via metabolic profiling and dynamic metabolome analysis with ¹³C-labeling. The concentrations of total ketone bodies in the media of cells treated with FA 8:0 or FA 10:0 were 3.22- or 3.69-fold higher than those obtained with FA 18:1 treatment, respectively. FA 12:0 treatment did not significantly increase ketone body levels compared to DMSO treatment (control), whereas FA 12:0 treatment increased intracellular triacylglycerol (TG) levels 15.4 times compared to the control. Metabolic profiles of FA 12:0-treated samples differed from those of the FA 8:0-treated and FA 10:0-treated samples, suggesting that metabolic assimilation of MCFAs differed significantly depending on the MCFA type. Furthermore, the dynamic metabolome analysis clearly revealed that FA 8:0 was rapidly and quantitatively oxidized to acetyl-CoA and assimilated into ketone bodies, citrate cycle intermediates, and glucogenic amino acids but not readily into TGs.

Optimization of 1,2,4-butanetriol production from xylose in Saccharomyces cerevisiae by metabolic engineering of NADH/NADPH balance

1,2,4-Butanetriol (BT) is used as a precursor for the synthesis of various pharmaceuticals and the energetic plasticizer 1,2,4-butanetriol trinitrate. In Saccharomyces cerevisiae, BT is biosynthesized from xylose via heterologous four enzymatic reactions catalyzed by xylose dehydrogenase, xylonate dehydratase, 2-ketoacid decarboxylase, and alcohol dehydrogenase. We here aimed to improve the BT yield in S. cerevisiae by genetic engineering. First, the amount of the key intermediate 2-keto-3-deoxy-xylonate as described previously was successfully reduced in 41% by multiple integrations of Lactococcus lactis 2-ketoacid decarboxylase gene kdcA into the yeast genome. Since the heterologous BT synthetic pathway is independent of yeast native metabolism, this manipulation has led to NADH/NADPH imbalance and deficiency during BT production. Overexpression of the NADH kinase POS5Δ17 lacking the mitochondrial targeting sequence to relieve NADH/NADPH imbalance resulted in the BT titer of 2.2 g/L (31% molar yield). Feeding low concentrations of glucose and xylose to support the supply of NADH resulted in BT titer of 6.6 g/L with (57% molar yield). Collectively, improving the NADH/NADPH ratio and supply from glucose are essential for the construction of a xylose pathway, such as the BT synthetic pathway, independent of native yeast metabolism.

Characterizing glucose, illumination, and nitrogen-deprivation phenotypes of Synechocystis PCC6803 with Raman spectroscopy

Background

Synechocystis sp. PCC6803 is a model cyanobacterium that has been studied widely and is considered for metabolic engineering applications. Here, Raman spectroscopy and Raman chemometrics (Rametrix™) were used to (i) study broad phenotypic changes in response to growth conditions, (ii) identify phenotypic changes associated with its circadian rhythm, and (iii) correlate individual Raman bands with biomolecules and verify these with more accepted analytical methods.

Methods

Synechocystis cultures were grown under various conditions, exploring dependencies on light and/or external carbon and nitrogen sources. The Rametrix™ LITE Toolbox for MATLAB® was used to process Raman spectra and perform principal component analysis (PCA) and discriminant analysis of principal components (DAPC). The Rametrix™ PRO Toolbox was used to validate these models through leave-one-out routines that classified a Raman spectrum when growth conditions were withheld from the model. Performance was measured by classification accuracy, sensitivity, and specificity. Raman spectra were also subjected to statistical tests (ANOVA and pairwise comparisons) to identify statistically relevant changes in Synechocystis phenotypes. Finally, experimental methods, including widely used analytical and spectroscopic assays were used to quantify the levels of glycogen, fatty acids, amino acids, and chlorophyll a for correlations with Raman data.

