scholarly journals Kinetics of the ancestral carbon metabolism pathways in deep-branching bacteria and archaea

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Tomonari Sumi ◽  
Kouji Harada
Keyword(s):  
Carbon Metabolism ◽  
Carbon Fixation ◽  
Citrate Synthase ◽  
Tricarboxylic Acid Cycle ◽  
Necessary Condition ◽  
Last Universal Common Ancestor ◽  
Universal Common Ancestor ◽  
Biomass Components ◽  
Kinetics Of ◽  
Reductive Tricarboxylic Acid Cycle

AbstractThe origin of life is believed to be chemoautotrophic, deriving all biomass components from carbon dioxide, and all energy from inorganic redox couples in the environment. The reductive tricarboxylic acid cycle (rTCA) and the Wood–Ljungdahl pathway (WL) have been recognized as the most ancient carbon fixation pathways. The rTCA of the chemolithotrophic Thermosulfidibacter takaii, which was recently demonstrated to take place via an unexpected reverse reaction of citrate synthase, was reproduced using a kinetic network model, and a competition between reductive and oxidative fluxes on rTCA due to an acetyl coenzyme A (ACOA) influx upon acetate uptake was revealed. Avoiding ACOA direct influx into rTCA from WL is, therefore, raised as a kinetically necessary condition to maintain a complete rTCA. This hypothesis was confirmed for deep-branching bacteria and archaea, and explains the kinetic factors governing elementary processes in carbon metabolism evolution from the last universal common ancestor.

scholarly journals Investigation of Carbon Metabolism in “Dehalococcoides ethenogenes” Strain 195 by Use of Isotopomer and Transcriptomic Analyses

2009 ◽  
Vol 191 (16) ◽  
pp. 5224-5231 ◽  
Author(s):  
Yinjie J. Tang ◽  
Shan Yi ◽  
Wei-Qin Zhuang ◽  
Stephen H. Zinder ◽  
Jay D. Keasling ◽  
...  
Keyword(s):  
Genome Annotation ◽  
Carbon Fixation ◽  
Coenzyme A ◽  
Citrate Synthase ◽  
Tricarboxylic Acid Cycle ◽  
Acetyl Coa ◽  
Experimental Conditions ◽  
Acetyl Coenzyme A ◽  
Acetyl Coenzyme ◽  
Dehalococcoides Ethenogenes

ABSTRACT Members of the genus “Dehalococcoides” are the only known microorganisms that can completely dechlorinate tetrachloroethene and trichloroethene to the innocuous end product, ethene. This study examines the central metabolism in “Dehalococcoides ethenogenes” strain 195 via 13C-labeled tracer experiments. Supported by the genome annotation and the transcript profile, isotopomer analysis of key metabolites clarifies ambiguities in the genome annotation and identifies an unusual biosynthetic pathway in strain 195. First, the 13C-labeling studies revealed that strain 195 contains complete amino acid biosynthesis pathways, even though current genome annotation suggests that several of these pathways are incomplete. Second, the tricarboxylic acid cycle of strain 195 is confirmed to be branched, and the Wood-Ljungdahl carbon fixation pathway is shown to not be functionally active under our experimental conditions; rather, CO2 is assimilated via two reactions, conversion of acetyl-coenzyme A (acetyl coenzyme A [acetyl-CoA]) to pyruvate catalyzed by pyruvate synthase (DET0724-0727) and pyruvate conversion to oxaloacetate via pyruvate carboxylase (DET0119-0120). Third, the 13C-labeling studies also suggested that isoleucine is synthesized from acetyl-CoA and pyruvate via citramalate synthase (CimA, EC 2.3.1.182), rather than from the common pathway via threonine ammonia-lyase (EC 4.3.1.19). Finally, evidence is presented that strain 195 may contain an undocumented citrate synthase (>95% Re-type stereospecific), i.e., a novel Re-citrate synthase that is apparently different from the one recently reported in Clostridium kluyveri.

scholarly journals Systems-informed genome mining for electroautotrophic microbial production

2020 ◽  
Author(s):  
Anthony J. Abel ◽  
Jacob M. Hilzinger ◽  
Adam P. Arkin ◽  
Douglas S. Clark
Keyword(s):  
Carbon Fixation ◽  
Microbial Respiration ◽  
Tricarboxylic Acid Cycle ◽  
Genome Mining ◽  
Tricarboxylic Acid ◽  
Nitrate Respiration ◽  
Fixation Rate ◽  
Acid Cycle ◽  
Carbon Molecules ◽  
Reductive Tricarboxylic Acid Cycle

