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Dowaidar M. Synthetic biology of metabolic cycles for Enhanced CO 2 capture and Sequestration. Bioorg Chem 2024; 153:107774. [PMID: 39260160 DOI: 10.1016/j.bioorg.2024.107774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2024] [Revised: 08/01/2024] [Accepted: 08/28/2024] [Indexed: 09/13/2024]
Abstract
In most organisms, the tri-carboxylic acid cycle (TCA cycle) is an essential metabolic system that is involved in both energy generation and carbon metabolism. Its uni-directionality, however, restricts its use in synthetic biology and carbon fixation. Here, it is describing the use of the modified TCA cycle, called the Tri-carboxylic acid Hooked to Ethylene by Enzyme Reactions and Amino acid Synthesis, the reductive tricarboxylic acid branch/4-hydroxybutyryl-CoA/ethylmalonyl-CoA/acetyl-CoA (THETA) cycle, in Escherichia coli for the purposes of carbon fixation and amino acid synthesis. Three modules make up the THETA cycle: (1) pyruvate to succinate transformation, (2) succinate to crotonyl-CoA change, and (3) crotonyl-CoA to acetyl-CoA and pyruvate change. It is presenting each module's viability in vivo and showing how it integrates into the E. coli metabolic network to support growth on minimal medium without the need for outside supplementation. Enzyme optimization, route redesign, and heterologous expression were used to get over metabolic roadblocks and produce functional modules. Furthermore, the THETA cycle may be improved by including components of the Carbon-Efficient Tri-Carboxylic Acid Cycle (CETCH cycle) to improve carbon fixation. THETA cycle's promise as a platform for applications in synthetic biology and carbon fixation.
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Affiliation(s)
- Moataz Dowaidar
- Bioengineering Department, King Fahd University of Petroleum and Minerals (KFUPM), Dhahran 31261, Saudi Arabia; Interdisciplinary Research Center for Hydrogen Technologies and Carbon Management, King Fahd University of Petroleum and Minerals (KFUPM), Dhahran, 31261, Saudi Arabia; Biosystems and Machines Research Center, King Fahd University of Petroleum and Minerals (KFUPM), Dhahran, 31261, Saudi Arabia.
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2
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Polleys CM, Singh P, Thieu HT, Genega EM, Jahanseir N, Zuckerman AL, Díaz FR, Patra A, Beheshti A, Georgakoudi I. Rapid, high-resolution, non-destructive assessments of metabolic and morphological homogeneity uniquely identify high-grade cervical precancerous lesions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.10.593564. [PMID: 38798665 PMCID: PMC11118292 DOI: 10.1101/2024.05.10.593564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Purpose Two-photon microscopy (2PM) is an emerging clinical imaging modality with the potential to non-invasively assess tissue metabolism and morphology in high-resolution. This study aimed to assess the translational potential of 2PM for improved detection of high-grade cervical precancerous lesions. Experimental Design 2P images attributed to reduced nicotinamide adenine dinucleotide (phosphate) (NAD(P)H) and oxidized flavoproteins (FP) were acquired from the full epithelial thickness of freshly excised human cervical tissue biopsies (N = 62). Fifteen biopsies harbored high-grade squamous intraepithelial lesions (HSILs), 14 biopsies harbored low-grade SILs (LSILs), and 33 biopsies were benign. Quadratic discriminant analysis (QDA) leveraged morphological and metabolic functional metrics extracted from these images to predict the presence of HSILs. We performed gene set enrichment analysis (GSEA) using datasets available on the Gene Expression Omnibus (GEO) to validate the presence of metabolic reprogramming in HSILs. Results Integrating metabolic and morphological 2P-derived metrics from finely sampled, full-thickness epithelia achieved a high 90.8 ± 6.1% sensitivity and 72.3 ± 11.3% specificity of HSIL detection. Notably, sensitivity (91.4 ± 12.0%) and specificity (77.5 ± 12.6%) were maintained when utilizing metrics from only two images at 12- and 72-μm from the tissue surface. Upregulation of glycolysis, fatty acid metabolism, and oxidative phosphorylation in HSIL tissues validated the metabolic reprogramming captured by 2P biomarkers. Conclusion Label-free 2P images from as few as two epithelial depths enable rapid and robust HSIL detection through the quantitative characterization of metabolic and morphological reprogramming, underscoring the potential of this tool for clinical evaluation of cervical precancers.
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Affiliation(s)
| | - Pramesh Singh
- Data Intensive Studies Center, Tufts University, Medford, MA 02155, USA
| | - Hong-Thao Thieu
- Department of Obstetrics and Gynecology, Tufts University School of Medicine, Tufts Medical Center, Boston, MA 02111, USA
| | - Elizabeth M. Genega
- Department of Pathology and Laboratory Medicine, Tufts University School of Medicine, Tufts Medical Center, Boston, MA 02111, USA
| | - Narges Jahanseir
- Department of Pathology and Laboratory Medicine, Tufts University School of Medicine, Tufts Medical Center, Boston, MA 02111, USA
| | - Andrea L. Zuckerman
- Department of Obstetrics and Gynecology, Tufts University School of Medicine, Tufts Medical Center, Boston, MA 02111, USA
| | - Francisca Rius Díaz
- Department of Preventive Medicine and Public Health, Faculty of Medicine, University of Málaga, 32 Louis Pasteur Boulevard, 29071 Málaga, Spain
| | - Abani Patra
- Data Intensive Studies Center, Tufts University, Medford, MA 02155, USA
| | - Afshin Beheshti
- Blue Marble Space Institute of Science, Seattle, WA, 98104 USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Irene Georgakoudi
- Department of Biomedical Engineering, Tufts University, Medford, MA 02155, USA
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3
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Chen Y, Han A, Wang M, Wei D, Wang W. Metabolic Engineering of Trichoderma reesei for l-Malic Acid Production. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:4043-4050. [PMID: 36812909 DOI: 10.1021/acs.jafc.2c09078] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
l-Malic acid has various applications in the chemical and food industries. The filamentous fungus Trichoderma reesei is known to be an efficient enzyme producer. Here, through metabolic engineering, T. reesei was constructed for the first time as an excellent cell factory for l-malic acid production. The heterologous overexpression of genes encoding the C4-dicarboxylate transporter from Aspergillus oryzae and Schizosaccharomyces pombe initiated l-malic acid production. The overexpression of pyruvate carboxylase from A. oryzae in the reductive tricarboxylic acid pathway further increased both the titer and yield of l-malic acid, resulting in the highest titer reported in a shake-flask culture. Furthermore, the deletion of malate thiokinase blocked l-malic acid degradation. Finally, the engineered T. reesei strain produced 220.5 g/L of l-malic acid in a 5 L fed-batch culture (productivity of 1.15 g/L/h). A T. reesei cell factory was created for the efficient production of l-malic acid.
