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Academic literature on the topic 'Wood-Ljungdahl metabolic pathway'
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Journal articles on the topic "Wood-Ljungdahl metabolic pathway"
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Song, Yoseb, Jin Soo Lee, Jongoh Shin, Gyu Min Lee, Sangrak Jin, Seulgi Kang, Jung-Kul Lee, et al. "Functional cooperation of the glycine synthase-reductase and Wood–Ljungdahl pathways for autotrophic growth of Clostridium drakei." Proceedings of the National Academy of Sciences 117, no. 13 (March 13, 2020): 7516–23. http://dx.doi.org/10.1073/pnas.1912289117.
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Among CO2-fixing metabolic pathways in nature, the linear Wood–Ljungdahl pathway (WLP) in phylogenetically diverse acetate-forming acetogens comprises the most energetically efficient pathway, requires the least number of reactions, and converts CO2 to formate and then into acetyl-CoA. Despite two genes encoding glycine synthase being well-conserved in WLP gene clusters, the functional role of glycine synthase under autotrophic growth conditions has remained uncertain. Here, using the reconstructed genome-scale metabolic model iSL771 based on the completed genome sequence, transcriptomics, 13C isotope-based metabolite-tracing experiments, biochemical assays, and heterologous expression of the pathway in another acetogen, we discovered that the WLP and the glycine synthase pathway are functionally interconnected to fix CO2, subsequently converting CO2 into acetyl-CoA, acetyl-phosphate, and serine. Moreover, the functional cooperation of the pathways enhances CO2 consumption and cellular growth rates via bypassing reducing power required reactions for cellular metabolism during autotrophic growth of acetogens.
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Martin, William, and Michael J. Russell. "On the origin of biochemistry at an alkaline hydrothermal vent." Philosophical Transactions of the Royal Society B: Biological Sciences 362, no. 1486 (November 3, 2006): 1887–926. http://dx.doi.org/10.1098/rstb.2006.1881.
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A model for the origin of biochemistry at an alkaline hydrothermal vent has been developed that focuses on the acetyl-CoA (Wood–Ljungdahl) pathway of CO 2 fixation and central intermediary metabolism leading to the synthesis of the constituents of purines and pyrimidines. The idea that acetogenesis and methanogenesis were the ancestral forms of energy metabolism among the first free-living eubacteria and archaebacteria, respectively, stands in the foreground. The synthesis of formyl pterins, which are essential intermediates of the Wood–Ljungdahl pathway and purine biosynthesis, is found to confront early metabolic systems with steep bioenergetic demands that would appear to link some, but not all, steps of CO 2 reduction to geochemical processes in or on the Earth's crust. Inorganically catalysed prebiotic analogues of the core biochemical reactions involved in pterin-dependent methyl synthesis of the modern acetyl-CoA pathway are considered. The following compounds appear as probable candidates for central involvement in prebiotic chemistry: metal sulphides, formate, carbon monoxide, methyl sulphide, acetate, formyl phosphate, carboxy phosphate, carbamate, carbamoyl phosphate, acetyl thioesters, acetyl phosphate, possibly carbonyl sulphide and eventually pterins. Carbon might have entered early metabolism via reactions hardly different from those in the modern Wood–Ljungdahl pathway, the pyruvate synthase reaction and the incomplete reverse citric acid cycle. The key energy-rich intermediates were perhaps acetyl thioesters, with acetyl phosphate possibly serving as the universal metabolic energy currency prior to the origin of genes. Nitrogen might have entered metabolism as geochemical NH 3 via two routes: the synthesis of carbamoyl phosphate and reductive transaminations of α-keto acids. Together with intermediates of methyl synthesis, these two routes of nitrogen assimilation would directly supply all intermediates of modern purine and pyrimidine biosynthesis. Thermodynamic considerations related to formyl pterin synthesis suggest that the ability to harness a naturally pre-existing proton gradient at the vent–ocean interface via an ATPase is older than the ability to generate a proton gradient with chemistry that is specified by genes.
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Fullerton, Heather, and Craig L. Moyer. "Comparative Single-Cell Genomics of Chloroflexi from the Okinawa Trough Deep-Subsurface Biosphere." Applied and Environmental Microbiology 82, no. 10 (March 11, 2016): 3000–3008. http://dx.doi.org/10.1128/aem.00624-16.