Results

PCA and DAPC models produced distinct clustering of Raman spectra, representing multiple Synechocystis phenotypes, based on (i) growth in the presence of 5 mM glucose, (ii) illumination (dark, light/dark [12 h/12 h], and continuous light at 20 µE), (iii) nitrogen deprivation (0–100% NaNO₃ of native BG-11 medium in continuous light), and (iv) throughout a 24 h light/dark (12 h/12 h) circadian rhythm growth cycle. Rametrix™ PRO was successful in identifying glucose-induced phenotypes with 95.3% accuracy, 93.4% sensitivity, and 96.9% specificity. Prediction accuracy was above random chance values for all other studies. Circadian rhythm analysis showed a return to the initial phenotype after 24 hours for cultures grown in light/dark (12 h/12 h) cycles; this did not occur for cultures grown in the dark. Finally, correlation coefficients (R > 0.7) were found for glycogen, all amino acids, and chlorophyll a when comparing specific Raman bands to other experimental results.

A shift in glutamine nitrogen metabolism contributes to the malignant progression of cancer

Glucose metabolism is remodeled in cancer, but the global pattern of cancer-specific metabolic changes remains unclear. Here we show, using the comprehensive measurement of metabolic enzymes by large-scale targeted proteomics, that the metabolism both carbon and nitrogen is altered during the malignant progression of cancer. The fate of glutamine nitrogen is shifted from the anaplerotic pathway into the TCA cycle to nucleotide biosynthesis, with this shift being controlled by glutaminase (GLS1) and phosphoribosyl pyrophosphate amidotransferase (PPAT). Interventions to reduce the PPAT/GLS1 ratio suppresses tumor growth of many types of cancer. A meta-analysis reveals that PPAT shows the strongest correlation with malignancy among all metabolic enzymes, in particular in neuroendocrine cancer including small cell lung cancer (SCLC). PPAT depletion suppresses the growth of SCLC lines. A shift in glutamine fate may thus be required for malignant progression of cancer, with modulation of nitrogen metabolism being a potential approach to SCLC treatment.

Glucose metabolism is known to be dysregulated in cancer. Here, the authors show that glutamine nitrogen is also affected in cancer and demonstrate that glutaminase 1 and phosphoribosyl pyrophosphate amidotransferase are the key enzymes that control this metabolic switch.

Nitrogen availability affects the dynamics of Microcystis blooms by regulating the downward transport of biomass

Nitrogen availability is one of the key factors affecting the dynamics of non-diazotrophic cyanobacterial blooms in eutrophic lakes. While previous studies mainly focused on the promoting effect of nitrogen on the growth of cyanobacteria, this study aimed to investigate the role of nitrogen availability in the downward transport of biomass and its effects on the dynamics of Microcystis blooms. We performed field enclosure experiments which demonstrated that nitrogen availability negatively affects the downward transport of biomass. With a nitrogen loading of 0.02 g N m^-2 d^-1, the Microcystis biomass in the water column decreased by 56.2% over a 4-day period. During the same period of time, the average sinking ratio was 0.23 d^-1; moreover, the termination of biomass growth was detected. At the notably higher nitrogen loading of 0.5 g N m^-2d^-1, the downward transport of biomass could still compensate for the biomass growth, although the average sinking ratio was lower at 0.16 d^-1. Additional laboratory culture experiments demonstrated that the increase in the downward transport of Microcystis occurred in parallel to an increase in the carbohydrate content and a decrease in gas vesicle content. Further proteomic analysis indicated that the carbohydrate accumulation induced by nitrogen deficiency was a result of the slowing down of catabolic consumption, especially the downregulation of glycolysis. Thus, our study suggests that increased intracellular carbohydrate accumulation at low nitrogen availability causes a higher sinking ratio of Microcystis, indicating that nitrogen limits the duration of Microcystis blooms; thus, decreased nitrogen availability may lead to increased sinking of biomass out of the water column, accelerating the dissipation of Microcystis blooms.

