scholarly journals Genetic evidence for two carbon fixation pathways in symbiotic and free-living bacteria: The Calvin-Benson-Bassham cycle and the reverse tricarboxylic acid cycle

2018 ◽  
Author(s):  
Maxim Rubin-Blum ◽  
Nicole Dubilier ◽  
Manuel Kleiner
Keyword(s):  
Carbon Fixation ◽  
Tricarboxylic Acid Cycle ◽  
Electron Flow ◽  
Tricarboxylic Acid ◽  
Riftia Pachyptila ◽  
Heterodisulfide Reductase ◽  
Free Living ◽  
Sulfur Oxidizer ◽  
Potential Benefits ◽  
Sulfur Oxidizing

AbstractVery few bacteria are able to fix carbon via both the reverse tricarboxylic acid (rTCA) and the Calvin-Benson-Bassham (CBB) cycles, such as symbiotic, sulfur-oxidizing bacteria that are the sole carbon source for the marine tubeworm Riftia pachyptila, the fastest growing invertebrate. To date, this co-existence of two carbon fixation pathways had not been found in a cultured bacterium and could thus not be studied in detail. Moreover, it was not clear if these two pathways were encoded in the same symbiont individual, or if two symbiont populations, each with one of the pathways, co-existed within tubeworms. With comparative genomics, we show that Thioflavicoccus mobilis, a cultured, free-living gammaproteobacterial sulfur oxidizer, possesses the genes for both carbon fixation pathways. Here, we also show that both the CBB and rTCA pathways are likely encoded in the genome of the sulfur-oxidizing symbiont of the tubeworm Escarpia laminata from deep-sea asphalt volcanoes in the Gulf of Mexico. Finally, we provide genomic and transcriptomic data suggesting a potential electron flow towards the rTCA cycle carboxylase 2-oxoglutarate:ferredoxin oxidoreductase, via a rare variant of NADH dehydrogenase/heterodisulfide reductase. This electron bifurcating complex, together with NAD(P)+ transhydrogenase and Na+ translocating Rnf membrane complexes may improve the efficiency of the rTCA cycle in both the symbiotic and the free-living sulfur oxidizer.ImportancePrimary production on Earth is dependent on autotrophic carbon fixation, which leads to the incorporation of carbon dioxide into biomass. Multiple metabolic pathways have been described for autotrophic carbon fixation, but most autotrophic organisms were assumed to have the genes for only one of these pathways. Our finding of a cultivable bacterium with two carbon fixation pathways in its genome opens the possibility to study the potential benefits of having two pathways and the interplay between these pathways. Additionally, this will allow the investigation of the unusual, and potentially very efficient mechanism of electron flow that could drive the rTCA cycle in these autotrophs. Such studies will deepen our understanding of carbon fixation pathways and could provide new avenues for optimizing carbon fixation in biotechnological applications.

scholarly journals Genetic Evidence for Two Carbon Fixation Pathways (the Calvin-Benson-Bassham Cycle and the Reverse Tricarboxylic Acid Cycle) in Symbiotic and Free-Living Bacteria

mSphere ◽  
2019 ◽  
Vol 4 (1) ◽  
Author(s):  
Maxim Rubin-Blum ◽  
Nicole Dubilier ◽  
Manuel Kleiner
Keyword(s):  
Carbon Fixation ◽  
Tricarboxylic Acid Cycle ◽  
Electron Flow ◽  
Tricarboxylic Acid ◽  
Heterodisulfide Reductase ◽  
Free Living ◽  
Content Type ◽  
Sulfur Oxidizer ◽  
Potential Benefits ◽  
Sulfur Oxidizing

