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Motovilov KA, Mostert AB. Melanin: Nature's 4th bioorganic polymer. SOFT MATTER 2024; 20:5635-5651. [PMID: 39012013 DOI: 10.1039/d4sm00491d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/17/2024]
Abstract
The pigments known as the melanins are widely recognized for their responsibility in the coloration of human skin, eyes, hair, and minimising the harmful effects of solar ultraviolet radiation. But specialists are aware that the melanins are present in all living kingdoms, barring viruses, and have functionality that extends beyond neutralizing ionising radiation. The ubiquitous presence of melanin in almost all human organs, recognized in recent years, as well as the presence of melanin in organisms that are evolutionarily distant from each other, indicate the fundamental importance of this class of material for all life forms. In this review, we argue for the need to accept melanins as the fourth primordial class of biological polymers, along with nucleic acids, proteins and polysaccharides. We consistently compare the properties of these canonical biological polymers with the properties of melanin and highlight key features that fundamentally distinguish melanins, their function and its mysteries.
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Affiliation(s)
- K A Motovilov
- Center for Photonics and 2D Materials, Moscow Institute of Physics and Technology, Institutsky Lane 9, Dolgoprudny 141701, Moscow Region, Russia.
| | - A B Mostert
- Department of Physics and Centre for Integrative Semiconductor Materials, Swansea University Bay Campus, Fabian Way, Swansea SA1 8EN, UK
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2
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Pomowski A, Dell'Acqua S, Wüst A, Pauleta SR, Moura I, Einsle O. Revisiting the metal sites of nitrous oxide reductase in a low-dose structure from Marinobacter nauticus. J Biol Inorg Chem 2024; 29:279-290. [PMID: 38720157 DOI: 10.1007/s00775-024-02056-y] [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: 01/28/2024] [Accepted: 04/10/2024] [Indexed: 05/24/2024]
Abstract
Copper-containing nitrous oxide reductase catalyzes a 2-electron reduction of the green-house gas N2O to yield N2. It contains two metal centers, the binuclear electron transfer site CuA, and the unique, tetranuclear CuZ center that is the site of substrate binding. Different forms of the enzyme were described previously, representing variations in oxidation state and composition of the metal sites. Hypothesizing that many reported discrepancies in the structural data may be due to radiation damage during data collection, we determined the structure of anoxically isolated Marinobacter nauticus N2OR from diffraction data obtained with low-intensity X-rays from an in-house rotating anode generator and an image plate detector. The data set was of exceptional quality and yielded a structure at 1.5 Å resolution in a new crystal form. The CuA site of the enzyme shows two distinct conformations with potential relevance for intramolecular electron transfer, and the CuZ cluster is present in a [4Cu:2S] configuration. In addition, the structure contains three additional types of ions, and an analysis of anomalous scattering contributions confirms them to be Ca2+, K+, and Cl-. The uniformity of the present structure supports the hypothesis that many earlier analyses showed inhomogeneities due to radiation effects. Adding to the earlier description of the same enzyme with a [4Cu:S] CuZ site, a mechanistic model is presented, with a structurally flexible CuZ center that does not require the complete dissociation of a sulfide prior to N2O binding.
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Affiliation(s)
- Anja Pomowski
- Institute for Biochemistry, Albert-Ludwigs-University Freiburg, Albertstrasse 21, 79104, Freiburg, Germany
| | - Simone Dell'Acqua
- Dipartimento Di Chimica, Università Di Pavia, Via Taramelli 12, 27100, Pavia, Italy
| | - Anja Wüst
- Institute for Biochemistry, Albert-Ludwigs-University Freiburg, Albertstrasse 21, 79104, Freiburg, Germany
| | - Sofia R Pauleta
- Microbial Stress Lab, UCIBIO-Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516, Caparica, Portugal
- Associate Laboratory i4HB-Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516, Caparica, Portugal
| | - Isabel Moura
- LAQV, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2529-516, Caparica, Portugal
| | - Oliver Einsle
- Institute for Biochemistry, Albert-Ludwigs-University Freiburg, Albertstrasse 21, 79104, Freiburg, Germany.
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3
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Zhang IH, Borer B, Zhao R, Wilbert S, Newman DK, Babbin AR. Uncultivated DPANN archaea are ubiquitous inhabitants of global oxygen-deficient zones with diverse metabolic potential. mBio 2024; 15:e0291823. [PMID: 38380943 PMCID: PMC10936187 DOI: 10.1128/mbio.02918-23] [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: 10/26/2023] [Accepted: 01/22/2024] [Indexed: 02/22/2024] Open
Abstract
Archaea belonging to the DPANN (Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, and Nanohaloarchaeota) superphylum have been found in an expanding number of environments and perform a variety of biogeochemical roles, including contributing to carbon, sulfur, and nitrogen cycling. Generally characterized by ultrasmall cell sizes and reduced genomes, DPANN archaea may form mutualistic, commensal, or parasitic interactions with various archaeal and bacterial hosts, influencing the ecology and functioning of microbial communities. While DPANN archaea reportedly comprise a sizeable fraction of the archaeal community within marine oxygen-deficient zone (ODZ) water columns, little is known about their metabolic capabilities in these ecosystems. We report 33 novel metagenome-assembled genomes (MAGs) belonging to the DPANN phyla Nanoarchaeota, Pacearchaeota, Woesearchaeota, Undinarchaeota, Iainarchaeota, and SpSt-1190 from pelagic ODZs in the Eastern Tropical North Pacific and the Arabian Sea. We find these archaea to be permanent, stable residents of all three major ODZs only within anoxic depths, comprising up to 1% of the total microbial community and up to 25%-50% of archaea as estimated from read mapping to MAGs. ODZ DPANN appear to be capable of diverse metabolic functions, including fermentation, organic carbon scavenging, and the cycling of sulfur, hydrogen, and methane. Within a majority of ODZ DPANN, we identify a gene homologous to nitrous oxide reductase. Modeling analyses indicate the feasibility of a nitrous oxide reduction metabolism for host-attached symbionts, and the small genome sizes and reduced metabolic capabilities of most DPANN MAGs suggest host-associated lifestyles within ODZs. IMPORTANCE Archaea from the DPANN (Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, and Nanohaloarchaeota) superphylum have diverse metabolic capabilities and participate in multiple biogeochemical cycles. While metagenomics and enrichments have revealed that many DPANN are characterized by ultrasmall genomes, few biosynthetic genes, and episymbiotic lifestyles, much remains unknown about their biology. We report 33 new DPANN metagenome-assembled genomes originating from the three global marine oxygen-deficient zones (ODZs), the first from these regions. We survey DPANN abundance and distribution within the ODZ water column, investigate their biosynthetic capabilities, and report potential roles in the cycling of organic carbon, methane, and nitrogen. We test the hypothesis that nitrous oxide reductases found within several ODZ DPANN genomes may enable ultrasmall episymbionts to serve as nitrous oxide consumers when attached to a host nitrous oxide producer. Our results indicate DPANN archaea as ubiquitous residents within the anoxic core of ODZs with the potential to produce or consume key compounds.
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Affiliation(s)
- Irene H. Zhang
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Benedict Borer
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Rui Zhao
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Steven Wilbert
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA
| | - Dianne K. Newman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, USA
| | - Andrew R. Babbin
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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4
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Rush KW, Eastman KAS, Welch EF, Bandarian V, Blackburn NJ. Capturing the Binuclear Copper State of Peptidylglycine Monooxygenase Using a Peptidyl-Homocysteine Lure. J Am Chem Soc 2024; 146:5074-5080. [PMID: 38363651 PMCID: PMC11096088 DOI: 10.1021/jacs.3c14705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2024]
Abstract
Peptidylglycine monooxygenase is a copper-dependent enzyme that catalyzes C-alpha hydroxylation of glycine extended pro-peptides, a critical post-translational step in peptide hormone processing. The canonical mechanism posits that dioxygen binds at the mononuclear M-center to generate a Cu(II)-superoxo species capable of H atom abstraction from the peptidyl substrate, followed by long-range electron tunneling from the CuH center. Recent crystallographic and biochemical data have challenged this mechanism, suggesting instead that an "open-to-closed" transition brings the copper centers closer, allowing reactivity within a binuclear intermediate. Here we present the first direct observation of an enzyme-bound binuclear copper species, captured by the use of an Ala-Ala-Phe-hCys inhibitor complex. This molecule reacts with the fully reduced enzyme to form a thiolate-bridged binuclear species characterized by EXAFS of the WT and its M314H variant and with the oxidized enzyme to form a novel mixed valence entity characterized by UV/vis and EPR. Mechanistic implications are discussed.
