1
|
Bak DW, Weerapana E. Proteomic strategies to interrogate the FeS proteome. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2024:119791. [PMID: 38925478 DOI: 10.1016/j.bbamcr.2024.119791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 05/23/2024] [Accepted: 06/19/2024] [Indexed: 06/28/2024]
Abstract
Iron‑sulfur (FeS) clusters, inorganic cofactors composed of iron and sulfide, participate in numerous essential redox, non-redox, structural, and regulatory biological processes within the cell. Though structurally and functionally diverse, the list of all proteins in an organism capable of binding one or more FeS clusters is referred to as its FeS proteome. Importantly, the FeS proteome is highly dynamic, with continuous cluster synthesis and delivery by complex FeS cluster biogenesis pathways. This cluster delivery is balanced out by processes that can result in loss of FeS cluster binding, such as redox state changes, iron availability, and oxygen sensitivity. Despite continued expansion of the FeS protein catalogue, it remains a challenge to reliably identify novel FeS proteins. As such, high-throughput techniques that can report on native FeS cluster binding are required to both identify new FeS proteins, as well as characterize the in vivo dynamics of FeS cluster binding. Due to the recent rapid growth in mass spectrometry, proteomics, and chemical biology, there has been a host of techniques developed that are applicable to the study of native FeS proteins. This review will detail both the current understanding of the FeS proteome and FeS cluster biology as well as describing state-of-the-art proteomic strategies for the study of FeS clusters within the context of a native proteome.
Collapse
Affiliation(s)
- Daniel W Bak
- Department of Chemistry, Boston College, Chestnut Hill, MA, United States of America.
| | - Eranthie Weerapana
- Department of Chemistry, Boston College, Chestnut Hill, MA, United States of America.
| |
Collapse
|
2
|
Hagen WR. The Development of Tungsten Biochemistry-A Personal Recollection. Molecules 2023; 28:molecules28104017. [PMID: 37241758 DOI: 10.3390/molecules28104017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 04/27/2023] [Accepted: 05/08/2023] [Indexed: 05/28/2023] Open
Abstract
The development of tungsten biochemistry is sketched from the viewpoint of personal participation. Following its identification as a bio-element, a catalogue of genes, enzymes, and reactions was built up. EPR spectroscopic monitoring of redox states was, and remains, a prominent tool in attempts to understand tungstopterin-based catalysis. A paucity of pre-steady-state data remains a hindrance to overcome to this day. Tungstate transport systems have been characterized and found to be very specific for W over Mo. Additional selectivity is presented by the biosynthetic machinery for tungstopterin enzymes. Metallomics analysis of hyperthermophilic archaeon Pyrococcus furiosus indicates a comprehensive inventory of tungsten proteins.
Collapse
Affiliation(s)
- Wilfred R Hagen
- Department of Biotechnology, Delft University of Technology, Building 58, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| |
Collapse
|
3
|
Winiarska A, Hege D, Gemmecker Y, Kryściak-Czerwenka J, Seubert A, Heider J, Szaleniec M. Tungsten Enzyme Using Hydrogen as an Electron Donor to Reduce Carboxylic Acids and NAD . ACS Catal 2022; 12:8707-8717. [PMID: 35874620 PMCID: PMC9295118 DOI: 10.1021/acscatal.2c02147] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Tungsten-dependent
aldehyde oxidoreductases (AORs) catalyze the
oxidation of aldehydes to acids and are the only known enzymes reducing
non-activated acids using electron donors with low redox potentials.
We report here that AOR from Aromatoleum aromaticum (AORAa) catalyzes the reduction of organic
acids not only with low-potential Eu(II) or Ti(III) complexes but
also with H2 as an electron donor. Additionally, AORAa catalyzes the H2-dependent reduction
of NAD+ or benzyl viologen. The rate of H2-dependent
NAD+ reduction equals to 10% of that of aldehyde oxidation,
representing the highest H2 turnover rate observed among
the Mo/W enzymes. As AORAa simultaneously
catalyzes the reduction of acids and NAD+, we designed
a cascade reaction utilizing a NAD(P)H-dependent alcohol dehydrogenase
to reduce organic acids to the corresponding alcohols with H2 as the only reductant. The newly discovered W-hydrogenase side activity
of AORAa may find applications in either
NADH recycling or conversion of carboxylic acids to more useful biochemicals.