ABSTRACT Very few bacteria are able to fix carbon via both the reverse tricarboxylic acid (rTCA) and the Calvin-Benson-Bassham (CBB) cycles, such as symbiotic, sulfur-oxidizing bacteria that are the sole carbon source for the marine tubeworm Riftia pachyptila, the fastest-growing invertebrate. To date, the coexistence of these two carbon fixation pathways had not been found in a cultured bacterium and could thus not be studied in detail. Moreover, it was not clear if these two pathways were encoded in the same symbiont individual, or if two symbiont populations, each with one of the pathways, coexisted within tubeworms. With comparative genomics, we show that Thioflavicoccus mobilis, a cultured, free-living gammaproteobacterial sulfur oxidizer, possesses the genes for both carbon fixation pathways. Here, we also show that both the CBB and rTCA pathways are likely encoded in the genome of the sulfur-oxidizing symbiont of the tubeworm Escarpia laminata from deep-sea asphalt volcanoes in the Gulf of Mexico. Finally, we provide genomic and transcriptomic data suggesting a potential electron flow toward the rTCA cycle carboxylase 2-oxoglutarate:ferredoxin oxidoreductase, via a rare variant of NADH dehydrogenase/heterodisulfide reductase in the E. laminata symbiont. This electron-bifurcating complex, together with NAD(P)+ transhydrogenase and Na+ translocating Rnf membrane complexes, may improve the efficiency of the rTCA cycle in both the symbiotic and the free-living sulfur oxidizer. IMPORTANCE Primary production on Earth is dependent on autotrophic carbon fixation, which leads to the incorporation of carbon dioxide into biomass. Multiple metabolic pathways have been described for autotrophic carbon fixation, but most autotrophic organisms were assumed to have the genes for only one of these pathways. Our finding of a cultivable bacterium with two carbon fixation pathways in its genome, the rTCA and the CBB cycle, opens the possibility to study the potential benefits of having these two pathways and the interplay between them. Additionally, this will allow the investigation of the unusual and potentially very efficient mechanism of electron flow that could drive the rTCA cycle in these autotrophs. Such studies will deepen our understanding of carbon fixation pathways and could provide new avenues for optimizing carbon fixation in biotechnological applications.

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

2019 ◽  
Vol 14 (1) ◽  
pp. 104-122 ◽  
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

Abstract Most autotrophs use the Calvin–Benson–Bassham (CBB) cycle for carbon fixation. In contrast, 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 may have lost most key genes of the rTCA cycle. Intriguingly, the phylogenies of campylobacterotal CBB cycle 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 cycle 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, suggesting that it uses this cycle for carbon fixation. Our discovery calls into question current assumptions about the distribution of carbon fixation pathways in microbial lineages, and the interpretation of stable isotope measurements in the environment.

scholarly journals Metabolic differences between symbiont subpopulations in the deep-sea tubeworm Riftia pachyptila

2020 ◽  
Author(s):  
Tjorven Hinzke ◽  
Manuel Kleiner ◽  
Mareike Meister ◽  
Rabea Schlüter ◽  
Christian Hentschker ◽  
...  
Keyword(s):  
Carbon Fixation ◽  
Statistical Evaluation ◽  
Gradient Centrifugation ◽  
Riftia Pachyptila ◽  
Metabolic Diversity ◽  
Host Animal ◽  
Host Interaction ◽  
Sulfur Oxidizing ◽  
Differentiation Stage ◽  
Vent Tube

AbstractThe hydrothermal vent tube worm Riftia pachyptila lives in intimate symbiosis with intracellular sulfur-oxidizing gammaproteobacteria. Although the symbiont population consists of a single 16S rRNA phylotype, bacteria in the same host animal exhibit a remarkable degree of metabolic diversity: They simultaneously utilize two carbon fixation pathways and various energy sources and electron acceptors. Whether these multiple metabolic routes are employed in the same symbiont cells, or rather in distinct symbiont subpopulations, was unclear. As Riftia symbionts vary considerably in cell size and shape, we enriched individual symbiont cell sizes by density gradient centrifugation in order to test whether symbiont cells of different sizes show different metabolic profiles. Metaproteomic analysis and statistical evaluation using clustering and random forests, supported by microscopy and flow cytometry, strongly suggest that Riftia symbiont cells of different sizes represent metabolically dissimilar stages of a physiological differentiation process: Small symbionts actively divide and may establish cellular symbiont-host interaction, as indicated by highest abundance of the cell division key protein FtsZ and highly abundant chaperones and porins in this initial phase. Large symbionts, on the other hand, apparently do not divide, but still replicate DNA, leading to DNA endoreduplication. Highest abundance of enzymes for CO2 fixation, carbon storage and biosynthesis in large symbionts indicates that in this late differentiation stage the symbiont’s metabolism is efficiently geared towards the production of organic material. We propose that this division of labor between smaller and larger symbionts benefits the productivity of the symbiosis as a whole.

scholarly journals Bacterial symbiont subpopulations have different roles in a deep-sea symbiosis

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Tjorven Hinzke ◽  
Manuel Kleiner ◽  
Mareike Meister ◽  
Rabea Schlüter ◽  
Christian Hentschker ◽  
...  
Keyword(s):  
Deep Sea ◽  
Hydrothermal Vent ◽  
Carbon Fixation ◽  
Density Gradient Centrifugation ◽  
Gradient Centrifugation ◽  
Bacterial Symbiont ◽  
Riftia Pachyptila ◽  
Physiological Diversity ◽  
Host Interaction ◽  
Sulfur Oxidizing