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ABSTRACTChloroflexismall-subunit (SSU) rRNA gene sequences are frequently recovered from subseafloor environments, but the metabolic potential of the phylum is poorly understood. The phylumChloroflexiis represented by isolates with diverse metabolic strategies, including anoxic phototrophy, fermentation, and reductive dehalogenation; therefore, function cannot be attributed to these organisms based solely on phylogeny. Single-cell genomics can provide metabolic insights into uncultured organisms, like the deep-subsurfaceChloroflexi. Nine SSU rRNA gene sequences were identified from single-cell sorts of whole-round core material collected from the Okinawa Trough at Iheya North hydrothermal field as part of Integrated Ocean Drilling Program (IODP) expedition 331 (Deep Hot Biosphere). Previous studies of subsurfaceChloroflexisingle amplified genomes (SAGs) suggested heterotrophic or lithotrophic metabolisms and provided no evidence for growth by reductive dehalogenation. Our nineChloroflexiSAGs (seven of which are from the orderAnaerolineales) indicate that, in addition to genes for the Wood-Ljungdahl pathway, exogenous carbon sources can be actively transported into cells. At least one subunit for pyruvate ferredoxin oxidoreductase was found in four of theChloroflexiSAGs. This protein can provide a link between the Wood-Ljungdahl pathway and other carbon anabolic pathways. Finally, one of the sevenAnaerolinealesSAGs contains a distinct reductive dehalogenase homologous (rdhA) gene.IMPORTANCEThrough the use of single amplified genomes (SAGs), we have extended the metabolic potential of an understudied group of subsurface microbes, theChloroflexi. These microbes are frequently detected in the subsurface biosphere, though their metabolic capabilities have remained elusive. In contrast to previously examinedChloroflexiSAGs, our genomes (several are from the orderAnaerolineales) were recovered from a hydrothermally driven system and therefore provide a unique window into the metabolic potential of this type of habitat. In addition, a reductive dehalogenase gene (rdhA) has been directly linked to marine subsurfaceChloroflexi, suggesting that reductive dehalogenation is not limited to the classDehalococcoidia. This discovery expands the nutrient-cycling and metabolic potential present within the deep subsurface and provides functional gene information relating to this enigmatic group.
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Jin, Sangrak, Jiyun Bae, Yoseb Song, Nicole Pearcy, Jongoh Shin, Seulgi Kang, Nigel P. Minton, Philippe Soucaille, and Byung-Kwan Cho. "Synthetic Biology on Acetogenic Bacteria for Highly Efficient Conversion of C1 Gases to Biochemicals." International Journal of Molecular Sciences 21, no. 20 (October 15, 2020): 7639. http://dx.doi.org/10.3390/ijms21207639.
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Synthesis gas, which is mainly produced from fossil fuels or biomass gasification, consists of C1 gases such as carbon monoxide, carbon dioxide, and methane as well as hydrogen. Acetogenic bacteria (acetogens) have emerged as an alternative solution to recycle C1 gases by converting them into value-added biochemicals using the Wood-Ljungdahl pathway. Despite the advantage of utilizing acetogens as biocatalysts, it is difficult to develop industrial-scale bioprocesses because of their slow growth rates and low productivities. To solve these problems, conventional approaches to metabolic engineering have been applied; however, there are several limitations owing to the lack of required genetic bioparts for regulating their metabolic pathways. Recently, synthetic biology based on genetic parts, modules, and circuit design has been actively exploited to overcome the limitations in acetogen engineering. This review covers synthetic biology applications to design and build industrial platform acetogens.
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Youssef, Noha H., Ibrahim F. Farag, Sydney Rudy, Ace Mulliner, Kara Walker, Ford Caldwell, Malik Miller, Wouter Hoff, and Mostafa Elshahed. "The Wood–Ljungdahl pathway as a key component of metabolic versatility in candidate phylum Bipolaricaulota (Acetothermia, OP1)." Environmental Microbiology Reports 11, no. 4 (April 2, 2019): 538–47. http://dx.doi.org/10.1111/1758-2229.12753.
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Cárdenas, Juan Pablo, Verónica Martínez, P. Covarrubias, David S. Holmes, and Raquel Quatrini. "Predicted CO/CO2 Fixation in Ferroplasma spp. via a Novel Chimaeric Pathway." Advanced Materials Research 71-73 (May 2009): 219–22. http://dx.doi.org/10.4028/www.scientific.net/amr.71-73.219.