AbstractMicrobial electrosynthesis (MES) systems can store renewable energy and CO2 in many-carbon molecules inaccessible to abiotic electrochemistry. Here, we develop a multiphysics model to investigate the fundamental and practical limits of MES enabled by direct electron uptake and we identify organisms in which this biotechnological CO2-fixation strategy can be realized. Systematic model comparisons of microbial respiration and carbon fixation strategies revealed that, under aerobic conditions, the CO2 fixation rate is limited to <6 μmol/cm2/hr by O2 mass transport despite efficient electron utilization. In contrast, anaerobic nitrate respiration enables CO2 fixation rates >50 μmol/cm2/hr for microbes using the reductive tricarboxylic acid cycle. Phylogenetic analysis, validated by recapitulating experimental demonstrations of electroautotrophy, uncovered multiple probable electroautotrophic organisms and a significant number of genetically tractable strains that require heterologous expression of <5 proteins to gain electroautotrophic function. The model and analysis presented here will guide microbial engineering and reactor design for practical MES systems.

scholarly journals Metals enable a non-enzymatic acetyl CoA pathway

2017 ◽  
Author(s):  
Sreejith J. Varma ◽  
Kamila B. Muchowska ◽  
Paul Chatelain ◽  
Joseph Moran
Keyword(s):  
Carbon Fixation ◽  
Acid Synthesis ◽  
Last Universal Common Ancestor ◽  
Amino Acid Synthesis ◽  
Evolutionary Origins ◽  
Universal Common Ancestor ◽  
Wide Range ◽  
Biological Conversion ◽  
Acetyl Coa Pathway ◽  
Late Invention

The evolutionary origins of carbon fixation, the biological conversion of CO2to metabolites, remain unclear. Phylogenetics indicates that the AcCoA pathway, the reductive fixation of CO2to acetyl and pyruvate, was a key biosynthetic route used by the Last Universal Common Ancestor (LUCA) to build its biochemistry. However, debate exists over whether CO2fixation is a relatively late invention of pre-LUCA evolution or whether it dates back to prebiotic chemistry. Here we show that zero-valent forms of the transition metals known to act as co-factors in the AcCoA pathway (Fe0, Ni0, Co0) fix CO2on their surface in a manner closely resembling the biological pathway, producing acetate and pyruvate in near mM concentrations following cleavage from the surface. The reaction is robust over a wide range of temperatures and pressures with acetate and pyruvate constituting the major products in solution at 1 bar of CO2and 30 °g;C. The discovered conditions also promote 7 of the 11 steps of the rTCA cycle and amino acid synthesis, providing a stunning direct connection between simple inorganic chemistry and ancient CO2-fixation pathways. The results strongly sup-port the notion that CO2-fixation pathways are an outgrowth of spontaneous geochemistry.

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.

Oxaloacetate-to-malate conversion by mineral photoelectrochemistry: implications for the viability of the reductive tricarboxylic acid cycle in prebiotic chemistry

2008 ◽  
Vol 7 (3-4) ◽  
pp. 271-278 ◽  
Author(s):  
Marcelo I. Guzman ◽  
Scot T. Martin
Keyword(s):  
Tricarboxylic Acid Cycle ◽  
Tricarboxylic Acid ◽  
Forward Rate ◽  
Early Earth ◽  
Arrhenius Behavior ◽  
Dependent Rate ◽  
High Viability ◽  
Increasing Temperature ◽  
Kinetics Of ◽  
Reductive Tricarboxylic Acid Cycle

AbstractThe carboxylic acids produced by the reductive tricarboxylic acid (rTCA) cycle are possibly a biosynthetic core of initial life, although several steps such as the reductive kinetics of oxaloacetate (OAA) to malate (MA) are problematic by conventional chemical routes. In this context, we studied the kinetics of this reaction as promoted by ZnS mineral photoelectrochemistry. The quantum efficiency φMA of MA production from the photoelectrochemical reduction of OAA followed φMA=0.13 [OAA] (2.1×10−3+[OAA])−1 and was independent of temperature (5 to 50°C). To evaluate the importance of this forward rate under a prebiotic scenario, we also studied the temperature-dependent rate of the backward thermal decarboxylation of OAA to pyruvate (PA), which followed an Arrhenius behavior as log (k−2)=11.74–4956/T, where k−2 is in units of s−1. These measured rates were employed in conjunction with the indirectly estimated carboxylation rate of PA to OAA to assess the possible importance of mineral photoelectrochemistry in the conversion of OAA to MA under several scenarios of prebiotic conditions on early Earth. As an example, our analysis shows that there is 90% efficiency with a forward velocity of 3 yr/cycle for the OAA→MA step of the rTCA cycle at 280 K. Efficiency and velocity both decrease for increasing temperature. These results suggest high viability for mineral photoelectrochemistry as an enzyme-free engine to drive the rTCA cycle through the early aeons of early Earth, at least for the investigated OAA→MA step.

