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Yang JI, Jung HC, Oh HM, Choi BG, Lee HS, Kang SG. NADP + or CO 2 reduction by frhAGB-encoded hydrogenase through interaction with formate dehydrogenase 3 in the hyperthermophilic archaeon Thermococcus onnurineus NA1. Appl Environ Microbiol 2023; 89:e0147423. [PMID: 37966269 PMCID: PMC10734459 DOI: 10.1128/aem.01474-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 09/23/2023] [Indexed: 11/16/2023] Open
Abstract
IMPORTANCE The strategy using structural homology with the help of structure prediction by AlphaFold was very successful in finding potential targets for the frhAGB-encoded hydrogenase of Thermococcus onnurineus NA1. The finding that the hydrogenase can interact with FdhB to reduce the cofactor NAD(P)+ is significant in that the enzyme can function to supply reducing equivalents, just as F420-reducing hydrogenases in methanogens use coenzyme F420 as an electron carrier. Additionally, it was identified that T. onnurineus NA1 could produce formate from H2 and CO2 by the concerted action of frhAGB-encoded hydrogenase and formate dehydrogenase Fdh3.
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Affiliation(s)
- Ji-in Yang
- Marine Biotechnology Research Center, Korea Institute of Ocean Science & Technology, Busan, South Korea
- Department of Applied Ocean Science, University of Science and Technology, Daejeon, South Korea
| | - Hae-Chang Jung
- Marine Biotechnology Research Center, Korea Institute of Ocean Science & Technology, Busan, South Korea
| | | | - Bo Gyoung Choi
- Marine Biotechnology Research Center, Korea Institute of Ocean Science & Technology, Busan, South Korea
| | - Hyun Sook Lee
- Marine Biotechnology Research Center, Korea Institute of Ocean Science & Technology, Busan, South Korea
- Department of Applied Ocean Science, University of Science and Technology, Daejeon, South Korea
| | - Sung Gyun Kang
- Marine Biotechnology Research Center, Korea Institute of Ocean Science & Technology, Busan, South Korea
- Department of Applied Ocean Science, University of Science and Technology, Daejeon, South Korea
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Phylogenomic Analysis of Metagenome-Assembled Genomes Deciphered Novel Acetogenic Nitrogen-Fixing Bathyarchaeota from Hot Spring Sediments. Microbiol Spectr 2022; 10:e0035222. [PMID: 35647693 PMCID: PMC9241837 DOI: 10.1128/spectrum.00352-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
This study describes the phylogenomic analysis and metabolic insights of metagenome-assembled genomes (MAGs) retrieved from hot spring sediment samples. The metagenome-assembled sequences recovered three near-complete genomes belonging to the archaeal phylum. Analysis of genome-wide core genes and 16S rRNA-based phylogeny placed the ILS200 and ILS300 genomes within the uncultivated and largely understudied bathyarchaeal phylum, whereas ILS100 represented the phylum Thaumarchaeota. The average nucleotide identity (ANI) of the bin ILS100 was 76% with Nitrososphaeria_archaeon_isolate_SpSt-1069. However, the bins ILS200 and ILS300 showed ANI values of 75% and 70% with Candidatus_Bathyarchaeota_archaeon_isolate_DRTY-6_2_bin_115 and Candidatus_Bathyarchaeota_archaeon_BA1_ba1_01, respectively. The genomic potential of Bathyarchaeota bins ILS200 and ILS300 showed genes necessary for the Wood-Ljungdahl pathway, and the gene encoding the methyl coenzyme M reductase (mcr) complex essential for methanogenesis was absent. The metabolic potential of the assembled genomes included genes involved in nitrogen assimilation, including nitrogenase and the genes necessary for the urea cycle. The presence of these genes suggested the metabolic potential of Bathyarchaeota to fix nitrogen under extreme environments. In addition, the ILS200 and ILS300 genomes carried genes involved in the tricarboxylic acid (TCA) cycle, glycolysis, and degradation of organic carbons. Finally, we conclude that the reconstructed Bathyarchaeota bins are autotrophic acetogens and organo-heterotrophs. IMPORTANCE We describe the Bathyarchaeota bins that are likely to be acetogens with a wide range of metabolic potential. These bins did not exhibit methanogenic machinery, suggesting methane production may not occur by all subgroup lineages of Bathyarchaeota. Phylogenetic analysis support that both ILS200 and ILS300 belonged to the Bathyarchaeota. The discovery of new bathyarchaeotal MAGs provides additional knowledge for understanding global carbon and nitrogen metabolism under extreme conditions.
