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Balci B, O'Neill RD, Shepard EM, Pagnier A, Marlott A, Mock MT, Broderick WE, Broderick JB. Semisynthetic maturation of [FeFe]-hydrogenase using [Fe 2(μ-SH) 2(CN) 2(CO) 4] 2-: key roles for HydF and GTP. Chem Commun (Camb) 2023. [PMID: 37376915 DOI: 10.1039/d3cc02169f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/29/2023]
Abstract
Here we describe maturation of the [FeFe]-hydrogenase from its [4Fe-4S]-bound precursor state by using the synthetic complex [Fe2(μ-SH)2(CN)2(CO)4]2- together with HydF and components of the glycine cleavage system, but in the absence of the maturases HydE and HydG. This semisynthetic and fully-defined maturation provides new insights into the nature of H-cluster biosynthesis.
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Affiliation(s)
- Batuhan Balci
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, MT 59717, USA.
| | - Roark D O'Neill
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, MT 59717, USA.
| | - Eric M Shepard
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, MT 59717, USA.
| | - Adrien Pagnier
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, MT 59717, USA.
| | - Alexander Marlott
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, MT 59717, USA.
| | - Michael T Mock
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, MT 59717, USA.
| | - William E Broderick
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, MT 59717, USA.
| | - Joan B Broderick
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, MT 59717, USA.
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2
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la Rosa GMD, García-Oliva F, Ovando-Vázquez C, Celis-García LB, López-Reyes L, López-Lozano NE. Amino Acids in the Root Exudates of Agave lechuguilla Torr. Favor the Recruitment and Enzymatic Activity of Nutrient-Improvement Rhizobacteria. MICROBIAL ECOLOGY 2022:10.1007/s00248-022-02162-x. [PMID: 36571608 DOI: 10.1007/s00248-022-02162-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 12/15/2022] [Indexed: 06/17/2023]
Abstract
Agave lechuguilla is a widely distributed plant in arid ecosystems. It has been suggested that its microbiome is partially responsible for its great adaptability to the oligotrophic environments of the Chihuahuan Desert. To lead the recruitment of beneficial rhizobacteria, the root exudates are essential; however, the amino acids contained within these compounds had been largely overlooked. Thus, we investigated how the variations of amino acids in the rhizosphere at different growth stages of A. lechuguilla affect the rhizobacterial community composition, its functions, and activity of the beneficial bacteria. In this regard, it was found that arginine and tyrosine were related to the composition of the rhizobacterial community associated to A. lechuguilla, where the most abundant genera were from the phylum Proteobacteria and Bacteroidetes. Moreover, Firmicutes was largely represented by Bacillus in the phosphorus-mineralizing bacteria community, which may indicate its great distribution and versatility in the harsh environments of the Chihuahuan Desert. In contrast, we found a high proportion of Unknown taxa of nitrogen-fixing bacteria, reflecting the enormous diversity in the rhizosphere of these types of plants that remains to be explored. This work also reports the influence of micronutrients and the amino acids methionine and arginine over the increased activity of the nitrogen-fixing and phosphorus-mineralizing bacteria in the rhizosphere of lechuguillas. In addition, the results highlight the multiple beneficial functions present in the microbiome that could help the host to tolerate arid conditions and improve nutrient availability.
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Affiliation(s)
- Guadalupe Medina-de la Rosa
- CONACyT-División de Ciencias Ambientales, Instituto Potosino de Investigación Científica Y Tecnológica, A.C., Camino a La Presa de San José 2055, Lomas 4Ta Secc, 78216, San Luis Potosí, S.L.P., Mexico
| | - Felipe García-Oliva
- Instituto de Investigaciones en Ecosistemas Y Sustentabilidad, Universidad Nacional Autónoma de México, 58190, Morelia, Mich, Mexico
| | - Cesaré Ovando-Vázquez
- CONACyT-Centro Nacional de Supercómputo, Instituto Potosino de Investigación Científica Y Tecnológica, A.C., 78216, San Luis Potosí, S.L.P., Mexico
| | - Lourdes B Celis-García
- CONACyT-División de Ciencias Ambientales, Instituto Potosino de Investigación Científica Y Tecnológica, A.C., Camino a La Presa de San José 2055, Lomas 4Ta Secc, 78216, San Luis Potosí, S.L.P., Mexico
| | - Lucía López-Reyes
- Centro de Investigación en Ciencias Microbiológicas, Benemérita Universidad Autónoma de Puebla, 72000, Puebla, Pue., Mexico
| | - Nguyen Esmeralda López-Lozano
- CONACyT-División de Ciencias Ambientales, Instituto Potosino de Investigación Científica Y Tecnológica, A.C., Camino a La Presa de San José 2055, Lomas 4Ta Secc, 78216, San Luis Potosí, S.L.P., Mexico.