scholarly journals Autotrophic and mixotrophic metabolism of an anammox bacterium revealed by in vivo 13C and 2H metabolic network mapping

2020 ◽  
Author(s):  
Christopher E. Lawson ◽  
Guylaine H. L. Nuijten ◽  
Rob M. de Graaf ◽  
Tyler B. Jacobson ◽  
Martin Pabst ◽  
...  
Keyword(s):  
Carbon Metabolism ◽  
Metabolic Networks ◽  
Metabolic Flux ◽  
Citrate Synthase ◽  
Side Population ◽  
Tricarboxylic Acid Cycle ◽  
Anammox Bacteria ◽  
Flux Analysis ◽  
Anammox Bacterium

Abstract Anaerobic ammonium-oxidizing (anammox) bacteria mediate a key step in the biogeochemical nitrogen cycle and have been applied worldwide for the energy-efficient removal of nitrogen from wastewater. However, outside their core energy metabolism, little is known about the metabolic networks driving anammox bacterial anabolism and use of different carbon and energy substrates beyond genome-based predictions. Here, we experimentally resolved the central carbon metabolism of the anammox bacterium Candidatus ‘Kuenenia stuttgartiensis’ using time-series 13C and 2H isotope tracing, metabolomics, and isotopically nonstationary metabolic flux analysis. Our findings confirm predicted metabolic pathways used for CO2 fixation, central metabolism, and amino acid biosynthesis in K. stuttgartiensis, and reveal several instances where genomic predictions are not supported by in vivo metabolic fluxes. This includes the use of the oxidative branch of an incomplete tricarboxylic acid cycle for alpha-ketoglutarate biosynthesis, despite the genome not having an annotated citrate synthase. We also demonstrate that K. stuttgartiensis is able to directly assimilate extracellular formate via the Wood–Ljungdahl pathway instead of oxidizing it completely to CO2 followed by reassimilation. In contrast, our data suggest that K. stuttgartiensis is not capable of using acetate as a carbon or energy source in situ and that acetate oxidation occurred via the metabolic activity of a low-abundance microorganism in the bioreactor’s side population. Together, these findings provide a foundation for understanding the carbon metabolism of anammox bacteria at a systems-level and will inform future studies aimed at elucidating factors governing their function and niche differentiation in natural and engineered ecosystems.

scholarly journals Evidence for Autotrophic CO2 Fixation via the Reductive Tricarboxylic Acid Cycle by Members of the ε Subdivision of Proteobacteria

2005 ◽  
Vol 187 (9) ◽  
pp. 3020-3027 ◽  
Author(s):  
Michael Hügler ◽  
Carl O. Wirsen ◽  
Georg Fuchs ◽  
Craig D. Taylor ◽  
Stefan M. Sievert
Keyword(s):  
Carbon Fixation ◽  
Tricarboxylic Acid Cycle ◽  
Calvin Cycle ◽  
Tricarboxylic Acid ◽  
Rrna Gene ◽  
Atp Citrate Lyase ◽  
Acid Cycle ◽  
Key Enzymes ◽  
Citrate Lyase ◽  
Reductive Tricarboxylic Acid Cycle

ABSTRACT Based on 16S rRNA gene surveys, bacteria of the ε subdivision of proteobacteria have been identified to be important members of microbial communities in a variety of environments, and quite a few have been demonstrated to grow autotrophically. However, no information exists on what pathway of autotrophic carbon fixation these bacteria might use. In this study, Thiomicrospira denitrificans and Candidatus Arcobacter sulfidicus, two chemolithoautotrophic sulfur oxidizers of the ε subdivision of proteobacteria, were examined for activities of the key enzymes of the known autotrophic CO2 fixation pathways. Both organisms contained activities of the key enzymes of the reductive tricarboxylic acid cycle, ATP citrate lyase, 2-oxoglutarate:ferredoxin oxidoreductase, and pyruvate:ferredoxin oxidoreductase. Furthermore, no activities of key enzymes of other CO2 fixation pathways, such as the Calvin cycle, the reductive acetyl coenzyme A pathway, and the 3-hydroxypropionate cycle, could be detected. In addition to the key enzymes, the activities of the other enzymes involved in the reductive tricarboxylic acid cycle could be measured. Sections of the genes encoding the α- and β-subunits of ATP citrate lyase could be amplified from both organisms. These findings represent the first direct evidence for the operation of the reductive tricarboxylic acid cycle for autotrophic CO2 fixation in ε-proteobacteria. Since ε-proteobacteria closely related to these two organisms are important in many habitats, such as hydrothermal vents, oxic-sulfidic interfaces, or oilfields, these results suggest that autotrophic CO2 fixation via the reductive tricarboxylic acid cycle might be more important than previously considered.

