scholarly journals Regulation of Autotrophic CO2 Fixation in the Archaeon Thermoproteus neutrophilus

2010 ◽  
Vol 192 (20) ◽  
pp. 5329-5340 ◽  
Author(s):  
W. Hugo Ramos-Vera ◽  
Valérie Labonté ◽  
Michael Weiss ◽  
Julia Pauly ◽  
Georg Fuchs
Keyword(s):  
Carbon Fixation ◽  
Protein A ◽  
Carbon Sources ◽  
Fumarate Hydratase ◽  
Central Carbon Metabolism ◽  
Gene Organization ◽  
Fumarate Reductase ◽  
Organic Substrates ◽  
Autotrophic Co2 Fixation ◽  
Whole Cells

ABSTRACT Thermoproteus neutrophilus, a hyperthermophilic, chemolithoautotrophic, anaerobic crenarchaeon, uses a novel autotrophic CO2 fixation pathway, the dicarboxylate/hydroxybutyrate cycle. The regulation of the central carbon metabolism was studied on the level of whole cells, enzyme activity, the proteome, transcription, and gene organization. The organism proved to be a facultative autotroph, which prefers organic acids as carbon sources that can easily feed into the metabolite pools of this cycle. Addition of the preferred carbon sources acetate, pyruvate, succinate, and 4-hydroxybutyrate to cultures resulted in stimulation of the growth rate and a diauxic growth response. The characteristic enzyme activities of the carbon fixation cycle, fumarate hydratase, fumarate reductase, succinyl coenzyme A (CoA) synthetase, and enzymes catalyzing the conversion of succinyl-CoA to crotonyl-CoA, were differentially downregulated in the presence of acetate and, to a lesser extent, in the presence of other organic substrates. This regulation pattern correlated well with the differential expression profile of the proteome as well as with the transcription of the encoding genes. The genes encoding phosphoenolpyruvate (PEP) carboxylase, fumarate reductase, and four enzymes catalyzing the conversion of succinyl-CoA to crotonyl-CoA are clustered. Two putative operons, one comprising succinyl-CoA reductase plus 4-hydroxybutyrate-CoA ligase genes and the other comprising 4-hydroxybutyryl-CoA dehydratase plus fumarate reductase genes, were divergently transcribed into leaderless mRNAs. The promoter regions were characterized and used for isolating DNA binding proteins. Besides an Alba protein, a 18-kDa protein characteristic for autotrophic Thermoproteales that bound specifically to the promoter region was identified. This system may be suitable for molecular analysis of the transcriptional regulation of autotrophy-related genes.

scholarly journals A Functional cra Gene Is Required forSalmonella enterica Serovar Typhimurium Virulence in BALB/c Mice

2000 ◽  
Vol 68 (6) ◽  
pp. 3772-3775 ◽  
Author(s):  
James H. Allen ◽  
Maryjane Utley ◽  
Han van den Bosch ◽  
Piet Nuijten ◽  
Maarten Witvliet ◽  
...  
Keyword(s):  
Carbon Metabolism ◽  
Salmonella Enterica ◽  
Protein A ◽  
Carbon Sources ◽  
Central Carbon Metabolism ◽  
Central Carbon ◽  
Serovar Typhimurium ◽  
Gluconeogenic Substrates

ABSTRACT A minitransposon mutant of Salmonella enterica serovar Typhimurium SR-11, SR-11 Fad−, is unable to utilize gluconeogenic substrates as carbon sources and is avirulent and immunogenic when administered perorally to BALB/c mice (M. J. Utley et al., FEMS Microbiol. Lett., 163:129–134, 1998). Here, evidence is presented that the mutation in SR-11 Fad− that renders the strain avirulent is in the cra gene, which encodes the Cra protein, a regulator of central carbon metabolism.

scholarly journals Autotrophic CO2 Fixation by Chloroflexus aurantiacus: Study of Glyoxylate Formation and Assimilation via the 3-Hydroxypropionate Cycle