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3
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Birchfield AS, McIntosh CA. The Effect of Recombinant Tags on Citrus paradisi Flavonol-Specific 3-O Glucosyltransferase Activity. PLANTS 2020; 9:plants9030402. [PMID: 32213838 PMCID: PMC7154896 DOI: 10.3390/plants9030402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 03/21/2020] [Accepted: 03/22/2020] [Indexed: 11/16/2022]
Abstract
Recombinant tags are used extensively in protein expression systems to allow purification through IMAC (Immobilized Metal Affinity Chromatography), identification through Western blot, and to facilitate crystal formation for structural analysis. While widely used, their role in enzyme characterization has raised concerns with respect to potential impact on activity. In this study, a flavonol-specific 3-O glucosyltransferase (Cp3GT) from grapefruit (Citrus paradisi) was expressed in Pichia pastoris, and was assayed in its untagged form and with a C-terminal c-myc/6x His tag under various conditions to determine the effect of tags. Prior characterization of pH optima for Cp3GT obtained through expression in Escherichia coli, containing an N-terminal thioredoxin/6x His tag, indicated an optimal pH of 7-7.5, which is indicative of a normal physiological pH and agrees with other glucosyltransferase (GT) pH optima. However, characterization of Cp3GT expressed using P. pastoris with a C-terminal c-myc-6x His tag showed a higher optimal pH of 8.5-9. This suggests a possible tag effect or an effect related to physiological differences between the cell expression systems. Results testing recombinant Cp3GT expressed in Pichia with and without C-terminal tags showed a possible tag effect with regard to substrate preference and interactions with metals, but no apparent effect on enzymatic kinetics or pH optima.
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McCarver AC, Lessner DJ. Molecular characterization of the thioredoxin system from Methanosarcina acetivorans. FEBS J 2014; 281:4598-611. [PMID: 25112424 DOI: 10.1111/febs.12964] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Revised: 07/25/2014] [Accepted: 08/07/2014] [Indexed: 11/28/2022]
Abstract
The thioredoxin system, composed of thioredoxin reductase (TrxR) and thioredoxin (Trx), is widely distributed in nature, where it serves key roles in electron transfer and in the defense against oxidative stress. Although recent evidence reveals Trx homologues are almost universally present among the methane-producing archaea (methanogens), a complete thioredoxin system has not been characterized from any methanogen. We examined the phylogeny of Trx homologues among methanogens and characterized the thioredoxin system from Methanosarcina acetivorans. Phylogenetic analysis of Trx homologues from methanogens revealed eight clades, with one clade containing Trxs broadly distributed among methanogens. The Methanococci and Methanobacteria each contain one additional Trx from another clade, respectively, whereas the Methanomicrobia contain an additional five distinct Trxs. Methanosarcina acetivorans, a member of the Methanomicrobia, contains a single TrxR (MaTrxR) and seven Trx homologues (MaTrx1-7), with representatives from five of the methanogen Trx clades. Purified recombinant MaTrxR had 5,5'-dithiobis(2-nitrobenzoic acid) (DTNB) reductase and oxidase activities. The apparent Km value for NADPH was 115-fold lower than that for NADH, consistent with NADPH as the physiological electron donor to MaTrxR. Purified recombinant MaTrx2, MaTrx6 and MaTrx7 exhibited dithiothreitol- and lipoamide-dependent insulin disulfide reductase activities. However, only MaTrx7, which is encoded adjacent to MaTrxR, could serve as a redox partner to MaTrxR. These results reveal that M. acetivorans harbors at least three functional and distinct Trxs, and a complete thioredoxin system composed of NADPH, MaTrxR and at least MaTrx7. This is the first characterization of a complete thioredoxin system from a methanogen, which provides a foundation to understand the system in methanogens.
