scholarly journals Top-down, knowledge-based genetic reduction of yeast central carbon metabolism

2021 ◽  
Author(s):  
Eline Postma ◽  
luuk Couwenberg ◽  
Roderick N. Van Roosmalen ◽  
Jordi Geelhoed ◽  
Philip de Groot ◽  
...  
Keyword(s):  
Carbon Metabolism ◽  
Large Scale ◽  
Tricarboxylic Acid Cycle ◽  
Synthetic Medium ◽  
Central Carbon Metabolism ◽  
Genetic Redundancy ◽  
Genetic Complexity ◽  
Wide Range ◽  
Central Carbon ◽  
Yeast Genes

Saccharomyces cerevisiae, whose evolutionary past includes a whole-genome duplication event, is characterised by a mosaic genome configuration with substantial apparent genetic redundancy. This apparent redundancy raises questions about the evolutionary driving force for genomic fixation of minor paralogs and complicates modular and combinatorial metabolic engineering strategies. While isoenzymes might be important in specific environments, they could be dispensable in controlled laboratory or industrial contexts. The present study explores the extent to which the genetic complexity of the central carbon metabolism (CCM) in S. cerevisiae, here defined as the combination of glycolysis, pentose phosphate pathway, tricarboxylic acid cycle and a limited number of related pathways and reactions, can be reduced by elimination of (iso)enzymes without major negative impacts on strain physiology. Cas9-mediated, groupwise deletion of 35 from the 111 genes yielded a minimal CCM strain, which despite the elimination of 32 % of CCM-related proteins, showed only a minimal change in phenotype on glucose-containing synthetic medium in controlled bioreactor cultures relative to a congenic reference strain. Analysis under a wide range of other growth and stress conditions revealed remarkably few phenotypic changes of the reduction of genetic complexity. Still, a well-documented context-dependent role of GPD1 in osmotolerance was confirmed. The minimal CCM strain provides a model system for further research into genetic redundancy of yeast genes and a platform for strategies aimed at large-scale, combinatorial remodelling of yeast CCM.

scholarly journals HexR Controls Glucose-Responsive Genes and Central Carbon Metabolism in Neisseria meningitidis

2015 ◽  
Vol 198 (4) ◽  
pp. 644-654 ◽  
Author(s):  
Ana Antunes ◽  
Giacomo Golfieri ◽  
Francesca Ferlicca ◽  
Marzia M. Giuliani ◽  
Vincenzo Scarlato ◽  
...  
Keyword(s):  
Energy Metabolism ◽  
Neisseria Meningitidis ◽  
Microarray Analysis ◽  
Carbon Metabolism ◽  
Tricarboxylic Acid Cycle ◽  
Transcriptional Regulator ◽  
Central Carbon Metabolism ◽  
Binding Motif ◽  
Content Type ◽  
Central Carbon

ABSTRACTNeisseria meningitidis, an exclusively human pathogen and the leading cause of bacterial meningitis, must adapt to different host niches during human infection.N. meningitidiscan utilize a restricted range of carbon sources, including lactate, glucose, and pyruvate, whose concentrations vary in host niches. Microarray analysis ofN. meningitidisgrown in a chemically defined medium in the presence or absence of glucose allowed us to identify genes regulated by carbon source availability. Most such genes are implicated in energy metabolism and transport, and some are implicated in virulence. In particular, genes involved in glucose catabolism were upregulated, whereas genes involved in the tricarboxylic acid cycle were downregulated. Several genes encoding surface-exposed proteins, including the MafA adhesins andNeisseriasurface protein A, were upregulated in the presence of glucose. Our microarray analysis led to the identification of a glucose-responsivehexR-like transcriptional regulator that controls genes of the central carbon metabolism ofN. meningitidisin response to glucose. We characterized the HexR regulon and showed that thehexRgene is accountable for some of the glucose-responsive regulation;in vitroassays with the purified protein showed that HexR binds to the promoters of the central metabolic operons of the bacterium. Based on DNA sequence alignment of the target sites, we propose a 17-bp pseudopalindromic consensus HexR binding motif. Furthermore,N. meningitidisstrains lackinghexRexpression were deficient in establishing successful bacteremia in an infant rat model of infection, indicating the importance of this regulator for the survival of this pathogenin vivo.IMPORTANCENeisseria meningitidisgrows on a limited range of nutrients during infection. We analyzed the gene expression ofN. meningitidisin response to glucose, the main energy source available in human blood, and we found that glucose regulates many genes implicated in energy metabolism and nutrient transport, as well as some implicated in virulence. We identified and characterized a transcriptional regulator (HexR) that controls metabolic genes ofN. meningitidisin response to glucose. We generated a mutant lacking HexR and found that the mutant was impaired in causing systemic infection in animal models. SinceN. meningitidislacks known bacterial regulators of energy metabolism, our findings suggest that HexR plays a major role in its biology by regulating metabolism in response to environmental signals.