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3
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Steward KF, Payne D, Kincannon W, Johnson C, Lensing M, Fausset H, Németh B, Shepard EM, Broderick WE, Broderick JB, Dubois J, Bothner B. Proteomic Analysis of Methanococcus voltae Grown in the Presence of Mineral and Nonmineral Sources of Iron and Sulfur. Microbiol Spectr 2022; 10:e0189322. [PMID: 35876569 PMCID: PMC9431491 DOI: 10.1128/spectrum.01893-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 06/17/2022] [Indexed: 11/28/2022] Open
Abstract
Iron sulfur (Fe-S) proteins are essential and ubiquitous across all domains of life, yet the mechanisms underpinning assimilation of iron (Fe) and sulfur (S) and biogenesis of Fe-S clusters are poorly understood. This is particularly true for anaerobic methanogenic archaea, which are known to employ more Fe-S proteins than other prokaryotes. Here, we utilized a deep proteomics analysis of Methanococcus voltae A3 cultured in the presence of either synthetic pyrite (FeS2) or aqueous forms of ferrous iron and sulfide to elucidate physiological responses to growth on mineral or nonmineral sources of Fe and S. The liquid chromatography-mass spectrometry (LCMS) shotgun proteomics analysis included 77% of the predicted proteome. Through a comparative analysis of intra- and extracellular proteomes, candidate proteins associated with FeS2 reductive dissolution, Fe and S acquisition, and the subsequent transport, trafficking, and storage of Fe and S were identified. The proteomic response shows a large and balanced change, suggesting that M. voltae makes physiological adjustments involving a range of biochemical processes based on the available nutrient source. Among the proteins differentially regulated were members of core methanogenesis, oxidoreductases, membrane proteins putatively involved in transport, Fe-S binding ferredoxin and radical S-adenosylmethionine proteins, ribosomal proteins, and intracellular proteins involved in Fe-S cluster assembly and storage. This work improves our understanding of ancient biogeochemical processes and can support efforts in biomining of minerals. IMPORTANCE Clusters of iron and sulfur are key components of the active sites of enzymes that facilitate microbial conversion of light or electrical energy into chemical bonds. The proteins responsible for transporting iron and sulfur into cells and assembling these elements into metal clusters are not well understood. Using a microorganism that has an unusually high demand for iron and sulfur, we conducted a global investigation of cellular proteins and how they change based on the mineral forms of iron and sulfur. Understanding this process will answer questions about life on early earth and has application in biomining and sustainable sources of energy.
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Affiliation(s)
- Katherine F. Steward
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | - Devon Payne
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, Montana, USA
| | - Will Kincannon
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | - Christina Johnson
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | - Malachi Lensing
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | - Hunter Fausset
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | - Brigitta Németh
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | - Eric M. Shepard
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | - William E. Broderick
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | - Joan B. Broderick
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | - Jen Dubois
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | - Brian Bothner
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
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4
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Shepard EM, Impano S, Duffus BR, Pagnier A, Duschene KS, Betz JN, Byer AS, Galambas A, McDaniel EC, Watts H, McGlynn SE, Peters JW, Broderick WE, Broderick JB. HydG, the "dangler" iron, and catalytic production of free CO and CN -: implications for [FeFe]-hydrogenase maturation. Dalton Trans 2021; 50:10405-10422. [PMID: 34240096 PMCID: PMC9154046 DOI: 10.1039/d1dt01359a] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The organometallic H-cluster of the [FeFe]-hydrogenase consists of a [4Fe-4S] cubane bridged via a cysteinyl thiolate to a 2Fe subcluster ([2Fe]H) containing CO, CN-, and dithiomethylamine (DTMA) ligands. The H-cluster is synthesized by three dedicated maturation proteins: the radical SAM enzymes HydE and HydG synthesize the non-protein ligands, while the GTPase