The hydrothermal vent tubeworm Riftia pachyptila hosts a single 16S rRNA phylotype of intracellular sulfur-oxidizing symbionts, which vary considerably in cell morphology and exhibit a remarkable degree of physiological diversity and redundancy, even in the same host. To elucidate whether multiple metabolic routes are employed in the same cells or rather in distinct symbiont subpopulations, we enriched symbionts according to cell size by density gradient centrifugation. Metaproteomic analysis, microscopy, and flow cytometry strongly suggest that Riftia symbiont cells of different sizes represent metabolically dissimilar stages of a physiological differentiation process: While small symbionts actively divide and may establish cellular symbiont-host interaction, large symbionts apparently do not divide, but still replicate DNA, leading to DNA endoreduplication. Moreover, in large symbionts, carbon fixation and biomass production seem to be metabolic priorities. We propose that this division of labor between smaller and larger symbionts benefits the productivity of the symbiosis as a whole.

scholarly journals Abiotic and biotic processes that drive carboxylation and decarboxylation reactions

2020 ◽  
Vol 105 (5) ◽  
pp. 609-615
Author(s):  
Cody S. Sheik ◽  
H. James Cleaves ◽  
Kristin Johnson-Finn ◽  
Donato Giovannelli ◽  
Thomas L. Kieft ◽  
...  
Keyword(s):  
Metabolic Pathways ◽  
Subduction Zones ◽  
Carbon Fixation ◽  
Prebiotic Chemistry ◽  
Tricarboxylic Acid Cycle ◽  
Tricarboxylic Acid ◽  
Short Term ◽  
Planetary Evolution ◽  
Broad Overview

Abstract Carboxylation and decarboxylation are two fundamental classes of reactions that impact the cycling of carbon in and on Earth’s crust. These reactions play important roles in both long-term (primarily abiotic) and short-term (primarily biotic) carbon cycling. Long-term cycling is important in the subsurface and at subduction zones where organic carbon is decomposed and outgassed or recycled back to the mantle. Short-term reactions are driven by biology and have the ability to rapidly convert CO2 to biomass and vice versa. For instance, carboxylation is a critical reaction in primary production and metabolic pathways like photosynthesis in which sunlight provides energy to drive carbon fixation, whereas decarboxylation is a critical reaction in metabolic pathways like respiration and the tricarboxylic acid cycle. Early life and prebiotic chemistry on Earth likely relied heavily upon the abiotic synthesis of carboxylic acids. Over time, life has diversified (de)carboxylation reactions and incorporated them into many facets of cellular metabolism. Here we present a broad overview of the importance of carboxylation and decarboxylation reactions from both abiotic and biotic perspectives to highlight the importance of these reactions and compounds to planetary evolution.

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 Abundance of Reverse Tricarboxylic Acid Cycle Genes in Free-Living Microorganisms at Deep-Sea Hydrothermal Vents

2004 ◽  
Vol 70 (10) ◽  
pp. 6282-6289 ◽  
Author(s):  
Barbara J. Campbell ◽  
S. Craig Cary
Keyword(s):  
Deep Sea ◽  
Hydrothermal Vents ◽  
Tricarboxylic Acid Cycle ◽  
Calvin Cycle ◽  
Tricarboxylic Acid ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Free Living ◽  
Bisphosphate Carboxylase ◽  
Acid Cycle

ABSTRACT Since the discovery of hydrothermal vents more than 25 years ago, the Calvin-Bassham-Benson (Calvin) cycle has been considered the principal carbon fixation pathway in this microbe-based ecosystem. However, on the basis of recent molecular data of cultured free-living and noncultured episymbiotic members of the epsilon subdivision of Proteobacteria and earlier carbon isotope data of primary consumers, an alternative autotrophic pathway may predominate. Here, genetic and culture-based approaches demonstrated the abundance of reverse tricarboxylic acid cycle genes compared to the abundance of Calvin cycle genes in microbial communities from two geographically distinct deep-sea hydrothermal vents. PCR with degenerate primers for three key genes in the reverse tricarboxylic acid cycle and form I and form II of ribulose 1,5-bisphosphate carboxylase/oxygenase (Calvin cycle marker gene) were utilized to demonstrate the abundance of the reverse tricarboxylic acid cycle genes in diverse vent samples. These genes were also expressed in at least one chimney sample. Diversity, similarity matrix, and phylogenetic analyses of cloned samples and amplified gene products from autotrophic enrichment cultures suggest that the majority of autotrophs that utilize the reverse tricarboxylic acid cycle are members of the epsilon subdivision of Proteobacteria. These results parallel the results of previously published molecular surveys of 16S rRNA genes, demonstrating the dominance of members of the epsilon subdivision of Proteobacteria in free-living hydrothermal vent communities. Members of the epsilon subdivision of Proteobacteria are also ubiquitous in many other microaerophilic to anaerobic sulfidic environments, such as the deep subsurface. Therefore, the reverse tricarboxylic acid cycle may be a major autotrophic pathway in these environments and significantly contribute to global autotrophic processes.