Collapse
Affiliation(s)
- Agnieszka Winiarska
- Jerzy Haber Institute of Catalysis and Surface Chemistry Polish Academy of Sciences, Kraków 30-239, Poland
| | - Dominik Hege
- Faculty of Biology, Philipps-Universität Marburg, Marburg D-35043, Germany
| | - Yvonne Gemmecker
- Faculty of Biology, Philipps-Universität Marburg, Marburg D-35043, Germany
| | - Joanna Kryściak-Czerwenka
- Jerzy Haber Institute of Catalysis and Surface Chemistry Polish Academy of Sciences, Kraków 30-239, Poland
| | - Andreas Seubert
- Faculty of Chemistry, Philipps-Universität Marburg, Marburg D-35043, Germany
| | - Johann Heider
- Faculty of Biology, Philipps-Universität Marburg, Marburg D-35043, Germany.,Center for Synthetic Microbiology, Philipps-Universität Marburg, Marburg D-35043, Germany
| | - Maciej Szaleniec
- Jerzy Haber Institute of Catalysis and Surface Chemistry Polish Academy of Sciences, Kraków 30-239, Poland
| |
Collapse
|
4
|
Abstract
Metalloproteins play diverse and critical functions in all living systems, and their dysfunctional forms are closely related to many human diseases. The development of methods that enable comprehensive mapping of metalloproteome is of great interest to help elucidate crucial roles of metalloproteins in both physiology and pathology, as well as to discover new metalloproteins. We herein briefly review recent progress in the field of metalloproteomics and provide future outlooks.
Collapse
Affiliation(s)
- Xin Zeng
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing 100871, China.,Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Yao Cheng
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing 100871, China.,College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Chu Wang
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing 100871, China.,College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.,Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| |
Collapse
|
5
|
Vali SW, Haja DK, Brand RA, Adams MWW, Lindahl PA. The Pyrococcus furiosus ironome is dominated by [Fe 4S 4] 2+ clusters or thioferrate-like iron depending on the availability of elemental sulfur. J Biol Chem 2021; 296:100710. [PMID: 33930466 PMCID: PMC8219758 DOI: 10.1016/j.jbc.2021.100710] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Revised: 04/12/2021] [Accepted: 04/22/2021] [Indexed: 11/28/2022] Open
Abstract
Pyrococcus furiosus is a hyperthermophilic anaerobic archaeon whose metabolism depends on whether elemental sulfur is (+S0) or is not (-S0) included in growth medium. Under +S0 conditions, expression of respiratory hydrogenase declines while respiratory membrane-bound sulfane reductase and the putative iron-storage protein IssA increase. Our objective was to investigate the iron content of WT and ΔIssA cells under these growth conditions using Mössbauer spectroscopy. WT-S0 cells contained ∼1 mM Fe, with ∼85% present as two spectroscopically distinct forms of S = 0 [Fe4S4]2+ clusters; the remainder was mainly high-spin FeII. WT+S0 cells contained 5 to 9 mM Fe, with 75 to 90% present as magnetically ordered thioferrate-like (TFL) iron nanoparticles. TFL iron was similar to chemically defined thioferrates; both consisted of FeIII ions coordinated by an S4 environment, and both exhibited strong coupling between particles causing high applied fields to have little spectral effect. At high temperatures with magnetic hyperfine interactions abolished, TFL iron exhibited two doublets overlapping those of [Fe4S4]2+ clusters in -S0 cells. This coincidence arose because of similar coordination environments of TFL iron and cluster iron. The TFL structure was more heterogeneous in the presence of IssA. Presented data suggest that IssA may coordinate insoluble iron sulfides as TFL iron, formed as a byproduct of anaerobic sulfur respiration under high iron conditions, which thereby reduces its toxicity to the cell. This was the first Mössbauer characterization of the ironome of an archaeon, and it illustrates differences relative to the iron content of better-studied bacteria such as Escherichia coli.
Collapse
Affiliation(s)
- Shaik Waseem Vali
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, USA
| | - Dominik K Haja
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, USA
| | - Richard A Brand
- Faculty of Physics, University of Duisburg-Essen, Duisburg, Germany; Institute of Nanotechnology, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany
| | - Michael W W Adams
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, USA
| | - Paul A Lindahl
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, USA; Department of Chemistry, Texas A&M University, College Station, Texas, USA.
| |
Collapse
|
6
|
Improving Arsenic Tolerance of Pyrococcus furiosus by Heterologous Expression of a Respiratory Arsenate Reductase. Appl Environ Microbiol 2020; 86:AEM.01728-20. [PMID: 32859593 DOI: 10.1128/aem.01728-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 08/16/2020] [Indexed: 11/20/2022] Open
Abstract
Arsenate is a notorious toxicant that is known to disrupt multiple biochemical pathways. Many microorganisms have developed mechanisms to detoxify arsenate using the ArsC-type arsenate reductase, and some even use arsenate as a terminal electron acceptor for respiration involving arsenate respiratory reductase (Arr). ArsC-type reductases have been studied extensively, but the phylogenetically unrelated Arr system is less investigated and has not been characterized from Archaea Here, we heterologously expressed the genes encoding Arr from the crenarchaeon Pyrobaculum aerophilum in the euryarchaeon Pyrococcus furiosus, both of which grow optimally near 100°C. Recombinant P. furiosus was grown on molybdenum (Mo)- or tungsten (W)-containing medium, and two types of recombinant Arr enzymes were purified, one containing Mo (Arr-Mo) and one containing W (Arr-W). Purified Arr-Mo had a 140-fold higher specific activity in arsenate [As(V)] reduction than Arr-W, and Arr-Mo also reduced arsenite [As(III)]. The P. furiosus strain expressing Arr-Mo (the Arr strain) was able to use arsenate as a terminal electron acceptor during growth on peptides. In addition, the Arr strain had increased tolerance compared to that of the parent strain to arsenate and also, surprisingly, to arsenite. Compared to the parent, the Arr strain accumulated intracellularly almost an order of magnitude more arsenic when cells were grown in the presence of arsenite. X-ray absorption spectroscopy (XAS) results suggest that the Arr strain of P. furiosus improves its tolerance to arsenite by increasing production of less-toxic arsenate and nontoxic methylated arsenicals compared to that by the parent.IMPORTANCE Arsenate respiratory reductases (Arr) are much less characterized than the detoxifying arsenate reductase system. The heterologous expression and characterization of an Arr from Pyrobaculum aerophilum in Pyrococcus furiosus provides new insights into the function of this enzyme. From in vivo studies, production of Arr not only enabled P. furiosus to use arsenate [As(V)] as a terminal electron acceptor, it also provided the organism with a higher resistance to arsenate and also, surprisingly, to arsenite [As(III)]. In contrast to the tungsten-containing oxidoreductase enzymes natively produced by P. furiosus, recombinant P. aerophilum Arr was much more active with molybdenum than with tungsten. It is also, to our knowledge, the only characterized Arr to be active with both molybdenum and tungsten in the active site.
