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Geng H, Xu Y, Dai X, Yang D. Abiotic and biotic roles of metals in the anaerobic digestion of sewage sludge: A review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:169313. [PMID: 38123094 DOI: 10.1016/j.scitotenv.2023.169313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 12/09/2023] [Accepted: 12/10/2023] [Indexed: 12/23/2023]
Abstract
Anaerobic digestion (AD) is a promising technique for sludge treatment and resource recovery. Metals are very important components of sludge and can have substantial effects on its complex nature and microbial activity. However, systematic reviews have not addressed how metals in sludge affect AD and how they can be regulated to improve AD. This paper comprehensively reviews the effects of metals on the AD of sludge from both abiotic and biotic perspectives. First, we introduce the contents and basic characteristics (e.g., chemical forms) of intrinsic metals in sewage sludge. Then, we summarise the main mechanism by which metals influence sludge properties and the methods for removing metals and thus improving AD. Next, we analyze the effects of both intrinsic and exogenous metals on the enzymes and microbial communities involved in anaerobic bioconversion, focusing on the types, critical concentrations and valence states of the metals. Finally, we propose ideas for future research on the roles of metals in the AD of sludge. In summary, this review systematically clarifies the roles of metals in the AD of sludge and provides a reference for improving AD by regulating these metals.
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Affiliation(s)
- Hui Geng
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Tongji University, Shanghai 200092, PR China
| | - Ying Xu
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Tongji University, Shanghai 200092, PR China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, PR China.
| | - Xiaohu Dai
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Tongji University, Shanghai 200092, PR China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, PR China
| | - Dianhai Yang
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Tongji University, Shanghai 200092, PR China
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2
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Varrella S, Tangherlini M, Corinaldesi C. Deep Hypersaline Anoxic Basins as Untapped Reservoir of Polyextremophilic Prokaryotes of Biotechnological Interest. Mar Drugs 2020; 18:md18020091. [PMID: 32019162 PMCID: PMC7074082 DOI: 10.3390/md18020091] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 01/27/2020] [Accepted: 01/28/2020] [Indexed: 12/18/2022] Open
Abstract
Deep-sea hypersaline anoxic basins (DHABs) are considered to be among the most extreme ecosystems on our planet, allowing only the life of polyextremophilic organisms. DHABs’ prokaryotes exhibit extraordinary metabolic capabilities, representing a hot topic for microbiologists and biotechnologists. These are a source of enzymes and new secondary metabolites with valuable applications in different biotechnological fields. Here, we review the current knowledge on prokaryotic diversity in DHABs, highlighting the biotechnological applications of identified taxa and isolated species. The discovery of new species and molecules from these ecosystems is expanding our understanding of life limits and is expected to have a strong impact on biotechnological applications.
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Affiliation(s)
- Stefano Varrella
- Department of Materials, Environmental Sciences and Urban Planning, Polytechnic University of Marche, 60131 Ancona, Italy;
| | | | - Cinzia Corinaldesi
- Department of Materials, Environmental Sciences and Urban Planning, Polytechnic University of Marche, 60131 Ancona, Italy;
- Correspondence:
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3
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Dipasquale L, Pradhan N, d’Ippolito G, Fontana A. Potential of Hydrogen Fermentative Pathways in Marine Thermophilic Bacteria: Dark Fermentation and Capnophilic Lactic Fermentation in Thermotoga and Pseudothermotoga Species. GRAND CHALLENGES IN MARINE BIOTECHNOLOGY 2018. [DOI: 10.1007/978-3-319-69075-9_6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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Hao X, Wei J, van Loosdrecht MCM, Cao D. Analysing the mechanisms of sludge digestion enhanced by iron. WATER RESEARCH 2017; 117:58-67. [PMID: 28390236 DOI: 10.1016/j.watres.2017.03.048] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 02/05/2017] [Accepted: 03/23/2017] [Indexed: 06/07/2023]
Abstract
Carbon-neutral operation of wastewater treatment plants (WWTPs) requires enhancing anaerobic digestion (AD) of excess sludge for a higher energy conversion efficiency. Among others, iron has been identified to function on enhancing methane production in AD. As an industrial residual, waste iron scraps (WISs) have been reported as potentially enhancing CH4 production in AD. With this study, the mechanisms of AD enhanced by WISs are analysed in a two-phase process: acidogenic phase (AP) and methanogenic phase (MP). Semi-continuous tests substantially excluded ORP reduction and hydrogen-evolution corrosion induced by WISs in enhancing CH4 production, although WISs (10 g Fe/L) could indeed increase CH4 production by 10.1% and 21.4% when added in AP and MP respectively. Detection on both FISH and enzymatic activities of involved microorganisms revealed that the stimulating effects of WISs on anaerobes (both catabolism and anabolism) could play an important (96.3%) role in enhancing CH4 production, which would facilitate hydrolysis of refractory organics and improvement of electron transport rate (ETR).