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Affiliation(s)
- Yumeng Chen
- State Key Lab of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Ao Han
- State Key Lab of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Meng Wang
- State Key Lab of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Dongzhi Wei
- State Key Lab of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Wei Wang
- State Key Lab of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
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4
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Diehl C, Gerlinger PD, Paczia N, Erb TJ. Synthetic anaplerotic modules for the direct synthesis of complex molecules from CO 2. Nat Chem Biol 2023; 19:168-175. [PMID: 36470994 PMCID: PMC9889269 DOI: 10.1038/s41589-022-01179-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 09/22/2022] [Indexed: 12/12/2022]
Abstract
Anaplerosis is an essential feature of metabolism that allows the continuous operation of natural metabolic networks, such as the citric acid cycle, by constantly replenishing drained intermediates. However, this concept has not been applied to synthetic in vitro metabolic networks, thus far. Here we used anaplerotic strategies to directly access the core sequence of the CETCH cycle, a new-to-nature in vitro CO2-fixation pathway that features several C3-C5 biosynthetic precursors. We drafted four different anaplerotic modules that use CO2 to replenish the CETCH cycle's intermediates and validated our designs by producing 6-deoxyerythronolide B (6-DEB), the C21-macrolide backbone of erythromycin. Our best design allowed the carbon-positive synthesis of 6-DEB via 54 enzymatic reactions in vitro at yields comparable to those with isolated 6-DEB polyketide synthase (DEBS). Our work showcases how new-to-nature anaplerotic modules can be designed and tailored to enhance and expand the synthetic capabilities of complex catalytic in vitro reaction networks.
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Affiliation(s)
- Christoph Diehl
- grid.419554.80000 0004 0491 8361Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Patrick D. Gerlinger
- grid.419554.80000 0004 0491 8361Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Nicole Paczia
- grid.419554.80000 0004 0491 8361Core Facility for Metabolomics and Small Molecule Mass Spectrometry, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Tobias J. Erb
- grid.419554.80000 0004 0491 8361Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany ,grid.452532.7SYNMIKRO Center for Synthetic Microbiology, Marburg, Germany
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5
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TMT-based proteomic analysis of the inactivation effect of high voltage atmospheric cold plasma treatment on Pseudomonas aeruginosa. Lebensm Wiss Technol 2022. [DOI: 10.1016/j.lwt.2022.113981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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6
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Lacroux J, Atteia A, Brugière S, Couté Y, Vallon O, Steyer JP, van Lis R. Proteomics unveil a central role for peroxisomes in butyrate assimilation of the heterotrophic Chlorophyte alga Polytomella sp. Front Microbiol 2022; 13:1029828. [PMID: 36353459 PMCID: PMC9637915 DOI: 10.3389/fmicb.2022.1029828] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Accepted: 10/05/2022] [Indexed: 09/08/2023] Open
Abstract
Volatile fatty acids found in effluents of the dark fermentation of biowastes can be used for mixotrophic growth of microalgae, improving productivity and reducing the cost of the feedstock. Microalgae can use the acetate in the effluents very well, but butyrate is poorly assimilated and can inhibit growth above 1 gC.L-1. The non-photosynthetic chlorophyte alga Polytomella sp. SAG 198.80 was found to be able to assimilate butyrate fast. To decipher the metabolic pathways implicated in butyrate assimilation, quantitative proteomics study was developed comparing Polytomella sp. cells grown on acetate and butyrate at 1 gC.L-1. After statistical analysis, a total of 1772 proteins were retained, of which 119 proteins were found to be overaccumulated on butyrate vs. only 46 on acetate, indicating that butyrate assimilation necessitates additional metabolic steps. The data show that butyrate assimilation occurs in the peroxisome via the β-oxidation pathway to produce acetyl-CoA and further tri/dicarboxylic acids in the glyoxylate cycle. Concomitantly, reactive oxygen species defense enzymes as well as the branched amino acid degradation pathway were strongly induced. Although no clear dedicated butyrate transport mechanism could be inferred, several membrane transporters induced on butyrate are identified as potential condidates. Metabolic responses correspond globally to the increased needs for central cofactors NAD, ATP and CoA, especially in the peroxisome and the cytosol.