scholarly journals Horizontal acquisition of a patchwork Calvin cycle by symbiotic and free-living Campylobacterota (formerly Epsilonproteobacteria)

2018 ◽  
Author(s):  
Adrien Assié ◽  
Nikolaus Leisch ◽  
Dimitri V. Meier ◽  
Harald Gruber-Vodicka ◽  
Halina E. Tegetmeyer ◽  
...  
Keyword(s):  
Stable Isotope ◽  
Carbon Fixation ◽  
Tricarboxylic Acid Cycle ◽  
Calvin Cycle ◽  
Tricarboxylic Acid ◽  
Multiple Sources ◽  
Free Living ◽  
Sulfur Oxidizing ◽  
Reductive Tricarboxylic Acid Cycle ◽  
Horizontal Acquisition

AbstractAlthough the majority of known autotrophs use the Calvin-Benson-Bassham (CBB) cycle for carbon fixation, all currently described autotrophs from the Campylobacterota (previously Epsilonproteobacteria) use the reductive tricarboxylic acid cycle (rTCA) instead. We discovered campylobacterotal epibionts (“Candidatus Thiobarba”) of deep-sea mussels that have acquired a complete CBB cycle and lost key genes of the rTCA cycle. Intriguingly, the phylogenies of campylobacterotal CBB genes suggest they were acquired in multiple transfers from Gammaproteobacteria closely related to sulfur-oxidizing endosymbionts associated with the mussels, as well as from Betaproteobacteria. We hypothesize that “Ca. Thiobarba” switched from the rTCA to a fully functional CBB cycle during its evolution, by acquiring genes from multiple sources, including co-occurring symbionts. We also found key CBB cycle genes in free-living Campylobacterota, suggesting that the CBB cycle may be more widespread in this phylum than previously known. Metatranscriptomics and metaproteomics confirmed high expression of CBB cycle genes in mussel-associated “Ca. Thiobarba”. Direct stable isotope fingerprinting showed that “Ca. Thiobarba” has typical CBB signatures, additional evidence that it uses this cycle for carbon fixation. Our discovery calls into question current assumptions about the distribution of carbon fixation pathways across the tree of life, and the interpretation of stable isotope measurements in the environment.

scholarly journals Autotrophic and mixotrophic metabolism of an anammox bacterium revealed by in vivo13C and 2H metabolic network mapping

2019 ◽  
Author(s):  
Christopher E. Lawson ◽  
Guylaine H.L. Nuijten ◽  
Rob M. de Graaf ◽  
Tyler B. Jacobson ◽  
Martin Pabst ◽  
...  
Keyword(s):  
Carbon Metabolism ◽  
Metabolic Networks ◽  
Metabolic Flux ◽  
Citrate Synthase ◽  
Side Population ◽  
Tricarboxylic Acid Cycle ◽  
Anammox Bacteria ◽  
Flux Analysis ◽  
Anammox Bacterium

AbstractAnaerobic ammonium-oxidizing (anammox) bacteria mediate a key step in the biogeochemical nitrogen cycle and have been applied worldwide for the energy-efficient removal of nitrogen from wastewater. However, outside their core energy metabolism, little is known about the metabolic networks driving anammox bacterial anabolism and mixotrophy beyond genome-based predictions. Here, we experimentally resolved the central carbon metabolism of the anammox bacterium Candidatus ‘Kuenenia stuttgartiensis’ using time-series 13C and 2H isotope tracing, metabolomics, and isotopically nonstationary metabolic flux analysis (INST-MFA). Our findings confirm predicted metabolic pathways used for CO2 fixation, central metabolism, and amino acid biosynthesis in K. stuttgartiensis, and reveal several instances where genomic predictions are not supported by in vivo metabolic fluxes. This includes the use of an oxidative tricarboxylic acid cycle, despite the genome not encoding a known citrate synthase. We also demonstrate that K. stuttgartiensis is able to directly assimilate extracellular formate via the Wood-Ljungdahl pathway instead of oxidizing it completely to CO2 followed by reassimilation. In contrast, our data suggests that K. stuttgartiensis is not capable of using acetate as a carbon or energy source in situ and that acetate oxidation occurred via the metabolic activity of a low-abundance microorganism in the bioreactor’s side population. Together, these findings provide a foundation for understanding the carbon metabolism of anammox bacteria at a systems-level and will inform future studies aimed at elucidating factors governing their function and niche differentiation in natural and engineered ecosystems.

Sign in / Sign up

Export Citation Format

Share Document