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Affiliation(s)
- Xiaodi Hao
- Sino-Dutch R&D Centre for Future Wastewater Treatment Technologies/Key Laboratory of Urban Stormwater System and Water Environment, Beijing University of Civil Engineering & Architecture, Beijing 100044, PR China.
| | - Jing Wei
- Sino-Dutch R&D Centre for Future Wastewater Treatment Technologies/Key Laboratory of Urban Stormwater System and Water Environment, Beijing University of Civil Engineering & Architecture, Beijing 100044, PR China
| | - Mark C M van Loosdrecht
- Sino-Dutch R&D Centre for Future Wastewater Treatment Technologies/Key Laboratory of Urban Stormwater System and Water Environment, Beijing University of Civil Engineering & Architecture, Beijing 100044, PR China; Dept. of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Daqi Cao
- Sino-Dutch R&D Centre for Future Wastewater Treatment Technologies/Key Laboratory of Urban Stormwater System and Water Environment, Beijing University of Civil Engineering & Architecture, Beijing 100044, PR China
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Yan Z, Fushinobu S, Wakagi T. Four Cys residues in heterodimeric 2-oxoacid:ferredoxin oxidoreductase are required for CoA-dependent oxidative decarboxylation but not for a non-oxidative decarboxylation. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1844:736-43. [PMID: 24491525 DOI: 10.1016/j.bbapap.2014.01.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 11/13/2013] [Revised: 01/22/2014] [Accepted: 01/24/2014] [Indexed: 11/26/2022]
Abstract
Heterodimeric 2-oxoacid:ferredoxin oxidoreductase (OFOR) from Sulfolobus tokodaii (StOFOR) has only one [4Fe-4S]²⁺ cluster, ligated by 4 Cys residues, C12, C15, C46, and C197. The enzyme has no other Cys. To elucidate the role of these Cys residues in holding of the iron-sulfur cluster in the course of oxidative decarboxylation of a 2-oxoacid, one or two of these Cys residues was/were substituted with Ala to yield C12A, C15A, C46A, C197A and C12/15A mutants. All the mutants showed the loss of iron-sulfur cluster, except the C197A one which retained some unidentified type of iron-sulfur cluster. On addition of pyruvate to OFOR, the wild type enzyme exhibited a chromophore at 320nm and a stable large EPR signal corresponding to a hydroxyethyl-ThDP radical, while the mutant enzymes did not show formation of any radical intermediate or production of acetyl-CoA, suggesting that the intact [4Fe-4S] cluster is necessary for these processes. The stable radical intermediate in wild type OFOR was rapidly decomposed upon addition of CoA in the absence of an electron acceptor. Non-oxidative decarboxylation of pyruvate, yielding acetaldehyde, has been reported to require CoA for other OFORs, but StOFOR catalyzed acetaldehyde production from pyruvate independent of CoA, regardless of whether the iron-sulfur cluster is intact [4Fe-4S] type or not. A comprehensive reaction scheme for StOFOR with a single cluster was proposed.
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Affiliation(s)
- Zhen Yan
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Japan
| | - Shinya Fushinobu
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Japan
| | - Takayoshi Wakagi
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Japan.
