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Shomar H, Bokinsky G. Harnessing iron‑sulfur enzymes for synthetic biology. Biochim Biophys Acta Mol Cell Res 2024; 1871:119718. [PMID: 38574823 DOI: 10.1016/j.bbamcr.2024.119718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 03/13/2024] [Accepted: 03/25/2024] [Indexed: 04/06/2024]
Abstract
Reactions catalysed by iron-sulfur (Fe-S) enzymes appear in a variety of biosynthetic pathways that produce valuable natural products. Harnessing these biosynthetic pathways by expression in microbial cell factories grown on an industrial scale would yield enormous economic and environmental benefits. However, Fe-S enzymes often become bottlenecks that limits the productivity of engineered pathways. As a consequence, achieving the production metrics required for industrial application remains a distant goal for Fe-S enzyme-dependent pathways. Here, we identify and review three core challenges in harnessing Fe-S enzyme activity, which all stem from the properties of Fe-S clusters: 1) limited Fe-S cluster supply within the host cell, 2) Fe-S cluster instability, and 3) lack of specialized reducing cofactor proteins often required for Fe-S enzyme activity, such as enzyme-specific flavodoxins and ferredoxins. We highlight successful methods developed for a variety of Fe-S enzymes and electron carriers for overcoming these difficulties. We use heterologous nitrogenase expression as a grand case study demonstrating how each of these challenges can be addressed. We predict that recent breakthroughs in protein structure prediction and design will prove well-suited to addressing each of these challenges. A reliable toolkit for harnessing Fe-S enzymes in engineered metabolic pathways will accelerate the development of industry-ready Fe-S enzyme-dependent biosynthesis pathways.
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Affiliation(s)
- Helena Shomar
- Institut Pasteur, université Paris Cité, Inserm U1284, Diversité moléculaire des microbes (Molecular Diversity of Microbes lab), 75015 Paris, France
| | - Gregory Bokinsky
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands.
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2
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Ongenae V, Kempff A, van Neer V, Shomar H, Tesson F, Rozen D, Briegel A, Claessen D. Genome sequence and characterization of Streptomyces phages Vanseggelen and Verabelle, representing two new species within the genus Camvirus. Sci Rep 2023; 13:20153. [PMID: 37978256 PMCID: PMC10656467 DOI: 10.1038/s41598-023-47634-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 11/16/2023] [Indexed: 11/19/2023] Open
Abstract
Despite the rising interest in bacteriophages, little is known about their infection cycle and lifestyle in a multicellular host. Even in the model system Streptomyces, only a small number of phages have been sequenced and well characterized so far. Here, we report the complete characterization and genome sequences of Streptomyces phages Vanseggelen and Verabelle isolated using Streptomyces coelicolor as a host. A wide range of Streptomyces strains could be infected by both phages, but neither of the two phages was able to infect members of the closely related sister genus Kitasatospora. The phages Vanseggelen and Verabelle have a double-stranded DNA genome with lengths of 48,720 and 48,126 bp, respectively. Both phage genomes contain 72 putative genes, and the presence of an integrase encoding protein indicates a lysogenic lifestyle. Characterization of the phages revealed their stability over a wide range of temperatures (30-45 °C) and pH values (4-10). In conclusion, Streptomyces phage Vanseggelen and Streptomyces phage Verabelle are newly isolated phages that can be classified as new species in the genus Camvirus, within the subfamily Arquattrovirinae.
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Affiliation(s)
- Véronique Ongenae
- Molecular Biotechnology, Institute of Biology, Leiden University, P.O. Box 9505, 2300 RA, Leiden, The Netherlands
- Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands
| | - Annabel Kempff
- Molecular Biotechnology, Institute of Biology, Leiden University, P.O. Box 9505, 2300 RA, Leiden, The Netherlands
- Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands
| | - Vera van Neer
- Molecular Biotechnology, Institute of Biology, Leiden University, P.O. Box 9505, 2300 RA, Leiden, The Netherlands
- Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands
| | - Helena Shomar
- MDM Lab, Department Genomes and Genetics, Pasteur Institute, Paris, France
- INSERM, U1284, Université Paris-Cité, Paris, France
| | | | - Daniël Rozen
- Molecular Biotechnology, Institute of Biology, Leiden University, P.O. Box 9505, 2300 RA, Leiden, The Netherlands.
- Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands.
| | - Ariane Briegel
- Molecular Biotechnology, Institute of Biology, Leiden University, P.O. Box 9505, 2300 RA, Leiden, The Netherlands.
- Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands.
| | - Dennis Claessen
- Molecular Biotechnology, Institute of Biology, Leiden University, P.O. Box 9505, 2300 RA, Leiden, The Netherlands.
- Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands.