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Affiliation(s)
| | - Ariane Atteia
- MARBEC, Univ Montpellier, CNRS, Ifremer, IRD, Sète, France
| | - Sabine Brugière
- Univ Grenoble Alpes, CEA, INSERM, UMR BioSanté U1292, CNRS, CEA, Grenoble, France
| | - Yohann Couté
- Univ Grenoble Alpes, CEA, INSERM, UMR BioSanté U1292, CNRS, CEA, Grenoble, France
| | - Olivier Vallon
- Institut de Biologie Physico-Chimique, UMR7141 CNRS-Sorbonne Université, Paris, France
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Cremers G, Jetten MSM, Op den Camp HJM, Lücker S. Metascan: METabolic Analysis, SCreening and ANnotation of Metagenomes. FRONTIERS IN BIOINFORMATICS 2022; 2:861505. [PMID: 36304333 PMCID: PMC9580885 DOI: 10.3389/fbinf.2022.861505] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 05/30/2022] [Indexed: 12/03/2022] Open
Abstract
Large scale next generation metagenomic sequencing of complex environmental samples paves the way for detailed analysis of nutrient cycles in ecosystems. For such an analysis, large scale unequivocal annotation is a prerequisite, which however is increasingly hampered by growing databases and analysis time. Hereto, we created a hidden Markov model (HMM) database by clustering proteins according to their KEGG indexing. HMM profiles for key genes of specific metabolic pathways and nutrient cycles were organized in subsets to be able to analyze each important elemental cycle separately. An important motivation behind the clustered database was to enable a high degree of resolution for annotation, while decreasing database size and analysis time. Here, we present Metascan, a new tool that can fully annotate and analyze deeply sequenced samples with an average analysis time of 11 min per genome for a publicly available dataset containing 2,537 genomes, and 1.1 min per genome for nutrient cycle analysis of the same sample. Metascan easily detected general proteins like cytochromes and ferredoxins, and additional pmoCAB operons were identified that were overlooked in previous analyses. For a mock community, the BEACON (F1) score was 0.72–0.93 compared to the information in NCBI GenBank. In combination with the accompanying database, Metascan provides a fast and useful annotation and analysis tool, as demonstrated by our proof-of-principle analysis of a complex mock community metagenome.
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8
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Duncan D, Auclair K. Itaconate: an antimicrobial metabolite of macrophages. CAN J CHEM 2022. [DOI: 10.1139/cjc-2021-0117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Itaconate is a conjugated 1,4-dicarboxylate produced by macrophages. This small molecule has recently received increasing attention due to its role in modulating the immune response of macrophages upon exposure to pathogens. Itaconate has also been proposed to play an antimicrobial function; however, this has not been explored as intensively. Consistent with the latter, itaconate is known to show antibacterial activity in vitro and was reported to inhibit isocitrate lyase, an enzyme required for survival of bacterial pathogens in mammalian systems. Recent studies have revealed bacterial growth inhibition under biologically relevant conditions. In addition, an antimicrobial role for itaconate is substantiated by the high concentration of itaconate found in bacteria-containing vacuoles, and by the production of itaconate-degrading enzymes in pathogens such as Salmonella enterica ser. Typhimurium, Pseudomonas aeruginosa, and Yersinia pestis. This review describes the current state of literature in understanding the role of itaconate as an antimicrobial agent in host–pathogen interactions.
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Affiliation(s)
- Dustin Duncan
- Department of Chemistry, McGill University, Montreal, QC H3A 0B8, Canada
- Department of Chemistry, McGill University, Montreal, QC H3A 0B8, Canada
| | - Karine Auclair
- Department of Chemistry, McGill University, Montreal, QC H3A 0B8, Canada
- Department of Chemistry, McGill University, Montreal, QC H3A 0B8, Canada
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9
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Ribeiro M, Ceballos S, Poeta P, Torres C, Igrejas G. Methicillin-Resistant Staphylococcus aureus Proteome Response to Antibiotic Stress Provides Insights for New Therapeutic Strategies. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2021; 25:711-724. [PMID: 34705556 DOI: 10.1089/omi.2021.0151] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Antimicrobial resistance is a global threat, with methicillin-resistant Staphylococcus aureus (MRSA) being one of the most representative drug-resistant pathogens. MRSA spread is increasing due to its ability to establish new reservoirs. To this end, the clonal complex (CC)-130 is an emerging genetic lineage, generally regarded as animal adapted and carrying the mecC gene, and sporadically found in humans. Although the MRSA antibiotic resistance mechanisms have been described, there are limited data on systems-wide omics responses to antibiotic stress, particularly at the proteome level. In this study, a gel-based quantitative proteomics approach was performed to assess the cellular responses of a mecC-harboring CC130 MRSA strain of human origin to subinhibitory doses of cefoxitin. We focused on the global response of MRSA to antibiotic stress and upon this treatment, 53 proteins were significantly differentially expressed. Most of the latter proteins were mapped to having functions in cellular metabolism while some glycolysis-related proteins showed a decreased expression after cefoxitin stress. On the contrary, pyruvate kinase, a potential antimicrobial drug target, was found upregulated. Also, quorum sensing, genetic information processing, and stress response proteins were found upregulated. Low-affinity penicillin-binding protein (mecC-encoded) was found in cefoxitin-treated samples. In conclusion, these new findings on cefoxitin-induced proteome changes provide important insights and molecular leads for innovation in treatment of MRSA specifically, and omics approaches to address antibiotic resistance generally.