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Previous physiological studies of the genus Ferroplasma have indicated that these microorganisms are capable of fixing CO2 in the presence of ferrous iron and low concentrations of yeast extract. Analysis of the gene complement of Ferroplasma acidarmanus fer1 and two partial genomes of Ferroplasma type I and II derived from the Iron Mountain acid mine drainage metagenome revealed the absence of several functional marker genes encoding key enzymes of three know alternative CO2 fixation routes present in archaea, i.e. the 3-hydroxypropionate cycle, the Ljungdahl–Wood pathway and the reverse TCA cycle. It is thus intriguing how these chemoautotrophic archaeal species deal with their requirements for carbon and suggests that they might have a distinct CO2 fixation route, as yet unreported. Using comparative genomics and metabolic reconstruction strategies, a putative pathway was detected for C1 fixation consisting of four main steps: 1) conversion of carbon monoxide to carbon dioxide with gain of energy and/or 2) reduction of carbon dioxide to formate, 3) incorporation of formate to tetrahydrofolate and 4) donation of the carbon moiety of tetrahydrofolate to glycine to produce serine. Steps 1 to 3 involve enzymes that correspond to some of the Ljungdahl–Wood pathway proteins, whereas step 4 resembles the well known “serine cycle”, utilized by methylotrophic microorganisms for formaldehyde fixation. Thus, this chimaeric pathway might represent the missing carbon fixation route in Ferroplasmatales. Herein, we discuss the implications of these findings in the context of central carbon metabolism requirements for biomass production in acidic environments.
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Rupakula, Aamani, Thomas Kruse, Sjef Boeren, Christof Holliger, Hauke Smidt, and Julien Maillard. "The restricted metabolism of the obligate organohalide respiring bacterium Dehalobacter restrictus: lessons from tiered functional genomics." Philosophical Transactions of the Royal Society B: Biological Sciences 368, no. 1616 (April 19, 2013): 20120325. http://dx.doi.org/10.1098/rstb.2012.0325.
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Dehalobacter restrictus strain PER-K23 is an obligate organohalide respiring bacterium, which displays extremely narrow metabolic capabilities. It grows only via coupling energy conservation to anaerobic respiration of tetra- and trichloroethene with hydrogen as sole electron donor. Dehalobacter restrictus represents the paradigmatic member of the genus Dehalobacter , which in recent years has turned out to be a major player in the bioremediation of an increasing number of organohalides, both in situ and in laboratory studies. The recent elucidation of the D. restrictus genome revealed a rather elaborate genome with predicted pathways that were not suspected from its restricted metabolism, such as a complete corrinoid biosynthetic pathway, the Wood–Ljungdahl (WL) pathway for CO 2 fixation, abundant transcriptional regulators and several types of hydrogenases. However, one important feature of the genome is the presence of 25 reductive dehalogenase genes, from which so far only one, pceA , has been characterized on genetic and biochemical levels. This study describes a multi-level functional genomics approach on D. restrictus across three different growth phases. A global proteomic analysis allowed consideration of general metabolic pathways relevant to organohalide respiration, whereas the dedicated genomic and transcriptomic analysis focused on the diversity, composition and expression of genes associated with reductive dehalogenases.
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Prat, Laure, Julien Maillard, Régis Grimaud, and Christof Holliger. "Physiological Adaptation of Desulfitobacterium hafniense Strain TCE1 to Tetrachloroethene Respiration." Applied and Environmental Microbiology 77, no. 11 (April 8, 2011): 3853–59. http://dx.doi.org/10.1128/aem.02471-10.
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ABSTRACTDesulfitobacteriumspp. are ubiquitous organisms with a broad metabolic versatility, and some isolates have the ability to use tetrachloroethene (PCE) as terminal electron acceptor. In order to identify proteins involved in this organohalide respiration process, a comparative proteomic analysis was performed. Soluble and membrane-associated proteins obtained from cells ofDesulfitobacterium hafniensestrain TCE1 that were growing on different combinations of the electron donors lactate and hydrogen and the electron acceptors PCE and fumarate were analyzed. Among proteins increasingly expressed in the presence of PCE compared to fumarate as electron acceptor, a total of 57 proteins were identified by mass spectrometry analysis, revealing proteins involved in stress response and associated regulation pathways, such as PspA, GroEL, and CodY, and also proteins potentially participating in carbon and energy metabolism, such as proteins of the Wood-Ljungdahl pathway and electron transfer flavoproteins. These proteomic results suggest thatD. hafniensestrain TCE1 adapts its physiology to face the relative unfavorable growth conditions during an apparent opportunistic organohalide respiration.
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Bomberg, Malin, Tiina Lamminmäki, and Merja Itävaara. "Microbial communities and their predicted metabolic characteristics in deep fracture groundwaters of the crystalline bedrock at Olkiluoto, Finland." Biogeosciences 13, no. 21 (November 3, 2016): 6031–47. http://dx.doi.org/10.5194/bg-13-6031-2016.