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Affiliation(s)
- Katherine W. Rush
- Department of Chemical Physiology and Biochemistry, Oregon Health & Science University, Portland, OR 97239, USA
| | | | - Evan F. Welch
- Department of Chemical Physiology and Biochemistry, Oregon Health & Science University, Portland, OR 97239, USA
| | - Vahe Bandarian
- Department of Chemistry, University of Utah, Salt Lake City, UT 84112, USA
| | - Ninian J. Blackburn
- Department of Chemical Physiology and Biochemistry, Oregon Health & Science University, Portland, OR 97239, USA
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5
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Zhang IH, Borer B, Zhao R, Wilbert S, Newman DK, Babbin AR. Uncultivated DPANN archaea are ubiquitous inhabitants of global oxygen deficient zones with diverse metabolic potential. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.30.564641. [PMID: 37961710 PMCID: PMC10634959 DOI: 10.1101/2023.10.30.564641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Archaea belonging to the DPANN superphylum have been found within an expanding number of environments and perform a variety of biogeochemical roles, including contributing to carbon, sulfur, and nitrogen cycling. Generally characterized by ultrasmall cell sizes and reduced genomes, DPANN archaea may form mutualistic, commensal, or parasitic interactions with various archaeal and bacterial hosts, influencing the ecology and functioning of microbial communities. While DPANN archaea reportedly comprise 15-26% of the archaeal community within marine oxygen deficient zone (ODZ) water columns, little is known about their metabolic capabilities in these ecosystems. We report 33 novel metagenome-assembled genomes belonging to DPANN phyla Nanoarchaeota, Pacearchaeota, Woesarchaeota, Undinarchaeota, Iainarchaeota, and SpSt-1190 from pelagic ODZs in the Eastern Tropical North Pacific and Arabian Sea. We find these archaea to be permanent, stable residents of all 3 major ODZs only within anoxic depths, comprising up to 1% of the total microbial community and up to 25-50% of archaea. ODZ DPANN appear capable of diverse metabolic functions, including fermentation, organic carbon scavenging, and the cycling of sulfur, hydrogen, and methane. Within a majority of ODZ DPANN, we identify a gene homologous to nitrous oxide reductase. Modeling analyses indicate the feasibility of a nitrous oxide reduction metabolism for host-attached symbionts, and the small genome sizes and reduced metabolic capabilities of most DPANN MAGs suggest host-associated lifestyles within ODZs.
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Affiliation(s)
- Irene H. Zhang
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Benedict Borer
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Rui Zhao
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Steven Wilbert
- Divisions of Biology and Biological Engineering and Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, USA
| | - Dianne K. Newman
- Divisions of Biology and Biological Engineering and Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, USA
| | - Andrew R. Babbin
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
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6
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Singh S, Rai N, Tiwari H, Gupta P, Verma A, Kumar R, Kailashiya V, Salvi P, Gautam V. Recent Advancements in the Formulation of Nanomaterials-Based Nanozymes, Their Catalytic Activity, and Biomedical Applications. ACS APPLIED BIO MATERIALS 2023; 6:3577-3599. [PMID: 37590090 DOI: 10.1021/acsabm.3c00253] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/19/2023]
Abstract
Nanozymes are nanoparticles with intrinsic enzyme-mimicking properties that have become more prevalent because of their ability to outperform conventional enzymes by overcoming their drawbacks related to stability, cost, and storage. Nanozymes have the potential to manipulate active sites of natural enzymes, which is why they are considered promising candidates to function as enzyme mimetics. Several microscopy- and spectroscopy-based techniques have been used for the characterization of nanozymes. To date, a wide range of nanozymes, including catalase, oxidase, peroxidase, and superoxide dismutase, have been designed to effectively mimic natural enzymes. The activity of nanozymes can be controlled by regulating the structural and morphological aspects of the nanozymes. Nanozymes have multifaceted benefits, which is why they are exploited on a large scale for their application in the biomedical sector. The versatility of nanozymes aids in monitoring and treating cancer, other neurodegenerative diseases, and metabolic disorders. Due to the compelling advantages of nanozymes, significant research advancements have been made in this area. Although a wide range of nanozymes act as potent mimetics of natural enzymes, their activity and specificities are suboptimal, and there is still room for their diversification for analytical purposes. Designing diverse nanozyme systems that are sensitive to one or more substrates through specialized techniques has been the subject of an in-depth study. Hence, we believe that stimuli-responsive nanozymes may open avenues for diagnosis and treatment by fusing the catalytic activity and intrinsic nanomaterial properties of nanozyme systems.
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Affiliation(s)
- Swati Singh
- Centre of Experimental Medicine and Surgery, Institute of Medical Sciences, Banaras Hindu University, Varanasi 221005, India
| | - Nilesh Rai
- Centre of Experimental Medicine and Surgery, Institute of Medical Sciences, Banaras Hindu University, Varanasi 221005, India
| | - Harshita Tiwari
- Centre of Experimental Medicine and Surgery, Institute of Medical Sciences, Banaras Hindu University, Varanasi 221005, India
| | - Priyamvada Gupta
- Centre of Experimental Medicine and Surgery, Institute of Medical Sciences, Banaras Hindu University, Varanasi 221005, India
| | - Ashish Verma
- Centre of Experimental Medicine and Surgery, Institute of Medical Sciences, Banaras Hindu University, Varanasi 221005, India
| | - Rajiv Kumar
- Centre of Experimental Medicine and Surgery, Institute of Medical Sciences, Banaras Hindu University, Varanasi 221005, India
| | - Vikas Kailashiya
- Department of Pathology, Institute of Medical Sciences, Banaras Hindu University, Varanasi 221005, Uttar Pradesh, India
| | - Prafull Salvi
- Agriculture Biotechnology Department, National Agri-Food Biotechnology Institute, Sahibzada Ajit Singh Nagar 140306, India
| | - Vibhav Gautam
- Centre of Experimental Medicine and Surgery, Institute of Medical Sciences, Banaras Hindu University, Varanasi 221005, India
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7
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Lycus P, Einsle O, Zhang L. Structural biology of proteins involved in nitrogen cycling. Curr Opin Chem Biol 2023; 74:102278. [PMID: 36889028 DOI: 10.1016/j.cbpa.2023.102278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/31/2023] [Accepted: 02/02/2023] [Indexed: 03/08/2023]
Abstract
Microbial metabolic processes drive the global nitrogen cycle through sophisticated and often unique metalloenzymes that facilitate difficult redox reactions at ambient temperature and pressure. Understanding the intricacies of these biological nitrogen transformations requires a detailed knowledge that arises from the combination of a multitude of powerful analytical techniques and functional assays. Recent developments in spectroscopy and structural biology have provided new, powerful tools for addressing existing and emerging questions, which have gained urgency due to the global environmental implications of these fundamental reactions. The present review focuses on the recent contributions of the wider area of structural biology to understanding nitrogen metabolism, opening new avenues for biotechnological applications to better manage and balance the challenges of the global nitrogen cycle.
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Affiliation(s)
- Pawel Lycus
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstrasse 21, 79104, Freiburg im Breisgau, Germany; Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Oliver Einsle
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstrasse 21, 79104, Freiburg im Breisgau, Germany.
| | - Lin Zhang
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstrasse 21, 79104, Freiburg im Breisgau, Germany.