scholarly journals Flor yeasts rewire the central carbon metabolism during wine alcoholic fermentation

2021 ◽  
Author(s):  
Emilien Peltier ◽  
Charlotte Vion ◽  
Omar Abou Saada ◽  
Anne Friedrich ◽  
Joseph Schacherer ◽  
...  
Keyword(s):  
Carbon Metabolism ◽  
Parental Strain ◽  
Tricarboxylic Acid Cycle ◽  
Phenotypic Variability ◽  
Central Carbon Metabolism ◽  
Metabolic Adaptation ◽  
Flor Yeast ◽  
Central Carbon ◽  
Flor Yeasts ◽  
Allelic Variations

AbstractThe identification of natural allelic variations controlling quantitative traits could contribute to decipher metabolic adaptation mechanisms within different populations of the same species. Such variations could result from man-mediated selection pressures and participate to the domestication. In this study, the genetic causes of the phenotypic variability of the central carbon metabolism Saccharomyces cerevisiae were investigated in the context of the enological fermentation. Carbon dioxide and glycerol production as well as malic acid consumption modulate the fermentation yield revealing a high level of genetic complexity. Their genetic determinism was found out by a multi environment QTL mapping approach allowing the identification of 14 quantitative trait loci from which 8 of them were validated down to the gene level by genetic engineering. Most of the validated genes had allelic variations involving flor yeast specific alleles. Those alleles were brought in the offspring by one parental strain that is closely related to the flor yeast genetic group while the second parental strain is part of the wine group. The causative genes identified are functionally linked to quantitative proteomic variations that would explain divergent metabolic features of wine and flor yeasts involving the tricarboxylic acid cycle (TCA), the glyoxylate shunt and the homeostasis of proton and redox cofactors. Overall, this work led to the identification of genetic factors that are hallmarks of adaptive divergence between flor yeast and wine yeast in the wine biotope. These alleles can also be used in the context of yeast selection to improve oenological traits linked to fermentation yield.

scholarly journals Modifying the Cyanobacterial Metabolism as a Key to Efficient Biopolymer Production in Photosynthetic Microorganisms

2020 ◽  
Vol 21 (19) ◽  
pp. 7204
Author(s):  
Maciej Ciebiada ◽  
Katarzyna Kubiak ◽  
Maurycy Daroch
Keyword(s):  
Carbon Metabolism ◽  
Extracellular Polymeric Substances ◽  
Carbon Fixation ◽  
Tricarboxylic Acid Cycle ◽  
Central Carbon Metabolism ◽  
Efficient Production ◽  
Heterotrophic Microorganisms ◽  
Central Carbon ◽  
Polymeric Compounds ◽  
Metabolic Properties

