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Complete Genome Sequences of the Soil Oxalotrophic Bacterium Cupriavidus oxalaticus Strain Ox1 and Its Derived mCherry-Tagged Strain. Microbiol Resour Announc 2022; 11:e0018122. [PMID: 35924938 PMCID: PMC9476978 DOI: 10.1128/mra.00181-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Here, we report the complete genome sequences of the soil oxalotrophic bacterium Cupriavidus oxalaticus Ox1 and a derived mCherry-tagged strain. The genome size is approximately 6.69 Mb, with a GC content of 66.9%. The genome sequence of C. oxalaticus Ox1 contains a complete operon for the degradation and assimilation of oxalate.
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Nattermann M, Burgener S, Pfister P, Chou A, Schulz L, Lee SH, Paczia N, Zarzycki J, Gonzalez R, Erb TJ. Engineering a Highly Efficient Carboligase for Synthetic One-Carbon Metabolism. ACS Catal 2021; 11:5396-5404. [PMID: 34484855 PMCID: PMC8411744 DOI: 10.1021/acscatal.1c01237] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 04/06/2021] [Indexed: 12/15/2022]
Abstract
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One of the biggest
challenges to realize a circular carbon economy
is the synthesis of complex carbon compounds from one-carbon (C1)
building blocks. Since the natural solution space of C1–C1
condensations is limited to highly complex enzymes, the development
of more simple and robust biocatalysts may facilitate the engineering
of C1 assimilation routes. Thiamine diphosphate-dependent enzymes
harbor great potential for this task, due to their ability to create
C–C bonds. Here, we employed structure-guided iterative saturation
mutagenesis to convert oxalyl-CoA decarboxylase (OXC) from Methylobacterium extorquens into a glycolyl-CoA synthase
(GCS) that allows for the direct condensation of the two C1 units
formyl-CoA and formaldehyde. A quadruple variant MeOXC4 showed a 100 000-fold
switch between OXC and GCS activities, a 200-fold increase in the
GCS activity compared to the wild type, and formaldehyde affinity
that is comparable to natural formaldehyde-converting enzymes. Notably,
MeOCX4 outcompetes all other natural and engineered enzymes for C1–C1
condensations by more than 40-fold in catalytic efficiency and is
highly soluble in Escherichia coli.
In addition to the increased GCS activity, MeOXC4 showed up to 300-fold
higher activity than the wild type toward a broad range of carbonyl
acceptor substrates. When applied in vivo, MeOXC4 enables the production
of glycolate from formaldehyde, overcoming the current bottleneck
of C1–C1 condensation in whole-cell bioconversions and paving
the way toward synthetic C1 assimilation routes in vivo.
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Affiliation(s)
- Maren Nattermann
- Department of Biochemistry & Synthetic Metabolism, Max-Planck-Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043 Marburg, Germany
| | - Simon Burgener
- Department of Biochemistry & Synthetic Metabolism, Max-Planck-Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043 Marburg, Germany
| | - Pascal Pfister
- Department of Biochemistry & Synthetic Metabolism, Max-Planck-Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043 Marburg, Germany
| | - Alexander Chou
- Department of Chemical and Biomedical Engineering, University of South Florida, Tampa, Florida 33620, United States
| | - Luca Schulz
- Department of Biochemistry & Synthetic Metabolism, Max-Planck-Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043 Marburg, Germany
| | - Seung Hwan Lee
- Department of Chemical and Biomedical Engineering, University of South Florida, Tampa, Florida 33620, United States
| | - Nicole Paczia
- Department of Biochemistry & Synthetic Metabolism, Max-Planck-Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043 Marburg, Germany
| | - Jan Zarzycki
- Department of Biochemistry & Synthetic Metabolism, Max-Planck-Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043 Marburg, Germany
| | - Ramon Gonzalez
- Department of Chemical and Biomedical Engineering, University of South Florida, Tampa, Florida 33620, United States
| | - Tobias J. Erb
- Department of Biochemistry & Synthetic Metabolism, Max-Planck-Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043 Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), 35043 Marburg, Germany
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3
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Oxalyl‐CoA Decarboxylase katalysiert die nukleophile ein‐Kohlenstoff‐Verlängerung von Aldehyden zu chiralen α‐Hydroxysäuren. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201915155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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4
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Burgener S, Cortina NS, Erb TJ. Oxalyl-CoA Decarboxylase Enables Nucleophilic One-Carbon Extension of Aldehydes to Chiral α-Hydroxy Acids. Angew Chem Int Ed Engl 2020; 59:5526-5530. [PMID: 31894608 PMCID: PMC7154664 DOI: 10.1002/anie.201915155] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Indexed: 11/11/2022]
Abstract
The synthesis of complex molecules from simple, renewable carbon units is the goal of a sustainable economy. Here we explored the biocatalytic potential of the thiamine-diphosphate-dependent (ThDP) oxalyl-CoA decarboxylase (OXC)/2-hydroxyacyl-CoA lyase (HACL) superfamily that naturally catalyzes the shortening of acyl-CoA thioester substrates through the release of the C1 -unit formyl-CoA. We show that the OXC/HACL superfamily contains promiscuous members that can be reversed to perform nucleophilic C1 -extensions of various aldehydes to yield the corresponding 2-hydroxyacyl-CoA thioesters. We improved the catalytic properties of Methylorubrum extorquens OXC by rational enzyme engineering and combined it with two newly described enzymes-a specific oxalyl-CoA synthetase and a 2-hydroxyacyl-CoA thioesterase. This enzymatic cascade enabled continuous conversion of oxalate and aromatic aldehydes into valuable (S)-α-hydroxy acids with enantiomeric excess up to 99 %.