Single-Stage Astaxanthin Production Enhances the Nonmevalonate Pathway and Photosynthetic Central Metabolism in Synechococcus sp. PCC 7002

The natural pigment astaxanthin is widely used in aquaculture, pharmaceutical, nutraceutical, and cosmetic industries due to superior antioxidant properties. The green alga Haematococcus pluvialis is currently used for commercial production of astaxanthin pigment. However, slow growing H. pluvialis requires a complex two-stage stress-induced process with high light intensity leading to increased contamination risks. In contrast, the fast-growing euryhaline cyanobacterium Synechococcus sp. PCC 7002 (Synechococcus 7002) is able to reach high density under stress-free phototrophic conditions, and is therefore a promising metabolic engineering platform for astaxanthin production. In the present study, genes encoding β-carotene hydroxylase and β-carotene ketolase, from the marine bacterium Brevundimonas sp. SD212, are integrated into the endogenous plasmid of Synechococcus 7002, and then expressed to biosynthesize astaxanthin. Although Synechococcus 7002 does not inherently produce astaxanthin, the recombinant ZW strain yields 3 mg/g dry cell weight astaxanthin from CO₂ as the sole carbon source, with significantly higher astaxanthin content than previous cyanobacteria reports. Synechococcus 7002 astaxanthin productivity reached 3.35 mg/L/day after just 2 days in a continuous autotrophic process, which is comparable to the best H. pluvialis astaxanthin productivities when factoring in growth times. Metabolomics analysis reveals increases in fractions of hexose-, pentose-, and triose phosphates along with intermediates involved in the nonmevalonate pathway. Dynamic metabolomics analysis of ¹³C labeled metabolites clearly indicates flux enhancements in the Calvin cycle and glycolysis resulting from the overexpression of astaxanthin biosynthetic genes. This study suggests that cyanobacteria may enhance central metabolism as well as the nonmevalonate pathway in an attempt to replenish depleted pigments such as β-carotene and zeaxanthin.

Short-Term Temporal Metabolic Behavior in Halophilic Cyanobacterium Synechococcus sp. Strain PCC 7002 after Salt Shock

In response to salt stress, cyanobacteria increases the gene expression of Na⁺/H⁺ antiporter and K⁺ uptake system proteins and subsequently accumulate compatible solutes. However, alterations in the concentrations of metabolic intermediates functionally related to the early stage of the salt stress response have not been investigated. The halophilic cyanobacterium Synechococcus sp. PCC 7002 was subjected to salt shock with 0.5 and 1 M NaCl, then we performed metabolomics analysis by capillary electrophoresis/mass spectrometry (CE/MS) and gas chromatography/mass spectrometry (GC/MS) after cultivation for 1, 3, 10, and 24 h. Gene expression profiling using a microarray after 1 h of salt shock was also conducted. We observed suppression of the Calvin cycle and activation of glycolysis at both NaCl concentrations. However, there were several differences in the metabolic changes after salt shock following exposure to 0.5 M and 1 M NaCl: (i): the main compatible solute, glucosylglycerol, accumulated quickly at 0.5 M NaCl after 1 h but increased gradually for 10 h at 1 M NaCl; (ii) the oxidative pentose phosphate pathway and the tricarboxylic acid cycle were activated at 0.5 M NaCl; and (iii) the multi-functional compound spermidine greatly accumulated at 1 M NaCl. Our results show that Synechococcus sp. PCC 7002 acclimated to different levels of salt through a salt stress response involving the activation of different metabolic pathways.

