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Liu M, Devlin JC, Hu J, Volkova A, Battaglia TW, Ho M, Asplin JR, Byrd A, Loke P, Li H, Ruggles KV, Tsirigos A, Blaser MJ, Nazzal L. Microbial genetic and transcriptional contributions to oxalate degradation by the gut microbiota in health and disease. eLife 2021; 10:e63642. [PMID: 33769280 PMCID: PMC8062136 DOI: 10.7554/elife.63642] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 03/23/2021] [Indexed: 12/14/2022] Open
Abstract
Over-accumulation of oxalate in humans may lead to nephrolithiasis and nephrocalcinosis. Humans lack endogenous oxalate degradation pathways (ODP), but intestinal microbes can degrade oxalate using multiple ODPs and protect against its absorption. The exact oxalate-degrading taxa in the human microbiota and their ODP have not been described. We leverage multi-omics data (>3000 samples from >1000 subjects) to show that the human microbiota primarily uses the type II ODP, rather than type I. Furthermore, among the diverse ODP-encoding microbes, an oxalate autotroph, Oxalobacter formigenes, dominates this function transcriptionally. Patients with inflammatory bowel disease (IBD) frequently suffer from disrupted oxalate homeostasis and calcium oxalate nephrolithiasis. We show that the enteric oxalate level is elevated in IBD patients, with highest levels in Crohn's disease (CD) patients with both ileal and colonic involvement consistent with known nephrolithiasis risk. We show that the microbiota ODP expression is reduced in IBD patients, which may contribute to the disrupted oxalate homeostasis. The specific changes in ODP expression by several important taxa suggest that they play distinct roles in IBD-induced nephrolithiasis risk. Lastly, we colonize mice that are maintained in the gnotobiotic facility with O. formigenes, using either a laboratory isolate or an isolate we cultured from human stools, and observed a significant reduction in host fecal and urine oxalate levels, supporting our in silico prediction of the importance of the microbiome, particularly O. formigenes in host oxalate homeostasis.
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Affiliation(s)
- Menghan Liu
- NYU Langone HealthNew YorkUnited States
- Vilcek Institute of Graduate Biomedical SciencesNew YorkUnited States
| | - Joseph C Devlin
- NYU Langone HealthNew YorkUnited States
- Vilcek Institute of Graduate Biomedical SciencesNew YorkUnited States
| | - Jiyuan Hu
- NYU Langone HealthNew YorkUnited States
| | - Angelina Volkova
- NYU Langone HealthNew YorkUnited States
- Vilcek Institute of Graduate Biomedical SciencesNew YorkUnited States
| | | | - Melody Ho
- NYU Langone HealthNew YorkUnited States
| | - John R Asplin
- Litholink Corporation, Laboratory Corporation of America HoldingsChicagoUnited States
| | - Allyson Byrd
- Department of Cancer Immunology, Genentech IncSouth San FranciscoUnited States
| | - P'ng Loke
- NYU Langone HealthNew YorkUnited States
| | - Huilin Li
- NYU Langone HealthNew YorkUnited States
| | | | | | - Martin J Blaser
- Center for Advanced Biotechnology and Medicine, Rutgers UniversityNew YorkUnited States
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Pierce E, Mansoorabadi SO, Can M, Reed GH, Ragsdale SW. Properties of Intermediates in the Catalytic Cycle of Oxalate Oxidoreductase and Its Suicide Inactivation by Pyruvate. Biochemistry 2017; 56:2824-2835. [PMID: 28514140 PMCID: PMC5463272 DOI: 10.1021/acs.biochem.7b00222] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Oxalate:ferredoxin oxidoreductase (OOR) is an unusual member of the thiamine pyrophosphate (TPP)-dependent 2-oxoacid:ferredoxin oxidoreductase (OFOR) family in that it catalyzes the coenzyme A (CoA)-independent conversion of oxalate into 2 equivalents of carbon dioxide. This reaction is surprising because binding of CoA to the