Collapse
|
7
|
Abstract
Tungsten is the heaviest element used in biological systems. It occurs in the active sites of several bacterial or archaeal enzymes and is ligated to an organic cofactor (metallopterin or metal binding pterin; MPT) which is referred to as tungsten cofactor (Wco). Wco-containing enzymes are found in the dimethyl sulfoxide reductase (DMSOR) and the aldehyde:ferredoxin oxidoreductase (AOR) families of MPT-containing enzymes. Some depend on Wco, such as aldehyde oxidoreductases (AORs), class II benzoyl-CoA reductases (BCRs) and acetylene hydratases (AHs), whereas others may incorporate either Wco or molybdenum cofactor (Moco), such as formate dehydrogenases, formylmethanofuran dehydrogenases or nitrate reductases. The obligately tungsten-dependent enzymes catalyze rather unusual reactions such as ones with extremely low-potential electron transfers (AOR, BCR) or an unusual hydration reaction (AH). In recent years, insights into the structure and function of many tungstoenzymes have been obtained. Though specific and unspecific ABC transporter uptake systems have been described for tungstate and molybdate, only little is known about further discriminative steps in Moco and Wco biosynthesis. In bacteria producing Moco- and Wco-containing enzymes simultaneously, paralogous isoforms of the metal insertase MoeA may be specifically involved in the molybdenum- and tungsten-insertion into MPT, and in targeting Moco or Wco to their respective apo-enzymes. Wco-containing enzymes are of emerging biotechnological interest for a number of applications such as the biocatalytic reduction of CO2, carboxylic acids and aromatic compounds, or the conversion of acetylene to acetaldehyde.
Collapse
|
8
|
Nissen LS, Basen M. The emerging role of aldehyde:ferredoxin oxidoreductases in microbially-catalyzed alcohol production. J Biotechnol 2019; 306:105-117. [DOI: 10.1016/j.jbiotec.2019.09.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 09/09/2019] [Accepted: 09/09/2019] [Indexed: 11/16/2022]
|
9
|
Characterization of thiosulfate reductase from Pyrobaculum aerophilum heterologously produced in Pyrococcus furiosus. Extremophiles 2019; 24:53-62. [PMID: 31278423 DOI: 10.1007/s00792-019-01112-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 06/26/2019] [Indexed: 10/26/2022]
Abstract
The genome of the archaeon Pyrobaculum aerophilum (Topt ~ 100 °C) contains an operon (PAE2859-2861) encoding a putative pyranopterin-containing oxidoreductase of unknown function and metal content. These genes (with one gene modified to encode a His-affinity tag) were inserted into the fermentative anaerobic archaeon, Pyrococcus furiosus (Topt ~ 100 °C). Dye-linked assays of cytoplasmic extracts from recombinant P. furiosus show that the P. aerophilum enzyme is a thiosulfate reductase (Tsr) and reduces thiosulfate but not polysulfide. The enzyme (Tsr-Mo) from molybdenum-grown cells contains Mo (Mo:W = 9:1) while the enzyme (Tsr-W) from tungsten-grown cells contains mainly W (Mo:W = 1:6). Purified Tsr-Mo has over ten times the activity (Vmax = 1580 vs. 141 µmol min-1 mg-1) and twice the affinity for thiosulfate (Km = ~ 100 vs. ~ 200 μM) than Tsr-W and is reduced at a lower potential (Epeak = - 255 vs - 402 mV). Tsr-Mo and Tsr-W proteins are heterodimers lacking the membrane anchor subunit (PAE2861). Recombinant P. furiosus expressing P. aerophilum Tsr could not use thiosulfate as a terminal electron acceptor. P. furiosus contains five pyranopterin-containing enzymes, all of which utilize W. P. aerophilum Tsr-Mo is the first example of an active Mo-containing enzyme produced in P. furiosus.