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Affiliation(s)
- Miguel Ribeiro
- Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro, Vila Real, Portugal.,Functional Genomics and Proteomics Unity, University of Trás-os-Montes and Alto Douro, Vila Real, Portugal.,LAQV-REQUIMTE, Faculty of Science and Technology, University Nova of Lisbon, Lisbon, Portugal
| | - Sara Ceballos
- Area Biochemistry and Molecular Biology, University of La Rioja, Logroño, Spain
| | - Patrícia Poeta
- LAQV-REQUIMTE, Faculty of Science and Technology, University Nova of Lisbon, Lisbon, Portugal.,Microbiology and Antibiotic Resistance Team (MicroART), Department of Veterinary Sciences, University of Trás-os-Montes and Alto Douro (UTAD), Vila Real, Portugal
| | - Carmen Torres
- Area Biochemistry and Molecular Biology, University of La Rioja, Logroño, Spain
| | - Gilberto Igrejas
- Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro, Vila Real, Portugal.,Functional Genomics and Proteomics Unity, University of Trás-os-Montes and Alto Douro, Vila Real, Portugal.,LAQV-REQUIMTE, Faculty of Science and Technology, University Nova of Lisbon, Lisbon, Portugal
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10
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Duncan D, Lupien A, Behr MA, Auclair K. Effect of pH on the antimicrobial activity of the macrophage metabolite itaconate. MICROBIOLOGY-SGM 2021; 167. [PMID: 34020726 DOI: 10.1099/mic.0.001050] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The production of itaconate by macrophages was only discovered in 2011. An increasing number of studies have since revealed essential biological functions for this small molecule, ranging from antimicrobial to immunomodulator. The antibacterial role of itaconate has however been questioned because the estimated concentration of itaconate in macrophages (low-millimolar) is lower than the minimum inhibitory concentration (MIC) of itaconate reported for several bacterial strains (low-to-mid-millimolar). We note that some of these investigations have tended to ignore the high acidity of this small diacid (pKas 3.85 and 5.45), thereby potentially biassing activity measurements. We measured the MIC of itaconate in Escherichia coli (not known to metabolize itaconate) and in Salmonella enterica serovar Typhimurium (known to metabolize itaconate) at varying pH values to probe the effect that pH has on itaconate toxicity. Herein, we demonstrate that the antimicrobial effect of itaconate is dependent upon the pH of the media and that itaconate does have antimicrobial activity at biologically relevant pH and concentrations. Under nutrient-poor conditions, the antimicrobial activity of itaconate in both E. coli and S. Typhimurium increased approximately 200-fold when the pH was dropped by one unit, whereas itaconate was not found to be toxic under nutrient rich conditions. Our results also reveal that the activity of itaconate is synergistic with acidity, yet is not a function of increased permeability with protonation. Similar experiments performed with succinate (a pKa-matched diacid) yielded drastically different results, consistent with a target-based mechanism of action for itaconate. Overall, our work shows the importance of controlling the pH when performing experiments with itaconic acid.
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Affiliation(s)
- Dustin Duncan
- Department of Chemistry, McGill University, Montreal, Quebec, Canada
| | - Andréanne Lupien
- McGill International TB Centre, McGill University, Montreal, Quebec, Canada.,Department of Medicine, McGill University, Montreal, Quebec, Canada
| | - Marcel A Behr
- McGill International TB Centre, McGill University, Montreal, Quebec, Canada.,Department of Medicine, McGill University, Montreal, Quebec, Canada
| | - Karine Auclair
- Department of Chemistry, McGill University, Montreal, Quebec, Canada
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11
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Huang J, Fraser ME. Tartryl-CoA inhibits succinyl-CoA synthetase. Acta Crystallogr F Struct Biol Commun 2020; 76:302-308. [PMID: 32627745 PMCID: PMC7336359 DOI: 10.1107/s2053230x20008201] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 06/20/2020] [Indexed: 11/10/2022] Open
Abstract
Succinyl-CoA synthetase (SCS) catalyzes the only substrate-level phosphorylation step in the tricarboxylic acid cycle. Human GTP-specific SCS (GTPSCS), an αβ-heterodimer, was produced in Escherichia coli. The purified protein crystallized from a solution containing tartrate, CoA and magnesium chloride, and a crystal diffracted to 1.52 Å resolution. Tartryl-CoA was discovered to be bound to GTPSCS. The CoA portion lies in the amino-terminal domain of the α-subunit and the tartryl end extends towards the catalytic histidine residue. The terminal carboxylate binds to the phosphate-binding site of GTPSCS.
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Affiliation(s)
- Ji Huang
- Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Marie E. Fraser
- Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
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12
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Heine V, Meinert-Berning C, Lück J, Mikowsky N, Voigt B, Riedel K, Steinbüchel A. The catabolism of 3,3'-thiodipropionic acid in Variovorax paradoxus strain TBEA6: A proteomic analysis. PLoS One 2019; 14:e0211876. [PMID: 30742653 PMCID: PMC6370202 DOI: 10.1371/journal.pone.0211876] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 01/23/2019] [Indexed: 01/11/2023] Open
Abstract
Variovorax paradoxus strain TBEA6 is one of the few organisms known to utilize 3,3'-thiodipropionate (TDP) as the only source of carbon and energy. It cleaves TDP to 3-mercaptopropionate (3MP), which is a direct precursor for polythioester synthesis. To establish this process in V. paradoxus TBEA6, it is crucial to unravel its TDP metabolism. Therefore, a proteomic approach with subsequent deletion of interesting genes in the bacterium was chosen. Cells were cultivated with D-gluconate, TDP or 3-sulfinopropionate as the only carbon sources. Proteins with high abundances in gels of cells cultivated with either of the organic sulfur compounds were analyzed further. Thereby, we did not only confirm parts of the already postulated TDP metabolism, but also eight new protein candidates for TDP degradation were detected. Deletions of the corresponding genes (two enoyl-CoA hydratases (Ech-20 and Ech-30), an FK506-binding protein, a putative acetolactate synthase, a carnitinyl-CoA dehydratase, and a putative crotonase family protein) were obtained. Only the deletions of both Ech-20 and Ech-30 led to a TDP negative phenotype. The deletion mutant of VPARA_05510, which encodes the putative crotonase family protein showed reduced growth with TDP. The three genes are located in one cluster with genes proven to be involved in TDP metabolism. Thermal shift assays showed an increased stability of Ech-20 with TDP-CoA but not with TDP. These results indicate that Ech-20 uses TDP-CoA as a substrate instead of TDP. Hence, we postulate a new putative pathway for TDP metabolism. Ech-30 interacts with neither TDP-CoA nor TDP but might interact with other CoA-activated intermediates of the proposed pathway. Further enzyme characterization is necessary to unravel the complete pathway from TDP to 3MP.