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Abstract. The microbial diversity in oligotrophic isolated crystalline Fennoscandian Shield bedrock fracture groundwaters is high, but the core community has not been identified. Here we characterized the bacterial and archaeal communities in 12 water conductive fractures situated at depths between 296 and 798 m by high throughput amplicon sequencing using the Illumina HiSeq platform. Between 1.7 × 104 and 1.2 × 106 bacterial or archaeal sequence reads per sample were obtained. These sequences revealed that up to 95 and 99 % of the bacterial and archaeal sequences obtained from the 12 samples, respectively, belonged to only a few common species, i.e. the core microbiome. However, the remaining rare microbiome contained over 3- and 6-fold more bacterial and archaeal taxa. The metabolic properties of the microbial communities were predicted using PICRUSt. The approximate estimation showed that the metabolic pathways commonly included fermentation, fatty acid oxidation, glycolysis/gluconeogenesis, oxidative phosphorylation, and methanogenesis/anaerobic methane oxidation, but carbon fixation through the Calvin cycle, reductive TCA cycle, and the Wood–Ljungdahl pathway was also predicted. The rare microbiome is an unlimited source of genomic functionality in all ecosystems. It may consist of remnants of microbial communities prevailing in earlier environmental conditions, but could also be induced again if changes in their living conditions occur.
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Schuchmann, Kai, and Volker Müller. "Energetics and Application of Heterotrophy in Acetogenic Bacteria." Applied and Environmental Microbiology 82, no. 14 (May 13, 2016): 4056–69. http://dx.doi.org/10.1128/aem.00882-16.
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ABSTRACTAcetogenic bacteria are a diverse group of strictly anaerobic bacteria that utilize the Wood-Ljungdahl pathway for CO2fixation and energy conservation. These microorganisms play an important part in the global carbon cycle and are a key component of the anaerobic food web. Their most prominent metabolic feature is autotrophic growth with molecular hydrogen and carbon dioxide as the substrates. However, most members also show an outstanding metabolic flexibility for utilizing a vast variety of different substrates. In contrast to autotrophic growth, which is hardly competitive, metabolic flexibility is seen as a key ability of acetogens to compete in ecosystems and might explain the almost-ubiquitous distribution of acetogenic bacteria in anoxic environments. This review covers the latest findings with respect to the heterotrophic metabolism of acetogenic bacteria, including utilization of carbohydrates, lactate, and different alcohols, especially in the model acetogenAcetobacterium woodii. Modularity of metabolism, a key concept of pathway design in synthetic biology, together with electron bifurcation, to overcome energetic barriers, appears to be the basis for the amazing substrate spectrum. At the same time, acetogens depend on only a relatively small number of enzymes to expand the substrate spectrum. We will discuss the energetic advantages of coupling CO2reduction to fermentations that exploit otherwise-inaccessible substrates and the ecological advantages, as well as the biotechnological applications of the heterotrophic metabolism of acetogens.
Dissertations / Theses on the topic "Wood-Ljungdahl metabolic pathway"
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Hu, Peng. "Thermodynamic, Sulfide, Redox Potential, and pH Effects on Syngas Fermentation." BYU ScholarsArchive, 2011. https://scholarsarchive.byu.edu/etd/2919.
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Recently, work in ethanol production is exploring the fermentation of syngas (primarily CO, CO2, and H2) following gasification of cellulosic biomass. The syngas fermentation by clostridium microbes utilizes the Wood-Ljungdahl metabolic pathway. Along this pathway, the intermediate Acetyl-CoA typically diverges to produce ethanol, acetic acid, and/or cell mass. To develop strategies for process optimization, a thermodynamic analysis was conducted that provided a detailed understanding of the favorability of the reactions along the metabolic pathway. Thermodynamic analysis provided identification of potentially limiting steps. Once these limiting reactions were identified, further thermodynamic analysis provided additional insights into the ways in which reaction conditions could be adjusted to improve product yield as well as minimize the effect of such bottlenecks. In this way, strategies to enhance product formation were effectively formed. A thermodynamic analysis regarding electron utilization suggested that it would be unlikely that H2 is utilized in favor of CO for electron production when both species are present. Therefore, CO conversion efficiency to products will be sacrificed during syngas fermentation since some of the CO will make electrons at the expense of product and cell mass formation. Furthermore, the analysis showed the thermodynamic difference of ethanol production, acetate production, and acetate to ethanol conversion, at varying reaction conditions, such as at different pH and redox potential levels. These differences were then incorporated into a strategy to optimize production of desired product, improve bioreactor design, and decrease the amount of by-product formed. Based on the thermodynamics analysis, experiments with varying experimental conditions were performed. The results showed that sulfide concentration in the media changed. In order to assess the effects of experimental conditions on syngas fermentation and decrease the experimental variability, experiments with controlled sulfide, redox potential, and pH were designed and the results indicated that these factors play key roles on cell growth, product formation and product distribution. Furthermore, experimental conditions had different effects on fermentation during different phases. For example, cell growth is much better at pH=5.8 than pH=4.5. However, the ethanol production rate at pH=4.5 is better than pH=5.8. A strategy involving controlling the pH and redox potential at different phases was effectively applied to improve ethanol production. This work provided significant insights on how varying experimental conditions can affect the syngas fermentation process.