Collapse
|
10
|
Dorn KV, Blaschkowski B, Bamberger H, van Slageren J, Doll K, Claus R, Matsumoto Y, Takagi H, Hartenbach I. Black Current: Structure, Characterization, and Optoelectronic Properties of Ce 3 Cl 3 [MoO 6 ]. Chemistry 2019; 25:7921-7926. [PMID: 30972829 DOI: 10.1002/chem.201901038] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Indexed: 11/06/2022]
Abstract
The admixture of CeO2 , Ce, CeCl3 , and MoO3 with an excess of LiCl as flux in evacuated silica ampules leads to large black single crystals as well as a black microcrystalline powder of Ce3 Cl3 [MoO6 ] after tempering at 850 °C for three days. The title compound crystallizes in the hexagonal space group P63 /m (a=934.93(4), c=538.86(2) pm) with two formula units per unit cell. The crystal structure consists of rather unusual trigonal-prismatic [MoO6 ]6- units besides Ce3+ ions in a tetra-capped trigonal-prismatic coordination, formed by four Cl- and six O2- ions. The black color is related to an optical band gap of 1.35(2) eV, which was determined by diffuse reflectance spectroscopy and confirmed by theoretical calculations. The low band gap between the 4f1 state of cerium (HOMO) and the 5d0 state of molybdenum (LUMO) gave rise to the idea of electronic excitation between these two states by IR irradiation, creating a drop in the resistivity of the material, which was detected by appropriate measurements.
Collapse
Affiliation(s)
- Katharina V Dorn
- Institute of Inorganic Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569, Stuttgart, Germany.,Department of Materials and Environmental Chemistry, Stockholm University, Svante Arrhenius Väg 16 C, 10691, Stockholm, Sweden
| | - Björn Blaschkowski
- Institute of Inorganic Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569, Stuttgart, Germany
| | - Heiko Bamberger
- Institute of Physical Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569, Stuttgart, Germany
| | - Joris van Slageren
- Institute of Physical Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569, Stuttgart, Germany
| | - Klaus Doll
- Institute of Theoretical Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569, Stuttgart, Germany
| | - Ralf Claus
- Max-Planck-Institute for Solid-State Research, Heisenbergstrasse 1, 70569, Stuttgart, Germany
| | - Yosuke Matsumoto
- Max-Planck-Institute for Solid-State Research, Heisenbergstrasse 1, 70569, Stuttgart, Germany
| | - Hidenori Takagi
- Max-Planck-Institute for Solid-State Research, Heisenbergstrasse 1, 70569, Stuttgart, Germany
| | - Ingo Hartenbach
- Institute of Inorganic Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569, Stuttgart, Germany
| |
Collapse
|
11
|
Qian HX, Liao RZ. QM/MM Study of Tungsten-Dependent Benzoyl-Coenzyme A Reductase: Rationalization of Regioselectivity and Predication of W vs Mo Selectivity. Inorg Chem 2018; 57:10667-10678. [DOI: 10.1021/acs.inorgchem.8b01328] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Hui-Xia Qian
- Key Laboratory of Material Chemistry for Energy Conversion and Storage, Ministry of Education, Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medica, Hubei Key Laboratory of Materials Chemistry and Service Failure, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Rong-Zhen Liao
- Key Laboratory of Material Chemistry for Energy Conversion and Storage, Ministry of Education, Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medica, Hubei Key Laboratory of Materials Chemistry and Service Failure, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan 430074, China
| |
Collapse
|
12
|
Okamura TA, Omi Y, Hirano Y, Onitsuka K. Comparative studies on the contribution of NHS hydrogen bonds in tungsten and molybdenum benzenedithiolate complexes. Dalton Trans 2018; 45:15651-15659. [PMID: 27722343 DOI: 10.1039/c6dt02250b] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A series of monooxotungsten(iv) and dioxotungsten(vi) benzenedithiolates, (NEt4)2[WIVO(1,2-S2-3-RCONHC6H3)2] (1-W; R = CH3 (a), t-Bu (b), or CF3 (c)) and (NEt4)2[WVIO2(1,2-S2-3-RCONHC6H3)2] (2-W), were synthesized and compared with the corresponding molybdenum analogues. Single crystals of trans-1b-W were successfully obtained, and the crystal structure was determined by X-ray analysis although 1b-Mo could not be crystallized. The NHS hydrogen bonds shifted the potential of the W(iv/v) redox couple to more positive values, and the strength of the hydrogen bond and the positive shift value were strongly correlated. The hydrogen bonds in both 1-W and 2-W were weaker than those in the corresponding molybdenum analogues; however, the effect of the hydrogen bonds on the redox potential was greater in 1-W.