Cyanobacteria are photoautotrophic bacteria commonly found in the natural environment. Due to the ecological benefits associated with the assimilation of carbon dioxide from the atmosphere and utilization of light energy, they are attractive hosts in a growing number of biotechnological processes. Biopolymer production is arguably one of the most critical areas where the transition from fossil-derived chemistry to renewable chemistry is needed. Cyanobacteria can produce several polymeric compounds with high applicability such as glycogen, polyhydroxyalkanoates, or extracellular polymeric substances. These important biopolymers are synthesized using precursors derived from central carbon metabolism, including the tricarboxylic acid cycle. Due to their unique metabolic properties, i.e., light harvesting and carbon fixation, the molecular and genetic aspects of polymer biosynthesis and their relationship with central carbon metabolism are somehow different from those found in heterotrophic microorganisms. A greater understanding of the processes involved in cyanobacterial metabolism is still required to produce these molecules more efficiently. This review presents the current state of the art in the engineering of cyanobacterial metabolism for the efficient production of these biopolymers.

scholarly journals Biochemical unity revisited: microbial central carbon metabolism holds new discoveries, multi-tasking pathways, and redundancies with a reason

2020 ◽  
Vol 401 (12) ◽  
pp. 1429-1441
Author(s):  
Lennart Schada von Borzyskowski ◽  
Iria Bernhardsgrütter ◽  
Tobias J. Erb
Keyword(s):  
Carbon Metabolism ◽  
Metabolic Pathways ◽  
Central Carbon Metabolism ◽  
Genetic Redundancy ◽  
Acetyl Coa ◽  
Central Carbon ◽  
Long Time ◽  
Biochemical Research ◽  
Biochemical Diversity ◽  
Central Reaction

AbstractFor a long time, our understanding of metabolism has been dominated by the idea of biochemical unity, i.e., that the central reaction sequences in metabolism are universally conserved between all forms of life. However, biochemical research in the last decades has revealed a surprising diversity in the central carbon metabolism of different microorganisms. Here, we will embrace this biochemical diversity and explain how genetic redundancy and functional degeneracy cause the diversity observed in central metabolic pathways, such as glycolysis, autotrophic CO2 fixation, and acetyl-CoA assimilation. We conclude that this diversity is not the exception, but rather the standard in microbiology.

scholarly journals Flor Yeasts Rewire the Central Carbon Metabolism During Wine Alcoholic Fermentation

2021 ◽  
Vol 2 ◽  
Author(s):  
Emilien Peltier ◽  
Charlotte Vion ◽  
Omar Abou Saada ◽  
Anne Friedrich ◽  
Joseph Schacherer ◽  
...  
Keyword(s):  
Carbon Metabolism ◽  
Tricarboxylic Acid Cycle ◽  
Phenotypic Variability ◽  
Central Carbon Metabolism ◽  
Genetic Group ◽  
Metabolic Adaptation ◽  
Flor Yeast ◽  
Central Carbon ◽  
Flor Yeasts ◽  
Allelic Variations

The identification of natural allelic variations controlling quantitative traits could contribute to decipher metabolic adaptation mechanisms within different populations of the same species. Such variations could result from human-mediated selection pressures and participate to the domestication. In this study, the genetic causes of the phenotypic variability of the central carbon metabolism of Saccharomyces cerevisiae were investigated in the context of the enological fermentation. The genetic determinism of this trait was found out by a quantitative trait loci (QTL) mapping approach using the offspring of two strains belonging to the wine genetic group of the species. A total of 14 QTL were identified from which 8 were validated down to the gene level by genetic engineering. The allelic frequencies of the validated genes within 403 enological strains showed that most of the validated QTL had allelic variations involving flor yeast specific alleles. Those alleles were brought in the offspring by one parental strain that contains introgressions from the flor yeast genetic group. The causative genes identified are functionally linked to quantitative proteomic variations that would explain divergent metabolic features of wine and flor yeasts involving the tricarboxylic acid cycle (TCA), the glyoxylate shunt and the homeostasis of proton and redox cofactors. Overall, this work led to the identification of genetic factors that are hallmarks of adaptive divergence between flor yeast and wine yeast in the wine biotope. These results also reveal that introgressions originated from intraspecific hybridization events promoted phenotypic variability of carbon metabolism observed in wine strains.