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8
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Mhaske A, Sharma S, Shukla R. Nanotheranostic: The futuristic therapy for copper mediated neurological sequelae. J Drug Deliv Sci Technol 2023. [DOI: 10.1016/j.jddst.2023.104193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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9
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Guo J, Fisher OS. Orchestrating copper binding: structure and variations on the cupredoxin fold. J Biol Inorg Chem 2022; 27:529-540. [PMID: 35994119 DOI: 10.1007/s00775-022-01955-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 08/07/2022] [Indexed: 11/26/2022]
Abstract
A large number of copper binding proteins coordinate metal ions using a shared three-dimensional fold called the cupredoxin domain. This domain was originally identified in Type 1 "blue copper" centers but has since proven to be a common domain architecture within an increasingly large and diverse group of copper binding domains. The cupredoxin fold has a number of qualities that make it ideal for coordinating Cu ions for purposes including electron transfer, enzyme catalysis, assembly of other copper sites, and copper sequestration. The structural core does not undergo major conformational changes upon metal binding, but variations within the coordination environment of the metal site confer a range of Cu-binding affinities, reduction potentials, and spectroscopic properties. Here, we discuss these proteins from a structural perspective, examining how variations within the overall cupredoxin fold and metal binding sites are linked to distinct spectroscopic properties and biological functions. Expanding far beyond the blue copper proteins, cupredoxin domains are used by a growing number of proteins and enzymes as a means of binding copper ions, with many more likely remaining to be identified.
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Affiliation(s)
- Jing Guo
- Department of Chemistry, Lehigh University, Bethlehem, PA, USA
| | - Oriana S Fisher
- Department of Chemistry, Lehigh University, Bethlehem, PA, USA.
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10
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Reaction of N-Acetylcysteine with Cu 2+: Appearance of Intermediates with High Free Radical Scavenging Activity: Implications for Anti-/Pro-Oxidant Properties of Thiols. Int J Mol Sci 2022; 23:ijms23116199. [PMID: 35682881 PMCID: PMC9181168 DOI: 10.3390/ijms23116199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 05/27/2022] [Accepted: 05/30/2022] [Indexed: 11/16/2022] Open
Abstract
We studied the kinetics of the reaction of N-acetyl-l-cysteine (NAC or RSH) with cupric ions at an equimolar ratio of the reactants in aqueous acid solution (pH 1.4−2) using UV/Vis absorption and circular dichroism (CD) spectroscopies. Cu2+ showed a strong catalytic effect on the 2,2′-azino-bis(3-ethylbenzothiazoline-6-sulfonate) radical (ABTSr) consumption and autoxidation of NAC. Difference spectra revealed the formation of intermediates with absorption maxima at 233 and 302 nm (ε302/Cu > 8 × 103 M−1 cm−1) and two positive Cotton effects centered at 284 and 302 nm. These intermediates accumulate during the first, O2-independent, phase of the NAC autoxidation. The autocatalytic production of another chiral intermediate, characterized by two positive Cotton effects at 280 and 333 nm and an intense negative one at 305 nm, was observed in the second reaction phase. The intermediates are rapidly oxidized by added ABTSr; otherwise, they are stable for hours in the reaction solution, undergoing a slow pH- and O2-dependent photosensitive decay. The kinetic and spectral data are consistent with proposed structures of the intermediates as disulfide-bridged dicopper(I) complexes of types cis-/trans-CuI2(RS)2(RSSR) and CuI2(RSSR)2. The electronic transitions observed in the UV/Vis and CD spectra are tentatively attributed to Cu(I) → disulfide charge transfer with an interaction of the transition dipole moments (exciton coupling). The catalytic activity of the intermediates as potential O2 activators via Cu(II) peroxo-complexes is discussed. A mechanism for autocatalytic oxidation of Cu(I)−thiolates promoted by a growing electronically coupled −[CuI2(RSSR)]n− polymer is suggested. The obtained results are in line with other reported observations regarding copper-catalyzed autoxidation of thiols and provide new insight into these complicated, not yet fully understood systems. The proposed hypotheses point to the importance of the Cu(I)−disulfide interaction, which may have a profound impact on biological systems.
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11
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Electrochemical Characterization of an Engineered Red Copper Protein Featuring an Unprecedented Entropic Control of the Reduction Potential. Bioelectrochemistry 2022; 146:108095. [DOI: 10.1016/j.bioelechem.2022.108095] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 03/04/2022] [Accepted: 03/10/2022] [Indexed: 12/12/2022]
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12
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Hu L, Wang X, Chen C, Chen J, Wang Z, Chen J, Hrynshpan D, Savitskaya T. NosZ gene cloning, reduction performance and structure of Pseudomonas citronellolis WXP-4 nitrous oxide reductase. RSC Adv 2022; 12:2549-2557. [PMID: 35425296 PMCID: PMC8979117 DOI: 10.1039/d1ra09008a] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 01/08/2022] [Indexed: 11/24/2022] Open
Abstract
Nitrous oxide reductase (N2OR) is the only known enzyme that can reduce the powerful greenhouse gas nitrous oxide (N2O) to harmless nitrogen at the final step of bacterial denitrification. To alleviate the N2O emission, emerging approaches aim at microbiome biotechnology. In this study, the genome sequence of facultative anaerobic bacteria Pseudomonas citronellolis WXP-4, which efficiently degrades N2O, was obtained by de novo sequencing for the first time, and then, four key reductase structure coding genes related to complete denitrification were identified. The single structural encoding gene nosZ with a length of 1914 bp from strain WXP-4 was cloned in Escherichia coli BL21(DE3), and the N2OR protein (76 kDa) was relatively highly efficiently expressed under the optimal inducing conditions of 1.0 mM IPTG, 5 h, and 30 °C. Denitrification experiment results confirmed that recombinant E. coli had strong denitrification ability and reduced 10 mg L−1 of N2O to N2 within 15 h under the optimal conditions of pH 7.0 and 40 °C, its corresponding N2O reduction rate was almost 2.3 times that of Alcaligenes denitrificans strain TB, but only 80% of that of wild strain WXP-4, meaning that nos gene cluster auxiliary gene deletion decreased the activity of N2OR. The 3D structure of N2OR predicted on the basis of sequence homology found that electron transfer center CuA had only five amino acid ligands, and the S2 of the catalytically active center CuZ only bound one CuI atom. The unique 3D structure was different from previous reports and may be closely related to the strong N2O reduction ability of strain WXP-4 and recombinant E. coli. The findings show a potential application of recombinant E. coli in alleviating the greenhouse effect and provide a new perspective for researching the relationship between structure and function of N2OR. Nitrous oxide reductase (N2OR) is the only known enzyme that can reduce the powerful greenhouse gas nitrous oxide (N2O) to harmless nitrogen at the final step of bacterial denitrification. The recombinant E. coli and wild strain WXP-4 demonstrate strong N2O reduction ability.![]()
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Affiliation(s)
- Liyong Hu
- College of Environment, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Xiaoping Wang
- College of Environment, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Cong Chen
- College of Environment, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Jianmeng Chen
- College of Environment, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Zeyu Wang
- Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Interdisciplinary Research Academy, Zhejiang Shuren University, Hangzhou, 310015, China
| | - Jun Chen
- Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Interdisciplinary Research Academy, Zhejiang Shuren University, Hangzhou, 310015, China
| | - Dzmitry Hrynshpan
- Research Institute of Physical and Chemical Problems, Belarusian State University, Minsk, 220030, Belarus
| | - Tatsiana Savitskaya
- Research Institute of Physical and Chemical Problems, Belarusian State University, Minsk, 220030, Belarus
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13
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Wang LK, Chen X, Wei W, Xu Q, Sun J, Mannina G, Song L, Ni BJ. Biological Reduction of Nitric Oxide for Efficient Recovery of Nitrous Oxide as an Energy Source. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:1992-2005. [PMID: 33430585 DOI: 10.1021/acs.est.0c04037] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Chemical absorption-biological reduction based on Fe(II)EDTA is a promising technology to remove nitric oxide (NO) from flue gases. However, limited effort has been made to enable direct energy recovery from NO through production of nitrous oxide (N2O) as a potential renewable energy rather than greenhouse gas. In this work, the enhanced energy recovery in the form of N2O via biological NO reduction was investigated by conducting short-term and long-term experiments at different Fe(II)EDTA-NO and organic carbon levels. The results showed both NO reductase and N2O reductase were inhibited at Fe(II)EDTA-NO concentration up to 20 mM, with the latter being inhibited more significantly, thus facilitating N2O accumulation. Furthermore, N2O accumulation was enhanced under carbon-limiting conditions because of electron competition during short-term experiments. Up to 47.5% of NO-N could be converted to gaseous N2O-N, representing efficient N2O recovery. Fe(II)EDTA-NO reduced microbial diversity and altered the community structure toward Fe(II)EDTA-NO-reducing bacteria-dominated culture during long-term experiments. The most abundant bacterial genus Pseudomonas, which was able to resist the toxicity of Fe(II)EDTA-NO, was significantly enriched, with its relative abundance increased from 1.0 to 70.3%, suggesting Pseudomonas could be the typical microbe for the energy recovery technology in NO-based denitrification.