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Affiliation(s)
- Addison C McCarver
- Department of Biological Sciences, University of Arkansas-Fayetteville, AR, USA
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Pedone E, Fiorentino G, Pirone L, Contursi P, Bartolucci S, Limauro D. Functional and structural characterization of protein disulfide oxidoreductase from Thermus thermophilus HB27. Extremophiles 2014; 18:723-31. [DOI: 10.1007/s00792-014-0652-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2014] [Accepted: 04/27/2014] [Indexed: 11/28/2022]
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Yan Z, Nam YW, Fushinobu S, Wakagi T. Sulfolobus tokodaii ST2133 is characterized as a thioredoxin reductase-like ferredoxin:NADP+ oxidoreductase. Extremophiles 2013; 18:99-110. [DOI: 10.1007/s00792-013-0601-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2013] [Accepted: 11/14/2013] [Indexed: 10/26/2022]
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Esposito L, Ruggiero A, Masullo M, Ruocco MR, Lamberti A, Arcari P, Zagari A, Vitagliano L. Crystallographic and spectroscopic characterizations of Sulfolobus solfataricus TrxA1 provide insights into the determinants of thioredoxin fold stability. J Struct Biol 2012; 177:506-12. [DOI: 10.1016/j.jsb.2011.10.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2011] [Revised: 10/20/2011] [Accepted: 10/30/2011] [Indexed: 10/15/2022]
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Oliveira MA, Discola KF, Alves SV, Medrano FJ, Guimarães BG, Netto LES. Insights into the specificity of thioredoxin reductase-thioredoxin interactions. A structural and functional investigation of the yeast thioredoxin system. Biochemistry 2010; 49:3317-26. [PMID: 20235561 DOI: 10.1021/bi901962p] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The enzymatic activity of thioredoxin reductase enzymes is endowed by at least two redox centers: a flavin and a dithiol/disulfide CXXC motif. The interaction between thioredoxin reductase and thioredoxin is generally species-specific, but the molecular aspects related to this phenomenon remain elusive. Here, we investigated the yeast cytosolic thioredoxin system, which is composed of NADPH, thioredoxin reductase (ScTrxR1), and thioredoxin 1 (ScTrx1) or thioredoxin 2 (ScTrx2). We showed that ScTrxR1 was able to efficiently reduce yeast thioredoxins (mitochondrial and cytosolic) but failed to reduce the human and Escherichia coli thioredoxin counterparts. To gain insights into this specificity, the crystallographic structure of oxidized ScTrxR1 was solved at 2.4 A resolution. The protein topology of the redox centers indicated the necessity of a large structural rearrangement for FAD and thioredoxin reduction using NADPH. Therefore, we modeled a large structural rotation between the two ScTrxR1 domains (based on the previously described crystal structure, PDB code 1F6M ). Employing diverse approaches including enzymatic assays, site-directed mutagenesis, amino acid sequence alignment, and structure comparisons, insights were obtained about the features involved in the species-specificity phenomenon, such as complementary electronic parameters between the surfaces of ScTrxR1 and yeast thioredoxin enzymes and loops and residues (such as Ser(72) in ScTrx2). Finally, structural comparisons and amino acid alignments led us to propose a new classification that includes a larger number of enzymes with thioredoxin reductase activity, neglected in the low/high molecular weight classification.
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Affiliation(s)
- Marcos A Oliveira
- Departamento de Biologia, Universidade Estadual Paulista, São Vicente, Brazil
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Kirkensgaard KG, Hägglund P, Finnie C, Svensson B, Henriksen A. Structure of Hordeum vulgare NADPH-dependent thioredoxin reductase 2. Unwinding the reaction mechanism. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2009; 65:932-41. [PMID: 19690371 PMCID: PMC2733882 DOI: 10.1107/s0907444909021817] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2009] [Accepted: 06/09/2009] [Indexed: 12/24/2022]
Abstract
Thioredoxins (Trxs) are protein disulfide reductases that regulate the intracellular redox environment and are important for seed germination in plants. Trxs are in turn regulated by NADPH-dependent thioredoxin reductases (NTRs), which provide reducing equivalents to Trx using NADPH to recycle Trxs to the active form. Here, the first crystal structure of a cereal NTR, HvNTR2 from Hordeum vulgare (barley), is presented, which is also the first structure of a monocot plant NTR. The structure was determined at 2.6 A resolution and refined to an R(cryst) of 19.0% and an R(free) of 23.8%. The dimeric protein is structurally similar to the structures of AtNTR-B from Arabidopsis thaliana and other known low-molecular-weight NTRs. However, the relative position of the two NTR cofactor-binding domains, the FAD and the NADPH domains, is not the same. The NADPH domain is rotated by 25 degrees and bent by a 38% closure relative to the FAD domain in comparison with AtNTR-B. The structure may represent an intermediate between the two conformations described previously: the flavin-oxidizing (FO) and the flavin-reducing (FR) conformations. Here, analysis of interdomain contacts as well as phylogenetic studies lead to the proposal of a new reaction scheme in which NTR-Trx interactions mediate the FO to FR transformation.