HydF serves as a scaffold for assembly of [2Fe]H prior to its delivery to the [FeFe]-hydrogenase containing the [4Fe-4S] cubane. HydG uses l-tyrosine as a substrate, cleaving it to produce p-cresol as well as the CO and CN- ligands to the H-cluster, although there is some question as to whether these are formed as free diatomics or as part of a [Fe(CO)2(CN)] synthon. Here we show that Clostridium acetobutylicum (C.a.) HydG catalyzes formation of multiple equivalents of free CO at rates comparable to those for CN- formation. Free CN- is also formed in excess molar equivalents over protein. A g = 8.9 EPR signal is observed for C.a. HydG reconstituted to load the 5th "dangler" iron of the auxiliary [4Fe-4S][FeCys] cluster and is assigned to this "dangler-loaded" cluster state. Free CO and CN- formation and the degree of activation of [FeFe]-hydrogenase all occur regardless of dangler loading, but are increased 10-35% in the dangler-loaded HydG; this indicates the dangler iron is not essential to this process but may affect relevant catalysis. During HydG turnover in the presence of myoglobin, the g = 8.9 signal remains unchanged, indicating that a [Fe(CO)2(CN)(Cys)] synthon is not formed at the dangler iron. Mutation of the only protein ligand to the dangler iron, H272, to alanine nearly completely abolishes both free CO formation and hydrogenase activation, however results show this is not due solely to the loss of the dangler iron. In experiments with wild type and H272A HydG, and with different degrees of dangler loading, we observe a consistent correlation between free CO/CN- formation and hydrogenase activation. Taken in full, our results point to free CO/CN-, but not an [Fe(CO)2(CN)(Cys)] synthon, as essential species in hydrogenase maturation.
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Affiliation(s)
- Eric M Shepard
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, MT 59717, USA.
| | - Stella Impano
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, MT 59717, USA.
| | - Benjamin R Duffus
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, MT 59717, USA.
| | - Adrien Pagnier
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, MT 59717, USA.
| | - Kaitlin S Duschene
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, MT 59717, USA.
| | - Jeremiah N Betz
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, MT 59717, USA.
| | - Amanda S Byer
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, MT 59717, USA.
| | - Amanda Galambas
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, MT 59717, USA.
| | - Elizabeth C McDaniel
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, MT 59717, USA.
| | - Hope Watts
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, MT 59717, USA.
| | - Shawn E McGlynn
- Earth-Life Science Institute, Tokyo Institute of Technology, Ookayama, Meguro-ku, Tokyo 152-8550, Japan
| | - John W Peters
- Institute of Biological Chemistry, Washington State University, Pullman, WA 99163, USA
| | - William E Broderick
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, MT 59717, USA.
| | - Joan B Broderick
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, MT 59717, USA.
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5
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Martin WF. Carbon-Metal Bonds: Rare and Primordial in Metabolism. Trends Biochem Sci 2020; 44:807-818. [PMID: 31104860 DOI: 10.1016/j.tibs.2019.04.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 04/16/2019] [Accepted: 04/18/2019] [Indexed: 12/13/2022]
Abstract
Submarine hydrothermal vents are rich in hydrogen (H2), an ancient source of electrons and chemical energy for life. Geochemical H2 stems from serpentinization, a process in which rock-bound iron reduces water to H2. Reactions involving H2 and carbon dioxide (CO2) in hydrothermal systems generate abiotic methane and formate; these reactions resemble the core energy metabolism of methanogens and acetogens. These organisms are strict anaerobic autotrophs that inhabit hydrothermal vents and harness energy via H2-dependent CO2 reduction. Serpentinization also generates native metals, which can reduce CO2 to formate and acetate in the laboratory. The enzymes that channel H2, CO2, and dinitrogen (N2) into methanogen and acetogen metabolism are the backbone of the most ancient metabolic pathways. Their active sites share carbon-metal bonds which, although rare in biology, are conserved relics of primordial biochemistry present at the origin of life.
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Affiliation(s)
- William F Martin
- Institute for Molecular Evolution, University of Düsseldorf, 40225 Düsseldorf, Germany.