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Affiliation(s)
- Li-Kun Wang
- State Key Laboratory of Pollution Control and Resources Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, PR China
- Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, PR China
| | - Xueming Chen
- College of Environment and Resources, Fuzhou University, Fujian 350116, PR China
| | - Wei Wei
- State Key Laboratory of Pollution Control and Resources Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, PR China
| | - Qiuxiang Xu
- State Key Laboratory of Pollution Control and Resources Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, PR China
- Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, PR China
| | - Jing Sun
- State Key Laboratory of Pollution Control and Resources Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, PR China
- Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, PR China
| | - Giorgio Mannina
- State Key Laboratory of Pollution Control and Resources Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, PR China
- Engineering Department, Palermo University, Viale delle Scienze, ed. 8, 90128 Palermo, Italy
| | - Lan Song
- School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, PR China
| | - Bing-Jie Ni
- State Key Laboratory of Pollution Control and Resources Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, PR China
- Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, PR China
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14
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Zhang L, Bill E, Kroneck PMH, Einsle O. A [3Cu:2S] cluster provides insight into the assembly and function of the Cu Z site of nitrous oxide reductase. Chem Sci 2021; 12:3239-3244. [PMID: 34164092 PMCID: PMC8179356 DOI: 10.1039/d0sc05204c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Nitrous oxide reductase (N2OR) is the only known enzyme reducing environmentally critical nitrous oxide (N2O) to dinitrogen (N2) as the final step of bacterial denitrification. The assembly process of its unique catalytic [4Cu:2S] cluster CuZ remains scarcely understood. Here we report on a mutagenesis study of all seven histidine ligands coordinating this copper center, followed by spectroscopic and structural characterization and based on an established, functional expression system for Pseudomonas stutzeri N2OR in Escherichia coli. While no copper ion was found in the CuZ binding site of variants H129A, H130A, H178A, H326A, H433A and H494A, the H382A variant carried a catalytically inactive [3Cu:2S] center, in which one sulfur ligand, SZ2, had relocated to form a weak hydrogen bond to the sidechain of the nearby lysine residue K454. This link provides sufficient stability to avoid the loss of the sulfide anion. The UV-vis spectra of this cluster are strikingly similar to those of the active enzyme, implying that the flexibility of SZ2 may have been observed before, but not recognized. The sulfide shift changes the metal coordination in CuZ and is thus of high mechanistic interest. Variants of all seven histidine ligands of the [4Cu:2S] active site of nitrous oxide reductase mostly result in loss of the metal site. However, a H382A variant retains a [3Cu:2S] cluster that hints towards a structural flexibility also present in the intact site.![]()
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Affiliation(s)
- Lin Zhang
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg Albertstrasse 21 79104 Freiburg im Breisgau Germany
| | - Eckhard Bill
- Max-Planck-Institut für Chemische Energiekonversion Stiftstr. 34-36 D-45470 Mülheim an der Ruhr Germany
| | | | - Oliver Einsle
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg Albertstrasse 21 79104 Freiburg im Breisgau Germany
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15
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Zhang L, Bill E, Kroneck PMH, Einsle O. Histidine-Gated Proton-Coupled Electron Transfer to the CuA Site of Nitrous Oxide Reductase. J Am Chem Soc 2020; 143:830-838. [DOI: 10.1021/jacs.0c10057] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Lin Zhang
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstraße 21, 79104 Freiburg im Breisgau, Germany
| | - Eckhard Bill
- Max-Planck-Institut für Chemische Energiekonversion, Stiftstraße 34-36, D-45470 Mülheim an der Ruhr, Germany
| | | | - Oliver Einsle
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstraße 21, 79104 Freiburg im Breisgau, Germany
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16
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Andrei A, Öztürk Y, Khalfaoui-Hassani B, Rauch J, Marckmann D, Trasnea PI, Daldal F, Koch HG. Cu Homeostasis in Bacteria: The Ins and Outs. MEMBRANES 2020; 10:E242. [PMID: 32962054 PMCID: PMC7558416 DOI: 10.3390/membranes10090242] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Revised: 09/11/2020] [Accepted: 09/15/2020] [Indexed: 12/16/2022]
Abstract
Copper (Cu) is an essential trace element for all living organisms and used as cofactor in key enzymes of important biological processes, such as aerobic respiration or superoxide dismutation. However, due to its toxicity, cells have developed elaborate mechanisms for Cu homeostasis, which balance Cu supply for cuproprotein biogenesis with the need to remove excess Cu. This review summarizes our current knowledge on bacterial Cu homeostasis with a focus on Gram-negative bacteria and describes the multiple strategies that bacteria use for uptake, storage and export of Cu. We furthermore describe general mechanistic principles that aid the bacterial response to toxic Cu concentrations and illustrate dedicated Cu relay systems that facilitate Cu delivery for cuproenzyme biogenesis. Progress in understanding how bacteria avoid Cu poisoning while maintaining a certain Cu quota for cell proliferation is of particular importance for microbial pathogens because Cu is utilized by the host immune system for attenuating pathogen survival in host cells.
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Affiliation(s)
- Andreea Andrei
- Institut für Biochemie und Molekularbiologie, ZBMZ, Medizinische Fakultät, Albert-Ludwigs Universität Freiburg; Stefan Meier Str. 17, 79104 Freiburg, Germany; (A.A.); (Y.O.); (J.R.); (D.M.)
- Fakultät für Biologie, Albert-Ludwigs Universität Freiburg; Schänzlestrasse 1, 79104 Freiburg, Germany
| | - Yavuz Öztürk
- Institut für Biochemie und Molekularbiologie, ZBMZ, Medizinische Fakultät, Albert-Ludwigs Universität Freiburg; Stefan Meier Str. 17, 79104 Freiburg, Germany; (A.A.); (Y.O.); (J.R.); (D.M.)
| | | | - Juna Rauch
- Institut für Biochemie und Molekularbiologie, ZBMZ, Medizinische Fakultät, Albert-Ludwigs Universität Freiburg; Stefan Meier Str. 17, 79104 Freiburg, Germany; (A.A.); (Y.O.); (J.R.); (D.M.)
| | - Dorian Marckmann
- Institut für Biochemie und Molekularbiologie, ZBMZ, Medizinische Fakultät, Albert-Ludwigs Universität Freiburg; Stefan Meier Str. 17, 79104 Freiburg, Germany; (A.A.); (Y.O.); (J.R.); (D.M.)
| | | | - Fevzi Daldal
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA;
| | - Hans-Georg Koch
- Institut für Biochemie und Molekularbiologie, ZBMZ, Medizinische Fakultät, Albert-Ludwigs Universität Freiburg; Stefan Meier Str. 17, 79104 Freiburg, Germany; (A.A.); (Y.O.); (J.R.); (D.M.)
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17
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Stein LY. The Long-Term Relationship between Microbial Metabolism and Greenhouse Gases. Trends Microbiol 2020; 28:500-511. [DOI: 10.1016/j.tim.2020.01.006] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 01/09/2020] [Accepted: 01/16/2020] [Indexed: 11/26/2022]
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18
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Morgada MN, Llases ME, Giannini E, Castro MA, Alzari PM, Murgida DH, Lisa MN, Vila AJ. Unexpected electron spin density on the axial methionine ligand in Cu A suggests its involvement in electron pathways. Chem Commun (Camb) 2020; 56:1223-1226. [PMID: 31897463 DOI: 10.1039/c9cc08883k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The CuA center is a paradigm for the study of long-range biological electron transfer. This metal center is an essential cofactor for terminal oxidases like cytochrome c oxidase, the enzymatic complex responsible for cellular respiration in eukaryotes and in most bacteria. CuA acts as an electron hub by transferring electrons from reduced cytochrome c to the catalytic site of the enzyme where dioxygen reduction takes place. Different electron transfer pathways have been proposed involving a weak axial methionine ligand residue, conserved in all CuA sites. This hypothesis has been challenged by theoretical calculations indicating the lack of electron spin density in this ligand. Here we report an NMR study with selectively labeled methionine in a native CuA. NMR spectroscopy discloses the presence of net electron spin density in the methionine axial ligand in the two alternative ground states of this metal center. Similar spin delocalization observed on two second sphere mutants further supports this evidence. These data provide a novel view of the electronic structure of CuA centers and support previously neglected electron transfer pathways.