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Affiliation(s)
- Kristine G. Kirkensgaard
- Carlsberg Laboratory, Denmark
- Enzyme and Protein Chemistry, Department of Systems BioIogy, Technical University of Denmark, Denmark
| | - Per Hägglund
- Enzyme and Protein Chemistry, Department of Systems BioIogy, Technical University of Denmark, Denmark
| | - Christine Finnie
- Enzyme and Protein Chemistry, Department of Systems BioIogy, Technical University of Denmark, Denmark
| | - Birte Svensson
- Enzyme and Protein Chemistry, Department of Systems BioIogy, Technical University of Denmark, Denmark
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Ruggiero A, Masullo M, Marasco D, Ruocco MR, Grimaldi P, Arcari P, Zagari A, Vitagliano L. The dimeric structure of Sulfolobus solfataricus
thioredoxin A2 and the basis of its thermostability. Proteins 2009; 77:1004-8. [DOI: 10.1002/prot.22559] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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Ruggiero A, Lanzotti MA, Ruocco MR, Grimaldi P, Marasco D, Arcari P, Masullo M, Zagari A, Vitagliano L. Crystallization and preliminary X-ray crystallographic analysis of two dimeric hyperthermostable thioredoxins isolated from Sulfolobus solfataricus. Acta Crystallogr Sect F Struct Biol Cryst Commun 2009; 65:604-7. [PMID: 19478442 PMCID: PMC2688421 DOI: 10.1107/s1744309109016200] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2009] [Accepted: 04/29/2009] [Indexed: 11/10/2022]
Abstract
The thioredoxin system of the archaeon Sulfolobus solfataricus involves a number of different proteins: two thioredoxin reductases (SsTrxRB2 and SsTrxRB3), two distinct thioredoxins (SsTrxA1 and SsTrxA2) and a disulfide oxidoreductase (SsPDO). Here, the crystallization and preliminary crystallographic analyses of SsTrxA1 and SsTrxA2, two dimeric proteins endowed with extraordinary thermal stability, are reported. In addition to the functional thioredoxin domain, both SsTrxA1 and SsTrxA2 present an extra N-terminal fragment of approximately 30 residues. Although crystallization trials have been conducted on both forms of the proteins, crystals that were suitable for X-ray crystallographic analyses have only been obtained for their truncated variants. The crystals of SsTrxA2 belonged to space group P2, with unit-cell parameters a = 28.27, b = 27.88, c = 62.06 A, beta = 92.34 degrees , and diffracted to 1.83 A resolution, whereas the crystals of SsTrxA1 belonged to space group P2(1), with unit-cell parameters a = 51.76, b = 75.09, c = 55.35 A, beta = 112.64 degrees , and diffracted to 1.90 A resolution. The structures of the two proteins have been solved by molecular replacement.
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Affiliation(s)
- Alessia Ruggiero
- Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, I-80134 Napoli, Italy
| | - Maria Angela Lanzotti
- Dipartimento delle Scienze Biologiche, Sezione di Biostrutture, Università degli Studi di Napoli Federico II, Via Mezzocannone 16, I-80134 Napoli, Italy
| | - Maria Rosaria Ruocco
- Dipartimento di Biochimica e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Via S. Pansini 5, I-80131 Napoli, Italy
| | - Pasquale Grimaldi
- Dipartimento di Biochimica e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Via S. Pansini 5, I-80131 Napoli, Italy
- Dipartimento di Scienze Farmacobiologiche, Università degli Studi ‘Magna Graecia’ di Catanzaro, Roccelletta di Borgia, I-88021 Catanzaro, Italy
| | - Daniela Marasco
- Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, I-80134 Napoli, Italy
- Dipartimento delle Scienze Biologiche, Sezione di Biostrutture, Università degli Studi di Napoli Federico II, Via Mezzocannone 16, I-80134 Napoli, Italy
| | - Paolo Arcari
- Dipartimento di Biochimica e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Via S. Pansini 5, I-80131 Napoli, Italy
- CEINGE Biotecnologie Avanzate s.c.a.r.l., Via Comunale Margherita 482, I-80145 Napoli, Italy
| | - Mariorosario Masullo
- Dipartimento di Biochimica e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Via S. Pansini 5, I-80131 Napoli, Italy
- Dipartimento di Scienze Farmacobiologiche, Università degli Studi ‘Magna Graecia’ di Catanzaro, Roccelletta di Borgia, I-88021 Catanzaro, Italy
| | - Adriana Zagari
- Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, I-80134 Napoli, Italy
- Dipartimento delle Scienze Biologiche, Sezione di Biostrutture, Università degli Studi di Napoli Federico II, Via Mezzocannone 16, I-80134 Napoli, Italy
- CEINGE Biotecnologie Avanzate s.c.a.r.l., Via Comunale Margherita 482, I-80145 Napoli, Italy
- CNISM Università degli Studi di Napoli Federico II, Italy
| | - Luigi Vitagliano
- Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, I-80134 Napoli, Italy
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