2001 ◽  
Vol 183 (14) ◽  
pp. 4305-4316 ◽  
Author(s):  
Sylvia Herter ◽  
Jan Farfsing ◽  
Nasser Gad'On ◽  
Christoph Rieder ◽  
Wolfgang Eisenreich ◽  
...  
Keyword(s):  
Carbon Fixation ◽  
Calvin Cycle ◽  
Carbon Assimilation ◽  
Growth Conditions ◽  
Chloroflexus Aurantiacus ◽  
Acetyl Coa ◽  
Autotrophic Co2 Fixation ◽  
Whole Cells ◽  
Coa Transferase ◽  
Malonyl Coa

ABSTRACT In the facultative autotrophic organism Chloroflexus aurantiacus, a phototrophic green nonsulfur bacterium, the Calvin cycle does not appear to be operative in autotrophic carbon assimilation. An alternative cyclic pathway, the 3-hydroxypropionate cycle, has been proposed. In this pathway, acetyl coenzyme A (acetyl-CoA) is assumed to be converted to malate, and two CO2 molecules are thereby fixed. Malyl-CoA is supposed to be cleaved to acetyl-CoA, the starting molecule, and glyoxylate, the carbon fixation product. Malyl-CoA cleavage is shown here to be catalyzed by malyl-CoA lyase; this enzyme activity is induced severalfold in autotrophically grown cells. Malate is converted to malyl-CoA via an inducible CoA transferase with succinyl-CoA as a CoA donor. Some enzyme activities involved in the conversion of malonyl-CoA via 3-hydroxypropionate to propionyl-CoA are also induced under autotrophic growth conditions. So far, no clue as to the first step in glyoxylate assimilation has been obtained. One possibility for the assimilation of glyoxylate involves the conversion of glyoxylate to glycine and the subsequent assimilation of glycine. However, such a pathway does not occur, as shown by labeling of whole cells with [1,2-13C2]glycine. Glycine carbon was incorporated only into glycine, serine, and compounds that contained C1 units derived therefrom and not into other cell compounds.

scholarly journals Lokiarchaeon exhibits homoacetogenesis

2019 ◽  
Author(s):  
William D. Orsi ◽  
Aurèle Vuillemin ◽  
Paula Rodriguez ◽  
Ömer K. Coskun ◽  
Gonzalo V. Gomez-Saez ◽  
...  
Keyword(s):  
Gene Expression ◽  
Host Cell ◽  
Extracellular Polymeric Substances ◽  
Carbon Fixation ◽  
Carbon Sources ◽  
Stable Isotope Probing ◽  
Organic Substrates ◽  
Sugar Fermentation ◽  
Expression Of Genes ◽  
Wide Range

AbstractThe proposed Asgard superphylum of Archaea comprises the closest archaeal relatives of eukaryotes, whose genomes hold clues pertaining to the nature host cell that acquired the mitochondrion at the origin of eukaryotes1-4. Genomes of the Asgard candidate Phylum ‘Candidatus Lokiarchaeota’ [Lokiarchaeon] suggest an acetogenic H2 –dependent lifestyle5 and mixotrophic capabilities6. However, data on the activity of Lokiarchaeon are currently lacking, and the ecology of the host cell that acquired the mitochondrion is debated4,7. Here, we show that in anoxic marine sediments underlying highly productive waters on the Namibian continental shelf Lokiarchaeon gene expression increases with depth below the seafloor, and was significantly different across a redox gradient spanning hypoxic to sulfidic conditions. Notably, Lokiarchaeon increased expression of genes involved in growth, carbohydrate metabolism, and the H2-dependent Wood-Ljungdahl (WLP) carbon fixation pathway under the most reducing (sulfidic) conditions. Quantitative stable isotope probing experiments revealed multiple populations of Lokiarchaeota utilizing both CO2 and diatomaceous extracellular polymeric substances (dEPS) as carbon sources over a 10-day incubation under anoxic conditions. This apparent anaerobic mixotrophic metabolism was consistent with the expression of Lokiarchaeon genes involved in transport and fermentation of sugars and amino acids. Remarkably, several Asgard populations were more enriched with 13C-dEPS compared to the community average, indicating a preference for dEPS as a growth substrate. The qSIP and gene expression data indicate a metabolism of “Candidatus Lokiarchaeota” similar to that of sugar fermenting homoacetogenic bacteria8, namely that Lokiarchaeon can couple fermentative H2 production from organic substrates with electron bifurcation and the autotrophic and H2-dependent WLP. Homoacetogenesis allows to access a wide range of substrates and relatively high ATP gain during acetogenic sugar fermentation8 thereby providing an ecological advantage for Lokiarchaeon in anoxic, energy limited settings.