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Affiliation(s)
- Marcos N Morgada
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR), Ocampo y Esmeralda, Rosario 2000, Argentina.
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19
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Timilsina A, Zhang C, Pandey B, Bizimana F, Dong W, Hu C. Potential Pathway of Nitrous Oxide Formation in Plants. FRONTIERS IN PLANT SCIENCE 2020; 11:1177. [PMID: 32849729 PMCID: PMC7412978 DOI: 10.3389/fpls.2020.01177] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 07/20/2020] [Indexed: 05/12/2023]
Abstract
Plants can produce and emit nitrous oxide (N2O), a potent greenhouse gas, into the atmosphere, and several field-based studies have concluded that this gas is emitted at substantial amounts. However, the exact mechanisms of N2O production in plant cells are unknown. Several studies have hypothesised that plants might act as a medium to transport N2O produced by soil-inhabiting microorganisms. Contrarily, aseptically grown plants and axenic algal cells supplied with nitrate (NO3) are reported to emit N2O, indicating that it is produced inside plant cells by some unknown physiological phenomena. In this study, the possible sites, mechanisms, and enzymes involved in N2O production in plant cells are discussed. Based on the experimental evidence from various studies, we determined that N2O can be produced from nitric oxide (NO) in the mitochondria of plants. NO, a signaling molecule, is produced through oxidative and reductive pathways in eukaryotic cells. During hypoxia and anoxia, NO3 in the cytosol is metabolised to produce nitrite (NO2), which is reduced to form NO via the reductive pathway in the mitochondria. Under low oxygen condition, NO formed in the mitochondria is further reduced to N2O by the reduced form of cytochrome c oxidase (CcO). This pathway is active only when cells experience hypoxia or anoxia, and it may be involved in N2O formation in plants and soil-dwelling animals, as reported previously by several studies. NO can be toxic at a high concentration. Therefore, the reduction of NO to N2O in the mitochondria might protect the integrity of the mitochondria, and thus, protect the cell from the toxicity of NO accumulation under hypoxia and anoxia. As NO3 is a major source of nitrogen for plants and all plants may experience hypoxic and anoxic conditions owing to soil environmental factors, a significant global biogenic source of N2O may be its formation in plants via the proposed pathway.
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Affiliation(s)
- Arbindra Timilsina
- Key Laboratory of Agricultural Water Resources, Hebei Key Laboratory of Soil Ecology, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, China
- University of Chinese Academy of Sciences, Beijing, China
- *Correspondence: Arbindra Timilsina, ; Chunsheng Hu,
| | - Chuang Zhang
- Key Laboratory of Agricultural Water Resources, Hebei Key Laboratory of Soil Ecology, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Bikram Pandey
- University of Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Mountain Ecological Restoration and Bio-resource Utilization and Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Fiston Bizimana
- Key Laboratory of Agricultural Water Resources, Hebei Key Laboratory of Soil Ecology, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Wenxu Dong
- Key Laboratory of Agricultural Water Resources, Hebei Key Laboratory of Soil Ecology, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, China
| | - Chunsheng Hu
- Key Laboratory of Agricultural Water Resources, Hebei Key Laboratory of Soil Ecology, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, China
- University of Chinese Academy of Sciences, Beijing, China
- *Correspondence: Arbindra Timilsina, ; Chunsheng Hu,
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20
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Alwan KB, Welch EF, Blackburn NJ. Catalytic M Center of Copper Monooxygenases Probed by Rational Design. Effects of Selenomethionine and Histidine Substitution on Structure and Reactivity. Biochemistry 2019; 58:4436-4446. [PMID: 31626532 DOI: 10.1021/acs.biochem.9b00823] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The M centers of the mononuclear monooxygenases peptidylglycine monooxygenase (PHM) and dopamine β-monooxygenase bind and activate dioxygen en route to substrate hydroxylation. Recently, we reported the rational design of a protein-based model in which the CusF metallochaperone was repurposed via a His to Met mutation to act as a structural and spectroscopic biomimic. The PHM M site exhibits a number of unusual attributes, including a His2Met ligand set, a fluxional Cu(I)-S(Met) bond, tight binding of exogenous ligands CO and N3-, and complete coupling of oxygen reduction to substrate hydroxylation even at extremely low turnover rates. In particular, mutation of the Met ligand to His completely eliminates the catalytic activity despite the propensity of CuI-His3 centers to bind and activate dioxygen in other metalloenzyme systems. Here, we further develop the CusF-based model to explore methionine variants in which Met is replaced by selenomethionine (SeM) and histidine. We examine the effects on coordinate structure and exogenous ligand binding via X-ray absorption spectroscopy and electron paramagnetic resonance and probe the consequences of mutations on redox chemistry via studies of the reduction by ascorbate and oxidation via molecular oxygen. The M-site model is three-coordinate in the Cu(I) state and binds CO to form a four-coordinate carbonyl. In the oxidized forms, the coordination changes to tetragonal five-coordinate with a long axial Met ligand that like the enzymes is undetectable at either the Cu or Se K edges. The EXAFS data at the Se K edge of the SeM variant provide unique information about the nature of the Cu-methionine bond that is likewise weak and fluxional. Kinetic studies document the sluggish reactivity of the Cu(I) complexes with molecular oxygen and rapid rates of reduction of the Cu(II) complexes by ascorbate, indicating a remarkable stability of the Cu(I) state in all three derivatives. The results show little difference between the Met ligand and its SeM and His congeners and suggest that the Met contributes to catalysis in ways that are more complex than simple perturbation of the redox chemistry. Overall, the results stimulate a critical re-examination of the canonical reaction mechanisms of the mononuclear copper monooxygenases.
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Affiliation(s)
- Katherine B Alwan
- Department of Chemical Physiology and Biochemistry , Oregon Health & Sciences University , Portland , Oregon 97239 , United States
| | - Evan F Welch
- Department of Chemical Physiology and Biochemistry , Oregon Health & Sciences University , Portland , Oregon 97239 , United States
| | - Ninian J Blackburn
- Department of Chemical Physiology and Biochemistry , Oregon Health & Sciences University , Portland , Oregon 97239 , United States
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21
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Bacterial nitrous oxide respiration: electron transport chains and copper transfer reactions. Adv Microb Physiol 2019; 75:137-175. [PMID: 31655736 DOI: 10.1016/bs.ampbs.2019.07.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Biologically catalyzed nitrous oxide (N2O, laughing gas) reduction to dinitrogen gas (N2) is a desirable process in the light of ever-increasing atmospheric concentrations of this important greenhouse gas and ozone depleting substance. A diverse range of bacterial species produce the copper cluster-containing enzyme N2O reductase (NosZ), which is the only known enzyme that converts N2O to N2. Based on phylogenetic analyses, NosZ enzymes have been classified into clade I or clade II and it has turned out that this differentiation is also applicable to nos gene clusters (NGCs) and some physiological traits of the corresponding microbial cells. The NosZ enzyme is the terminal reductase of anaerobic N2O respiration, in which electrons derived from a donor substrate are transferred to NosZ by means of an electron transport chain (ETC) that conserves energy through proton motive force generation. This chapter presents models of the ETCs involved in clade I and clade II N2O respiration as well as of the respective NosZ maturation and maintenance processes. Despite differences in NGCs and growth yields of N2O-respiring microorganisms, the deduced bioenergetic framework in clade I and clade II N2O respiration is assumed to be equivalent. In both cases proton motive quinol oxidation by N2O is thought to be catalyzed by the Q cycle mechanism of a membrane-bound Rieske/cytochrome bc complex. However, clade I and clade II organisms are expected to differ significantly in terms of auxiliary electron transport processes as well as NosZ active site maintenance and repair.