Collapse
Affiliation(s)
- Taka-Aki Okamura
- Department of Macromolecular Science, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan.
| | - Yui Omi
- Department of Macromolecular Science, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan.
| | - Yasunori Hirano
- Department of Macromolecular Science, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan.
| | - Kiyotaka Onitsuka
- Department of Macromolecular Science, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan.
| |
Collapse
|
13
|
Synthesis and solution structure of desoxotungsten(IV) and monooxotungsten(VI) benzenedithiolate complexes containing two intramolecular NH⋯S hydrogen bonds. Inorganica Chim Acta 2017. [DOI: 10.1016/j.ica.2017.08.036] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
14
|
Maia LB, Moura I, Moura JJ. Molybdenum and tungsten-containing formate dehydrogenases: Aiming to inspire a catalyst for carbon dioxide utilization. Inorganica Chim Acta 2017. [DOI: 10.1016/j.ica.2016.07.010] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
|
15
|
Ammam F, Tremblay PL, Lizak DM, Zhang T. Effect of tungstate on acetate and ethanol production by the electrosynthetic bacterium Sporomusa ovata. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:163. [PMID: 27493685 PMCID: PMC4973070 DOI: 10.1186/s13068-016-0576-0] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 07/27/2016] [Indexed: 05/19/2023]
Abstract
BACKGROUND Microbial electrosynthesis (MES) and gas fermentation are bioenergy technologies in which a microbial catalyst reduces CO2 into organic carbon molecules with electrons from the cathode of a bioelectrochemical system or from gases such as H2. The acetogen Sporomusa ovata has the capacity of reducing CO2 into commodity chemicals by both gas fermentation and MES. Acetate is often the only product generated by S. ovata during autotrophic growth. RESULTS In this study, trace elements in S. ovata growth medium were optimized to improve MES and gas fermentation productivity. Augmenting tungstate concentration resulted in a 2.9-fold increase in ethanol production by S. ovata during H2:CO2-dependent growth. It also promoted electrosynthesis of ethanol in a S. ovata-driven MES reactor and increased acetate production 4.4-fold compared to unmodified medium. Furthermore, fatty acids propionate and butyrate were successfully converted to their corresponding alcohols 1-propanol and 1-butanol by S. ovata during gas fermentation. Increasing tungstate concentration enhanced conversion efficiency for both propionate and butyrate. Gene expression analysis suggested that tungsten-containing aldehyde ferredoxin oxidoreductases (AORs) and a tungsten-containing formate dehydrogenase (FDH) were involved in the improved biosynthesis of acetate, ethanol, 1-propanol, and 1-butanol. AORs and FDH contribute to the fatty acids re-assimilation pathway and the Wood-Ljungdahl pathway, respectively. CONCLUSIONS This study presented here shows that optimization of microbial catalyst growth medium can improve productivity and lead to the biosynthesis of different products by gas fermentation and MES. It also provides insights on the metabolism of biofuels production in acetogens and demonstrates that S. ovata has an important untapped metabolic potential for the production of other chemicals than acetate via CO2-converting bioprocesses including MES.
Collapse
Affiliation(s)
- Fariza Ammam
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2970 Hørsholm, Denmark
| | - Pier-Luc Tremblay
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2970 Hørsholm, Denmark
- School of Chemistry, Chemical Engineering and Life Science, Wuhan University of Technology, Wuhan, 430070 People’s Republic of China
| | - Dawid M. Lizak
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2970 Hørsholm, Denmark
| | - Tian Zhang
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2970 Hørsholm, Denmark
- School of Chemistry, Chemical Engineering and Life Science, Wuhan University of Technology, Wuhan, 430070 People’s Republic of China
| |
Collapse
|
16
|
Hagedoorn PL. Microbial Metalloproteomics. Proteomes 2015; 3:424-439. [PMID: 28248278 PMCID: PMC5217388 DOI: 10.3390/proteomes3040424] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Revised: 11/04/2015] [Accepted: 11/23/2015] [Indexed: 12/12/2022] Open
Abstract
Metalloproteomics is a rapidly developing field of science that involves the comprehensive analysis of all metal-containing or metal-binding proteins in a biological sample. The purpose of this review is to offer a comprehensive overview of the research involving approaches that can be categorized as inductively coupled plasma (ICP)-MS based methods, X-ray absorption/fluorescence, radionuclide based methods and bioinformatics. Important discoveries in microbial proteomics will be reviewed, as well as the outlook to new emerging approaches and research areas.
Collapse
Affiliation(s)
- Peter-Leon Hagedoorn
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, Delft 2628 BC, The Netherlands.
| |
Collapse
|
17
|
A New Class of Tungsten-Containing Oxidoreductase in Caldicellulosiruptor, a Genus of Plant Biomass-Degrading Thermophilic Bacteria. Appl Environ Microbiol 2015; 81:7339-47. [PMID: 26276113 DOI: 10.1128/aem.01634-15] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2015] [Accepted: 07/30/2015] [Indexed: 12/18/2022] Open
Abstract
Caldicellulosiruptor bescii grows optimally at 78°C and is able to decompose high concentrations of lignocellulosic plant biomass without the need for thermochemical pretreatment. C. bescii ferments both C5 and C6 sugars primarily to hydrogen gas, lactate, acetate, and CO2 and is of particular interest for metabolic engineering applications given the recent availability of a genetic system. Developing optimal strains for technological use requires a detailed understanding of primary metabolism, particularly when the goal is to divert all available reductant (electrons) toward highly reduced products such as biofuels. During an analysis of the C. bescii genome sequence for oxidoreductase-type enzymes, evidence was uncovered to suggest that the primary redox metabolism of C. bescii has a completely uncharacterized aspect involving tungsten, a rarely used element in biology. An active tungsten utilization pathway in C. bescii was demonstrated by the heterologous production of a tungsten-requiring, aldehyde-oxidizing enzyme (AOR) from the hyperthermophilic archaeon Pyrococcus furiosus. Furthermore, C. bescii also contains a tungsten-based AOR-type enzyme, here termed XOR, which is phylogenetically unique, representing a completely new member of the AOR tungstoenzyme family. Moreover, in C. bescii, XOR represents ca. 2% of the cytoplasmic protein. XOR is proposed to play a key, but as yet undetermined, role in the primary redox metabolism of this cellulolytic microorganism.