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Affiliation(s)
- Viktoria Heine
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität, Münster, Germany
| | - Christina Meinert-Berning
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität, Münster, Germany
| | - Janina Lück
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität, Münster, Germany
| | - Nadine Mikowsky
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität, Münster, Germany
| | - Birgit Voigt
- Institut für Mikrobiologie, Ernst-Moritz-Arndt-Universität, Greifswald, Germany
| | - Katharina Riedel
- Institut für Mikrobiologie, Ernst-Moritz-Arndt-Universität, Greifswald, Germany
| | - Alexander Steinbüchel
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität, Münster, Germany
- Environmental Science Department, King Abdulaziz University, Jeddah, Saudi Arabia
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13
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Kallscheuer N, Gätgens J, Lübcke M, Pietruszka J, Bott M, Polen T. Improved production of adipate with Escherichia coli by reversal of β-oxidation. Appl Microbiol Biotechnol 2016; 101:2371-2382. [PMID: 27933454 DOI: 10.1007/s00253-016-8033-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Revised: 11/23/2016] [Accepted: 11/26/2016] [Indexed: 11/28/2022]
Abstract
The linear C6 dicarboxylic acid adipic acid is an important bulk chemical in the petrochemical industry as precursor of the polymer nylon-6,6-polyamide. In recent years, efforts were made towards the biotechnological production of adipate from renewable carbon sources using microbial cells. One strategy is to produce adipate via a reversed β-oxidation pathway. Hitherto, the adipate titers were very low due to limiting enzyme activities for this pathway. In most cases, the CoA intermediates are non-natural substrates for the tested enzymes and were therefore barely converted. We here tested heterologous enzymes in Escherichia coli to overcome these limitations and to improve the production of adipate via a reverse β-oxidation pathway. We tested in vitro selected enzymes for the efficient reduction of the enoyl-CoA and in the final reaction for the thioester cleavage. The genes encoding the enzymes which showed in vitro the highest activity were then used to construct an expression plasmid for a synthetic adipate pathway. Expression of paaJ, paaH, paaF, dcaA, and tesB in E. coli BL21(DE3) resulted in the production of up to 36 mg/L of adipate after 30 h of cultivation. Beside the activities of the pathway enzymes, the availability of metabolic precursors may limit the synthesis of adipate, providing another key target for further strain engineering towards high-yield production of adipate with E. coli.
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Affiliation(s)
- Nicolai Kallscheuer
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany.
| | - Jochem Gätgens
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Marvin Lübcke
- Institute of Bioorganic Chemistry, Heinrich-Heine-Universität, Düsseldorf, 52425, Jülich, Germany
| | - Jörg Pietruszka
- Institute of Bioorganic Chemistry, Heinrich-Heine-Universität, Düsseldorf, 52425, Jülich, Germany
| | - Michael Bott
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Tino Polen
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany.
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Allen KD, White RH. Occurrence and biosynthesis of 3-mercaptopropionic acid in Methanocaldococcus jannaschii. FEMS Microbiol Lett 2016; 363:fnw217. [PMID: 27634308 DOI: 10.1093/femsle/fnw217] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/12/2016] [Indexed: 12/30/2022] Open
Abstract
In a non-targeted analysis of thiol-containing compounds in the hyperthermophilic methanogen Methanocaldococcus jannaschii, we discovered three unexpected metabolites: 3-mercaptopropionic acid (MPA), 2-hydroxy-4-mercaptobutyric acid (HMBA) and 4-mercapto-2-oxobutyric acid (MOB). HMBA and MOB have never been reported as natural products, while MPA is highly prevalent in aquatic environments as a result of biotic and abiotic processing of sulfur-containing compounds. This report provides evidence that HMBA and MOB are part of a biosynthetic pathway to generate MPA in M. jannaschii We show that HMBA can be biosynthesized from malate semialdehyde and hydrogen sulfide, likely using a mechanism similar to that proposed for coenzyme M, coenzyme B and homocysteine biosynthesis in methanogens, where an aldehyde is converted to a thiol. The L-sulfolactate dehydrogenase, derived from the MJ1425 gene, is shown to catalyze the NAD-dependent oxidation of HMBA to MOB. Finally, we demonstrate that HMBA can be used as a biosynthetic precursor to MPA in M. jannaschii cell extracts. This proposed pathway may contribute to the wide occurrence of MPA in marine environments and indicates that MPA must serve some important function in M. jannaschii.