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6
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Eram MS, Ma K. Decarboxylation of pyruvate to acetaldehyde for ethanol production by hyperthermophiles. Biomolecules 2013; 3:578-96. [PMID: 24970182 PMCID: PMC4030962 DOI: 10.3390/biom3030578] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Revised: 08/02/2013] [Accepted: 08/15/2013] [Indexed: 11/16/2022] Open
Abstract
Pyruvate decarboxylase (PDC encoded by pdc) is a thiamine pyrophosphate (TPP)-containing enzyme responsible for the conversion of pyruvate to acetaldehyde in many mesophilic organisms. However, no pdc/PDC homolog has yet been found in fully sequenced genomes and proteomes of hyper/thermophiles. The only PDC activity reported in hyperthermophiles was a bifunctional, TPP- and CoA-dependent pyruvate ferredoxin oxidoreductase (POR)/PDC enzyme from the hyperthermophilic archaeon Pyrococcus furiosus. Another enzyme known to be involved in catalysis of acetaldehyde production from pyruvate is CoA-acetylating acetaldehyde dehydrogenase (AcDH encoded by mhpF and adhE). Pyruvate is oxidized into acetyl-CoA by either POR or pyruvate formate lyase (PFL), and AcDH catalyzes the reduction of acetyl-CoA to acetaldehyde in mesophilic organisms. AcDH is present in some mesophilic (such as clostridia) and thermophilic bacteria (e.g., Geobacillus and Thermoanaerobacter). However, no AcDH gene or protein homologs could be found in the released genomes and proteomes of hyperthermophiles. Moreover, no such activity was detectable from the cell-free extracts of different hyperthermophiles under different assay conditions. In conclusion, no commonly-known PDCs was found in hyperthermophiles. Instead of the commonly-known PDC, it appears that at least one multifunctional enzyme is responsible for catalyzing the non-oxidative decarboxylation of pyruvate to acetaldehyde in hyperthermophiles.
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Affiliation(s)
- Mohammad S Eram
- Department of Biology, University of Waterloo, 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada.
| | - Kesen Ma
- Department of Biology, University of Waterloo, 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada.
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Reed GH, Ragsdale SW, Mansoorabadi SO. Radical reactions of thiamin pyrophosphate in 2-oxoacid oxidoreductases. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2011; 1824:1291-8. [PMID: 22178227 DOI: 10.1016/j.bbapap.2011.11.010] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2011] [Accepted: 11/28/2011] [Indexed: 11/27/2022]
Abstract
Thiamin pyrophosphate (TPP) is essential in carbohydrate metabolism in all forms of life. TPP-dependent decarboxylation reactions of 2-oxo-acid substrates result in enamine adducts between the thiazolium moiety of the coenzyme and decarboxylated substrate. These central enamine intermediates experience different fates from protonation in pyruvate decarboxylase to oxidation by the 2-oxoacid dehydrogenase complexes, the pyruvate oxidases, and 2-oxoacid oxidoreductases. Virtually all of the TPP-dependent enzymes, including pyruvate decarboxylase, can be assayed by 1-electron redox reactions linked to ferricyanide. Oxidation of the enamines is thought to occur via a 2-electron process in the 2-oxoacid dehydrogenase complexes, wherein acyl group transfer is associated with reduction of the disulfide of the lipoamide moiety. However, discrete 1-electron steps occur in the oxidoreductases, where one or more [4Fe-4S] clusters mediate the electron transfer reactions to external electron acceptors. These radical intermediates can be detected in the absence of the acyl-group acceptor, coenzyme A (CoASH). The π-electron system of the thiazolium ring stabilizes the radical. The extensively delocalized character of the radical is evidenced by quantitative analysis of nuclear hyperfine splitting tensors as detected by electron paramagnetic resonance (EPR) spectroscopy and by electronic structure calculations. The second electron transfer step is markedly accelerated by the presence of CoASH. While details of the second electron transfer step and its facilitation by CoASH remain elusive, expected redox properties of potential intermediates limit possible scenarios. This article is part of a Special Issue entitled: Radical SAM enzymes and Radical Enzymology.