scholarly journals Coassimilation of Organic Substrates via the Autotrophic 3-Hydroxypropionate Bi-Cycle in Chloroflexus aurantiacus

2011 ◽  
Vol 77 (17) ◽  
pp. 6181-6188 ◽  
Author(s):  
Jan Zarzycki ◽  
Georg Fuchs
Keyword(s):  
Microbial Mats ◽  
Carbon Fixation ◽  
Glyoxylate Cycle ◽  
Cell Mass ◽  
Central Carbon Metabolism ◽  
Chloroflexus Aurantiacus ◽  
Organic Substrates ◽  
Fermentation Products ◽  
Photoautotrophic Growth ◽  
Content Type

ABSTRACTChloroflexus aurantiacusis a facultative autotrophic green nonsulfur bacterium that grows phototrophically in thermal springs and forms microbial mats with cyanobacteria. Cyanobacteria produce glycolate during the day (photorespiration) and excrete fermentation products at night.C. aurantiacususes the 3-hydroxypropionate bi-cycle for autotrophic carbon fixation. This pathway was thought to be also suited for the coassimilation of various organic substrates such as glycolate, acetate, propionate, 3-hydroxypropionate, lactate, butyrate, or succinate. To test this possibility, we added these compounds at a 5 mM concentration to autotrophically pregrown cells. Although the provided amounts of H2and CO2allowed continuing photoautotrophic growth, cells immediately consumed most substrates at rates equaling the rate of autotrophic carbon fixation. Using [14C]acetate, half of the labeled organic carbon was incorporated into cell mass. Our data suggest thatC. aurantiacususes the 3-hydroxypropionate bi-cycle, together with the glyoxylate cycle, to channel organic substrates into the central carbon metabolism. Enzyme activities of the 3-hydroxypropionate bi-cycle were marginally affected when cells were grown heterotrophically with such organic substrates. The 3-hydroxypropionate bi-cycle inChloroflexiis unique and was likely fostered in an environment in which traces of organic compounds can be coassimilated. Other bacteria living under oligotrophic conditions acquired genes of a rudimentary 3-hydroxypropionate bi-cycle, possibly for the same purpose. Examples areChloroherpeton thalassium,Erythrobactersp. strain NAP-1,Nitrococcus mobilis, and marine gammaproteobacteria of the OM60/NOR5 clade such asCongregibacter litoralis.

scholarly journals Modelization of Nutrient Removal Processes at a Large WWTP Using a Modified ASM2d Model

2018 ◽  
Vol 15 (12) ◽  
pp. 2817 ◽  
Author(s):  
Jakub Drewnowski ◽  
Jacek Makinia ◽  
Lukasz Kopec ◽  
Francisco-Jesus Fernandez-Morales
Keyword(s):  
Nutrient Removal ◽  
Carbon Sources ◽  
Oxygen Demand ◽  
Full Scale ◽  
Biological Nutrient Removal ◽  
Organic Substrates ◽  
Modified Model ◽  
Rate Limiting Step ◽  
Uptake Rates ◽  
Rate Limiting