acyl-TPP intermediate of other OFORs results in formation of a CoA ester, and in the case of pyruvate:ferredoxin oxidoreductase (PFOR), CoA binding generates the central metabolic intermediate acetyl-CoA and promotes a 105-fold acceleration of the rate of electron transfer. Here we describe kinetic, spectroscopic, and computational results to show that CoA has no effect on catalysis by OOR and describe the chemical rationale for why this cofactor is unnecessary in this enzymatic transformation. Our results demonstrate that, like PFOR, OOR binds pyruvate and catalyzes decarboxylation to form the same hydroxyethylidine-TPP (HE-TPP) intermediate and one-electron transfer to generate the HE-TPP radical. However, in OOR, this intermediate remains stranded at the active site as a covalent inhibitor. These and other results indicate that, like other OFOR family members, OOR generates an oxalate-derived adduct with TPP (oxalyl-TPP) that undergoes decarboxylation and one-electron transfer to form a radical intermediate remaining bound to TPP (dihydroxymethylidene-TPP). However, unlike in PFOR, where CoA binding drives formation of the product, in OOR, proton transfer and a conformational change in the "switch loop" alter the redox potential of the radical intermediate sufficiently to promote the transfer of an electron into the iron-sulfur cluster network, leading directly to a second decarboxylation and completing the catalytic cycle.
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Affiliation(s)
- Elizabeth Pierce
- Department of Biological Chemistry, University of Michigan , Ann Arbor, Michigan 48109-0606, United States
| | - Steven O Mansoorabadi
- Department of Chemistry and Biochemistry, Auburn University , 179 Chemistry Building, Auburn, Alabama 36849, United States
| | - Mehmet Can
- Department of Biological Chemistry, University of Michigan , Ann Arbor, Michigan 48109-0606, United States
| | - George H Reed
- Department of Biochemistry, University of Wisconsin-Madison , 440 Henry Mall, Madison, Wisconsin 53726, United States
| | - Stephen W Ragsdale
- Department of Biological Chemistry, University of Michigan , Ann Arbor, Michigan 48109-0606, United States
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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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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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Espinoza LAT, ter Haseborg E, Weber M, Karle E, Peschke R, Frimmel FH. Effect of selected metal ions on the photocatalytic degradation of bog lake water natural organic matter. WATER RESEARCH 2011; 45:1039-1048. [PMID: 21093013 DOI: 10.1016/j.watres.2010.10.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2010] [Revised: 09/14/2010] [Accepted: 10/13/2010] [Indexed: 05/30/2023]
Abstract
Herein we report the photocatalytic degradation of natural organic matter from a bog lake (Lake Hohloh, Black Forest, Germany) in the presence of 0, 5, and 10 μmol L(-1) of added Cu(2+), Mn(2+), Zn(2+) and Fe(3+). The reactions were followed by size exclusion chromatography with organic carbon detection (SEC-DOC) and by measurements of low molecular weight organic acids. Addition of Cu(2+) had the largest effect of all four studied metals, leading to a retardation in the molecular size changes in NOM: degradation of the larger molecular weight fraction was inhibited leading to reduced production of smaller molecular weight metabolites. Similarly, addition of Cu(2+) reduced the production of formic and oxalic acids, and reduced the bioavailability of the partially degraded NOM.
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Affiliation(s)
- Luis A Tercero Espinoza
- Water Chemistry, Engler-Bunte-Institut, Karlsruhe Institute of Technology, Engler-Bunte-Ring 1, 76131 Karlsruhe, Germany.