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Affiliation(s)
- Simon Burgener
- Department of Biochemistry & Synthetic Metabolism, Max-Planck-Institute for terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043, Marburg, Germany
| | - Niña Socorro Cortina
- Department of Biochemistry & Synthetic Metabolism, Max-Planck-Institute for terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043, Marburg, Germany
| | - Tobias J Erb
- Department of Biochemistry & Synthetic Metabolism, Max-Planck-Institute for terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043, Marburg, Germany
- LOEWE-Center for Synthetic Microbiology, Philipps-University Marburg, Karl-von-Frisch-Str. 8, 35043, Marburg, Germany
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5
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One-carbon chemistry of oxalate oxidoreductase captured by X-ray crystallography. Proc Natl Acad Sci U S A 2015; 113:320-5. [PMID: 26712008 DOI: 10.1073/pnas.1518537113] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Thiamine pyrophosphate (TPP)-dependent oxalate oxidoreductase (OOR) metabolizes oxalate, generating two molecules of CO2 and two low-potential electrons, thus providing both the carbon and reducing equivalents for operation of the Wood-Ljungdahl pathway of acetogenesis. Here we present structures of OOR in which two different reaction intermediate bound states have been trapped: the covalent adducts between TPP and oxalate and between TPP and CO2. These structures, along with the previously determined structure of substrate-free OOR, allow us to visualize how active site rearrangements can drive catalysis. Our results suggest that OOR operates via a bait-and-switch mechanism, attracting substrate into the active site through the presence of positively charged and polar residues, and then altering the electrostatic environment through loop and side chain movements to drive catalysis. This simple but elegant mechanism explains how oxalate, a molecule that humans and most animals cannot break down, can be used for growth by acetogenic bacteria.
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6
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Gibson M, Brignole EJ, Pierce E, Can M, Ragsdale SW, Drennan CL. The Structure of an Oxalate Oxidoreductase Provides Insight into Microbial 2-Oxoacid Metabolism. Biochemistry 2015; 54:4112-20. [PMID: 26061898 PMCID: PMC4498597 DOI: 10.1021/acs.biochem.5b00521] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Thiamine pyrophosphate (TPP), a derivative of vitamin B1, is a versatile and ubiquitous cofactor. When coupled with [4Fe-4S] clusters in microbial 2-oxoacid:ferredoxin oxidoreductases (OFORs), TPP is involved in catalyzing low-potential redox reactions that are important for the synthesis of key metabolites and the reduction of N2, H(+), and CO2. We have determined the high-resolution (2.27 Å) crystal structure of the TPP-dependent oxalate oxidoreductase (OOR), an enzyme that allows microbes to grow on oxalate, a widely occurring dicarboxylic acid that is found in soil and freshwater and is responsible for kidney stone disease in humans. OOR catalyzes the anaerobic oxidation of oxalate, harvesting the low-potential electrons for use in anaerobic reduction and fixation of CO2. We compare the OOR structure to that of the only other structurally characterized OFOR family member, pyruvate:ferredoxin oxidoreductase. This side-by-side structural analysis highlights the key similarities and differences that are relevant for the chemistry of this entire class of TPP-utilizing enzymes.