The biodegradation of particulate substrates starts by a hydrolytic stage. Hydrolysis is a slow reaction and usually becomes the rate limiting step of the organic substrates biodegradation. The objective of this work was to evaluate a novel hydrolysis concept based on a modification of the activated sludge model (ASM2d) and to compare it with the original ASM2d model. The hydrolysis concept was developed in order to accurately predict the use of internal carbon sources in enhanced biological nutrient removal (BNR) processes at a full scale facility located in northern Poland. Both hydrolysis concepts were compared based on the accuracy of their predictions for the main processes taking place at a full-scale facility. From the comparison, it was observed that the modified ASM2d model presented similar predictions to those of the original ASM2d model on the behavior of chemical oxygen demand (COD), NH4-N, NO3-N, and PO4-P. However, the modified model proposed in this work yield better predictions of the oxygen uptake rate (OUR) (up to 5.6 and 5.7%) as well as in the phosphate release and uptake rates.

scholarly journals Freshwater Chlorobia Exhibit Metabolic Specialization among Cosmopolitan and Endemic Populations

mSystems ◽  
2021 ◽  
Vol 6 (3) ◽  
Author(s):  
Sarahi L. Garcia ◽  
Maliheh Mehrshad ◽  
Moritz Buck ◽  
Jackson M. Tsuji ◽  
Josh D. Neufeld ◽  
...  
Keyword(s):  
Carbon Fixation ◽  
Carbon Sources ◽  
Natural Populations ◽  
Freshwater Ecosystems ◽  
Electron Donors ◽  
Functional Ecology ◽  
Lake Ecosystems ◽  
Tropical Regions ◽  
Metabolic Versatility ◽  
Globally Distributed

ABSTRACT Photosynthetic bacteria from the class Chlorobia (formerly phylum Chlorobi) sustain carbon fixation in anoxic water columns. They harvest light at extremely low intensities and use various inorganic electron donors to fix carbon dioxide into biomass. Until now, most information on the functional ecology and local adaptations of Chlorobia members came from isolates and merely 26 sequenced genomes that may not adequately represent natural populations. To address these limitations, we analyzed global metagenomes to profile planktonic Chlorobia cells from the oxyclines of 42 freshwater bodies, spanning subarctic to tropical regions and encompassing all four seasons. We assembled and compiled over 500 genomes, including metagenome-assembled genomes (MAGs), single-amplified genomes (SAGs), and reference genomes from cultures, clustering them into 71 metagenomic operational taxonomic units (mOTUs or “species”). Of the 71 mOTUs, 57 were classified within the genus Chlorobium, and these mOTUs represented up to ∼60% of the microbial communities in the sampled anoxic waters. Several Chlorobium-associated mOTUs were globally distributed, whereas others were endemic to individual lakes. Although most clades encoded the ability to oxidize hydrogen, many lacked genes for the oxidation of specific sulfur and iron substrates. Surprisingly, one globally distributed Scandinavian clade encoded the ability to oxidize hydrogen, sulfur, and iron, suggesting that metabolic versatility facilitated such widespread colonization. Overall, these findings provide new insight into the biogeography of the Chlorobia and the metabolic traits that facilitate niche specialization within lake ecosystems. IMPORTANCE The reconstruction of genomes from metagenomes has helped explore the ecology and evolution of environmental microbiota. We applied this approach to 274 metagenomes collected from diverse freshwater habitats that spanned oxic and anoxic zones, sampling seasons, and latitudes. We demonstrate widespread and abundant distributions of planktonic Chlorobia-associated bacteria in hypolimnetic waters of stratified freshwater ecosystems and show they vary in their capacities to use different electron donors. Having photoautotrophic potential, these Chlorobia members could serve as carbon sources that support metalimnetic and hypolimnetic food webs.