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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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Abstract
Acetogens utilize the acetyl-CoA Wood-Ljungdahl pathway as a terminal electron-accepting, energy-conserving, CO(2)-fixing process. The decades of research to resolve the enzymology of this pathway (1) preceded studies demonstrating that acetogens not only harbor a novel CO(2)-fixing pathway, but are also ecologically important, and (2) overshadowed the novel microbiological discoveries of acetogens and acetogenesis. The first acetogen to be isolated, Clostridium aceticum, was reported by Klaas Tammo Wieringa in 1936, but was subsequently lost. The second acetogen to be isolated, Clostridium thermoaceticum, was isolated by Francis Ephraim Fontaine and co-workers in 1942. C. thermoaceticum became the most extensively studied acetogen and was used to resolve the enzymology of the acetyl-CoA pathway in the laboratories of Harland Goff Wood and Lars Gerhard Ljungdahl. Although acetogenesis initially intrigued few scientists, this novel process fostered several scientific milestones, including the first (14)C-tracer studies in biology and the discovery that tungsten is a biologically active metal. The acetyl-CoA pathway is now recognized as a fundamental component of the global carbon cycle and essential to the metabolic potentials of many different prokaryotes. The acetyl-CoA pathway and variants thereof appear to be important to primary production in certain habitats and may have been the first autotrophic process on earth and important to the evolution of life. The purpose of this article is to (1) pay tribute to those who discovered acetogens and acetogenesis, and to those who resolved the acetyl-CoA pathway, and (2) highlight the ecology and physiology of acetogens within the framework of their scientific roots.
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Affiliation(s)
- Harold L Drake
- Department of Ecological Microbiology, University of Bayreuth, 95440 Bayreuth, Germany.
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Degradation of glyoxylate and glycolate with ATP synthesis by a thermophilic anaerobic bacterium, Moorella sp. strain HUC22-1. Appl Environ Microbiol 2007; 74:1447-52. [PMID: 18083850 DOI: 10.1128/aem.01421-07] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The thermophilic homoacetogenic bacterium Moorella sp. strain HUC22-1 ferments glyoxylate to acetate roughly according to the reaction 2 glyoxylate --> acetate + 2 CO(2). A batch culture with glyoxylate and yeast extract yielded 11.7 g per mol of cells per substrate, which was much higher than that obtained with H(2) plus CO(2). Crude extracts of glyoxylate-grown cells catalyzed the ADP- and NADP-dependent condensation of glyoxylate and acetyl coenzyme A (acetyl-CoA) to pyruvate and CO(2) and converted pyruvate to acetyl-CoA and CO(2), which are the key reactions of the malyl-CoA pathway. ATP generation was also detected during the key enzyme reactions of this pathway. Furthermore, this bacterium consumed l-malate, an intermediate in the malyl-CoA pathway, and produced acetate. These findings suggest that Moorella sp. strain HUC22-1 can generate ATP by substrate-level phosphorylation during glyoxylate catabolism through the malyl-CoA pathway.
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Abstract
Moorella thermoacetica (originally isolated as Clostridium thermoaceticum) has served as the primary acetogenic bacterium for the resolution of the acetyl coenzyme A (acetyl-CoA) or Wood-Lijungdahl pathway, a metabolic pathway that (i) autotrophically assimilates CO2 and (ii) is centrally important to the turnover of carbon in many habitats. The purpose of this article is to highlight the diverse physiological features of this model acetogen and to examine some of the consequences of its metabolic capabilities.
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Affiliation(s)
- Harold L Drake
- Department of Ecological Microbiology, University of Bayreuth, Germany.
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Drake HL, Daniel SL. Physiology of the thermophilic acetogen Moorella thermoacetica. Res Microbiol 2004; 155:422-36. [PMID: 15249059 DOI: 10.1016/j.resmic.2004.03.003] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2004] [Accepted: 03/12/2004] [Indexed: 10/26/2022]
Abstract
Moorella thermoacetica (originally isolated as Clostridium thermoaceticum) has served as the primary acetogenic bacterium for the resolution of the acetyl coenzyme A (acetyl-CoA) or Wood-Ljungdahl pathway, a metabolic pathway that (i) autotrophically assimilates CO2 and (ii) is centrally important to the turnover of carbon in many habitats. The purpose of this article is to highlight the diverse physiological features of this model acetogen and to examine some of the consequences of its metabolic capabilities.
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Affiliation(s)
- Harold L Drake
- Department of Ecological Microbiology, University of Bayreuth, 95440 Bayreuth, Germany.
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