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6
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H-cluster assembly intermediates built on HydF by the radical SAM enzymes HydE and HydG. J Biol Inorg Chem 2019; 24:783-792. [PMID: 31493152 DOI: 10.1007/s00775-019-01709-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 08/13/2019] [Indexed: 12/12/2022]
Abstract
[FeFe]-hydrogenase catalyzes the reversible reduction of protons to H2 at a complex metallocofactor site, the H-cluster. Biosynthesis of this active-site H-cluster requires three maturation enzymes: the radical S-adenosylmethionine enzymes HydE and HydG synthesize the nonprotein ligands, while the GTPase HydF provides a scaffold for assembly of the 2Fe subcluster of the H-cluster ([2Fe]H) prior to its transfer to hydrogenase. To delineate the assembly and delivery steps for the 2Fe precursor cluster coordinated to HydF ([2Fe]F), we have heterologously expressed HydF in the presence of HydE alone (HydFE) or HydG alone (HydFG), and characterized the resulting purified HydFE and HydFG using UV-visible, EPR, and FTIR spectroscopies and biochemical assays. The iron-sulfur clusters on HydF are modified by co-expression with HydE or HydG, as evidenced by the changes in the visible, EPR, and FTIR spectral features. Further, biochemical assays show that HydFE is capable of activating HydAΔEFG to a limited extent (~ 1% of WT) even though the normal source of CO and CN- ligands of [2Fe]H (HydG) was absent. Activation assays performed with HydFG, in contrast, exhibit no ability to mature HydAΔEFG. It appears that in the case of HydFE, trace diatomics from the cellular environment are incorporated into a [2Fe]F-like precursor on HydF in the absence of HydG. We conclude that the product of HydE, presumably the dithiomethylamine ligand of [2Fe]H, is absolutely essential to the activation process, while the diatomic products of HydG can be provided from alternate sources.
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7
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Abstract
Described is the preparation of the first iron carbide-sulfides. The cluster [Fe6C(CO)15(SO2)]2- ([2]2-), which is generated quantitatively from [Fe6C(CO)16]2- ([1]2-), was O-methylated to give the sulfinite [2Me]-. Demethoxylation of [2Me]- with BF3 gave the face-capped octahedral cluster Fe6C(CO)15(SO) (3). In solution, 3 spontaneously converted to the sulfide Fe6C(CO)16(S) (4), an edge-fused double cluster with Fe5C and Fe3S subunits. Although 4 undergoes 1e- reduction reversibly, 2e- reduction (or base hydrolysis) of 4 gives closo-[Fe6C(CO)14(S)]2- ([5]2-). The synthetic entries into the Fe6CS x manifold may underpin the preparation of active-site analogues of the FeMoco and FeVco cofactors.
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Affiliation(s)
- Liang Liu
- School of Chemical Sciences , University of Illinois , Urbana , Illinois 61801 , United States
| | - Thomas B Rauchfuss
- School of Chemical Sciences , University of Illinois , Urbana , Illinois 61801 , United States
| | - Toby J Woods
- School of Chemical Sciences , University of Illinois , Urbana , Illinois 61801 , United States
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8
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Abstract
Enzyme-mediated cascade reactions are widespread in biosynthesis. To facilitate comparison with the mechanistic categorizations of cascade reactions by synthetic chemists and delineate the common underlying chemistry, we discuss four types of enzymatic cascade reactions: those involving nucleophilic, electrophilic, pericyclic, and radical reactions. Two subtypes of enzymes that generate radical cascades exist at opposite ends of the oxygen abundance spectrum. Iron-based enzymes use O2 to generate high valent iron-oxo species to homolyze unactivated C-H bonds in substrates to initiate skeletal rearrangements. At anaerobic end, enzymes reversibly cleave S-adenosylmethionine (SAM) to generate the 5'-deoxyadenosyl radical as a powerful oxidant to initiate C-H bond homolysis in bound substrates. The latter enzymes are termed radical SAM enzymes. We categorize the former as "thwarted oxygenases".