scholarly journals Physiological Proteomics of the Uncultured Endosymbiont of Riftia pachyptila

Science ◽  
2007 ◽  
Vol 315 (5809) ◽  
pp. 247-250 ◽  
Author(s):  
Stephanie Markert ◽  
Cordelia Arndt ◽  
Horst Felbeck ◽  
Dörte Becher ◽  
Stefan M. Sievert ◽  
...  
Keyword(s):  
Deep Sea ◽  
Tricarboxylic Acid Cycle ◽  
Sulfide Oxidation ◽  
Calvin Cycle ◽  
Tricarboxylic Acid ◽  
Riftia Pachyptila ◽  
Proteomic Approach ◽  
Reductive Tricarboxylic Acid Cycle ◽  
Metagenome Sequence

The bacterial endosymbiont of the deep-sea tube worm Riftia pachyptila has never been successfully cultivated outside its host. In the absence of cultivation data, we have taken a proteomic approach based on the metagenome sequence to study the metabolism of this peculiar microorganism in detail. As one result, we found that three major sulfide oxidation proteins constitute ∼12% of the total cytosolic proteome, which highlights the essential role of these enzymes for the symbiont's energy metabolism. Unexpectedly, the symbiont uses the reductive tricarboxylic acid cycle in addition to the previously identified Calvin cycle for CO2 fixation.

scholarly journals Co-occurring activity of two autotrophic pathways in symbionts of hydrothermal vent tubeworm Riftia pachyptila

2021 ◽  
Author(s):  
Juliana M. Leonard ◽  
Jessica Mitchell ◽  
Roxanne A. Beinart ◽  
Jennifer A. Delaney ◽  
Jon G. Sanders ◽  
...  
Keyword(s):  
High Pressure ◽  
Hydrothermal Vent ◽  
Dissolved Inorganic Carbon ◽  
Tricarboxylic Acid Cycle ◽  
Riftia Pachyptila ◽  
Acid Cycle ◽  
Citrate Lyase ◽  
Sulfur Oxidizing ◽  
Reductive Tricarboxylic Acid Cycle

Genome and proteome data predict the presence of both the reductive citric acid cycle (rCAC; also called the reductive tricarboxylic acid cycle) and Calvin-Benson-Bassham cycle (CBB) in “ Candidatus Endoriftia persephonae”, the autotrophic sulfur-oxidizing bacterial endosymbiont from giant hydrothermal vent tubeworm Riftia pachyptila. We tested whether these cycles were differentially induced by sulfide supply, since the synthesis of biosynthetic intermediates by the rCAC is less energetically expensive than the CBB. R. pachyptila were incubated under in situ conditions in high-pressure aquaria under low (28-40 μmol hr −1 ) or high (180 - 276 μmol hr −1 ) rates of sulfide supply. Symbiont-bearing trophosome samples excised from R. pachyptila maintained under either condition were capable of similar rates of CO 2 fixation. Activities of rCAC enzyme ATP-dependent citrate lyase and CBB enzyme RubisCO did not differ between the two conditions, though transcript abundances for ATP-dependent citrate lyase were 4 to 5-fold higher under low sulfide conditions. δ 13 C values of internal dissolved inorganic carbon pools were variable, and did not correlate with sulfide supply rate. In samples taken from freshly collected R. pachyptila, δ 13 C values of lipids fell between those collected for organisms using either the rCAC or CBB cycles exclusively. These observations are consistent with co-occurring activities of rCAC and CBB cycles in this symbiosis. IMPORTANCE Previous to this study, the activities of the rCAC and CBB in R. pachyptila had largely been inferred from –omics studies of R. pachyptila without direct assessment of in situ conditions prior to collection. In this study, R. pachyptila were maintained and monitored in high-pressure aquaria prior to measuring their CO 2 -fixation parameters. Results suggest that ranges in sulfide concentrations similar to those experienced in situ do not exert a strong influence on the relative activities of the rCAC and CBB. This observation highlights the importance of further study of this symbiosis and other organisms with multiple CO 2 -fixing pathways, which recent genomics and biochemical studies suggest are likely to be more prevalent than anticipated.

Sign in / Sign up

Export Citation Format

Share Document