Simple, fast and accurate method for the determination of glycogen in the model unicellular cyanobacterium Synechocystis sp. PCC 6803

Glycogen is a highly soluble branched polymer composed of glucose monomers linked by glycosidic bonds that represents, together with starch, one of the main energy storage compounds in living organisms. While starch is present in plant cells, glycogen is present in bacteria, protozoa, fungi and animal cells. Due to its essential function, it has been the subject of intense research for almost two centuries. Different procedures for the isolation and quantification of glycogen, according to the origin of the sample and/or the purpose of the study, have been reported in the literature. The objective of this study is to optimize the methodology for the determination of glycogen in cyanobacteria, as the interest in cyanobacterial glycogen has increased in recent years due to the biotechnological application of these microorganisms. In the present work, the methodology reported for the quantification of glycogen in cyanobacteria has been reviewed and an extensive empirical analysis has been performed showing how this methodology can be optimized significantly to reduce time and improve reliability and reproducibility. Based on these results, a simple and fast protocol for quantification of glycogen in the model unicellular cyanobacterium Synechocystis sp. PCC 6803 is presented, which could also be successfully adapted to other cyanobacteria.

Disruption of the Gene trx-m1 Impedes the Growth of Anabaena sp. PCC 7120 under Nitrogen Starvation

Cyanobacteria possess a sophisticated photosynthesis-based metabolism with admirable plasticity. This plasticity is possible via the deep regulation network, the thiol-redox regulations operated by thioredoxin (hereafter, Trx). In this context, we characterized the Trx-m1-deficient mutant strain of Anabaena sp., PCC 7120 (shortly named A.7120), cultivated under nitrogen limitation. Trx-m1 appears to coordinate the nitrogen response and its absence induces large changes in the proteome. Our data clearly indicate that Trx-m1 is crucial for the diazotrophic growth of A.7120. The lack of Trx-m1 resulted in a large differentiation of heterocysts (>20% of total cells), which were barely functional probably due to a weak expression of nitrogenase. In addition, heterocysts of the mutant strain did not display the usual cellular structure of nitrogen-fixative cells. This unveiled why the mutant strain was not able to grow under nitrogen starvation.

Production and structural characterization of a new type of polysaccharide from nitrogen-limited Arthrospira platensis cultivated in outdoor industrial-scale open raceway ponds

BACKGROUND

Carbohydrates are major biomass source in fuel-targeted biorefinery. Arthrospira platensis is the largest commercialized microalgae with good environmental tolerance and high biomass production. However, the traditional target of A. platensis cultivation is the protein, which is the downstream product of carbohydrates. Aiming to provide the alternative non-food carbohydrates source, the feasible manipulation technology on the cultivation is needed, as well as new separation methodology to achieve maximum utilization of overall biomass.

RESULTS

The present study aimed to demonstrate the feasibility of industrially producing carbohydrate-enriched A. platensis and characterize the structure of the polysaccharide involved. Cultivated in industrial-scale outdoor open raceway ponds under nitrogen limitation, A. platensis accumulated maximally 64.3%DW of carbohydrate. The maximum biomass and carbohydrate productivity reached 27.5 g m^-2 day^-1 and 26.2 g m^-2 day^-1, respectively. The efficient extraction and purification of the polysaccharides include a high-pressure homogenization-assisted hot water extraction followed by flocculation with a non-toxic flocculant ZTC1 + 1, with the polysaccharide purity and total recovery reaching 81% and 75%, respectively. The purified polysaccharide was mainly composed of (1→3)(1→4)- or (1→3)(1→2)-α-glucan with a molecular weight of 300-700 kDa, which differed from the commonly acknowledged glycogen.

CONCLUSIONS

By the way of controlled nitrogen limitation, the high carbohydrate production of A. platensis in the industrial scale was achieved. The α-glucan from A. platensis could be a potential glucose source for industrial applications. A non-toxic separation method of carbohydrate was applied to maintain the possibility of utilization of residue in high-value field.

Utilization of shrimp wastewater for poly-β-hydroxybutyrate production by Synechocystis sp. PCC 6803 strain ΔSphU cultivated in photobioreactor

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Shrimp wastewater is a rich source of P- and N-compounds suitable for cyanobacterial growth.