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Affiliation(s)
- Christopher T Walsh
- Stanford University Chemistry, Engineering, and Medicine for Human Health (CheM-H), Stanford University, Stanford, CA, 94305, USA
| | - Bradley S Moore
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, 92093, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, 92093, USA
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9
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Affiliation(s)
- Christopher T. Walsh
- Stanford University Chemistry, Engineering, and Medicine for Human Health (CheM-H)Stanford University Stanford CA 94305 USA
| | - Bradley S. Moore
- Center for Marine Biotechnology and BiomedicineScripps Institution of OceanographyUniversity of California, San Diego La Jolla CA 92093 USA
- Skaggs School of Pharmacy and Pharmaceutical SciencesUniversity of California, San Diego La Jolla CA 92093 USA
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10
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Scott AG, Szilagyi RK, Mulder DW, Ratzloff MW, Byer AS, King PW, Broderick WE, Shepard EM, Broderick JB. Compositional and structural insights into the nature of the H-cluster precursor on HydF. Dalton Trans 2018; 47:9521-9535. [PMID: 29964288 DOI: 10.1039/c8dt01654b] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Assembly of an active [FeFe]-hydrogenase requires dedicated maturation enzymes that generate the active-site H-cluster: the radical SAM enzymes HydE and HydG synthesize the unusual non-protein ligands - carbon monoxide, cyanide, and dithiomethylamine - while the GTPase HydF serves as a scaffold for assembly of the 2Fe subcluster containing these ligands. In the current study, enzymatically cluster-loaded HydF ([2Fe]F) is produced by co-expression with HydE and HydG in an Escherichia coli host followed by isolation and examination by FTIR and EPR spectroscopy. FTIR reveals the presence of well-defined terminal CO and CN- ligands; however, unlike in the [FeFe]-hydrogenase, no bridging CO is observed. Exposure of this loaded HydF to exogenous CO or H2 produces no significant changes to the FTIR spectrum, indicating that, unlike in the [FeFe]-hydrogenase, the 2Fe cluster in loaded HydF is coordinatively saturated and relatively unreactive. EPR spectroscopy reveals the presence of both [4Fe-4S] and [2Fe-2S] clusters on this loaded HydF, but provides no direct evidence for these being linked to the [2Fe]F. Using the chemical reactivity and FTIR data, a large collection of computational models were evaluated. Their scaled quantum chemical vibrational spectra allowed us to score various [2Fe]F structures in terms of their ability to reproduce the diatomic stretching frequencies observed in the FTIR experimental spectra. Collectively, the results provide new insights that support the presence of a diamagnetic, but spin-polarized FeI-FeI oxidation state for the [2Fe]F precursor cluster that is coordinated by 4 CO and 2 CN- ligands, and bridged to an adjacent iron-sulfur cluster through one of the CN- ligands.
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Affiliation(s)
- Anna G Scott
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717, USA.
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11
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Li Q, Lalaoui N, Woods TJ, Rauchfuss TB, Arrigoni F, Zampella G. Electron-Rich, Diiron Bis(monothiolato) Carbonyls: C-S Bond Homolysis in a Mixed Valence Diiron Dithiolate. Inorg Chem 2018; 57:4409-4418. [PMID: 29620876 DOI: 10.1021/acs.inorgchem.8b00094] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The synthesis and redox properties are presented for the electron-rich bis(monothiolate)s Fe2(SR)2(CO)2(dppv)2 for R = Me ([1]0), Ph ([2]0), CH2Ph ([3]0). Whereas related derivatives adopt C2-symmetric Fe2(CO)2P4 cores, [1]0-[3]0 have Cs symmetry resulting from the unsymmetrical steric properties of the axial vs equatorial R groups. Complexes [1]0-[3]0 undergo 1e- oxidation upon treatment with ferrocenium salts to give the mixed valence cations [Fe2(SR)2(CO)2(dppv)2]+. As established crystallographically, [3]+ adopts a rotated structure, characteristic of related mixed valence diiron complexes. Unlike [1]+ and [2]+ and many other [Fe2(SR)2L6]+ derivatives, [3]+ undergoes C-S bond homolysis, affording the diferrous sulfido-thiolate [Fe2(SCH2Ph)(S)(CO)2(dppv)2]+ ([4]+). According to X-ray crystallography, the first coordination spheres of [3]+ and [4]+ are similar, but the Fe-sulfido bonds are short in [4]+. The conversion of [3]+ to [4]+ follows first-order kinetics, with k = 2.3 × 10-6 s-1 (30 °C). When the conversion is conducted in THF, the organic products are toluene and dibenzyl. In the presence of TEMPO, the conversion of [3]+ to [4]+ is accelerated about 10×, the main organic product being TEMPO-CH2Ph. DFT calculations predict that the homolysis of a C-S bond is exergonic for [Fe2(SCH2Ph)2(CO)2(PR3)4]+ but endergonic for the neutral complex as well as less substituted cations. The unsaturated character of [4]+ is indicated by its double carbonylation to give [Fe2(SCH2Ph)(S)(CO)4(dppv)2]+ ([5]+), which adopts a bioctahedral structure.