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Affiliation(s)
- George H Reed
- Department of Biochemistry, University of Wisconsin-Madison, 1710 University Avenue, Madison, WI 53726, USA.
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Ikeda T, Yamamoto M, Arai H, Ohmori D, Ishii M, Igarashi Y. Enzymatic and electron paramagnetic resonance studies of anabolic pyruvate synthesis by pyruvate: ferredoxin oxidoreductase from Hydrogenobacter thermophilus. FEBS J 2009; 277:501-10. [PMID: 20015072 DOI: 10.1111/j.1742-4658.2009.07506.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Pyruvate: ferredoxin oxidoreductase (POR; EC 1.2.7.1) catalyzes the thiamine pyrophosphate-dependent oxidative decarboxylation of pyruvate to form acetyl-CoA and CO(2). The thermophilic, obligate chemolithoautotrophic hydrogen-oxidizing bacterium, Hydrogenobacter thermophilus TK-6, assimilates CO(2) via the reductive tricarboxylic acid cycle. In this cycle, POR acts as pyruvate synthase catalyzing the reverse reaction (i.e. reductive carboxylation of acetyl-CoA) to form pyruvate. The pyruvate synthesis reaction catalyzed by POR is an energetically unfavorable reaction and requires a strong reductant. Moreover, the reducing equivalents must be supplied via its physiological electron mediator, a small iron-sulfur protein ferredoxin. Therefore, the reaction is difficult to demonstrate in vitro and the reaction mechanism has been poorly understood. In the present study, we coupled the decarboxylation of 2-oxoglutarate catalyzed by 2-oxoglutarate: ferredoxin oxidoreductase (EC 1.2.7.3), which generates sufficiently low-potential electrons to reduce ferredoxin, to drive the energy-demanding pyruvate synthesis by POR. We demonstrate that H. thermophilus POR catalyzes pyruvate synthesis from acetyl-CoA and CO(2), confirming the operation of the reductive tricarboxylic acid cycle in this bacterium. We also measured the electron paramagnetic resonance spectra of the POR intermediates in both the forward and reverse reactions, and demonstrate the intermediacy of a 2-(1-hydroxyethyl)- or 2-(1-hydroxyethylidene)-thiamine pyrophosphate radical in both reactions. The reaction mechanism of the reductive carboxylation of acetyl-CoA is also discussed.
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Affiliation(s)
- Takeshi Ikeda
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Japan
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9
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Mansoorabadi SO, Seravalli J, Furdui C, Krymov V, Gerfen GJ, Begley TP, Melnick J, Ragsdale SW, Reed GH. EPR spectroscopic and computational characterization of the hydroxyethylidene-thiamine pyrophosphate radical intermediate of pyruvate:ferredoxin oxidoreductase. Biochemistry 2006; 45:7122-31. [PMID: 16752902 PMCID: PMC2505060 DOI: 10.1021/bi0602516] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The radical intermediate of pyruvate:ferredoxin oxidoreductase (PFOR) from Moorella thermoacetica was characterized using electron paramagnetic resonance (EPR) spectroscopy at X-band and D-band microwave frequencies. EPR spectra, obtained with various combinations of isotopically labeled substrate (pyruvate) and coenzyme (thiamine pyrophosphate (TPP)), were analyzed by spectral simulations. Parameters obtained from the simulations were compared with those predicted from electronic structure calculations on various radical structures. The g-values and 14N/15N-hyperfine splittings obtained from the spectra are consistent with a planar, hydroxyethylidene-thiamine pyrophosphate (HE-TPP) pi-radical, in which spin is delocalized onto the thiazolium sulfur and nitrogen atoms. The 1H-hyperfine splittings from the methyl group of pyruvate and the 13C-hyperfine splittings from C2 of both pyruvate and TPP are consistent with a model in which the pyruvate-derived oxygen atom of the HE-TPP radical forms a hydrogen bond. The hyperfine splitting constants and g-values are not compatible with those predicted for a nonplanar, sigma/n-type cation radical.