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Affiliation(s)
- Marcus
I. Gibson
- Department
of Chemistry, Massachusetts Institute of
Technology, 77 Massachusetts
Avenue, Cambridge, Massachusetts 02139, United States
| | - Edward J. Brignole
- Department
of Chemistry, Massachusetts Institute of
Technology, 77 Massachusetts
Avenue, Cambridge, Massachusetts 02139, United States,Howard
Hughes Medical Institute, Massachusetts
Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Elizabeth Pierce
- Department
of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Mehmet Can
- Department
of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Stephen W. Ragsdale
- Department
of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Catherine L. Drennan
- Department
of Chemistry, Massachusetts Institute of
Technology, 77 Massachusetts
Avenue, Cambridge, Massachusetts 02139, United States,Howard
Hughes Medical Institute, Massachusetts
Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States,Department
of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States,E-mail: . Telephone: (617) 253-5622
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7
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Function and X-ray crystal structure of Escherichia coli YfdE. PLoS One 2013; 8:e67901. [PMID: 23935849 PMCID: PMC3720670 DOI: 10.1371/journal.pone.0067901] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Accepted: 05/21/2013] [Indexed: 02/05/2023] Open
Abstract
Many food plants accumulate oxalate, which humans absorb but do not metabolize, leading to the formation of urinary stones. The commensal bacterium Oxalobacter formigenes consumes oxalate by converting it to oxalyl-CoA, which is decarboxylated by oxalyl-CoA decarboxylase (OXC). OXC and the class III CoA-transferase formyl-CoA:oxalate CoA-transferase (FCOCT) are widespread among bacteria, including many that have no apparent ability to degrade or to resist external oxalate. The EvgA acid response regulator activates transcription of the Escherichia coli yfdXWUVE operon encoding YfdW (FCOCT), YfdU (OXC), and YfdE, a class III CoA-transferase that is ~30% identical to YfdW. YfdW and YfdU are necessary and sufficient for oxalate-induced protection against a subsequent acid challenge; neither of the other genes has a known function. We report the purification, in vitro characterization, 2.1-Å crystal structure, and functional assignment of YfdE. YfdE and UctC, an orthologue from the obligate aerobe Acetobacter aceti, perform the reversible conversion of acetyl-CoA and oxalate to oxalyl-CoA and acetate. The annotation of YfdE as acetyl-CoA:oxalate CoA-transferase (ACOCT) expands the scope of metabolic pathways linked to oxalate catabolism and the oxalate-induced acid tolerance response. FCOCT and ACOCT active sites contain distinctive, conserved active site loops (the glycine-rich loop and the GNxH loop, respectively) that appear to encode substrate specificity.
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8
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Gnanandarajah JS, Johnson TJ, Kim HB, Abrahante JE, Lulich JP, Murtaugh MP. Comparative faecal microbiota of dogs with and without calcium oxalate stones. J Appl Microbiol 2012; 113:745-56. [PMID: 22788835 DOI: 10.1111/j.1365-2672.2012.05390.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2012] [Revised: 07/03/2012] [Accepted: 07/04/2012] [Indexed: 12/13/2022]
Abstract
AIMS The absence of enteric oxalate-metabolizing bacterial species (OMBS) increases the likelihood of calcium oxalate (CaOx) urolithiasis in humans and dogs. The goal of this study was to compare the gut microbiota of healthy dogs and CaOx stone formed dogs (CaOx-dogs), especially with respect to OMBS. METHODS AND RESULTS Faecal samples from healthy and CaOx-dogs were obtained to analyse the hindgut microbiota by sequencing the V3 region of bacterial 16S rDNA. In total, 1223 operational taxonomic units (OTUs) were identified at 97% identity. Only 38% of these OTUs were shared by both groups. Significant differences in the relative abundance of 152 OTUs and 36 genera were observed between the two groups of dogs. CONCLUSIONS The faecal microbiota of healthy dogs is distinct from that of CaOx-dogs, indicating that the microbiota is altered in CaOx-dogs. SIGNIFICANCE AND IMPACT OF THE STUDY This is the first study that has compared the gut microbial diversity in healthy and CaOx-dogs. Results of this study indicate the future need for functional and comparative analyses of the total array of oxalate-metabolizing genes between healthy and CaOx stone formers, rather than focusing on specific bacterial species, to understand the critical role of OMBS in CaOx urolithiasis.
