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Shobnam N, Saksena S, Ratley G, Yadav M, Chaudhary PP, Sun AA, Howe KN, Gadkari M, Franco LM, Ganesan S, McCann KJ, Hsu AP, Kanakabandi K, Ricklefs S, Lack J, Yu W, Similuk M, Walkiewicz MA, Gardner DD, Barta K, Tullos K, Myles IA. Topical Steroid Withdrawal is a Targetable Excess of Mitochondrial NAD. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.04.17.24305846. [PMID: 38712043 PMCID: PMC11071640 DOI: 10.1101/2024.04.17.24305846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Background Topical corticosteroids (TCS) are first-line therapies for numerous skin conditions. Topical Steroid Withdrawal (TSW) is a controversial diagnosis advocated by patients with prolonged TCS exposure who report severe systemic reactions upon treatment cessation. However, to date there have been no systematic clinical or mechanistic studies to distinguish TSW from other eczematous disorders. Methods A re-analysis of a previous survey with eczematous skin disease was performed to evaluate potential TSW distinguishing symptoms. We subsequently conducted a pilot study of 16 patients fitting the proposed diagnostic criteria. We then performed: tissue metabolomics, transcriptomics, and immunostaining on skin biopsies; serum metabolomics and cytokine assessments; shotgun metagenomics on microbiome skin swabs; genome sequencing; followed by functional, mechanistic studies using human skin cell lines and mice. Results Clinically distinct TSW symptoms included burning, flushing, and thermodysregulation. Metabolomics and transcriptomics both implicated elevated NAD+ oxidation stemming from increased expression of mitochondrial complex I and conversion of tryptophan into kynurenine metabolites. These abnormalities were induced by glucocorticoid exposure both in vitro and in a cohort of healthy controls (N=19) exposed to TCS. Targeting complex I via either metformin or the herbal compound berberine improved outcomes in both cell culture and in an open-label case series for patients with TSW. Conclusion Taken together, our results suggest that TSW has a distinct dermatopathology. While future studies are needed to validate these results in larger cohorts, this work provides the first mechanistic evaluation into TSW pathology, and offers insights into clinical identification, pharmacogenomic candidates, and directed therapeutic strategies.
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Kostelac A, Taborda A, Martins LO, Haltrich D. Evolution and separation of actinobacterial pyranose and C-glycoside-3-oxidases. Appl Environ Microbiol 2024; 90:e0167623. [PMID: 38179968 PMCID: PMC10807413 DOI: 10.1128/aem.01676-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 11/21/2023] [Indexed: 01/06/2024] Open
Abstract
FAD-dependent pyranose oxidase (POx) and C-glycoside-3-oxidase (CGOx) are both members of the glucose-methanol-choline superfamily of oxidoreductases and belong to the same sequence space. Pyranose oxidases had been studied for their oxidation of monosaccharides such as D-glucose, but recently, a bacterial C-glycoside-3-oxidase that is phylogenetically related to POx and that reacts with C-glycosides such as carminic acid, mangiferin or puerarin has been described. Since these actinobacterial CGOx enzymes belong to the same sequence space as bacterial POx, they must have evolved from the same ancestor. Here, we performed a phylogenetic analysis of actinobacterial sequences and resurrected seven ancestral enzymes of the POx/CGOx sequence space to study the evolutionary trajectory of substrate preferences for monosaccharides and C-glycosides. Clade I, with its dimeric member POx from Kitasatospora aureofaciens, shows strict preference for monosaccharides (D-glucose and D-xylose) and does not react with any of the glycosides tested. No extant member of clade II has been studied to date. The two extant members of clades III and IV, monomeric POx/CGOx from Pseudoarthrobacter siccitolerans and Streptomyces canus, oxidized both monosaccharides as well as various C-glycosides (homoorientin, isovitexin, mangiferin, and puerarin). Steady-state kinetic parameters of several clades III and IV ancestral enzymes indicate that the generalist ancestor N35 slowly evolved to present-day enzymes with a much higher preference for C-glycosides than monosaccharides. Based on structural predictions of ancestors, we hypothesize that the strict specificity of bacterial clade I POx (and also fungal POx) is the result of oligomerization, which in turn results from the evolution of protein segments that were shown to be important for oligomerization, the arm, and the head domain.IMPORTANCEC-Glycosides often form active compounds in various plants. Breakage of the C-C bond in these glycosides to release the aglycone is challenging and proceeds via a two-step reaction, the oxidation of the sugar and subsequent cleavage of the C-C bond. Recently, an enzyme from a soil bacterium, FAD-dependent C-glycoside-3-oxidase (CGOx), was shown to catalyze the initial oxidation reaction. Here, we show that CGOx belongs to the same sequence space as pyranose oxidase (POx), and that an actinobacterial ancestor of the POx/CGOx family evolved into four clades, two of which show a high preference for C-glycosides.