Characterization of endoplasmic reticulum by co-localization of BiP and dicarbocyanine dyes

1992 ◽  
Vol 101 (2) ◽  
pp. 315-322 ◽  
Author(s):  
M. Terasaki ◽  
T.S. Reese
Keyword(s):  
Endoplasmic Reticulum ◽  
Cultured Cells ◽  
Protein A ◽  
Epithelial Cell Line ◽  
Cultured Fibroblasts ◽  
Whole Cells ◽  
Membrane Compartments ◽  
Immunoglobulin Binding Protein ◽  
Immunoglobulin Binding ◽  
Peripheral Regions

The original concept of endoplasmic reticulum derived from the observation of a reticular network in cultured fibroblasts by electron microscopy of whole cells. It was previously reported that the fluorescent dye, DiOC6(3), stains a similar network as well as mitochondria and other organelles in living cells. Here, we investigate the significance of the structures labeled by DiO6(3) in CV-1 cells, a monkey epithelial cell line. First, we show that the network stained in living CV-1 cells is preserved by glutaraldehyde fixation and then we co-label it with an antibody against BiP (immunoglobulin binding protein), a protein commonly accepted to be present in the endoplasmic reticulum. Anti-BiP labeled the same network as that labeled by DiOC6(3), so this network now is identified as being part of the endoplasmic reticulum. DiOC6(3) labels many other membrane compartments in addition to the endoplasmic reticulum. This, along with its lipophilic properties, suggests that DiOC6(3) stains all intracellular membranes. However, the extensive reticular network in the thin peripheral regions of cultured cells is easily distinguished from these other membranes. Thus, staining by DiOC6(3) is a useful method for localizing the endoplasmic reticulum, particularly in thin peripheral regions of cultured cells.

scholarly journals YvcK of Bacillus subtilis is required for a normal cell shape and for growth on Krebs cycle intermediates and substrates of the pentose phosphate pathway

Microbiology ◽  
2005 ◽  
Vol 151 (11) ◽  
pp. 3777-3791 ◽  
Author(s):  
Boris Görke ◽  
Elodie Foulquier ◽  
Anne Galinier
Keyword(s):  
Bacillus Subtilis ◽  
Pentose Phosphate Pathway ◽  
Carbon Metabolism ◽  
Carbon Sources ◽  
Krebs Cycle ◽  
Normal Growth ◽  
Central Carbon Metabolism ◽  
Pentose Phosphate ◽  
Homologous Protein ◽  
Krebs Cycle Intermediates

The HPr-like protein Crh has so far been detected only in the bacillus group of bacteria. In Bacillus subtilis, its gene is part of an operon composed of six ORFs, three of which exhibit strong similarity to genes of unknown function present in many bacteria. The promoter of the operon was determined and found to be constitutively active. A deletion analysis revealed that gene yvcK, encoded by this operon, is essential for growth on Krebs cycle intermediates and on carbon sources metabolized via the pentose phosphate pathway. In addition, cells lacking YvcK acquired media-dependent filamentous or L-shape-like aberrant morphologies. The presence of high magnesium concentrations restored normal growth and cell morphology. Furthermore, suppressor mutants cured from these growth defects appeared spontaneously with a high frequency. Such suppressing mutations were identified in a transposon mutagenesis screen and found to reside in seven different loci. Two of them mapped in genes of central carbon metabolism, including zwf, which encodes glucose-6-phosphate dehydrogenase and cggR, the product of which regulates the synthesis of glyceraldehyde-3-phosphate dehydrogenase. All these results suggest that YvcK has an important role in carbon metabolism, probably in gluconeogenesis required for the synthesis of cell wall precursor molecules. Interestingly, the Escherichia coli homologous protein, YbhK, can substitute for YvcK in B. subtilis, suggesting that the two proteins have been functionally conserved in these different bacteria.

scholarly journals Comparative metabolomics of Phialemonium curvatum as an omnipotent fungus cultivated on crude palm oil versus glucose

2020 ◽  
Vol 19 (1) ◽  
Author(s):  
Arief Izzairy Zamani ◽  
Susann Barig ◽  
Sarah Ibrahim ◽  
Hirzun Mohd. Yusof ◽  
Julia Ibrahim ◽  
...  
Keyword(s):  
Carbon Source ◽  
Organic Acids ◽  
Vegetable Oil ◽  
Carbon Metabolism ◽  
Sole Carbon Source ◽  
Carbon Sources ◽  
Tca Cycle ◽  
Central Carbon Metabolism ◽  
Targeted Metabolomics ◽  
Central Carbon