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Affiliation(s)
- J S Gnanandarajah
- Departments of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, St Paul, MN 55108, USA
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9
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Oxalyl-coenzyme A reduction to glyoxylate is the preferred route of oxalate assimilation in Methylobacterium extorquens AM1. J Bacteriol 2012; 194:3144-55. [PMID: 22493020 DOI: 10.1128/jb.00288-12] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Oxalate catabolism is conducted by phylogenetically diverse organisms, including Methylobacterium extorquens AM1. Here, we investigate the central metabolism of this alphaproteobacterium during growth on oxalate by using proteomics, mutant characterization, and (13)C-labeling experiments. Our results confirm that energy conservation proceeds as previously described for M. extorquens AM1 and other characterized oxalotrophic bacteria via oxalyl-coenzyme A (oxalyl-CoA) decarboxylase and formyl-CoA transferase and subsequent oxidation to carbon dioxide via formate dehydrogenase. However, in contrast to other oxalate-degrading organisms, the assimilation of this carbon compound in M. extorquens AM1 occurs via the operation of a variant of the serine cycle as follows: oxalyl-CoA reduction to glyoxylate and conversion to glycine and its condensation with methylene-tetrahydrofolate derived from formate, resulting in the formation of C3 units. The recently discovered ethylmalonyl-CoA pathway operates during growth on oxalate but is nevertheless dispensable, indicating that oxalyl-CoA reductase is sufficient to provide the glyoxylate required for biosynthesis. Analysis of an oxalyl-CoA synthetase- and oxalyl-CoA-reductase-deficient double mutant revealed an alternative, although less efficient, strategy for oxalate assimilation via one-carbon intermediates. The alternative process consists of formate assimilation via the tetrahydrofolate pathway to fuel the serine cycle, and the ethylmalonyl-CoA pathway is used for glyoxylate regeneration. Our results support the notion that M. extorquens AM1 has a plastic central metabolism featuring multiple assimilation routes for C1 and C2 substrates, which may contribute to the rapid adaptation of this organism to new substrates and the eventual coconsumption of substrates under environmental conditions.
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10
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Pierce E, Becker DF, Ragsdale SW. Identification and characterization of oxalate oxidoreductase, a novel thiamine pyrophosphate-dependent 2-oxoacid oxidoreductase that enables anaerobic growth on oxalate. J Biol Chem 2010; 285:40515-24. [PMID: 20956531 PMCID: PMC3003350 DOI: 10.1074/jbc.m110.155739] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2010] [Revised: 10/15/2010] [Indexed: 11/06/2022] Open
Abstract
Moorella thermoacetica is an anaerobic acetogen, a class of bacteria that is found in the soil, the animal gastrointestinal tract, and the rumen. This organism engages the Wood-Ljungdahl pathway of anaerobic CO(2) fixation for heterotrophic or autotrophic growth. This paper describes a novel enzyme, oxalate oxidoreductase (OOR), that enables M. thermoacetica to grow on oxalate, which is produced in soil and is a common component of kidney stones. Exposure to oxalate leads to the induction of three proteins that are subunits of OOR, which oxidizes oxalate coupled to the production of two electrons and CO(2) or bicarbonate. Like other members of the 2-oxoacid:ferredoxin oxidoreductase family, OOR contains thiamine pyrophosphate and three [Fe(4)S(4)] clusters. However, unlike previously characterized members of this family, OOR does not use coenzyme A as a substrate. Oxalate is oxidized with a k(cat) of 0.09 s(-1) and a K(m) of 58 μM at pH 8. OOR also oxidizes a few other 2-oxoacids (which do not induce OOR) also without any requirement for CoA. The enzyme transfers its reducing equivalents to a broad range of electron acceptors, including ferredoxin and the nickel-dependent carbon monoxide dehydrogenase. In conjunction with the well characterized Wood-Ljungdahl pathway, OOR should be sufficient for oxalate metabolism by M. thermoacetica, and it constitutes a novel pathway for oxalate metabolism.