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Affiliation(s)
- Kylie D Allen
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Robert H White
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
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15
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Huang J, Fraser ME. Structural basis for the binding of succinate to succinyl-CoA synthetase. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2016; 72:912-21. [PMID: 27487822 DOI: 10.1107/s2059798316010044] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 06/20/2016] [Indexed: 01/19/2023]
Abstract
Succinyl-CoA synthetase catalyzes the only step in the citric acid cycle that provides substrate-level phosphorylation. Although the binding sites for the substrates CoA, phosphate, and the nucleotides ADP and ATP or GDP and GTP have been identified, the binding site for succinate has not. To determine this binding site, pig GTP-specific succinyl-CoA synthetase was crystallized in the presence of succinate, magnesium ions and CoA, and the structure of the complex was determined by X-ray crystallography to 2.2 Å resolution. Succinate binds in the carboxy-terminal domain of the β-subunit. The succinate-binding site is near both the active-site histidine residue that is phosphorylated in the reaction and the free thiol of CoA. The carboxy-terminal domain rearranges when succinate binds, burying this active site. However, succinate is not in position for transfer of the phosphoryl group from phosphohistidine. Here, it is proposed that when the active-site histidine residue has been phosphorylated by GTP, the phosphohistidine displaces phosphate and triggers the movement of the carboxylate of succinate into position to be phosphorylated. The structure shows why succinyl-CoA synthetase is specific for succinate and does not react appreciably with citrate nor with the other C4-dicarboxylic acids of the citric acid cycle, fumarate and oxaloacetate, but shows some activity with L-malate.
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Affiliation(s)
- Ji Huang
- Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Marie E Fraser
- Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
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16
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Németh B, Doczi J, Csete D, Kacso G, Ravasz D, Adams D, Kiss G, Nagy AM, Horvath G, Tretter L, Mócsai A, Csépányi-Kömi R, Iordanov I, Adam-Vizi V, Chinopoulos C. Abolition of mitochondrial substrate-level phosphorylation by itaconic acid produced by LPS-induced Irg1 expression in cells of murine macrophage lineage. FASEB J 2015; 30:286-300. [PMID: 26358042 DOI: 10.1096/fj.15-279398] [Citation(s) in RCA: 92] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Accepted: 08/31/2015] [Indexed: 01/28/2023]
Abstract
Itaconate is a nonamino organic acid exhibiting antimicrobial effects. It has been recently identified in cells of macrophage lineage as a product of an enzyme encoded by immunoresponsive gene 1 (Irg1), acting on the citric acid cycle intermediate cis-aconitate. In mitochondria, itaconate can be converted by succinate-coenzyme A (CoA) ligase to itaconyl-CoA at the expense of ATP (or GTP), and is also a weak competitive inhibitor of complex II. Here, we investigated specific bioenergetic effects of increased itaconate production mediated by LPS-induced stimulation of Irg1 in murine bone marrow-derived macrophages (BMDM) and RAW-264.7 cells. In rotenone-treated macrophage cells, stimulation by LPS led to impairment in substrate-level phosphorylation (SLP) of in situ mitochondria, deduced by a reversal in the directionality of the adenine nucleotide translocase operation. In RAW-264.7 cells, the LPS-induced impairment in SLP was reversed by short-interfering RNA(siRNA)-but not scrambled siRNA-treatment directed against Irg1. LPS dose-dependently inhibited oxygen consumption rates (61-91%) and elevated glycolysis rates (>21%) in BMDM but not RAW-264.7 cells, studied under various metabolic conditions. In isolated mouse liver mitochondria treated with rotenone, itaconate dose-dependently (0.5-2 mM) reversed the operation of adenine nucleotide translocase, implying impairment in SLP, an effect that was partially mimicked by malonate. However, malonate yielded greater ADP-induced depolarizations (3-19%) than itaconate. We postulate that itaconate abolishes SLP due to 1) a "CoA trap" in the form of itaconyl-CoA that negatively affects the upstream supply of succinyl-CoA from the α-ketoglutarate dehydrogenase complex; 2) depletion of ATP (or GTP), which are required for the thioesterification by succinate-CoA ligase; and 3) inhibition of complex II leading to a buildup of succinate which shifts succinate-CoA ligase equilibrium toward ATP (or GTP) utilization. Our results support the notion that Irg1-expressing cells of macrophage lineage lose the capacity of mitochondrial SLP for producing itaconate during mounting of an immune defense.
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Affiliation(s)
- Beáta Németh
- *Department of Medical Biochemistry and Department of Physiology, Semmelweis University, Budapest, Hungary; and Lendület Neurobiochemistry Research Group, Lendület Inflammation Physiology Research Group, Laboratory for Neurobiochemistry, and Lendület Ion Channel Research Group, Hungarian Academy of Sciences, Budapest, Hungary
| | - Judit Doczi
- *Department of Medical Biochemistry and Department of Physiology, Semmelweis University, Budapest, Hungary; and Lendület Neurobiochemistry Research Group, Lendület Inflammation Physiology Research Group, Laboratory for Neurobiochemistry, and Lendület Ion Channel Research Group, Hungarian Academy of Sciences, Budapest, Hungary
| | - Dániel Csete
- *Department of Medical Biochemistry and Department of Physiology, Semmelweis University, Budapest, Hungary; and Lendület Neurobiochemistry Research Group, Lendület Inflammation Physiology Research Group, Laboratory for Neurobiochemistry, and Lendület Ion Channel Research Group, Hungarian Academy of Sciences, Budapest, Hungary