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Affiliation(s)
- Qianli Li
- School of Chemical Sciences , University of Illinois , Urbana , Illinois 61801 , United States
| | - Noémie Lalaoui
- School of Chemical Sciences , University of Illinois , Urbana , Illinois 61801 , United States
| | - Toby J Woods
- School of Chemical Sciences , University of Illinois , Urbana , Illinois 61801 , United States
| | - Thomas B Rauchfuss
- School of Chemical Sciences , University of Illinois , Urbana , Illinois 61801 , United States
| | - Federica Arrigoni
- Department of Biotechnology and Biosciences , University of Milano-Bicocca , Piazza della Scienza 2 , 20126 - Milan , Italy
| | - Giuseppe Zampella
- Department of Biotechnology and Biosciences , University of Milano-Bicocca , Piazza della Scienza 2 , 20126 - Milan , Italy
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12
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Haskamp V, Karrie S, Mingers T, Barthels S, Alberge F, Magalon A, Müller K, Bill E, Lubitz W, Kleeberg K, Schweyen P, Bröring M, Jahn M, Jahn D. The radical SAM protein HemW is a heme chaperone. J Biol Chem 2018; 293:2558-2572. [PMID: 29282292 PMCID: PMC5818191 DOI: 10.1074/jbc.ra117.000229] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Revised: 12/14/2017] [Indexed: 11/06/2022] Open
Abstract
Radical S-adenosylmethionine (SAM) enzymes exist in organisms from all kingdoms of life, and all of these proteins generate an adenosyl radical via the homolytic cleavage of the S-C(5') bond of SAM. Of particular interest are radical SAM enzymes, such as heme chaperones, that insert heme into respiratory enzymes. For example, heme chaperones insert heme into target proteins but have been studied only for the formation of cytochrome c-type hemoproteins. Here, we report that a radical SAM protein, the heme chaperone HemW from bacteria, is required for the insertion of heme b into respiratory chain enzymes. As other radical SAM proteins, HemW contains three cysteines and one SAM coordinating an [4Fe-4S] cluster, and we observed one heme per subunit of HemW. We found that an intact iron-sulfur cluster was required for HemW dimerization and HemW-catalyzed heme transfer but not for stable heme binding. A bacterial two-hybrid system screen identified bacterioferritins and the heme-containing subunit NarI of the respiratory nitrate reductase NarGHI as proteins that interact with HemW. We also noted that the bacterioferritins potentially serve as heme donors for HemW. Of note, heme that was covalently bound to HemW was actively transferred to a heme-depleted, catalytically inactive nitrate reductase, restoring its nitrate-reducing enzyme activity. Finally, the human HemW orthologue radical SAM domain-containing 1 (RSAD1) stably bound heme. In conclusion, our findings indicate that the radical SAM protein family HemW/RSAD1 is a heme chaperone catalyzing the insertion of heme into hemoproteins.
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Affiliation(s)
| | | | | | | | - François Alberge
- Laboratoire de Chimie Bactérienne UMR7283, CNRS, Aix-Marseille Université, 13009 Marseille, France, and
| | - Axel Magalon
- Laboratoire de Chimie Bactérienne UMR7283, CNRS, Aix-Marseille Université, 13009 Marseille, France, and
| | | | - Eckhard Bill
- Max Planck Institute for Chemical Energy Conversion, D-45470 Mülheim an der Ruhr, Germany
| | - Wolfgang Lubitz
- Max Planck Institute for Chemical Energy Conversion, D-45470 Mülheim an der Ruhr, Germany
| | | | | | | | | | - Dieter Jahn
- Braunschweig Centre of Integrated Systems Biology (BRICS), University Braunschweig, D-38106 Braunschweig, Germany,
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13
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Haskett TL, Ramsay JP, Bekuma AA, Sullivan JT, O'Hara GW, Terpolilli JJ. Evolutionary persistence of tripartite integrative and conjugative elements. Plasmid 2017; 92:30-36. [DOI: 10.1016/j.plasmid.2017.06.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 06/28/2017] [Accepted: 06/28/2017] [Indexed: 10/19/2022]
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14
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Shepard EM, Byer AS, Aggarwal P, Betz JN, Scott AG, Shisler KA, Usselman RJ, Eaton GR, Eaton SS, Broderick JB. Electron Spin Relaxation and Biochemical Characterization of the Hydrogenase Maturase HydF: Insights into [2Fe-2S] and [4Fe-4S] Cluster Communication and Hydrogenase Activation. Biochemistry 2017; 56:3234-3247. [PMID: 28525271 PMCID: PMC5490485 DOI: 10.1021/acs.biochem.7b00169] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Nature utilizes [FeFe]-hydrogenase enzymes to catalyze the interconversion between H2 and protons and electrons. Catalysis occurs at the H-cluster, a carbon monoxide-, cyanide-, and dithiomethylamine-coordinated 2Fe subcluster bridged via a cysteine to a [4Fe-4S] cluster. Biosynthesis of this unique metallocofactor is accomplished by three maturase enzymes denoted HydE, HydF, and HydG. HydE and HydG belong to the radical S-adenosylmethionine superfamily of enzymes and synthesize the nonprotein ligands of the H-cluster. These enzymes interact with HydF, a GTPase that acts as a scaffold or carrier protein during 2Fe subcluster assembly. Prior characterization of HydF demonstrated the protein exists in both dimeric and tetrameric states and coordinates both [4Fe-4S]2+/+ and [2Fe-2S]2+/+ clusters [Shepard, E. M., Byer, A. S., Betz, J. N., Peters, J. W., and