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Affiliation(s)
- Elizabeth Pierce
- From the Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109-0606 and
| | - Donald F. Becker
- the Department of Biochemistry, University of Nebraska, Lincoln, Nebraska 68588-0664
| | - Stephen W. Ragsdale
- From the Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109-0606 and
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11
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Blackmore MA, Quayle JR, Walker IO. Choice between autotrophy and heterotrophy in Pseudomonas oxalaticus. Utilization of oxalate by cells after adaptation from growth on formate to growth on oxalate. Biochem J 2010; 107:699-704. [PMID: 16742592 PMCID: PMC1198723 DOI: 10.1042/bj1070699] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
1. The labelling patterns of phosphoglycerate obtained from formate-grown or oxalate-grown Pseudomonas oxalaticus after exposure for 15sec. to [(14)C]formate or [(14)C]oxalate respectively were determined. 2. The phosphoglycerate obtained from the formate-grown cells contained 78% of the radioactivity in the carboxyl group. This is in accord with that predicted for operation of the ribulose diphosphate cycle of carbon dioxide fixation. 3. The labelling pattern of the phosphoglycerate obtained from the oxalate-grown cells approached uniformity, as predicted for the heterotrophic pathway of oxalate assimilation. The departure from complete uniformity may have been due to concurrent (14)CO(2) fixation into C(4) dicarboxylic acids. 4. The labelling pattern of phosphoglycerate obtained from cells that had just started to grow on oxalate after adaptation from formate was determined after incubation of the cells for 15sec. with [(14)C]oxalate. This pattern approached uniformity. 5. The pathway of incorporation of (14)CO(2) into cells that had just started to grow on oxalate after adaptation from formate, in the presence of either formate or oxalate as energy source, was studied by chromatographic and radio-autographic analysis. 6. It is concluded from the isotopic data that a mixed heterotrophic-autotrophic metabolism, with the former mode predominating, operates in the initial stages of growth on oxalate after adaptation from growth on formate.
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Affiliation(s)
- M A Blackmore
- Department of Microbiology, University of Sheffield, and Department of Biochemistry, University of Oxford
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12
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Blackmore MA, Quayle JR. Choice between autotrophy and heterotrophy in Pseudomonas oxalaticus. Growth in mixed substrates. Biochem J 2010; 107:705-13. [PMID: 16742593 PMCID: PMC1198724 DOI: 10.1042/bj1070705] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
1. The type of metabolism adopted by Pseudomonas oxalaticus during growth on a variety of carbon sources was studied. 2. The only substrate upon which autotrophic growth was observed is formate. 3. In mixtures of formate and those substrates upon which the organism can grow faster than on formate, e.g. succinate, lactate or citrate, heterotrophic metabolism results. 4. In mixtures of formate and those substrates upon which the organism can grow at a similar rate to that on formate, e.g. glycollate or glyoxylate, the predominant mode of metabolism adopted is heterotrophic utilization of the C(2) substrate coupled with oxidation of formate as ancillary energy source. 5. P. oxalaticus grows on oxalate 30% slower than on formate. In mixtures of formate and oxalate, the predominant mode of metabolism adopted is autotrophic utilization of formate coupled with oxidation of oxalate as ancillary energy source. 6. In mixtures of formate and those substrates upon which the organism grows at a much lower rate than on formate, e.g. glycerol and malonate, the predominant mode of metabolism adopted is autotrophic utilization of formate. 7. It is concluded that synthesis of the enzymes involved in autotrophic metabolism is controlled by a combination of induction and metabolite repression.
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Werther T, Zimmer A, Wille G, Golbik R, Weiss MS, König S. New insights into structure-function relationships of oxalyl CoA decarboxylase from Escherichia coli. FEBS J 2010. [DOI: 10.1111/j.1742-4658.2010.07673.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Svedruzić D, Jónsson S, Toyota CG, Reinhardt LA, Ricagno S, Lindqvist Y, Richards NGJ. The enzymes of oxalate metabolism: unexpected structures and mechanisms. Arch Biochem Biophys 2005; 433:176-92. [PMID: 15581576 DOI: 10.1016/j.abb.2004.08.032] [Citation(s) in RCA: 106] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2004] [Revised: 08/31/2004] [Indexed: 10/26/2022]
Abstract
Oxalate degrading enzymes have a number of potential applications, including medical diagnosis and treatments for hyperoxaluria and other oxalate-related diseases, the production of transgenic plants for human consumption, and bioremediation of the environment. This review seeks to provide a brief overview of current knowledge regarding the major classes of enzymes and related proteins that are employed in plants, fungi, and bacteria to convert oxalate into CO(2) and/or formate. Not only do these enzymes employ intriguing chemical strategies for cleaving the chemically unreactive C-C bond in oxalate, but they also offer the prospect of providing new insights into the molecular processes that underpin the evolution of biological catalysts.