Collapse
|
18
|
Proteomic Insights into Sulfur Metabolism in the Hydrogen-Producing Hyperthermophilic Archaeon Thermococcus onnurineus NA1. Int J Mol Sci 2015; 16:9167-95. [PMID: 25915030 PMCID: PMC4463584 DOI: 10.3390/ijms16059167] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Accepted: 04/14/2015] [Indexed: 11/17/2022] Open
Abstract
The hyperthermophilic archaeon Thermococcus onnurineus NA1 has been shown to produce H₂ when using CO, formate, or starch as a growth substrate. This strain can also utilize elemental sulfur as a terminal electron acceptor for heterotrophic growth. To gain insight into sulfur metabolism, the proteome of T. onnurineus NA1 cells grown under sulfur culture conditions was quantified and compared with those grown under H₂-evolving substrate culture conditions. Using label-free nano-UPLC-MSE-based comparative proteomic analysis, approximately 38.4% of the total identified proteome (589 proteins) was found to be significantly up-regulated (≥1.5-fold) under sulfur culture conditions. Many of these proteins were functionally associated with carbon fixation, Fe-S cluster biogenesis, ATP synthesis, sulfur reduction, protein glycosylation, protein translocation, and formate oxidation. Based on the abundances of the identified proteins in this and other genomic studies, the pathways associated with reductive sulfur metabolism, H₂-metabolism, and oxidative stress defense were proposed. The results also revealed markedly lower expression levels of enzymes involved in the sulfur assimilation pathway, as well as cysteine desulfurase, under sulfur culture condition. The present results provide the first global atlas of proteome changes triggered by sulfur, and may facilitate an understanding of how hyperthermophilic archaea adapt to sulfur-rich, extreme environments.
Collapse
|
19
|
Molybdenum Availability in the Ecosystems (Geochemistry Aspects, When and How Did It Appear?). SPRINGERBRIEFS IN MOLECULAR SCIENCE 2015. [DOI: 10.1007/978-94-017-9972-0_2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
|
20
|
Changes in metabolic pathways of Desulfovibrio alaskensis G20 cells induced by molybdate excess. J Biol Inorg Chem 2014; 20:311-22. [PMID: 25488518 DOI: 10.1007/s00775-014-1224-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Accepted: 11/25/2014] [Indexed: 01/06/2023]
Abstract
The activity of sulfate-reducing bacteria (SRB) intensifies the problems associated to corrosion of metals and the solution entails significant economic costs. Although molybdate can be used to control the negative effects of these organisms, the mechanisms triggered in the cells exposed to Mo-excess are poorly understood. In this work, the effects of molybdate ions on the growth and morphology of the SRB Desulfovibrio alaskensis G20 (DaG20) were investigated. In addition, the cellular localization, ion uptake and regulation of protein expression were studied. We found that molybdate concentrations ranging between 50 and 150 µM produce a twofold increase in the doubling time with this effect being more significant at 200 µM molybdate (five times increase in the doubling time). It was also observed that 500 µM molybdate completely inhibits the cellular growth. On the context of protein regulation, we found that several enzymes involved in energy metabolism, cellular division and metal uptake processes were particularly influenced under the conditions tested. An overall description of some of the mechanisms involved in the DaG20 adaptation to molybdate-stress conditions is discussed.