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Affiliation(s)
- Anja Kostelac
- Department of Food Science and Technology, BOKU—University of Natural Resources and Life Sciences, Vienna, Austria
- Doctoral Programme BioToP—Biomolecular Technology of Proteins, BOKU—University of Natural Resources and Life Sciences, Vienna, Austria
| | - André Taborda
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Oeiras, Portugal
| | - Lígia O. Martins
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Oeiras, Portugal
| | - Dietmar Haltrich
- Department of Food Science and Technology, BOKU—University of Natural Resources and Life Sciences, Vienna, Austria
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3
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Nicoll C, Mascotti M. Investigating the biochemical signatures and physiological roles of the FMO family using molecular phylogeny. BBA ADVANCES 2023; 4:100108. [PMID: 38034983 PMCID: PMC10682829 DOI: 10.1016/j.bbadva.2023.100108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 10/16/2023] [Accepted: 10/18/2023] [Indexed: 12/02/2023] Open
Abstract
Group B flavin-dependent monooxygenases are employed in swathes of different physiological functions. Despite their collectively large substrate profile, they all harness a flavin-based C4a-(hydro)peroxy intermediate for function. Within this class are the flavin-containing monooxygenases (FMOs), representing an integral component within the secondary metabolism of all living things - xenobiotic detoxification. Their broad substrate profile makes them ideal candidates for detoxifying procedures as they can tackle a range of compounds. Recent studies have illustrated that several FMOs, however, have unique substrate profiles and differing physiological functions that implicate new roles within secondary and primary metabolism. Herein this article, by employing phylogenetic approaches, and inspecting structures of AlphaFold generated models, we have constructed a biochemical blueprint of the FMO family. FMOs are clustered in four distinct groups, with two being predominantly dedicated to xenobiotic detoxification. Furthermore, we observe that differing enzymatic activities are not constricted to a 'golden' set of residues but instead an intricate constellation of primary and secondary sphere residues. We believe that this work delineates the core phylogeny of the Group B monooxygenases and will prove useful for classifying newly sequenced genes and provide directions to future biochemical investigations.
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Affiliation(s)
- C.R. Nicoll
- Department of Biology and Biotechnology Lazzaro Spallanzani, University of Pavia, Via Ferrata 9, 27100, Pavia, Italy
| | - M.L. Mascotti
- Molecular Enzymology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747, AG Groningen, The Netherlands
- IMIBIO-SL CONICET, Facultad de Química Bioquímica y Farmacia, Universidad Nacional de San Luis, Ejercito de los Andes 950, D5700HHW, San Luis, Argentina
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4
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Nicoll CR, Massari M, Fraaije MW, Mascotti ML, Mattevi A. Impact of ancestral sequence reconstruction on mechanistic and structural enzymology. Curr Opin Struct Biol 2023; 82:102669. [PMID: 37544113 DOI: 10.1016/j.sbi.2023.102669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 06/19/2023] [Accepted: 07/10/2023] [Indexed: 08/08/2023]
Abstract
Ancestral sequence reconstruction (ASR) provides insight into the changes within a protein sequence across evolution. More specifically, it can illustrate how specific amino acid changes give rise to different phenotypes within a protein family. Over the last few decades it has established itself as a powerful technique for revealing molecular common denominators that govern enzyme function. Here, we describe the strength of ASR in unveiling catalytic mechanisms and emerging phenotypes for a range of different proteins, also highlighting biotechnological applications the methodology can provide.
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Affiliation(s)
- Callum R Nicoll
- Department of Biology and Biotechnology Lazzaro Spallanzani, University of Pavia, Via Ferrata 9, 27100, Pavia, Italy
| | - Marta Massari
- Department of Biology and Biotechnology Lazzaro Spallanzani, University of Pavia, Via Ferrata 9, 27100, Pavia, Italy
| | - Marco W Fraaije
- Molecular Enzymology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747, AG Groningen, the Netherlands. https://twitter.com/fraaije1
| | - Maria Laura Mascotti
- Molecular Enzymology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747, AG Groningen, the Netherlands; IMIBIO-SL CONICET, Facultad de Química Bioquímica y Farmacia, Universidad Nacional de San Luis, Ejército de los Andes 950, D5700HHW, San Luis, Argentina
| | - Andrea Mattevi
- Department of Biology and Biotechnology Lazzaro Spallanzani, University of Pavia, Via Ferrata 9, 27100, Pavia, Italy.
