Cellular assays identify barriers impeding iron-sulfur enzyme activity in a non-native prokaryotic host
Iron-sulfur (Fe-S) clusters are ancient and ubiquitous protein cofactors and play irreplaceable roles in many metabolic and regulatory processes. Fe-S clusters are built and distributed to Fe-S enzymes by dedicated protein networks. The core components of these networks are widely conserved and high...
| Main Authors: | , , , , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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eLife Sciences Publications Ltd
2022-03-01
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| Series: | eLife |
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| Online Access: | https://elifesciences.org/articles/70936 |
| _version_ | 1811200482807382016 |
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| author | Francesca D'Angelo Elena Fernández-Fueyo Pierre Simon Garcia Helena Shomar Martin Pelosse Rita Rebelo Manuel Ferhat Büke Siyi Liu Niels van den Broek Nicolas Duraffourg Carol de Ram Martin Pabst Emmanuelle Bouveret Simonetta Gribaldo Béatrice Py Sandrine Ollagnier de Choudens Frédéric Barras Gregory Bokinsky |
| author_facet | Francesca D'Angelo Elena Fernández-Fueyo Pierre Simon Garcia Helena Shomar Martin Pelosse Rita Rebelo Manuel Ferhat Büke Siyi Liu Niels van den Broek Nicolas Duraffourg Carol de Ram Martin Pabst Emmanuelle Bouveret Simonetta Gribaldo Béatrice Py Sandrine Ollagnier de Choudens Frédéric Barras Gregory Bokinsky |
| author_sort | Francesca D'Angelo |
| collection | DOAJ |
| description | Iron-sulfur (Fe-S) clusters are ancient and ubiquitous protein cofactors and play irreplaceable roles in many metabolic and regulatory processes. Fe-S clusters are built and distributed to Fe-S enzymes by dedicated protein networks. The core components of these networks are widely conserved and highly versatile. However, Fe-S proteins and enzymes are often inactive outside their native host species. We sought to systematically investigate the compatibility of Fe-S networks with non-native Fe-S enzymes. By using collections of Fe-S enzyme orthologs representative of the entire range of prokaryotic diversity, we uncovered a striking correlation between phylogenetic distance and probability of functional expression. Moreover, coexpression of a heterologous Fe-S biogenesis pathway increases the phylogenetic range of orthologs that can be supported by the foreign host. We also find that Fe-S enzymes that require specific electron carrier proteins are rarely functionally expressed unless their taxon-specific reducing partners are identified and co-expressed. We demonstrate how these principles can be applied to improve the activity of a radical S-adenosyl methionine(rSAM) enzyme from a Streptomyces antibiotic biosynthesis pathway in Escherichia coli. Our results clarify how oxygen sensitivity and incompatibilities with foreign Fe-S and electron transfer networks each impede heterologous activity. In particular, identifying compatible electron transfer proteins and heterologous Fe-S biogenesis pathways may prove essential for engineering functional Fe-S enzyme-dependent pathways. |
| first_indexed | 2024-04-12T02:04:55Z |
| format | Article |
| id | doaj.art-bff937dfc81944c48a5763b78bc936c6 |
| institution | Directory Open Access Journal |
| issn | 2050-084X |
| language | English |
| last_indexed | 2024-04-12T02:04:55Z |
| publishDate | 2022-03-01 |
| publisher | eLife Sciences Publications Ltd |
| record_format | Article |
| series | eLife |
| spelling | doaj.art-bff937dfc81944c48a5763b78bc936c62022-12-22T03:52:35ZengeLife Sciences Publications LtdeLife2050-084X2022-03-011110.7554/eLife.70936Cellular assays identify barriers impeding iron-sulfur enzyme activity in a non-native prokaryotic hostFrancesca D'Angelo0https://orcid.org/0000-0001-5880-1087Elena Fernández-Fueyo1Pierre Simon Garcia2Helena Shomar3https://orcid.org/0000-0002-1090-2871Martin Pelosse4Rita Rebelo Manuel5https://orcid.org/0000-0001-8068-2053Ferhat Büke6Siyi Liu7Niels van den Broek8Nicolas Duraffourg9Carol de Ram10Martin Pabst11Emmanuelle Bouveret12Simonetta Gribaldo13https://orcid.org/0000-0002-7662-021XBéatrice Py14Sandrine Ollagnier de Choudens15https://orcid.org/0000-0002-0080-6659Frédéric Barras16https://orcid.org/0000-0003-3458-2574Gregory Bokinsky17https://orcid.org/0000-0002-7256-4492Unit Stress Adaptation and Metabolism of Enterobacteria, Department of Microbiology, Université de Paris, UMR CNRS 2001, Institut Pasteur, Paris, FranceDepartment of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, NetherlandsUnit Stress Adaptation and Metabolism of Enterobacteria, Department of Microbiology, Université de Paris, UMR CNRS 2001, Institut Pasteur, Paris, France; Institut Pasteur, Université de Paris, CNRS UMR6047, Evolutionary Biology of the Microbial Cell, Department of