Collapse
|
21
|
Molybdenum and tungsten-dependent formate dehydrogenases. J Biol Inorg Chem 2014; 20:287-309. [DOI: 10.1007/s00775-014-1218-2] [Citation(s) in RCA: 90] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2014] [Accepted: 11/09/2014] [Indexed: 11/25/2022]
|
22
|
Blomberg MRA, Borowski T, Himo F, Liao RZ, Siegbahn PEM. Quantum chemical studies of mechanisms for metalloenzymes. Chem Rev 2014; 114:3601-58. [PMID: 24410477 DOI: 10.1021/cr400388t] [Citation(s) in RCA: 431] [Impact Index Per Article: 43.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Margareta R A Blomberg
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University , SE-106 91 Stockholm, Sweden
| | | | | | | | | |
Collapse
|
23
|
New family of tungstate-responsive transcriptional regulators in sulfate-reducing bacteria. J Bacteriol 2013; 195:4466-75. [PMID: 23913324 DOI: 10.1128/jb.00679-13] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The trace elements molybdenum and tungsten are essential components of cofactors of many metalloenzymes. However, in sulfate-reducing bacteria, high concentrations of molybdate and tungstate oxyanions inhibit growth, thus requiring the tight regulation of their homeostasis. By a combination of bioinformatic and experimental techniques, we identified a novel regulator family, tungstate-responsive regulator (TunR), controlling the homeostasis of tungstate and molybdate in sulfate-reducing deltaproteobacteria. The effector-sensing domains of these regulators are similar to those of the known molybdate-responsive regulator ModE, while their DNA-binding domains are homologous to XerC/XerD site-specific recombinases. Using a comparative genomics approach, we identified DNA motifs and reconstructed regulons for 40 TunR family members. Positional analysis of TunR sites and putative promoters allowed us to classify most TunR proteins into two groups: (i) activators of modABC genes encoding a high-affinity molybdenum and tungsten transporting system and (ii) repressors of genes for toluene sulfonate uptake (TSUP) family transporters. The activation of modA and modBC genes by TunR in Desulfovibrio vulgaris Hildenborough was confirmed in vivo, and we discovered that the activation was diminished in the presence of tungstate. A predicted 30-bp TunR-binding motif was confirmed by in vitro binding assays. A novel TunR family of bacterial transcriptional factors controls tungstate and molybdate homeostasis in sulfate-reducing deltaproteobacteria. We proposed that TunR proteins participate in protection of the cells from the inhibition by these oxyanions. To our knowledge, this is a unique case of a family of bacterial transcriptional factors evolved from site-specific recombinases.
Collapse
|
24
|
Why is the molybdenum-substituted tungsten-dependent formaldehyde ferredoxin oxidoreductase not active? A quantum chemical study. J Biol Inorg Chem 2013; 18:175-181. [PMID: 23183892 DOI: 10.1007/s00775-012-0961-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2012] [Accepted: 11/13/2012] [Indexed: 01/12/2023]
Abstract
Formaldehyde ferredoxin oxidoreductase is a tungsten-dependent enzyme that catalyzes the oxidative degradation of formaldehyde to formic acid. The molybdenum ion can be incorporated into the active site to displace the tungsten ion, but is without activity. Density functional calculations have been employed to understand the incapacitation of the enzyme caused by molybdenum substitution. The calculations show that the enzyme with molybdenum (Mo-FOR) has higher redox potential than that with tungsten, which makes the formation of the Mo(VI)=O complex endothermic by 14 kcal/mol. Following our previously suggested mechanism for this enzyme, the formaldehyde substrate oxidation was also investigated for Mo-FOR using the same quantum-mechanics-only model, except for the displacement of tungsten by molybdenum. The calculations demonstrate that formaldehyde oxidation occurs via a sequential two-step mechanism. Similarly to the tungsten-catalyzed reaction, the Mo(VI)=O species performs the nucleophilic attack on the formaldehyde carbon, followed by proton transfer in concert with two-electron reduction of the metal center. The first step is rate-limiting, with a total barrier of 28.2 kcal/mol. The higher barrier is mainly due to the large energy penalty for the formation of the Mo(VI)=O species.
Collapse
|
25
|
Gonzalez PJ, Rivas MG, Mota CS, Brondino CD, Moura I, Moura JJ. Periplasmic nitrate reductases and formate dehydrogenases: Biological control of the chemical properties of Mo and W for fine tuning of reactivity, substrate specificity and metabolic role. Coord Chem Rev 2013. [DOI: 10.1016/j.ccr.2012.05.020] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
26
|
Sevcenco AM, Hagen WR, Hagedoorn PL. Microbial Metalloproteomes Explored Using MIRAGE. Chem Biodivers 2012; 9:1967-80. [DOI: 10.1002/cbdv.201100412] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|
27
|
Tsang CN, Bianga J, Sun H, Szpunar J, Lobinski R. Probing of bismuth antiulcer drug targets in H. pylori by laser ablation-inductively coupled plasma mass spectrometry. Metallomics 2012; 4:277-83. [PMID: 22286050 DOI: 10.1039/c2mt00169a] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
A method that allows partial denaturation of protein ligands in Bi- and Zn-protein complexes, leaving the metal coordination centre intact, was developed. It was based on the reduction of the S-S bridges with tris(2-carboxyl)phosphine followed by derivatization with iodoacetamide. Consequently conditions that allow the separation of Bi- and Zn-protein complexes using SDS electrophoresis were found. The separation efficiency was much higher than that in non-denaturating blue native electrophoresis. The method allowed the detection of seven Bi-binding protein candidates in H. pylori treated with bismuth subcitrate, some of which-fructose-bisphosphate aldolase (33.6 kDa), urease alpha subunit (26.4 kDa), and the 16.8 kDa proteins: 30S ribosomal protein S6 and neutrophil activating protein (NapA)-were bio-induced during the treatment. The method also allowed the monitoring of the changes in the Zn-proteome during treatment of H. pylori with the Bi-drug, which was found to increase the concentration of the Zn-binding proteins with particularly strong expression of the urease, S-adenosylmethionine synthetase and the above 16.8 kDa proteins.