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Affiliation(s)
- Drazenka Svedruzić
- Department of Chemistry, University of Florida, Gainesville, FL 32611-7200, USA
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15
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Jonsson S, Ricagno S, Lindqvist Y, Richards NGJ. Kinetic and mechanistic characterization of the formyl-CoA transferase from Oxalobacter formigenes. J Biol Chem 2004; 279:36003-12. [PMID: 15213226 DOI: 10.1074/jbc.m404873200] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Oxalobacter formigenes is an obligate anaerobe that colonizes the human gastrointestinal tract and employs oxalate breakdown to generate ATP in a novel process involving the interplay of two coupled enzymes and a membrane-bound oxalate:formate antiporter. Formyl-CoA transferase is a critical enzyme in oxalate-dependent ATP synthesis and is the first Class III CoA-transferase for which a high resolution, three-dimensional structure has been determined (Ricagno, S., Jonsson, S., Richards, N., and Lindqvist, Y. (2003) EMBO J. 22, 3210-3219). We now report the first detailed kinetic characterizations of recombinant, wild type formyl-CoA transferase and a number of site-specific mutants, which suggest that catalysis proceeds via a series of anhydride intermediates. Further evidence for this mechanistic proposal is provided by the x-ray crystallographic observation of an acylenzyme intermediate that is formed when formyl-CoA transferase is incubated with oxalyl-CoA. The catalytic mechanism of formyl-CoA transferase is therefore established and is almost certainly employed by all other members of the Class III CoA-transferase family.
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Affiliation(s)
- Stefan Jonsson
- Department of Chemistry, University of Florida, Gainesville, Florida 32611-7200, USA
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16
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Daniel SL, Pilsl C, Drake HL. Oxalate metabolism by the acetogenic bacteriumMoorella thermoacetica. FEMS Microbiol Lett 2004; 231:39-43. [PMID: 14769464 DOI: 10.1016/s0378-1097(03)00924-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2003] [Revised: 11/26/2003] [Accepted: 12/02/2003] [Indexed: 11/18/2022] Open
Abstract
Whole-cell and cell-extract experiments were performed to study the mechanism of oxalate metabolism in the acetogenic bacterium Moorella thermoacetica. In short-term, whole-cell assays, oxalate consumption was low unless cell suspensions were supplemented with CO(2), KNO(3), or Na(2)S(2)O(3). Cell extracts catalyzed the oxalate-dependent reduction of benzyl viologen. Oxalate consumption occurred concomitant to benzyl viologen reduction; when benzyl viologen was omitted, oxalate was not appreciably consumed. Based on benzyl viologen reduction, specific activities of extracts averaged 0.6 micromol oxalate oxidized min(-1) mg protein(-1). Extracts also catalyzed the formate-dependent reduction of NADP(+); however, oxalate-dependent reduction of NADP(+) was negligible. Oxalate- or formate-dependent reduction of NAD(+) was not observed. Addition of coenzyme A (CoA), acetyl-CoA, or succinyl-CoA to the assay had a minimal effect on the oxalate-dependent reduction of benzyl viologen. These results suggest that oxalate metabolism by M. thermoacetica requires a utilizable electron acceptor and that CoA-level intermediates are not involved.
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Affiliation(s)
- Steven L Daniel
- Department of Biological Sciences, Eastern Illinois University, Charleston, IL 61920, USA.
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17
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Metzler DE, Metzler CM, Sauke DJ. The Organization of Metabolism. Biochemistry 2001. [DOI: 10.1016/b978-012492543-4/50020-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Croes K, Van Veldhoven PP, Mannaerts GP, Casteels M. Production of formyl-CoA during peroxisomal alpha-oxidation of 3-methyl-branched fatty acids. FEBS Lett 1997; 407:197-200. [PMID: 9166898 DOI: 10.1016/s0014-5793(97)00343-8] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
alpha-Oxidation of 3-methyl-substituted fatty acids was studied in purified rat liver peroxisomes. The experiments revealed that formyl-CoA is formed during the alpha-oxidation process. The amount of formyl-CoA found constituted 2-5% of the amount of formate formed. Under the conditions used, no activation of exogenously added formate occurred in purified peroxisomes, whereas 95.5% of added synthetic formyl-CoA was converted to formate. These data indicate that during alpha-oxidation first formyl-CoA is formed, which is then hydrolysed to formate.