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5
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Evolution of enzyme functionality in the flavin-containing monooxygenases. Nat Commun 2023; 14:1042. [PMID: 36823138 PMCID: PMC9950137 DOI: 10.1038/s41467-023-36756-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 02/15/2023] [Indexed: 02/25/2023] Open
Abstract
Among the molecular mechanisms of adaptation in biology, enzyme functional diversification is indispensable. By allowing organisms to expand their catalytic repertoires and adopt fundamentally different chemistries, animals can harness or eliminate new-found substances and xenobiotics that they are exposed to in new environments. Here, we explore the flavin-containing monooxygenases (FMOs) that are essential for xenobiotic detoxification. Employing a paleobiochemistry approach in combination with enzymology techniques we disclose the set of historical substitutions responsible for the family's functional diversification in tetrapods. Remarkably, a few amino acid replacements differentiate an ancestral multi-tasking FMO into a more specialized monooxygenase by modulating the oxygenating flavin intermediate. Our findings substantiate an ongoing premise that enzymatic function hinges on a subset of residues that is not limited to the active site core.
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6
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Livada J, Vargas AM, Martinez CA, Lewis RD. Ancestral Sequence Reconstruction Enhances Gene Mining Efforts for Industrial Ene Reductases by Expanding Enzyme Panels with Thermostable Catalysts. ACS Catal 2023. [DOI: 10.1021/acscatal.2c03859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Affiliation(s)
- Jovan Livada
- Pfizer Global Research and Development, Chemical Research Development, MS 4073 Eastern Point Road, Groton, Connecticut 06340, United States
| | - Ariana M. Vargas
- Pfizer Global Research and Development, Chemical Research Development, MS 4073 Eastern Point Road, Groton, Connecticut 06340, United States
| | - Carlos A. Martinez
- Pfizer Global Research and Development, Chemical Research Development, MS 4073 Eastern Point Road, Groton, Connecticut 06340, United States
| | - Russell D. Lewis
- Pfizer Global Research and Development, Chemical Research Development, MS 4073 Eastern Point Road, Groton, Connecticut 06340, United States
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Clifton BE, Kozome D, Laurino P. Efficient Exploration of Sequence Space by Sequence-Guided Protein Engineering and Design. Biochemistry 2023; 62:210-220. [PMID: 35245020 DOI: 10.1021/acs.biochem.1c00757] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The rapid growth of sequence databases over the past two decades means that protein engineers faced with optimizing a protein for any given task will often have immediate access to a vast number of related protein sequences. These sequences encode information about the evolutionary history of the protein and the underlying sequence requirements to produce folded, stable, and functional protein variants. Methods that can take advantage of this information are an increasingly important part of the protein engineering tool kit. In this Perspective, we discuss the utility of sequence data in protein engineering and design, focusing on recent advances in three main areas: the use of ancestral sequence reconstruction as an engineering tool to generate thermostable and multifunctional proteins, the use of sequence data to guide engineering of multipoint mutants by structure-based computational protein design, and the use of unlabeled sequence data for unsupervised and semisupervised machine learning, allowing the generation of diverse and functional protein sequences in unexplored regions of sequence space. Altogether, these methods enable the rapid exploration of sequence space within regions enriched with functional proteins and therefore have great potential for accelerating the engineering of stable, functional, and diverse proteins for industrial and biomedical applications.
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Affiliation(s)
- Ben E Clifton
- Protein Engineering and Evolution Unit, Okinawa Institute of Science and Technology, 1919-1 Tancha, Onna, Okinawa 904-0495, Japan
| | - Dan Kozome
- Protein Engineering and Evolution Unit, Okinawa Institute of Science and Technology, 1919-1 Tancha, Onna, Okinawa 904-0495, Japan
| | - Paola Laurino
- Protein Engineering and Evolution Unit, Okinawa Institute of Science and Technology, 1919-1 Tancha, Onna, Okinawa 904-0495, Japan
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8
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Cheropkina H, Catucci G, Marucco A, Fenoglio I, Gilardi G, Sadeghi SJ. Human flavin-containing monooxygenase 1 and its long-sought hydroperoxyflavin intermediate. Biochem Pharmacol 2021; 193:114763. [PMID: 34509493 DOI: 10.1016/j.bcp.2021.114763] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 09/03/2021] [Accepted: 09/07/2021] [Indexed: 01/22/2023]
Abstract
Out of the five isoforms of human flavin-containing monooxygenase (hFMO), FMO1 and FMO3 are the most relevant to Phase I drug metabolism. They are involved in the oxygenation of xenobiotics including drugs and pesticides using NADPH and FAD as cofactors. Majority of the characterization of these enzymes has involved hFMO3, where intermediates of its catalytic cycle have been described. On the other hand, research efforts have so far failed in capturing the same key intermediate that is responsible for the monooxygenation activity of hFMO1. In this work we demonstrate spectrophotometrically the formation of a highly stable C4a-hydroperoxyflavin intermediate of hFMO1 upon reduction by NADPH and in the presence of O2. The measured half-life of this flavin intermediate revealed it to be stable and not fully re-oxidized even after 30 min at 15 °C in the absence of substrate, the highest stability ever observed for a human FMO. In addition, the uncoupling reactions of hFMO1 show that this enzyme is <1% uncoupled in the presence of substrate, forming small amounts of H2O2 with no observable superoxide as confirmed by EPR spin trapping experiments. This behaviour is different from hFMO3, that is shown to form both H2O2 and superoxide anion radical as a result of ∼50% uncoupling. These data are consistent with the higher stability of the hFMO1 intermediate in comparison to hFMO3. Taken together, these data demonstrate the different behaviours of these two closely related enzymes with consequences for drug metabolism as well as possible toxicity due to reactive oxygen species.