Broderick, J. B. (2016) Biochemistry 55, 3514-3527]. Herein, electron paramagnetic resonance (EPR) is utilized to characterize the [2Fe-2S]+ and [4Fe-4S]+ clusters bound to HydF. Examination of spin relaxation times using pulsed EPR in HydF samples exhibiting both [4Fe-4S]+ and [2Fe-2S]+ cluster EPR signals supports a model in which the two cluster types either are bound to widely separated sites on HydF or are not simultaneously bound to a single HydF species. Gel filtration chromatographic analyses of HydF spectroscopic samples strongly suggest the [2Fe-2S]+ and [4Fe-4S]+ clusters are coordinated to the dimeric form of the protein. Lastly, we examined the 2Fe subcluster-loaded form of HydF and showed the dimeric state is responsible for [FeFe]-hydrogenase activation. Together, the results indicate a specific role for the HydF dimer in the H-cluster biosynthesis pathway.
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Affiliation(s)
- Eric M Shepard
- Department of Chemistry and Biochemistry, Montana State University , Bozeman, Montana 59717, United States
| | - Amanda S Byer
- Department of Chemistry and Biochemistry, Montana State University , Bozeman, Montana 59717, United States
| | - Priyanka Aggarwal
- Department of Chemistry and Biochemistry, University of Denver , Denver, Colorado 80208, United States
| | - Jeremiah N Betz
- Department of Chemistry and Biochemistry, Montana State University , Bozeman, Montana 59717, United States
| | - Anna G Scott
- Department of Chemistry and Biochemistry, Montana State University , Bozeman, Montana 59717, United States
| | - Krista A Shisler
- Department of Chemistry and Biochemistry, Montana State University , Bozeman, Montana 59717, United States
| | - Robert J Usselman
- Department of Chemistry and Biochemistry, Montana State University , Bozeman, Montana 59717, United States
| | - Gareth R Eaton
- Department of Chemistry and Biochemistry, University of Denver , Denver, Colorado 80208, United States
| | - Sandra S Eaton
- Department of Chemistry and Biochemistry, University of Denver , Denver, Colorado 80208, United States
| | - Joan B Broderick
- Department of Chemistry and Biochemistry, Montana State University , Bozeman, Montana 59717, United States
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15
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Ji X, Li Y, Xie L, Lu H, Ding W, Zhang Q. Expanding Radical SAM Chemistry by Using Radical Addition Reactions and SAM Analogues. Angew Chem Int Ed Engl 2016; 55:11845-8. [DOI: 10.1002/anie.201605917] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2016] [Revised: 08/11/2016] [Indexed: 12/12/2022]
Affiliation(s)
- Xinjian Ji
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations; School of Life Sciences; Lanzhou University; Lanzhou 730000 China
- Department of Chemistry; Fudan University; Shanghai 200433 China
| | - Yongzhen Li
- Department of Chemistry; Fudan University; Shanghai 200433 China
| | - Liqi Xie
- Department of Chemistry; Fudan University; Shanghai 200433 China
| | - Haojie Lu
- Department of Chemistry; Fudan University; Shanghai 200433 China
| | - Wei Ding
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations; School of Life Sciences; Lanzhou University; Lanzhou 730000 China
| | - Qi Zhang
- Department of Chemistry; Fudan University; Shanghai 200433 China
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16
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Ji X, Li Y, Xie L, Lu H, Ding W, Zhang Q. Expanding Radical SAM Chemistry by Using Radical Addition Reactions and SAM Analogues. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201605917] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Xinjian Ji
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations; School of Life Sciences; Lanzhou University; Lanzhou 730000 China
- Department of Chemistry; Fudan University; Shanghai 200433 China
| | - Yongzhen Li
- Department of Chemistry; Fudan University; Shanghai 200433 China
| | - Liqi Xie
- Department of Chemistry; Fudan University; Shanghai 200433 China
| | - Haojie Lu
- Department of Chemistry; Fudan University; Shanghai 200433 China
| | - Wei Ding
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations; School of Life Sciences; Lanzhou University; Lanzhou 730000 China
| | - Qi Zhang
- Department of Chemistry; Fudan University; Shanghai 200433 China
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17
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Ding W, Ji X, Li Y, Zhang Q. Catalytic Promiscuity of the Radical S-adenosyl-L-methionine Enzyme NosL. Front Chem 2016; 4:27. [PMID: 27446906 PMCID: PMC4916742 DOI: 10.3389/fchem.2016.00027] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 06/09/2016] [Indexed: 12/19/2022] Open
Abstract
Catalytic promiscuity plays a key role in enzyme evolution and the acquisition of novel biological functions. Because of the high reactivity of radical species, in our view enzymes involving radical-mediated mechanisms could intrinsically be more prone to catalytic promiscuity. This mini-review summarizes the recent advances in the study of NosL, a radical S-adenosyl-L-methionine (SAM)-dependent L-tryptophan (L-Trp) lyase. We demonstrate here the interesting chemistry and remarkable catalytic promiscuity of NosL, and attempt to highlight the high evolvability of radical SAM enzymes and the potential to engineer these enzymes for novel and improved activities.