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Affiliation(s)
- K Croes
- Katholieke Universiteit Leuven, Afdeling Farmacologie, Campus Gasthuisberg, Belgium
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Sidhu H, Allison M, Peck AB. Identification and classification of Oxalobacter formigenes strains by using oligonucleotide probes and primers. J Clin Microbiol 1997; 35:350-3. [PMID: 9003594 PMCID: PMC229578 DOI: 10.1128/jcm.35.2.350-353.1997] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Genomic DNAs of various strains of Oxalobacter formigenes were subjected to restriction endonuclease fragment length polymorphism- and PCR-based amplification analyses with DNA probes and primers complementary to sequences within either the oxc gene, encoding oxalyl coenzyme A (oxalyl-CoA) decarboxylase, or the frc gene, encoding formyl-CoA transferase. Oligonucleotide probes based on nonconserved sequences of oxc or frc were able to divide O. formigenes strains into at least two groups, consistent with the current separation of O. formigenes strains into groups I and II on the basis of 16S rRNA sequence similarities and lipid content. In contrast, an oligonucleotide probe based on the conserved 5' end of oxc appeared to bind all group I and the majority of group II strains. PCR amplification of the oxc gene showed even greater sensitivity in detecting O. formigenes and provided support for further division of the strains into subgroups. In addition, these oligonucleotides failed to hybridize to or amplify PCR products from whole fecal DNA isolated from fresh stool samples from an individual not colonized with O. formigenes, indicating unique specificity. Thus, these DNA analyses permit both detection as well as classification of O. formigenes strains.
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Affiliation(s)
- H Sidhu
- Department of Pathology & Laboratory Medicine, University of Florida, Gainesville 32610, USA
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Baetz AL, Allison MJ. Purification and characterization of formyl-coenzyme A transferase from Oxalobacter formigenes. J Bacteriol 1990; 172:3537-40. [PMID: 2361939 PMCID: PMC213325 DOI: 10.1128/jb.172.7.3537-3540.1990] [Citation(s) in RCA: 67] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Formyl-coenzyme A (formyl-CoA) transferase was purified from Oxalobacter formigenes by high-pressure liquid chromatography with hydrophobic interaction chromatography and by DEAE anion-exchange chromatography. The enzyme was a single entity on sodium dodecyl sulfate-polyacrylamide gel electrophoresis and gel permeation chromatography (Mr, 44,000). It had an isoelectric point of 4.7. The enzyme catalyzed the transfer of CoA from formyl-CoA to either oxalate or succinate. Apparent Km and Vmax values, respectively, were 3.0 mM and 29.6 mumols/min per mg for formyl-CoA with an excess of succinate. The maximum specific activity was 2.15 mumols of CoA transferred from formyl-CoA to oxalate per min per mg of protein.
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Affiliation(s)
- A L Baetz
- National Animal Disease Center, U.S. Department of Agriculture, Ames, Iowa 50010
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Baetz AL, Allison MJ. Purification and characterization of oxalyl-coenzyme A decarboxylase from Oxalobacter formigenes. J Bacteriol 1989; 171:2605-8. [PMID: 2708315 PMCID: PMC209940 DOI: 10.1128/jb.171.5.2605-2608.1989] [Citation(s) in RCA: 87] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Oxalyl-coenzyme A (oxalyl-CoA) decarboxylase was purified from Oxalobacter formigenes by high-pressure liquid chromatography with hydrophobic interaction chromatography, DEAE anion-exchange chromatography, and gel permeation chromatography. The enzyme is made up of four identical subunits (Mr, 65,000) to give the active enzyme (Mr, 260,000). The enzyme catalyzed the thiamine PPi-dependent decarboxylation of oxalyl-CoA to formate and carbon dioxide. Apparent Km and Vmax values, respectively, were 0.24 mM and 0.25 mumol/min for oxalyl-CoA and 1.1 pM and 0.14 mumol/min for thiamine pyrophosphate. The maximum specific activity was 13.5 microM oxalyl-CoA decarboxylated per min per mg of protein.
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Affiliation(s)
- A L Baetz
- National Animal Disease Center, U.S. Department of Agriculture, Ames, Iowa 50010
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Skorczynski SS, Hamilton GA. Oxalyl thiolesters and N-oxalylcysteine are normal mammalian metabolites. Biochem Biophys Res Commun 1986; 141:1051-7. [PMID: 3814115 DOI: 10.1016/s0006-291x(86)80150-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
A method for the quantitative analysis of N-oxalylcysteine and oxalyl thiolesters (RSCOCOO-) in biological samples is described. These compounds were found in all rat tissues examined (kidney, liver, brain, heart, muscle and fat), with the amount of N-oxalylcysteine ranging up to 18 nmoles/g wet weight and that of oxalyl thiolesters up to 65 nmoles/g wet weight. The identification of such compounds in animal tissues adds further credence to the hypothesis that they may be important metabolic effectors.