Microbiology, Paris, FranceDepartment of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, NetherlandsUniv. Grenoble Alpes, CNRS, CEA, IRIG, Laboratoire de Chimie et Biologie des Métaux, Grenoble, FranceDepartment of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, NetherlandsDepartment of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, NetherlandsAix-Marseille Université-CNRS, Laboratoire de Chimie Bactérienne UMR 7283, Institut de Microbiologie de la Méditerranée, Institut Microbiologie Bioénergies Biotechnologie, Marseille, FranceDepartment of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, NetherlandsUniv. Grenoble Alpes, CNRS, CEA, IRIG, Laboratoire de Chimie et Biologie des Métaux, Grenoble, FranceDepartment of Biotechnology, Delft University of Technology, Delft, NetherlandsDepartment of Biotechnology, Delft University of Technology, Delft, NetherlandsUnit Stress Adaptation and Metabolism of Enterobacteria, Department of Microbiology, Université de Paris, UMR CNRS 2001, Institut Pasteur, Paris, FranceInstitut Pasteur, Université de Paris, CNRS UMR6047, Evolutionary Biology of the Microbial Cell, Department of Microbiology, Paris, FranceAix-Marseille Université-CNRS, Laboratoire de Chimie Bactérienne UMR 7283, Institut de Microbiologie de la Méditerranée, Institut Microbiologie Bioénergies Biotechnologie, Marseille, FranceUniv. Grenoble Alpes, CNRS, CEA, IRIG, Laboratoire de Chimie et Biologie des Métaux, Grenoble, FranceUnit Stress Adaptation and Metabolism of Enterobacteria, Department of Microbiology, Université de Paris, UMR CNRS 2001, Institut Pasteur, Paris, FranceDepartment of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, NetherlandsIron-sulfur (Fe-S) clusters are ancient and ubiquitous protein cofactors and play irreplaceable roles in many metabolic and regulatory processes. Fe-S clusters are built and distributed to Fe-S enzymes by dedicated protein networks. The core components of these networks are widely conserved and highly versatile. However, Fe-S proteins and enzymes are often inactive outside their native host species. We sought to systematically investigate the compatibility of Fe-S networks with non-native Fe-S enzymes. By using collections of Fe-S enzyme orthologs representative of the entire range of prokaryotic diversity, we uncovered a striking correlation between phylogenetic distance and probability of functional expression. Moreover, coexpression of a heterologous Fe-S biogenesis pathway increases the phylogenetic range of orthologs that can be supported by the foreign host. We also find that Fe-S enzymes that require specific electron carrier proteins are rarely functionally expressed unless their taxon-specific reducing partners are identified and co-expressed. We demonstrate how these principles can be applied to improve the activity of a radical S-adenosyl methionine(rSAM) enzyme from a Streptomyces antibiotic biosynthesis pathway in Escherichia coli. Our results clarify how oxygen sensitivity and incompatibilities with foreign Fe-S and electron transfer networks each impede heterologous activity. In particular, identifying compatible electron transfer proteins and heterologous Fe-S biogenesis pathways may prove essential for engineering functional Fe-S enzyme-dependent pathways.https://elifesciences.org/articles/70936iron-sulfur enzymehorizontal gene transfermicrobial engineeringelectron transfer protein |
| spellingShingle | Francesca D'Angelo Elena Fernández-Fueyo Pierre Simon Garcia Helena Shomar Martin Pelosse Rita Rebelo Manuel Ferhat Büke Siyi Liu Niels van den Broek Nicolas Duraffourg Carol de Ram Martin Pabst Emmanuelle Bouveret Simonetta Gribaldo Béatrice Py Sandrine Ollagnier de Choudens Frédéric Barras Gregory Bokinsky Cellular assays identify barriers impeding iron-sulfur enzyme activity in a non-native prokaryotic host eLife iron-sulfur enzyme horizontal gene transfer microbial engineering electron transfer protein |
| title | Cellular assays identify barriers impeding iron-sulfur enzyme activity in a non-native prokaryotic host |
| title_full | Cellular assays identify barriers impeding iron-sulfur enzyme activity in a non-native prokaryotic host |
| title_fullStr | Cellular assays identify barriers impeding iron-sulfur enzyme activity in a non-native prokaryotic host |
| title_full_unstemmed | Cellular assays identify barriers impeding iron-sulfur enzyme activity in a non-native prokaryotic host |
| title_short | Cellular assays identify barriers impeding iron-sulfur enzyme activity in a non-native prokaryotic host |
| title_sort | cellular assays identify barriers impeding iron sulfur enzyme activity in a non native prokaryotic host |
| topic | iron-sulfur enzyme horizontal gene transfer microbial engineering electron transfer protein |
| url | https://elifesciences.org/articles/70936 |
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