Lighting Up Live-Cell and In Vivo Central Carbon Metabolism with Genetically Encoded Fluorescent Sensors

2020 ◽  
Vol 13 (1) ◽  
pp. 293-314 ◽  
Author(s):  
Zhuo Zhang ◽  
Xiawei Cheng ◽  
Yuzheng Zhao ◽  
Yi Yang
Keyword(s):  
Carbon Metabolism ◽  
Tricarboxylic Acid Cycle ◽  
Cell Metabolism ◽  
Central Carbon Metabolism ◽  
Fluorescent Sensors ◽  
Pentose Phosphate ◽  
Spatiotemporal Information ◽  
Extant Species ◽  
Central Carbon

As the core component of cell metabolism, central carbon metabolism, consisting of glycolysis, the pentose phosphate pathway, and the tricarboxylic acid cycle converts nutrients into metabolic precursors for biomass and energy to sustain the life of virtually all extant species. The metabolite levels or distributions in central carbon metabolism often change dynamically with cell fates, development, and disease progression. However, traditional biochemical methods require cell lysis, making it challenging to obtain spatiotemporal information about metabolites in living cells and in vivo. Genetically encoded fluorescent sensors allow the rapid, sensitive, specific, and real-time readout of metabolite dynamics in living organisms, thereby offering the potential to fill the gap in current techniques. In this review, we introduce recent progress made in the development of genetically encoded fluorescent sensors for central carbon metabolism and discuss their advantages, disadvantages, and applications. Moreover, several future directions of metabolite sensors are also proposed.

scholarly journals Activation of the NRF2 antioxidant program generates an imbalance in central carbon metabolism in cancer

eLife ◽  
2017 ◽  
Vol 6 ◽  
Author(s):  
Volkan I Sayin ◽  
Sarah E LeBoeuf ◽  
Simranjit X Singh ◽  
Shawn M Davidson ◽  
Douglas Biancur ◽  
...  
Keyword(s):  
Cancer Cells ◽  
Carbon Metabolism ◽  
Human Cancer ◽  
Tricarboxylic Acid Cycle ◽  
Central Carbon Metabolism ◽  
Metabolic Demand ◽  
Human Cancer Cells ◽  
Central Carbon ◽  
Metabolic Imbalance

During tumorigenesis, the high metabolic demand of cancer cells results in increased production of reactive oxygen species. To maintain oxidative homeostasis, tumor cells increase their antioxidant production through hyperactivation of the NRF2 pathway, which promotes tumor cell growth. Despite the extensive characterization of NRF2-driven metabolic rewiring, little is known about the metabolic liabilities generated by this reprogramming. Here, we show that activation of NRF2, in either mouse or human cancer cells, leads to increased dependency on exogenous glutamine through increased consumption of glutamate for glutathione synthesis and glutamate secretion by xc- antiporter system. Together, this limits glutamate availability for the tricarboxylic acid cycle and other biosynthetic reactions creating a metabolic bottleneck. Cancers with genetic or pharmacological activation of the NRF2 antioxidant pathway have a metabolic imbalance between supporting increased antioxidant capacity over central carbon metabolism, which can be therapeutically exploited.

scholarly journals Flavin-Containing Monooxygenases Are Conserved Regulators of Stress Resistance and Metabolism

2021 ◽  
Vol 9 ◽  
Author(s):  
Shijiao Huang ◽  
Marshall B. Howington ◽  
Craig J. Dobry ◽  
Charles R. Evans ◽  
Scott F. Leiser
Keyword(s):  
Stress Resistance ◽  
Mitochondrial Respiration ◽  
Carbon Metabolism ◽  
Central Carbon Metabolism ◽  
Cellular Mechanisms ◽  
Wide Range ◽  
Central Carbon ◽  
Endogenous Role ◽  
Cellular Metabolic Activity ◽  
Metabolic Activities