| | - Gergely Kacso
- *Department of Medical Biochemistry and Department of Physiology, Semmelweis University, Budapest, Hungary; and Lendület Neurobiochemistry Research Group, Lendület Inflammation Physiology Research Group, Laboratory for Neurobiochemistry, and Lendület Ion Channel Research Group, Hungarian Academy of Sciences, Budapest, Hungary
| | - Dora Ravasz
- *Department of Medical Biochemistry and Department of Physiology, Semmelweis University, Budapest, Hungary; and Lendület Neurobiochemistry Research Group, Lendület Inflammation Physiology Research Group, Laboratory for Neurobiochemistry, and Lendület Ion Channel Research Group, Hungarian Academy of Sciences, Budapest, Hungary
| | - Daniel Adams
- *Department of Medical Biochemistry and Department of Physiology, Semmelweis University, Budapest, Hungary; and Lendület Neurobiochemistry Research Group, Lendület Inflammation Physiology Research Group, Laboratory for Neurobiochemistry, and Lendület Ion Channel Research Group, Hungarian Academy of Sciences, Budapest, Hungary
| | - Gergely Kiss
- *Department of Medical Biochemistry and Department of Physiology, Semmelweis University, Budapest, Hungary; and Lendület Neurobiochemistry Research Group, Lendület Inflammation Physiology Research Group, Laboratory for Neurobiochemistry, and Lendület Ion Channel Research Group, Hungarian Academy of Sciences, Budapest, Hungary
| | - Adam M Nagy
- *Department of Medical Biochemistry and Department of Physiology, Semmelweis University, Budapest, Hungary; and Lendület Neurobiochemistry Research Group, Lendület Inflammation Physiology Research Group, Laboratory for Neurobiochemistry, and Lendület Ion Channel Research Group, Hungarian Academy of Sciences, Budapest, Hungary
| | - Gergo Horvath
- *Department of Medical Biochemistry and Department of Physiology, Semmelweis University, Budapest, Hungary; and Lendület Neurobiochemistry Research Group, Lendület Inflammation Physiology Research Group, Laboratory for Neurobiochemistry, and Lendület Ion Channel Research Group, Hungarian Academy of Sciences, Budapest, Hungary
| | - Laszlo Tretter
- *Department of Medical Biochemistry and Department of Physiology, Semmelweis University, Budapest, Hungary; and Lendület Neurobiochemistry Research Group, Lendület Inflammation Physiology Research Group, Laboratory for Neurobiochemistry, and Lendület Ion Channel Research Group, Hungarian Academy of Sciences, Budapest, Hungary
| | - Attila Mócsai
- *Department of Medical Biochemistry and Department of Physiology, Semmelweis University, Budapest, Hungary; and Lendület Neurobiochemistry Research Group, Lendület Inflammation Physiology Research Group, Laboratory for Neurobiochemistry, and Lendület Ion Channel Research Group, Hungarian Academy of Sciences, Budapest, Hungary
| | - Roland Csépányi-Kömi
- *Department of Medical Biochemistry and Department of Physiology, Semmelweis University, Budapest, Hungary; and Lendület Neurobiochemistry Research Group, Lendület Inflammation Physiology Research Group, Laboratory for Neurobiochemistry, and Lendület Ion Channel Research Group, Hungarian Academy of Sciences, Budapest, Hungary
| | - Iordan Iordanov
- *Department of Medical Biochemistry and Department of Physiology, Semmelweis University, Budapest, Hungary; and Lendület Neurobiochemistry Research Group, Lendület Inflammation Physiology Research Group, Laboratory for Neurobiochemistry, and Lendület Ion Channel Research Group, Hungarian Academy of Sciences, Budapest, Hungary
| | - Vera Adam-Vizi
- *Department of Medical Biochemistry and Department of Physiology, Semmelweis University, Budapest, Hungary; and Lendület Neurobiochemistry Research Group, Lendület Inflammation Physiology Research Group, Laboratory for Neurobiochemistry, and Lendület Ion Channel Research Group, Hungarian Academy of Sciences, Budapest, Hungary
| | - Christos Chinopoulos
- *Department of Medical Biochemistry and Department of Physiology, Semmelweis University, Budapest, Hungary; and Lendület Neurobiochemistry Research Group, Lendület Inflammation Physiology Research Group, Laboratory for Neurobiochemistry, and Lendület Ion Channel Research Group, Hungarian Academy of Sciences, Budapest, Hungary
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Mesaconase Activity of Class I Fumarase Contributes to Mesaconate Utilization by Burkholderia xenovorans. Appl Environ Microbiol 2015; 81:5632-8. [PMID: 26070669 DOI: 10.1128/aem.00822-15] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Accepted: 06/02/2015] [Indexed: 11/20/2022] Open
Abstract
Pseudomonas aeruginosa, Yersinia pestis, and many other bacteria are able to utilize the C5-dicarboxylic acid itaconate (methylenesuccinate). Itaconate degradation starts with its activation to itaconyl coenzyme A (itaconyl-CoA), which is further hydrated to (S)-citramalyl-CoA, and citramalyl-CoA is finally cleaved into acetyl-CoA and pyruvate. The xenobiotic-degrading betaproteobacterium Burkholderia xenovorans possesses a P. aeruginosa-like itaconate degradation gene cluster and is able to grow on itaconate and its isomer mesaconate (methylfumarate). Although itaconate degradation proceeds in B. xenovorans in the same way as in P. aeruginosa, the pathway of mesaconate utilization is not known. Here, we show that mesaconate is metabolized through its hydration to (S)-citramalate. The latter compound is then metabolized to acetyl-CoA and pyruvate with the participation of two enzymes of the itaconate degradation pathway, a promiscuous itaconate-CoA transferase able to activate (S)-citramalate in addition to itaconate and (S)-citramalyl-CoA lyase. The first reaction of the pathway, the mesaconate hydratase (mesaconase) reaction, is catalyzed by a class I fumarase. As this enzyme (Bxe_A3136) has similar efficiencies (kcat/Km) for both fumarate and mesaconate hydration, we conclude that B. xenovorans class I fumarase is in fact a promiscuous fumarase/mesaconase. This promiscuity is physiologically relevant, as it allows the growth of this bacterium on mesaconate as a sole carbon and energy source.