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22
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Canonica F, Hennecke H, Glockshuber R. Biochemical pathway for the biosynthesis of the Cu A center in bacterial cytochrome c oxidase. FEBS Lett 2019; 593:2977-2989. [PMID: 31449676 DOI: 10.1002/1873-3468.13587] [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: 08/05/2019] [Revised: 08/21/2019] [Accepted: 08/22/2019] [Indexed: 01/25/2023]
Abstract
The di-copper center CuA is an essential metal cofactor in cytochrome oxidase (Cox) of mitochondria and many prokaryotes, mediating one-electron transfer from cytochrome c to the site for oxygen reduction. CuA is located in subunit II (CoxB) of Cox and protrudes into the periplasm of Gram-negative bacteria or the mitochondrial intermembrane space. How the two copper ions are brought together to build CoxB·CuA is the subject of this review. It had been known that the reductase TlpA and the metallochaperones ScoI and PcuC are required for CuA formation in bacteria, but the mechanism of copper transfer has emerged only recently for the Bradyrhizobium diazoefficiens system. It consists of the following steps: (a) TlpA keeps the active site cysteine pair of CoxB in its dithiol state as a prerequisite for metal insertion; (b) ScoI·Cu2+ rapidly forms a transient complex with apo-CoxB; (c) PcuC, loaded with Cu1+ and Cu2+ , dissociates this complex to CoxB·Cu2+ , and a second PcuC·Cu1+ ·Cu2+ transfers Cu1+ to CoxB·Cu2+ , yielding mature CoxB·CuA . Variants of this pathway might exist in other bacteria or mitochondria.
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Affiliation(s)
- Fabia Canonica
- Institute of Molecular Biology and Biophysics, ETH Zurich, Switzerland
| | | | - Rudi Glockshuber
- Institute of Molecular Biology and Biophysics, ETH Zurich, Switzerland
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23
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Llases ME, Lisa MN, Morgada MN, Giannini E, Alzari PM, Vila AJ. Arabidopsis thaliana Hcc1 is a Sco-like metallochaperone for Cu A assembly in Cytochrome c Oxidase. FEBS J 2019; 287:749-762. [PMID: 31348612 DOI: 10.1111/febs.15016] [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: 05/30/2019] [Revised: 07/03/2019] [Accepted: 07/22/2019] [Indexed: 01/13/2023]
Abstract
The assembly of the CuA site in Cytochrome c Oxidase (COX) is a critical step for aerobic respiration in COX-dependent organisms. Several gene products have been associated with the assembly of this copper site, the most conserved of them belonging to the Sco family of proteins, which have been shown to perform different roles in different organisms. Plants express two orthologs of Sco proteins: Hcc1 and Hcc2. Hcc1 is known to be essential for plant development and for COX maturation, but its precise function has not been addressed until now. Here, we report the biochemical, structural and functional characterization of Arabidopsis thaliana Hcc1 protein (here renamed Sco1). We solved the crystal structure of the Cu+1 -bound soluble domain of this protein, revealing a tri coordinated environment involving a CxxxCxn H motif. We show that AtSco1 is able to work as a copper metallochaperone, inserting two Cu+1 ions into the CuA site in a model of CoxII. We also show that AtSco1 does not act as a thiol-disulfide oxido-reductase. Overall, this information sheds new light on the biochemistry of Sco proteins, highlighting the diversity of functions among them despite their high structural similarities. DATABASE: PDB entry 6N5U (Crystal structure of Arabidopsis thaliana ScoI with copper bound).
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Affiliation(s)
- María-Eugenia Llases
- Instituto de Biología Molecular y Celular de Rosario (IBR CONICET-UNR), Rosario, Argentina
| | - María-Natalia Lisa
- Instituto de Biología Molecular y Celular de Rosario (IBR CONICET-UNR), Rosario, Argentina.,Plataforma de Biología Estructural y Metabolómica (PLABEM), Rosario, Argentina
| | - Marcos N Morgada
- Instituto de Biología Molecular y Celular de Rosario (IBR CONICET-UNR), Rosario, Argentina.,Area Biofísica, Departamento de Química Biológica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Argentina
| | - Estefanía Giannini
- Instituto de Biología Molecular y Celular de Rosario (IBR CONICET-UNR), Rosario, Argentina
| | - Pedro M Alzari
- Unité de Microbiologie Structurale, Institut Pasteur, Université Paris Diderot, Paris, France
| | - Alejandro J Vila
- Instituto de Biología Molecular y Celular de Rosario (IBR CONICET-UNR), Rosario, Argentina.,Plataforma de Biología Estructural y Metabolómica (PLABEM), Rosario, Argentina.,Area Biofísica, Departamento de Química Biológica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Argentina
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24
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Biochemistry of Copper Site Assembly in Heme-Copper Oxidases: A Theme with Variations. Int J Mol Sci 2019; 20:ijms20153830. [PMID: 31387303 PMCID: PMC6696091 DOI: 10.3390/ijms20153830] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2019] [Revised: 07/15/2019] [Accepted: 07/16/2019] [Indexed: 01/18/2023] Open
Abstract
Copper is an essential cofactor for aerobic respiration, since it is required as a redox cofactor in Cytochrome c Oxidase (COX). This ancient and highly conserved enzymatic complex from the family of heme-copper oxidase possesses two copper sites: CuA and CuB. Biosynthesis of the oxidase is a complex, stepwise process that requires a high number of assembly factors. In this review, we summarize the state-of-the-art in the assembly of COX, with special emphasis in the assembly of copper sites. Assembly of the CuA site is better understood, being at the same time highly variable among organisms. We also discuss the current challenges that prevent the full comprehension of the mechanisms of assembly and the pending issues in the field.
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25
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Stetsiuk O, Petrusenko SR, Sorace L, Lupan A, Attia AAA, Kokozay VN, El-Ghayoury A, Avarvari N. Versatile coordination behaviour of the chloro-tetrazine-picolylamine ligand: mixed-valence binuclear Cu(i)/Cu(ii) complexes. Dalton Trans 2019; 48:11966-11977. [PMID: 31313787 DOI: 10.1039/c9dt02379h] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The 3-Cl-6-amino-(2'-picolyl)-1,2,4,5-tetrazine ligand HL1 has been synthesized and structurally characterized. Its versatile coordination behavior has been evidenced through reactions with Cu(Hfac)2 and Cu(triflate)2 precursors, which provided mixed-valence bimetallic Cu1.5Cu1.5 complexes [Cu2(μ-Cl)(L1)2] 2 and [Cu2(μ-triflate)(L1)2] 5. Changing the Cu(ii) precursor and the solvent leads to the formation of mononuclear octahedral Cu(ii) complexes [CuCl2(HL1)2]·2CH3CN 3 and [Cu(Hfac)2(HL1)] 4, in which only the amino-pyridine unit is involved in the coordination of the metal center. In contrast, in complexes 2 and 5, the ligands are deprotonated and bridge the metal centers as pyridine-amido-tetrazine fragments, while a bridging chloride or triflate ligand completes the coordination sphere of the metal ions. The Cu-Cu distances of 2.4313(4) Å in 2 and 2.5198(10) Å in 5 lie among the shorter values within mixed-valence bimetallic Cu complexes. Mixed-valence character is strongly supported by DFT calculations, showing the equal repartition of the unpaired electron between the two metal centers.
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Affiliation(s)
- Oleh Stetsiuk
- MOLTECH-Anjou, UMR 6200, CNRS, UNIV Angers, 2 bd Lavoisier, 49045 ANGERS Cedex, France. and Department of Inorganic Chemistry, Taras Shevchenko National University of Kyiv, Volodymyrska str. 64/13, Kyiv 01601, Ukraine
| | - Svitlana R Petrusenko
- Department of Inorganic Chemistry, Taras Shevchenko National University of Kyiv, Volodymyrska str. 64/13, Kyiv 01601, Ukraine
| | - Lorenzo Sorace
- Dipartimento di Chimica "Ugo Schiff" and UdR INSTM, Università di Firenze, 50019 Sesto Fiorentino, Italy
| | - Alexandru Lupan
- Faculty of Chemistry and Chemical Engineering, Babes-Bolyai University, Cluj-Napoca, Romania
| | - Amr A A Attia
- Faculty of Chemistry and Chemical Engineering, Babes-Bolyai University, Cluj-Napoca, Romania
| | - Vladimir N Kokozay
- Department of Inorganic Chemistry, Taras Shevchenko National University of Kyiv, Volodymyrska str. 64/13, Kyiv 01601, Ukraine
| | - Abdelkrim El-Ghayoury
- MOLTECH-Anjou, UMR 6200, CNRS, UNIV Angers, 2 bd Lavoisier, 49045 ANGERS Cedex, France.
| | - Narcis Avarvari
- MOLTECH-Anjou, UMR 6200, CNRS, UNIV Angers, 2 bd Lavoisier, 49045 ANGERS Cedex, France.