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Affiliation(s)
| | - Javier Seravalli
- Department of Biochemistry, University of Nebraska, Lincoln, NE 68588-0664
| | - Cristina Furdui
- Department of Biochemistry, University of Nebraska, Lincoln, NE 68588-0664
| | - Vladimir Krymov
- Department of Physiology & Biophysics, Albert Einstein College of Medicine, Bronx, NY 10461-1602
| | - Gary J. Gerfen
- Department of Physiology & Biophysics, Albert Einstein College of Medicine, Bronx, NY 10461-1602
| | - Tadhg P. Begley
- Department of Chemistry and Chemical Biology, Baker Laboratory, Cornell University, Ithaca, NY 14853
| | - Jonathan Melnick
- Department of Chemistry and Chemical Biology, Baker Laboratory, Cornell University, Ithaca, NY 14853
| | | | - George H. Reed
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53726-4087
- To whom correspondence should be addressed. Telephone: (608) 262-0509; Fax: (608) 265-2904;
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Chabrière E, Vernède X, Guigliarelli B, Charon MH, Hatchikian EC, Fontecilla-Camps JC. Crystal structure of the free radical intermediate of pyruvate:ferredoxin oxidoreductase. Science 2001; 294:2559-63. [PMID: 11752578 DOI: 10.1126/science.1066198] [Citation(s) in RCA: 110] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
In anaerobic organisms, the decarboxylation of pyruvate, a crucial component of intermediary metabolism, is catalyzed by the metalloenzyme pyruvate: ferredoxin oxidoreductase (PFOR) resulting in the generation of low potential electrons and the subsequent acetylation of coenzyme A (CoA). PFOR is the only enzyme for which a stable acetyl thiamine diphosphate (ThDP)-based free radical reaction intermediate has been identified. The 1.87 A-resolution structure of the radical form of PFOR from Desulfovibrio africanus shows that, despite currently accepted ideas, the thiazole ring of the ThDP cofactor is markedly bent, indicating a drastic reduction of its aromaticity. In addition, the bond connecting the acetyl group to ThDP is unusually long, probably of the one-electron type already described for several cation radicals but not yet found in a biological system. Taken together, our data, along with evidence from the literature, suggest that acetyl-CoA synthesis by PFOR proceeds via a condensation mechanism involving acetyl (PFOR-based) and thiyl (CoA-based) radicals.
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Affiliation(s)
- E Chabrière
- Laboratoire de Cristallographie et Cristallogenèse des Protéines, Institut de Biologie Structurale Jean-Pierre Ebel, Commissariat à l'Energie Atomique, Université Joseph Fourier, CNRS, 41, rue Jules Horowitz, 38027 Grenoble Cedex 1, France
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Furdui C, Ragsdale SW. The role of pyruvate ferredoxin oxidoreductase in pyruvate synthesis during autotrophic growth by the Wood-Ljungdahl pathway. J Biol Chem 2000; 275:28494-9. [PMID: 10878009 DOI: 10.1074/jbc.m003291200] [Citation(s) in RCA: 118] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Pyruvate:ferredoxin oxidoreductase (PFOR) catalyzes the oxidative decarboxylation of pyruvate to acetyl-CoA and CO(2). The catalytic proficiency of this enzyme for the reverse reaction, pyruvate synthase, is poorly understood. Conversion of acetyl-CoA to pyruvate links the Wood-Ljungdahl pathway of autotrophic CO(2) fixation to the reductive tricarboxylic acid cycle, which in these autotrophic anaerobes is the stage for biosynthesis of all cellular macromolecules. The results described here demonstrate that the Clostridium thermoaceticum PFOR is a highly efficient pyruvate synthase. The Michaelis-Menten parameters for pyruvate synthesis by PFOR are: V(max) = 1.6 unit/mg (k(cat) = 3.2 s(-1)), K(m)(Acetyl-CoA) = 9 micrometer, and K(m)(CO(2)) = 2 mm. The intracellular concentrations of acetyl-CoA, CoASH, and pyruvate have been measured. The predicted rate of pyruvate synthesis at physiological concentrations of substrates clearly is sufficient to support the role of PFOR as a pyruvate synthase in vivo. Measurements of its k(cat)/K(m) values demonstrate that ferredoxin is a highly efficient electron carrier in both the oxidative and reductive reactions. On the other hand, rubredoxin is a poor substitute in the oxidative direction and is inept in donating electrons for pyruvate synthesis.