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Wübbeler JH, Hiessl S, Meinert C, Poehlein A, Schuldes J, Daniel R, Steinbüchel A. The genome of Variovorax paradoxus strain TBEA6 provides new understandings for the catabolism of 3,3'-thiodipropionic acid and hence the production of polythioesters. J Biotechnol 2015; 209:85-95. [PMID: 26073999 DOI: 10.1016/j.jbiotec.2015.06.390] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Revised: 06/01/2015] [Accepted: 06/09/2015] [Indexed: 11/30/2022]
Abstract
The betaproteobacterium Variovorax paradoxus strain TBEA6 is capable of using 3,3'-thiodipropionic acid (TDP) as sole carbon and energy source for growth. This thioether is employed for several industrial applications. It can be applied as precursor for the biotechnical production of polythioesters (PTE), which represent persistent bioplastics. Consequently, the genome of V. paradoxus strain TBEA6 was sequenced. The draft genome sequence comprises approximately 7.2Mbp and 6852 predicted open reading frames. Furthermore, transposon mutagenesis to unravel the catabolism of TDP in strain TBEA6 was performed. Screening of 20,000 mutants mapped the insertions of Tn5::mob in 32 mutants, which all showed no growth with TDP as sole carbon source. Based on the annotated genome sequence together with transposon-induced mutagenesis, defined gene deletions, in silico analyses and comparative genomics, a comprehensive pathway for the catabolism of TDP is proposed: TDP is imported via the tripartite tricarboxcylate transport system and/or the TRAP-type dicarboxylate transport system. The initial cleavage of TDP into 3-hydroxypropionic acid (3HP) and 3-mercaptopropionic acid (3MP), which serves as precursor substrate for PTE synthesis, is most probably performed by the FAD-dependent oxidoreductase Fox. 3HP is presumably catabolized via malonate semialdehyde, whereas 3MP is oxygenated by the 3MP-dioxygenase Mdo yielding 3-sulfinopropionic acid (3SP). Afterwards, 3SP is linked to coenzyme A. The next step is the abstraction of sulfite by a desulfinase, and the resulting propionyl-CoA enters the central metabolism. Sulfite is oxidized to sulfate by the sulfite-oxidizing enzyme SoeABC and is subsequently excreted by the cells by the sulfate exporter Pse.
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Affiliation(s)
- Jan Hendrik Wübbeler
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, 48149 Münster, Germany
| | - Sebastian Hiessl
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, 48149 Münster, Germany
| | - Christina Meinert
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, 48149 Münster, Germany
| | - Anja Poehlein
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institut für Mikrobiologie und Genetik, Georg-August-Universität Göttingen, Göttingen, Germany
| | - Jörg Schuldes
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institut für Mikrobiologie und Genetik, Georg-August-Universität Göttingen, Göttingen, Germany
| | - Rolf Daniel
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institut für Mikrobiologie und Genetik, Georg-August-Universität Göttingen, Göttingen, Germany
| | - Alexander Steinbüchel
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, 48149 Münster, Germany; Faculty of Biology, King Abdulaziz University, Jeddah, Saudi Arabia.
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19
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Wübbeler JH, Steinbüchel A. New pathways for bacterial polythioesters. Curr Opin Biotechnol 2014; 29:85-92. [DOI: 10.1016/j.copbio.2014.02.017] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2013] [Revised: 02/24/2014] [Accepted: 02/25/2014] [Indexed: 11/25/2022]
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20
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Identification of 3-sulfinopropionyl coenzyme A (CoA) desulfinases within the Acyl-CoA dehydrogenase superfamily. J Bacteriol 2013; 196:882-93. [PMID: 24317404 DOI: 10.1128/jb.01265-13] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
In a previous study, the essential role of 3-sulfinopropionyl coenzyme A (3SP-CoA) desulfinase acyl-CoA dehydrogenase (Acd) in Advenella mimigardefordensis strain DPN7(T) (AcdDPN7) during degradation of 3,3'-dithiodipropionic acid (DTDP) was elucidated. DTDP is a sulfur-containing precursor substrate for biosynthesis of polythioesters (PTEs). AcdDPN7 showed high amino acid sequence similarity to acyl-CoA dehydrogenases but was unable to catalyze a dehydrogenation reaction. Hence, it was investigated in the present study whether 3SP-CoA desulfinase activity is an uncommon or a widespread property within the acyl-CoA dehydrogenase superfamily. Therefore, proteins of the acyl-CoA dehydrogenase superfamily from Advenella kashmirensis WT001, Bacillus cereus DSM31, Cupriavidus necator N-1, Escherichia coli BL21, Pseudomonas putida KT2440, Burkholderia xenovorans LB400, Ralstonia eutropha H16, Variovorax paradoxus B4, Variovorax paradoxus S110, and Variovorax paradoxus TBEA6 were expressed in E. coli strains. All purified acyl-CoA dehydrogenases appeared as homotetramers, as revealed by size exclusion chromatography. AcdS110, AcdB4, AcdH16, and AcdKT2440 were able to dehydrogenate isobutyryl-CoA. AcdKT2440 additionally dehydrogenated butyryl-CoA and valeryl-CoA, whereas AcdDSM31 dehydrogenated only butyryl-CoA and valeryl-CoA. No dehydrogenation reactions were observed with propionyl-CoA, isovaleryl-CoA, succinyl-CoA, and glutaryl-CoA for any of the investigated acyl-CoA dehydrogenases. Only AcdTBEA6, AcdN-1, and AcdLB400 desulfinated 3SP-CoA and were thus identified as 3SP-CoA desulfinases within the acyl-CoA dehydrogenase family, although none of these three Acds dehydrogenated any of the tested acyl-CoA thioesters. No appropriate substrates were identified for AcdBL21 and AcdWT001. Spectrophotometric assays provided apparent Km and Vmax values for active substrates and indicated the applicability of phylogenetic analyses to predict the substrate range of uncharacterized acyl-CoA dehydrogenases. Furthermore, C. necator N-1 was found to utilize 3SP as the sole source of carbon and energy.
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