Abstract Background Sugars and triglycerides are common carbon sources for microorganisms. Nonetheless, a systematic comparative interpretation of metabolic changes upon vegetable oil or glucose as sole carbon source is still lacking. Selected fungi that can grow in acidic mineral salt media (MSM) with vegetable oil had been identified recently. Hence, this study aimed to investigate the overall metabolite changes of an omnipotent fungus and to reveal changes at central carbon metabolism corresponding to both carbon sources. Results Targeted and non-targeted metabolomics for both polar and semi-polar metabolites of Phialemonium curvatum AWO2 (DSM 23903) cultivated in MSM with palm oil (MSM-P) or glucose (MSM-G) as carbon sources were obtained. Targeted metabolomics on central carbon metabolism of tricarboxylic acid (TCA) cycle and glyoxylate cycle were analysed using LC–MS/MS-TripleQ and GC–MS, while untargeted metabolite profiling was performed using LC–MS/MS-QTOF followed by multivariate analysis. Targeted metabolomics analysis showed that glyoxylate pathway and TCA cycle were recruited at central carbon metabolism for triglyceride and glucose catabolism, respectively. Significant differences in organic acids concentration of about 4- to 8-fold were observed for citric acid, succinic acid, malic acid, and oxaloacetic acid. Correlation of organic acids concentration and key enzymes involved in the central carbon metabolism was further determined by enzymatic assays. On the other hand, the untargeted profiling revealed seven metabolites undergoing significant changes between MSM-P and MSM-G cultures. Conclusions Overall, this study has provided insights on the understanding on the effect of triglycerides and sugar as carbon source in fungi global metabolic pathway, which might become important for future optimization of carbon flux engineering in fungi to improve organic acids production when vegetable oil is applied as the sole carbon source.

scholarly journals Substrate-dependent CO2 fixation in heterotrophic bacteria revealed by stable isotope labelling

2020 ◽  
Vol 96 (6) ◽  
Author(s):  
Marina Spona-Friedl ◽  
Alexander Braun ◽  
Claudia Huber ◽  
Wolfgang Eisenreich ◽  
Christian Griebler ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Heterotrophic Bacteria ◽  
Tricarboxylic Acid Cycle ◽  
Carbon Sources ◽  
Organic Substrate ◽  
Gas Chromatography Mass Spectrometry ◽  
Logarithmic Phase ◽  
Natural Environments ◽  
Organic Substrates ◽  
Stable Isotope Labelling

ABSTRACT Virtually all heterotrophs incorporate carbon dioxide by anaplerotic fixation. Little explored, however, is the interdependency of pathways and rates of CO2fixation on the concurrent usage of organic substrate(s). Potentially, this could reveal which substrates out of a pool of dissolved organic carbon are utilised by environmental microorganisms. To explore this possibility, Bacillus subtilis W23 was grown in a minimal medium with normalised amounts of either glucose, lactate or malate as only organic substrates, each together with 1 g/L NaH13CO3. Incorporation of H13CO3− was traced by elemental analysis-isotope ratio mass spectrometry of biomass and gas chromatography-mass spectrometry of protein-derived amino acids. Until the late logarithmic phase, 13C incorporation into the tricarboxylic acid cycle increased with time and occurred via [4–13C]oxaloacetate formed by carboxylation of pyruvate. The levels of 13C incorporation were highest for growth on glucose and lowest on malate. Incorporation of 13C into gluconeogenesis products was mainly detected in the lactate and malate experiment, whereas glucose down-regulated this path. A proof-of-principle study with a natural groundwater community confirmed the ability to determine incorporation from H13CO3− by natural communities leading to specific labelling patterns. This underlines the potential of the labelling approach to characterise carbon sources of heterotrophic microorganisms in their natural environments.

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