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Phosphate in shrimp wastewater can be efficiently removed by Synechocystis ΔSphU.

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ΔSphU accumulates high PHB with commercial value when shrimp wastewater contains low nitrate level.

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Shrimp wastewater can be used for biodegradable plastic production by cyanobacterial cell.

The wastewater discharge from the intensive shrimp aquaculture contains high concentration of nutrients, which can lead to eutrophication. This study aimed to reuse the shrimp wastewater for low cost cyanobacterial cultivation to produce biodegradable plastic poly-β-hydroxybutyrate (PHB). The Synechocystis sp. PCC 6803 (ΔSphU) lacking phosphate regulator (SphU) could utilize nutrients in shrimp wastewater for promoting biomass yield of 500 mg L⁻¹ after 14 days. The ΔSphU showed the highest phosphate uptake rate of 20.16 mggDw⁻¹d⁻¹ at the first day of photobioreactor running. In addition, the nutrient removal efficiencies were 96.99% for phosphate, 80.10% for nitrate, 67.90% for nitrite and 98.07% for ammonium. The reduction of nitrate in shrimp wastewater due to nitrogen assimilation could induce PHB accumulation in ΔSphU. The highest PHB content was 32.48% (w/w) DW, with the maximum PHB productivity of 12.73 mg L⁻¹d⁻¹. The produced PHB of ΔSphU had material properties similar to those of the commercial PHB.

Biophotovoltaics: Green Power Generation From Sunlight and Water

Biophotovoltaics is a relatively new discipline in microbial fuel cell research. The basic idea is the conversion of light energy into electrical energy using photosynthetic microorganisms. The microbes will use their photosynthetic apparatus and the incoming light to split the water molecule. The generated protons and electrons are harvested using a bioelectrochemical system. The key challenge is the extraction of electrons from the microbial electron transport chains into a solid-state anode. On the cathode, a corresponding electrochemical counter reaction will consume the protons and electrons, e.g., through the oxygen reduction to water, or hydrogen formation. In this review, we are aiming to summarize the current state of the art and point out some limitations. We put a specific emphasis on cyanobacteria, as these microbes are considered future workhorses for photobiotechnology and are currently the most widely applied microbes in biophotovoltaics research. Current progress in biophotovoltaics is limited by very low current outputs of the devices while a lack of comparability and standardization of the experimental set-up hinders a systematic optimization of the systems. Nevertheless, the fundamental questions of redox homeostasis in photoautotrophs and the potential to directly harvest light energy from a highly efficient photosystem, rather than through oxidation of inefficiently produced biomass are highly relevant aspects of biophotovoltaics.

Nitrogen limitation affects the sinking property of Microcystis by promoting carbohydrate accumulation

Nitrogen limitation has been proven to inhibit Microcystis proliferation, and the significant decline in Microcystis blooms in late summer or autumn has been considered to be related to the nitrogen depletion in water. Sinking loss is another factor that influences the dynamics of cyanobacteria in lakes. However, to date, it is still unclear how the sinking property of Microcystis responds to nitrogen availability. Our results suggest that nitrogen limitation would directly influence sinking property of Microcystis, through a significant increase in the specific density of cells. In the short term, carbohydrate accumulation was mainly responsible for the high specific density, showing a high correlation among the NO₃^--N concentration, specific density and carbohydrate content. Furthermore, carbohydrates could rapidly accumulate after one light/dark cycle, which was mainly due to the reduction in carbohydrate consumption in the darkness under nitrogen limitation. Under nitrogen-light coupling conditions, the specific density ranged from 1.060 to 1.068, except for the treatment with high-nitrogen plus low-light, which showed the value of 1.032. More importantly, when coupled with low nitrogen, the low light did not decrease the carbohydrate content and the specific density, which implied that the sinking cells could not migrate back to the surface. Accordingly, a hypothesis was proposed that the carbohydrate accumulation induced by low nitrogen availability caused an increase in specific density, which invalidates the buoyancy regulation, and cells sink continually out of the water column. This study explores a new understanding on the disappearance mechanisms of Microcystis blooms in the late summer and fall.