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26
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Canonica F, Klose D, Ledermann R, Sauer MM, Abicht HK, Quade N, Gossert AD, Chesnov S, Fischer HM, Jeschke G, Hennecke H, Glockshuber R. Structural basis and mechanism for metallochaperone-assisted assembly of the Cu A center in cytochrome oxidase. SCIENCE ADVANCES 2019; 5:eaaw8478. [PMID: 31392273 PMCID: PMC6669012 DOI: 10.1126/sciadv.aaw8478] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 06/26/2019] [Indexed: 06/10/2023]
Abstract
The mechanisms underlying the biogenesis of the structurally unique, binuclear Cu1.5+•Cu1.5+ redox center (CuA) on subunit II (CoxB) of cytochrome oxidases have been a long-standing mystery. Here, we reconstituted the CoxB•CuA center in vitro from apo-CoxB and the holo-forms of the copper transfer chaperones ScoI and PcuC. A previously unknown, highly stable ScoI•Cu2+•CoxB complex was shown to be rapidly formed as the first intermediate in the pathway. Moreover, our structural data revealed that PcuC has two copper-binding sites, one each for Cu1+ and Cu2+, and that only PcuC•Cu1+•Cu2+ can release CoxB•Cu2+ from the ScoI•Cu2+•CoxB complex. The CoxB•CuA center was then formed quantitatively by transfer of Cu1+ from a second equivalent of PcuC•Cu1+•Cu2+ to CoxB•Cu2+. This metalation pathway is consistent with all available in vivo data and identifies the sources of the Cu ions required for CuA center formation and the order of their delivery to CoxB.
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Affiliation(s)
- Fabia Canonica
- Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
| | - Daniel Klose
- Laboratory of Physical Chemistry, ETH Zurich, Zurich, Switzerland
| | | | - Maximilian M. Sauer
- Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
| | - Helge K. Abicht
- Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
| | - Nick Quade
- Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
| | - Alvar D. Gossert
- Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
| | - Serge Chesnov
- Functional Genomics Center Zurich, University of Zurich/ETH Zurich, Zurich, Switzerland
| | | | - Gunnar Jeschke
- Laboratory of Physical Chemistry, ETH Zurich, Zurich, Switzerland
| | - Hauke Hennecke
- Institute of Microbiology, ETH Zurich, Zurich, Switzerland
| | - Rudi Glockshuber
- Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
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27
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Functional assembly of nitrous oxide reductase provides insights into copper site maturation. Proc Natl Acad Sci U S A 2019; 116:12822-12827. [PMID: 31189605 DOI: 10.1073/pnas.1903819116] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The multicopper enzyme nitrous oxide reductase reduces the greenhouse gas N2O to uncritical N2 as the final step of bacterial denitrification. Its two metal centers require an elaborate assembly machinery that so far has precluded heterologous production as a prerequisite for bioremediatory applications in agriculture and wastewater treatment. Here, we report on the production of active holoenzyme in Escherichia coli using a two-plasmid system to produce the entire biosynthetic machinery as well as the structural gene for the enzyme. Using this recombinant system to probe the role of individual maturation factors, we find that the ABC transporter NosFY and the accessory NosD protein are essential for the formation of the [4Cu:2S] site CuZ, but not the electron transfer site CuA Depending on source organism, the heterologous host E. coli can, in some cases, compensate for the lack of the Cu chaperone NosL, while in others this protein is strictly required, underlining the case for designing a recombinant system to be entirely self-contained.
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28
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Dikanov SA, Berry SM, Lu Y. HYSCORE Insights into the Distribution of the Unpaired Spin Density in an Engineered Cu A Site in Azurin and Its His120Gly Variant. Inorg Chem 2019; 58:4437-4445. [PMID: 30869885 DOI: 10.1021/acs.inorgchem.8b03604] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A comparative study of the 1H and 14N hyperfine interactions between the CuA site in an engineered CuA center in azurin (WT-CuAAz) and its His120Gly variant (H120G-CuAAz) using the two-dimensional ESEEM technique, HYSCORE, is reported. HYSCORE spectroscopy has clarified conflicting results in previous electron paramagnetic resonance (EPR) and electron nuclear double resonance (ENDOR) studies and found clear differences between the two CuA azurins. Specifically, a hyperfine coupling AN⊥ of 15.3 MHz was determined for the first time from the frequencies of double-quantum transitions of 14N histidine nitrogens coordinated to CuA in WT-CuAAz. In contrast, such coupling was not observed in the spectra of H120G-CuAAz, indicating at least a several megahertz increase in AN⊥ for the coordinated nitrogen in this variant. In addition, 14N HYSCORE spectra of WT-CuAAz show interaction with only one type of weakly coupled nitrogen assigned to the remote Nε atom of coordinated imidazole residues based on the quadrupole coupling constant ( e2 Qq/4 h) of ∼0.4 MHz. The spectrum of H120G-CuAAz resolves additional features typical for backbone peptide nitrogens with larger e2 Qq/4 h values of ∼0.7 MHz. Hyperfine couplings with these nitrogens vary between ∼0.4 and 0.7 MHz. In addition, the two resolved cross-peaks from Cβ protons in H120G-CuAAz display only ∼1 MHz shifts relative to the corresponding peaks in WT-CuAAz. These new findings have provided the first experimental evidence of the previous density functional theory analysis that predicted changes in the delocalized electron spin population of ∼0.02-0.03 (i.e., ∼10%) on copper and sulfur atoms of the CuA center in H120 variants relative to WT-CuAAz and resolved contradicting results between EPR and ENDOR studies of the valence distribution in CuAAz and its variants.
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Affiliation(s)
- Sergei A Dikanov
- Department of Veterinary Clinical Medicine , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Steven M Berry
- Department of Chemistry and Biochemistry , University of Minnesota Duluth , Duluth , Minnesota 55812 , United States
| | - Yi Lu
- Department of Chemistry , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
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29
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Zitare UA, Szuster J, Santalla MC, Llases ME, Morgada MN, Vila AJ, Murgida DH. Fine Tuning of Functional Features of the Cu A Site by Loop-Directed Mutagenesis. Inorg Chem 2019; 58:2149-2157. [PMID: 30644741 DOI: 10.1021/acs.inorgchem.8b03244] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Here we report the spectroscopic and electrochemical characterization of three novel chimeric CuA proteins in which either one or the three loops surrounding the metal ions in the Thermus thermophilus protein have been replaced by homologous human and plant sequences while preserving the set of coordinating amino acids. These conservative modifications mimic basic differences between CuA sites from different organisms and allow for fine tuning the energy gap between alternative electronic ground states of CuA.. This results in a systematic modulation of thermodynamic and kinetic electron transfer (ET) parameters and in the selection of one of two possible redox-active molecular orbitals, which differ in the ET reorganization energy by a factor of 2. Moreover, the ET mechanism is found to be frictionally controlled, and the modifications introduced into the different chimeras do not affect the frictional activation parameter.