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Affiliation(s)
- Hanna Cheropkina
- Department of Life Sciences and Systems Biology, University of Torino, Italy
| | - Gianluca Catucci
- Department of Life Sciences and Systems Biology, University of Torino, Italy
| | - Arianna Marucco
- Department of Life Sciences and Systems Biology, University of Torino, Italy
| | | | - Gianfranco Gilardi
- Department of Life Sciences and Systems Biology, University of Torino, Italy
| | - Sheila J Sadeghi
- Department of Life Sciences and Systems Biology, University of Torino, Italy.
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9
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Spence MA, Kaczmarski JA, Saunders JW, Jackson CJ. Ancestral sequence reconstruction for protein engineers. Curr Opin Struct Biol 2021; 69:131-141. [PMID: 34023793 DOI: 10.1016/j.sbi.2021.04.001] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 03/22/2021] [Accepted: 04/07/2021] [Indexed: 12/11/2022]
Abstract
In addition to its value in the study of molecular evolution, ancestral sequence reconstruction (ASR) has emerged as a useful methodology for engineering proteins with enhanced properties. Proteins generated by ASR often exhibit unique or improved activity, stability, and/or promiscuity, all of which are properties that are valued by protein engineers. Comparison between extant proteins and evolutionary intermediates generated by ASR also allows protein engineers to identify substitutions that have contributed to functional innovation or diversification within protein families. As ASR becomes more widely adopted as a protein engineering approach, it is important to understand the applications, limitations, and recent developments of this technique. This review highlights recent exemplifications of ASR, as well as technical aspects of the reconstruction process that are relevant to protein engineering.
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Affiliation(s)
- Matthew A Spence
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Joe A Kaczmarski
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Jake W Saunders
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Colin J Jackson
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia; ARC Centre of Excellence for Innovations in Peptide & Protein Science, Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia; ARC Centre of Excellence for Innovations in Synthetic Biology, Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia.
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10
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Paul CE, Eggerichs D, Westphal AH, Tischler D, van Berkel WJH. Flavoprotein monooxygenases: Versatile biocatalysts. Biotechnol Adv 2021; 51:107712. [PMID: 33588053 DOI: 10.1016/j.biotechadv.2021.107712] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 01/27/2021] [Accepted: 02/06/2021] [Indexed: 12/13/2022]
Abstract
Flavoprotein monooxygenases (FPMOs) are single- or two-component enzymes that catalyze a diverse set of chemo-, regio- and enantioselective oxyfunctionalization reactions. In this review, we describe how FPMOs have evolved from model enzymes in mechanistic flavoprotein research to biotechnologically relevant catalysts that can be applied for the sustainable production of valuable chemicals. After a historical account of the development of the FPMO field, we explain the FPMO classification system, which is primarily based on protein structural properties and electron donor specificities. We then summarize the most appealing reactions catalyzed by each group with a focus on the different types of oxygenation chemistries. Wherever relevant, we report engineering strategies that have been used to improve the robustness and applicability of FPMOs.
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Affiliation(s)
- Caroline E Paul
- Biocatalysis, Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Daniel Eggerichs
- Microbial Biotechnology, Faculty of Biology and Biotechnology, Ruhr-Universität Bochum, Universitätsstrasse 150, 44780 Bochum, Germany
| | - Adrie H Westphal
- Laboratory of Biochemistry, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Dirk Tischler
- Microbial Biotechnology, Faculty of Biology and Biotechnology, Ruhr-Universität Bochum, Universitätsstrasse 150, 44780 Bochum, Germany
| | - Willem J H van Berkel
- Laboratory of Food Chemistry, Wageningen University, Bornse Weilanden 9, 6708 WG Wageningen, The Netherlands.
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