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Affiliation(s)
- Wei Ding
- Department of Chemistry, Fudan University Shanghai, China
| | - Xinjian Ji
- Department of Chemistry, Fudan University Shanghai, China
| | - Yongzhen Li
- Department of Chemistry, Fudan University Shanghai, China
| | - Qi Zhang
- Department of Chemistry, Fudan University Shanghai, China
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18
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Ding W, Li Q, Jia Y, Ji X, Qianzhu H, Zhang Q. Emerging Diversity of the Cobalamin-Dependent Methyltransferases Involving Radical-Based Mechanisms. Chembiochem 2016; 17:1191-7. [PMID: 27028019 DOI: 10.1002/cbic.201600107] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Indexed: 11/10/2022]
Abstract
Cobalamins comprise a group of cobalt-containing organometallic cofactors that play important roles in cellular metabolism. Although many cobalamin-dependent methyltransferases (e.g., methionine synthase MetH) have been extensively studied, a new group of methyltransferases that are cobalamin-dependent and utilize radical chemistry in catalysis is just beginning to be appreciated. In this Concept article, we summarize recent advances in the understanding of the radical-based and cobalamin-dependent methyltransferases and discuss the functional and mechanistic diversity of this emerging class of enzymes.
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Affiliation(s)
- Wei Ding
- Key Laboratory of Cell Activities and Stress Adaptations, (Ministry of Education), School of Life Sciences, Lanzhou University, Lanzhou, 730000, China.,Department of Chemistry, Fudan University, Shanghai, 200433, China
| | - Qien Li
- Key Laboratory of Cell Activities and Stress Adaptations, (Ministry of Education), School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Youli Jia
- Key Laboratory of Cell Activities and Stress Adaptations, (Ministry of Education), School of Life Sciences, Lanzhou University, Lanzhou, 730000, China.,Department of Chemistry, Fudan University, Shanghai, 200433, China
| | - Xinjian Ji
- Department of Chemistry, Fudan University, Shanghai, 200433, China
| | - Haocheng Qianzhu
- Department of Chemistry, Fudan University, Shanghai, 200433, China
| | - Qi Zhang
- Department of Chemistry, Fudan University, Shanghai, 200433, China.
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19
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Banerjee R. Introduction to the thematic minireview series on radical S-adenosylmethionine (SAM) enzymes. J Biol Chem 2014; 290:3962-3. [PMID: 25477525 DOI: 10.1074/jbc.r114.630251] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In the early days, radical enzyme reactions that use S-adenosylmethionine (SAM) coordinated to an Fe-S cluster, which Perry Frey described as a "poor man's coenzyme B12," were believed to be relatively rare chemical curiosities. Today, bioinformatics analyses have revealed the wide prevalence and sheer numbers of radical SAM enzymes, conferring superfamily status. In this thematic minireview series, the JBC presents six articles on radical SAM enzymes that accomplish wide-ranging chemical transformations. We learn that despite the diversity of the reactions catalyzed, family members share some common structural and mechanistic themes. Still in its infancy, continued explorations promise to be fertile grounds for discoveries that will undoubtedly further broaden our understanding of the catalytic repertoire and deepen our understanding of the chemical strategies used by radical SAM enzymes.
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Affiliation(s)
- Ruma Banerjee
- From the Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan 48109-0600
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