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Affiliation(s)
- C Furdui
- Department of Biochemistry, Beadle Center, University of Nebraska, Lincoln, Nebraska 68588-0664, USA
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Jolley KA, Maddocks DG, Gyles SL, Mullan Z, Tang SL, Dyall-Smith ML, Hough DW, Danson MJ. 2-Oxoacid dehydrogenase multienzyme complexes in the halophilic Archaea? Gene sequences and protein structural predictions. MICROBIOLOGY (READING, ENGLAND) 2000; 146 ( Pt 5):1061-1069. [PMID: 10832633 DOI: 10.1099/00221287-146-5-1061] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
All Archaea catalyse the conversion of pyruvate to acetyl-CoA via a simple pyruvate oxidoreductase. This is in contrast to the Eukarya and most aerobic bacteria, which use the pyruvate dehydrogenase multienzyme complex [PDHC], consisting of multiple copies of three component enzymes: E1 (pyruvate decarboxylase), E2 (lipoate acetyl-transferase) and E3 (dihydrolipoamide dehydrogenase, DHLipDH). Until now no PDHC activity has been found in the Archaea, although DHLipDH has been discovered in the extremely halophilic Archaea and its gene sequence has been determined. In this paper, the discovery and sequencing of an operon containing the DHLipDH gene in the halophilic archaeon Haloferax volcanii are reported. Upstream of the DHLipDH gene are 3 ORFs which show highest sequence identities with the E1alpha, E1beta and E2 genes of the PDHC from gram-positive organisms. Structural predictions of the proposed protein product of the E2 gene show a domain structure characteristic of the E2 component in PDHCs, and catalytically important residues, including the lysine to which the lipoic acid cofactor is covalently bound, are conserved. Northern analyses indicate the transcription of the whole operon, but no PDHC enzymic activity could be detected in cell extracts. The presence in the E2 gene of an insertion (equivalent to approximately 100 aa) not found in bacterial or eukaryal E2 proteins, might be predicted to prevent multienzyme complex assembly. This is the first detailed report of the genes for a putative 2-oxoacid dehydrogenase complex in the Archaea, and the evolutionary and metabolic consequences of these findings are discussed.
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Affiliation(s)
- Keith A Jolley
- Centre for Extremophile Research, Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, UK1
| | - Deborah G Maddocks
- Centre for Extremophile Research, Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, UK1
| | - Shan L Gyles
- Centre for Extremophile Research, Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, UK1
| | - Zoë Mullan
- Centre for Extremophile Research, Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, UK1
| | - Sen-Lin Tang
- Department of Microbiology & Immunology, University of Melbourne, Parkville, Australia2
| | - Michael L Dyall-Smith
- Department of Microbiology & Immunology, University of Melbourne, Parkville, Australia2
| | - David W Hough
- Centre for Extremophile Research, Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, UK1
| | - Michael J Danson
- Centre for Extremophile Research, Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, UK1
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13
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Charon MH, Volbeda A, Chabriere E, Pieulle L, Fontecilla-Camps JC. Structure and electron transfer mechanism of pyruvate:ferredoxin oxidoreductase. Curr Opin Struct Biol 1999; 9:663-9. [PMID: 10607667 DOI: 10.1016/s0959-440x(99)00027-5] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The first crystal structure of pyruvate:ferredoxin oxidoreductase to be determined has provided significant new information on its structural organization and redox chemistry. Spectroscopic analyses of a radical reaction intermediate have shed more light on its thiamin-based mechanism of catalysis. Different approaches have been used to study the interaction between the enzyme and ferredoxin, its redox partner.
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Affiliation(s)
- M H Charon
- Laboratoire de Cristallographie et de Cristallogenèse des Protéines, Institut de Biologie Structurale J-P Ebel (CEA, CNRS), Grenoble, 38027, France.
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