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Gunshore S, Hamilton GA. Inhibition of the catalytic subunit of phosphorylase phosphatase by oxalyl thioesters and its possible relevance to the mechanism of insulin action. Biochem Biophys Res Commun 1986; 134:93-9. [PMID: 3004447 DOI: 10.1016/0006-291x(86)90531-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Oxalyl thioesters, especially S-oxalylglutathione, are shown to be effective inhibitors of the catalytic subunit of phosphorylase phosphatase. The amount of inhibition was found to be time dependent and partially reversed by thiols, thus suggesting that at least part of the inhibition is due to oxalylation of an enzymic thiol group. The possibility that the inhibition of the phosphatase by oxalyl thioesters may be important in vivo and that oxalyl thioesters may be functioning as negative intracellular messengers for insulin is discussed.
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Metabolic regulation in Pseudomonas oxalaticus OX1. Diauxic growth on mixtures of oxalate and formate or acetate. Arch Microbiol 1980. [DOI: 10.1007/bf00427736] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Chandra TS, Shethna YI. Oxalate and formate in Alcaligenes and Pseudomonas species. Antonie Van Leeuwenhoek 1975; 41:465-77. [PMID: 1083207 DOI: 10.1007/bf02565090] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Oxalate is metabolized by the glycerate pathway involving glyoxylate carboligase in Alcaligenes LOx and Pseudomonas KOx, and by the serine pathway involving hydroxypyruvate reductase in Ps.MOx and Ps.AM1 (var. 470). Although A.LOx does not grow on formate, stimulation of growth was observed in the presence of amino acids and a few Kreb's cycle intermediates. A.LOx possesses two different mechanisms for the oxidation of formate: (1) the constitutive formate oxidase which is present in the particulate fraction of oxalate-grown and succinate-plus-formate-grown cells; (2) the inducible NAD-linked formate dehydrogenase present in the 100 000 x g supernatant fraction of the cell-free extracts of oxalate-grown cells alone. The two systems occur simultaneously in oxalate-grown cells. The effect of inhibitors on formate oxidase activity and the other enzyme activities of the particulate formate-oxidizing fraction indicate that the oxidation of formate is linked to the respiratory chain.
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Scrutton MC. Chapter XII Assay of Enzymes of CO2 Metabolism. METHODS IN MICROBIOLOGY 1971. [DOI: 10.1016/s0580-9517(08)70584-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
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Chapter IV Evaluation of Methods Used to Determine Metabolic Pathways. METHODS IN MICROBIOLOGY 1971. [DOI: 10.1016/s0580-9517(08)70576-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register]
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Blackmore MA, Quayle JR. Microbial growth on oxalate by a route not involving glyoxylate carboligase. Biochem J 1970; 118:53-9. [PMID: 5472155 PMCID: PMC1179078 DOI: 10.1042/bj1180053] [Citation(s) in RCA: 74] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
1. The metabolism of oxalate by the pink-pigmented organisms, Pseudomonas AM1, Pseudomonas AM2, Protaminobacter ruber and Pseudomonas extorquens has been compared with that of the non-pigmented Pseudomonas oxalaticus. 2. During growth on oxalate, all the organisms contain oxalyl-CoA decarboxylase, formate dehydrogenase and oxalyl-CoA reductase. This is consistent with oxidation of oxalate to carbon dioxide taking place via oxalyl-CoA, formyl-CoA and formate as intermediates, and also reduction of oxalate to glyoxylate taking place via oxalyl-CoA. 3. The pink-pigmented organisms, when grown on oxalate, contain l-serine-glyoxylate aminotransferase and hydroxypyruvate reductase but do not contain glyoxylate carboligase. The converse of this obtains in oxalate-grown Ps. oxalaticus. This indicates that, in contrast with Ps. oxalaticus, synthesis of C(3) compounds from oxalate by the pink-pigmented organisms occurs by a variant of the ;serine pathway' used by Pseudomonas AM1 during growth on C(1) compounds. 4. Evidence in favour of this scheme is provided by the finding that a mutant of Pseudomonas AM1 that lacks hydroxypyruvate reductase is not able to grow on oxalate.
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