Flavin-Containing Monooxygenases are conserved xenobiotic-detoxifying enzymes. Recent studies have revealed endogenous functions of FMOs in regulating longevity in Caenorhabditis elegans and in regulating aspects of metabolism in mice. To explore the cellular mechanisms of FMO’s endogenous function, here we demonstrate that all five functional mammalian FMOs may play similar endogenous roles to improve resistance to a wide range of toxic stresses in both kidney and liver cells. We further find that stress-activated c-Jun N-terminal kinase activity is enhanced in FMO-overexpressing cells, which may lead to increased survival under stress. Furthermore, FMO expression modulates cellular metabolic activity as measured by mitochondrial respiration, glycolysis, and metabolomics analyses. FMO expression augments mitochondrial respiration and significantly changes central carbon metabolism, including amino acid and energy metabolism pathways. Together, our findings demonstrate an important endogenous role for the FMO family in regulation of cellular stress resistance and major cellular metabolic activities including central carbon metabolism.

scholarly journals Proteomic and biochemical responses to different concentrations of CO2 suggest the existence of multiple carbon metabolism strategies in Phaeodactylum tricornutum

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Songcui Wu ◽  
Wenhui Gu ◽  
Shuao Jia ◽  
Lepu Wang ◽  
Lijun Wang ◽  
...  
Keyword(s):  
Carbon Metabolism ◽  
Phaeodactylum Tricornutum ◽  
Carbon Fixation ◽  
Urea Cycle ◽  
Tricarboxylic Acid Cycle ◽  
Central Carbon Metabolism ◽  
Protein Abundance ◽  
Photosynthetic Pathway ◽  
Central Carbon ◽  
Related Proteins

Abstract Background Diatoms are well known for high photosynthetic efficiency and rapid growth rate, which are not only important oceanic primary producer, but also ideal feedstock for microalgae industrialization. Their high success is mainly due to the rapid response of photosynthesis to inorganic carbon fluctuations. Thus, an in-depth understanding of the photosynthetic carbon fixation mechanism of diatoms will be of great help to microalgae-based applications. This work directed toward the analysis of whether C4 photosynthetic pathway functions in the model marine diatom Phaeodactylum tricornutum, which possesses biophysical CO2-concentrating mechanism (CCM) as well as metabolic enzymes potentially involved in C4 photosynthetic pathway. Results For P. tricornutum, differential proteome, enzyme activities and transcript abundance of carbon metabolism-related genes especially biophysical and biochemical CCM-related genes in response to different concentrations of CO2 were tracked in this study. The upregulated protein abundance of a carbonic anhydrases and a bicarbonate transporter suggested biophysical CCM activated under low CO2 (LC). The upregulation of a number of key C4-related enzymes in enzymatic activity, transcript and protein abundance under LC indicated the induction of a mitochondria-mediated CCM in P. tricornutum. Moreover, protein abundance of a number of glycolysis, tricarboxylic acid cycle, photorespiration and ornithine–urea cycle related proteins upregulated under LC, while numbers of proteins involved in the Calvin cycle and pentose phosphate pathway were downregulated. Under high CO2 (HC), protein abundance of most central carbon metabolism and photosynthesis-related proteins were upregulated. Conclusions The proteomic and biochemical responses to different concentrations of CO2 suggested multiple carbon metabolism strategies exist in P. tricornutum. Namely, LC might induce a mitochondrial-mediated C4-like CCM and the improvement of glycolysis, tricarboxylic acid cycle, photorespiration and ornithine–urea cycle activity contribute to the energy supply and carbon and nitrogen recapture in P. tricornutum to cope with the CO2 limitation, while P. tricornutum responds to the HC environment by improving photosynthesis and central carbon metabolism activity. These findings can not only provide evidences for revealing the global picture of biophysical and biochemical CCM in P. tricornutum, but also provide target genes for further microalgal strain modification to improve carbon fixation and biomass yield in algal-based industry.

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