Collapse
Affiliation(s)
- Cheuk-Nam Tsang
- Department of Chemistry, The University of Hong Kong, Hong Kong, PR China
| | | | | | | | | |
Collapse
|
28
|
|
29
|
Magalon A, Fedor JG, Walburger A, Weiner JH. Molybdenum enzymes in bacteria and their maturation. Coord Chem Rev 2011. [DOI: 10.1016/j.ccr.2010.12.031] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
|
30
|
Tungsten and molybdenum regulation of formate dehydrogenase expression in Desulfovibrio vulgaris Hildenborough. J Bacteriol 2011; 193:2909-16. [PMID: 21498650 DOI: 10.1128/jb.00042-11] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Formate is an important energy substrate for sulfate-reducing bacteria in natural environments, and both molybdenum- and tungsten-containing formate dehydrogenases have been reported in these organisms. In this work, we studied the effect of both metals on the levels of the three formate dehydrogenases encoded in the genome of Desulfovibrio vulgaris Hildenborough, with lactate, formate, or hydrogen as electron donors. Using Western blot analysis, quantitative real-time PCR, activity-stained gels, and protein purification, we show that a metal-dependent regulatory mechanism is present, resulting in the dimeric FdhAB protein being the main enzyme present in cells grown in the presence of tungsten and the trimeric FdhABC₃ protein being the main enzyme in cells grown in the presence of molybdenum. The putatively membrane-associated formate dehydrogenase is detected only at low levels after growth with tungsten. Purification of the three enzymes and metal analysis shows that FdhABC₃ specifically incorporates Mo, whereas FdhAB can incorporate both metals. The FdhAB enzyme has a much higher catalytic efficiency than the other two. Since sulfate reducers are likely to experience high sulfide concentrations that may result in low Mo bioavailability, the ability to use W is likely to constitute a selective advantage.
Collapse
|
31
|
Effects of molybdate and tungstate on expression levels and biochemical characteristics of formate dehydrogenases produced by Desulfovibrio alaskensis NCIMB 13491. J Bacteriol 2011; 193:2917-23. [PMID: 21478344 DOI: 10.1128/jb.01531-10] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Formate dehydrogenases (FDHs) are enzymes that catalyze the formate oxidation to carbon dioxide and that contain either Mo or W in a mononuclear form in the active site. In the present work, the influence of Mo and W salts on the production of FDH by Desulfovibrio alaskensis NCIMB 13491 was studied. Two different FDHs, one containing W (W-FDH) and a second incorporating either Mo or W (Mo/W-FDH), were purified. Both enzymes were isolated from cells grown in a medium supplemented with 1 μM molybdate, whereas only the W-FDH was purified from cells cultured in medium supplemented with 10 μM tungstate. We demonstrated that the genes encoding the Mo/W-FDH are strongly downregulated by W and slightly upregulated by Mo. Metal effects on the expression level of the genes encoding the W-FDH were less significant. Furthermore, the expression levels of the genes encoding proteins involved in molybdate and tungstate transport are downregulated under the experimental conditions evaluated in this work. The molecular and biochemical properties of these enzymes and the selective incorporation of either Mo or W are discussed.
Collapse
|
32
|
Affiliation(s)
- Carola Schulzke
- School of Chemistry, Trinity College Dublin, Dublin 2, Ireland
| |
Collapse
|
33
|
Sevcenco AM, Pinkse MWH, Wolterbeek HT, Verhaert PDEM, Hagen WR, Hagedoorn PL. Exploring the microbial metalloproteome using MIRAGE. Metallomics 2011; 3:1324-30. [DOI: 10.1039/c1mt00154j] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
34
|
Exploring the active site of the tungsten, iron-sulfur enzyme acetylene hydratase. J Bacteriol 2010; 193:1229-36. [PMID: 21193613 DOI: 10.1128/jb.01057-10] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The soluble tungsten, iron-sulfur enzyme acetylene hydratase (AH) from mesophilic Pelobacter acetylenicus is a member of the dimethyl sulfoxide (DMSO) reductase family. It stands out from its class as it catalyzes a nonredox reaction, the addition of H₂O to acetylene (H-C≡C-H) to form acetaldehyde (CH₃CHO). Caught in its active W(IV) state, the high-resolution three-dimensional structure of AH offers an excellent starting point to tackle its unique chemistry and to identify catalytic amino acid residues within the active site cavity: Asp13 close to W(IV) coordinated to two molybdopterin-guanosine-dinucleotide ligands, Lys48 which couples the [4Fe-4S] cluster to the W site, and Ile142 as part of a hydrophobic ring at the end of the substrate access channel designed to accommodate the substrate acetylene. A protocol was developed to express AH in Escherichia coli and to produce active-site variants which were characterized with regard to activity and occupancy of the tungsten and iron-sulfur centers. By this means, fusion of the N-terminal chaperone binding site of the E. coli nitrate reductase NarG to the AH gene improved the yield and activity of AH and its variants significantly. Results from site-directed mutagenesis of three key residues, Asp13, Lys48, and Ile142, document their important role in catalysis of this unusual tungsten enzyme.
Collapse
|