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Affiliation(s)
- Ulises A Zitare
- Departamento de Química Inorgánica, Analítica y Química Física, Facultad de Ciencias Exactas y Naturales , Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE) , Universidad de Buenos Aires and CONICET, 1428 Buenos Aires , Argentina
| | - Jonathan Szuster
- Departamento de Química Inorgánica, Analítica y Química Física, Facultad de Ciencias Exactas y Naturales , Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE) , Universidad de Buenos Aires and CONICET, 1428 Buenos Aires , Argentina
| | - María C Santalla
- Departamento de Química Inorgánica, Analítica y Química Física, Facultad de Ciencias Exactas y Naturales , Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE) , Universidad de Buenos Aires and CONICET, 1428 Buenos Aires , Argentina
| | - María E Llases
- Departamento de Química Biológica, Facultad de Ciencias Bioquímicas y Farmacéuticas , Instituto de Biología Molecular y Celular de Rosario (IBR) , Universidad Nacional de Rosario and CONICET, 2000 Rosario , Argentina
| | - Marcos N Morgada
- Departamento de Química Biológica, Facultad de Ciencias Bioquímicas y Farmacéuticas , Instituto de Biología Molecular y Celular de Rosario (IBR) , Universidad Nacional de Rosario and CONICET, 2000 Rosario , Argentina
| | - Alejandro J Vila
- Departamento de Química Biológica, Facultad de Ciencias Bioquímicas y Farmacéuticas , Instituto de Biología Molecular y Celular de Rosario (IBR) , Universidad Nacional de Rosario and CONICET, 2000 Rosario , Argentina
| | - Daniel H Murgida
- Departamento de Química Inorgánica, Analítica y Química Física, Facultad de Ciencias Exactas y Naturales , Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE) , Universidad de Buenos Aires and CONICET, 1428 Buenos Aires , Argentina
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30
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Leguto AJ, Smith MA, Morgada MN, Zitare UA, Murgida DH, Lancaster KM, Vila AJ. Dramatic Electronic Perturbations of Cu A Centers via Subtle Geometric Changes. J Am Chem Soc 2019; 141:1373-1381. [PMID: 30582893 DOI: 10.1021/jacs.8b12335] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
CuA is a binuclear copper site acting as electron entry port in terminal heme-copper oxidases. In the oxidized form, CuA is a mixed valence pair whose electronic structure can be described using a potential energy surface with two minima, σu* and πu, that are variably populated at room temperature. We report that mutations in the first and second coordination spheres of the binuclear metallocofactor can be combined in an additive manner to tune the energy gap and, thus, the relative populations of the two lowest-lying states. A series of designed mutants span σu*/πu energy gaps ranging from 900 to 13 cm-1. The smallest gap corresponds to a variant with an effectively degenerate ground state. All engineered sites preserve the mixed-valence character of this metal center and the electron transfer functionality. An increase of the Cu-Cu distance less than 0.06 Å modifies the σu*/πu energy gap by almost 2 orders of magnitude, with longer distances eliciting a larger population of the πu state. This scenario offers a stark contrast to synthetic systems, as model compounds require a lengthening of 0.5 Å in the Cu-Cu distance to stabilize the πu state. These findings show that the tight control of the protein environment allows drastic perturbations in the electronic structure of CuA sites with minor geometric changes.
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Affiliation(s)
- Alcides J Leguto
- Instituto de Biología Molecular y Celular de Rosario (IBR), Departamento de Química Biológica, Facultad de Ciencias Bioquímicas y Farmacéuticas , Universidad Nacional de Rosario and CONICET , 2000 Rosario , Argentina
| | - Meghan A Smith
- Department of Chemistry and Chemical Biology , Cornell University , Ithaca , New York 14853 , United States
| | - Marcos N Morgada
- Instituto de Biología Molecular y Celular de Rosario (IBR), Departamento de Química Biológica, Facultad de Ciencias Bioquímicas y Farmacéuticas , Universidad Nacional de Rosario and CONICET , 2000 Rosario , Argentina
| | - Ulises A Zitare
- Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE), Departamento de Química Inorgánica, Analítica y Química Física, Facultad de Ciencias Exactas y Naturales , Universidad de Buenos Aires and CONICET , 1428 Buenos Aires , Argentina
| | - Daniel H Murgida
- Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE), Departamento de Química Inorgánica, Analítica y Química Física, Facultad de Ciencias Exactas y Naturales , Universidad de Buenos Aires and CONICET , 1428 Buenos Aires , Argentina
| | - Kyle M Lancaster
- Department of Chemistry and Chemical Biology , Cornell University , Ithaca , New York 14853 , United States
| | - Alejandro J Vila
- Instituto de Biología Molecular y Celular de Rosario (IBR), Departamento de Química Biológica, Facultad de Ciencias Bioquímicas y Farmacéuticas , Universidad Nacional de Rosario and CONICET , 2000 Rosario , Argentina
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31
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Fisher OS, Kenney GE, Ross MO, Ro SY, Lemma BE, Batelu S, Thomas PM, Sosnowski VC, DeHart CJ, Kelleher NL, Stemmler TL, Hoffman BM, Rosenzweig AC. Characterization of a long overlooked copper protein from methane- and ammonia-oxidizing bacteria. Nat Commun 2018; 9:4276. [PMID: 30323281 PMCID: PMC6189053 DOI: 10.1038/s41467-018-06681-5] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 09/20/2018] [Indexed: 12/24/2022] Open
Abstract
Methane-oxidizing microbes catalyze the oxidation of the greenhouse gas methane using the copper-dependent enzyme particulate methane monooxygenase (pMMO). Isolated pMMO exhibits lower activity than whole cells, however, suggesting that additional components may be required. A pMMO homolog, ammonia monooxygenase (AMO), converts ammonia to hydroxylamine in ammonia-oxidizing bacteria (AOB) which produce another potent greenhouse gas, nitrous oxide. Here we show that PmoD, a protein encoded within many pmo operons that is homologous to the AmoD proteins encoded within AOB amo operons, forms a copper center that exhibits the features of a well-defined CuA site using a previously unobserved ligand set derived from a cupredoxin homodimer. PmoD is critical for copper-dependent growth on methane, and genetic analyses strongly support a role directly related to pMMO and AMO. These findings identify a copper-binding protein that may represent a missing link in the function of enzymes critical to the global carbon and nitrogen cycles. Methane- and ammonia-oxidizing bacteria use the integral membrane, copper-dependent enzymes particulate methane monooxygenase (pMMO) and ammonia monooxygenase (AMO) to oxidize methane and ammonia. Here the authors structurally characterize the copper-binding protein PmoD, which contains an unusual CuA site and their genetic analyses strongly support a pMMO and AMO related function of PmoD.
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Affiliation(s)
- Oriana S Fisher
- Departments of Molecular Biosciences and Chemistry, Northwestern University, Evanston, 60208, IL, USA
| | - Grace E Kenney
- Departments of Molecular Biosciences and Chemistry, Northwestern University, Evanston, 60208, IL, USA
| | - Matthew O Ross
- Departments of Molecular Biosciences and Chemistry, Northwestern University, Evanston, 60208, IL, USA
| | - Soo Y Ro
- Departments of Molecular Biosciences and Chemistry, Northwestern University, Evanston, 60208, IL, USA
| | - Betelehem E Lemma
- Departments of Molecular Biosciences and Chemistry, Northwestern University, Evanston, 60208, IL, USA
| | - Sharon Batelu
- Department of Pharmaceutical Sciences, Wayne State University, Detroit, 48201, MI, USA
| | - Paul M Thomas
- Departments of Molecular Biosciences and Chemistry, Northwestern University, Evanston, 60208, IL, USA
| | - Victoria C Sosnowski
- Departments of Molecular Biosciences and Chemistry, Northwestern University, Evanston, 60208, IL, USA
| | - Caroline J DeHart
- Departments of Molecular Biosciences and Chemistry, Northwestern University, Evanston, 60208, IL, USA
| | - Neil L Kelleher
- Departments of Molecular Biosciences and Chemistry, Northwestern University, Evanston, 60208, IL, USA
| | - Timothy L Stemmler
- Department of Pharmaceutical Sciences, Wayne State University, Detroit, 48201, MI, USA
| | - Brian M Hoffman
- Departments of Molecular Biosciences and Chemistry, Northwestern University, Evanston, 60208, IL, USA
| | - Amy C Rosenzweig
- Departments of Molecular Biosciences and Chemistry, Northwestern University, Evanston, 60208, IL, USA.
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32
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Freisinger E, Sigel RKO. Celebrating Helmut Sigel. J Biol Inorg Chem 2017; 23:1-5. [PMID: 29218638 DOI: 10.1007/s00775-017-1523-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Affiliation(s)
- Eva Freisinger
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland.
| | - Roland K O Sigel
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland.
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