Increased flux in acetyl-CoA synthetic pathway and TCA cycle of Kluyveromyces marxianus under respiratory conditions

Yeasts are extremely useful, not only for fermentation but also for a wide spectrum of fuel and chemical productions. We analyzed the overall metabolic turnover and transcript dynamics in glycolysis and the TCA cycle, revealing the difference in adaptive pyruvate metabolic response between a Crabtree-negative species, Kluyveromyces marxianus, and a Crabtree-positive species, Saccharomyces cerevisiae, during aerobic growth. Pyruvate metabolism was inclined toward ethanol production under aerobic conditions in S. cerevisiae, while increased transcript abundances of the genes involved in ethanol metabolism and those encoding pyruvate dehydrogenase were seen in K. marxianus, indicating the augmentation of acetyl-CoA synthesis. Furthermore, different metabolic turnover in the TCA cycle was observed in the two species: malate and fumarate production in S. cerevisiae was higher than in K. marxianus, irrespective of aeration; however, fluxes of both the reductive and oxidative TCA cycles were enhanced in K. marxianus by aeration, implying both the cycles contribute to efficient electron flux without producing ethanol. Additionally, decreased hexokinase activity under aerobic conditions is expected to be important for maintenance of suitable carbon flux. These findings demonstrate differences in the key metabolic trait of yeasts employing respiration or fermentation, and provide important insight into the metabolic engineering of yeasts.

Carbon Fate and Flux in Prochlorococcus under Nitrogen Limitation

Primary production by Prochlorococcus, the smallest known free-living photosynthetic organism in terms of both physical and genomic size, is thought to have a significant role in global carbon cycles. Despite its small size and low growth rate, Prochlorococcus numerically dominates the phytoplankton community in the nutrient-poor oligotrophic ocean, the largest biome of the Earth's surface. How nutrient limitation, and nitrogen limitation in particular, affects the fate and flux of carbon fixed by Prochlorococcus is currently unknown. To address this gap in knowledge, we compared the bulk rates of photosynthesis and organic carbon release, the concentrations of intracellular metabolites, and the rates of assimilated carbon into the metabolite pools between replete and N-limited chemostat cultures. Total photosynthesis of our N-limited cultures was less than half of those observed in replete cultures, and nitrogen limitation also appears to cause a larger proportion of total fixed carbon to be released to the environment. Our data suggest this occurs in concert with the maintenance of large slow-moving pools of metabolites, including nitrogen-rich molecules such as glutamate. Additionally, we report field data suggesting metabolisms of Prochlorococcus are comparable to results we observe in our laboratory studies. Accounting for these observations, potential metabolic mechanisms utilized by Prochlorococcus are discussed as we build upon our understanding of nutrient-limited photosynthesis and carbon metabolism. IMPORTANCE Photosynthetic microbes are the predominant sources of organic carbon in the sunlit regions of the ocean. During photosynthesis, nitrogen and carbon metabolism are coordinated to synthesize nitrogen-containing organics such as amino acids and nucleic acids. In large regions of the ocean, nitrogen is thought to limit the growth of phytoplankton. The impact of nitrogen limitation on the synthesis of organic carbon is not well understood, especially for the most abundant photosynthetic organism in the nitrogen-limited regions of the ocean, Prochlorococcus. This study compares the carbon metabolism of nitrogen-replete and nitrogen-limited Prochlorococcus spp. to determine how nitrogen availability influences inorganic carbon assimilation into an organic form. Metabolomics and physiological data revealed that cells under nitrogen limitation have reduced metabolic flux and total carbon fixation rates while maintaining elevated metabolite pool levels and releasing a larger proportion of total fixed carbon to the environment.