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Hardy A, Shomar H, Bernheim A. [Bacterial immunity: Uncovering a new world]. Med Sci (Paris) 2023; 39:862-868. [PMID: 38018930 DOI: 10.1051/medsci/2023163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2023] Open
Abstract
Viruses are parasites that infect all living organisms, and bacteria are no exception. To defend themselves against their viruses (phages), bacteria have developed numerous and sophisticated defense mechanisms, our understanding of which is rapidly growing. In the 2000s, only a handful of mechanisms were known and only two of them seemed to be found in most bacteria. In 2018, a new key method based on genome analysis revealed that there were likely many others. Indeed, over the past five years, more than 150 new mechanisms have been discovered. It is now estimated that there are probably thousands. This remarkable diversity, paralleled with the tremendous viral diversity, is evident both in terms of possible combinations of systems in bacterial genomes and in molecular mechanisms. One of the most surprising observations emerging from the exploration of this diversity is the discovery of striking similarities between certain bacterial defense systems and antiviral systems in humans, as well as plant (and eukaryotes in general) immune systems. Contrary to the previously accepted paradigm, organisms as diverse as fungi, plants, bacteria and humans share certain molecular strategies to fight viral infections, suggesting that an underestimated part of eukaryotic antiviral immunity could have evolved from bacterial antiviral defense systems.
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Affiliation(s)
- Aël Hardy
- Institut Pasteur, université Paris Cité, Inserm U1284, Diversité moléculaire des microbes (Molecular Diversity of Microbes lab), 75015 Paris, France
| | - Helena Shomar
- Institut Pasteur, université Paris Cité, Inserm U1284, Diversité moléculaire des microbes (Molecular Diversity of Microbes lab), 75015 Paris, France
| | - Aude Bernheim
- Institut Pasteur, université Paris Cité, Inserm U1284, Diversité moléculaire des microbes (Molecular Diversity of Microbes lab), 75015 Paris, France
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Georjon H, Tesson F, Shomar H, Bernheim A. Genomic characterization of the antiviral arsenal of Actinobacteria. Microbiology (Reading) 2023; 169:001374. [PMID: 37531269 PMCID: PMC10482375 DOI: 10.1099/mic.0.001374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 07/18/2023] [Indexed: 08/04/2023]
Abstract
Phages are ubiquitous in nature, and bacteria with very different genomics, metabolisms, and lifestyles are subjected to their predation. Yet, the defence systems that allow bacteria to resist their phages have rarely been explored experimentally outside a very limited number of model organisms. Actinobacteria (Actinomycetota) are a phylum of GC-rich Gram-positive bacteria, which often produce an important diversity of secondary metabolites. Despite being ubiquitous in a wide range of environments, from soil to fresh and sea water but also the gut microbiome, relatively little is known about the anti-phage arsenal of Actinobacteria. In this work, we used DefenseFinder to systematically detect 131 anti-phage defence systems in 22803 fully sequenced prokaryotic genomes, among which are 2253 Actinobacteria of more than 700 species. We show that, like other bacteria, Actinobacteria encode many diverse anti-phage systems that are often encoded on mobile genetic elements. We further demonstrate that most detected defence systems are absent or rarer in Actinobacteria than in other bacteria, while a few rare systems are enriched (notably gp29-gp30 and Wadjet). We characterize the spatial distribution of anti-phage systems on Streptomyces chromosomes and show that some defence systems (e.g. RM systems) tend to be encoded in the core region, while others (e.g. Lamassu and Wadjet) are enriched towards the extremities. Overall, our results suggest that Actinobacteria might be a source of novel anti-phage systems and provide clues to characterize mechanistic aspects of known anti-phage systems.
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Affiliation(s)
- Héloïse Georjon
- Molecular Diversity of Microbes Lab, Institut Pasteur, Université Paris Cité, Inserm U1284, Paris, France
| | - Florian Tesson
- Molecular Diversity of Microbes Lab, Institut Pasteur, Université Paris Cité, Inserm U1284, Paris, France
- UMR 1137, IAME, Université de Paris, INSERM, Paris, France
| | - Helena Shomar
- Molecular Diversity of Microbes Lab, Institut Pasteur, Université Paris Cité, Inserm U1284, Paris, France
| | - Aude Bernheim
- Molecular Diversity of Microbes Lab, Institut Pasteur, Université Paris Cité, Inserm U1284, Paris, France
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D'Angelo F, Fernández-Fueyo E, Garcia PS, Shomar H, Pelosse M, Manuel RR, Büke F, Liu S, van den Broek N, Duraffourg N, de Ram C, Pabst M, Bouveret E, Gribaldo S, Py B, Ollagnier de Choudens S, Barras F, Bokinsky G. Cellular assays identify barriers impeding iron-sulfur enzyme activity in a non-native prokaryotic host. eLife 2022; 11:70936. [PMID: 35244541 PMCID: PMC8896826 DOI: 10.7554/elife.70936] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 02/03/2022] [Indexed: 11/24/2022] Open
Abstract
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.
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Affiliation(s)
- Francesca D'Angelo
- Unit Stress Adaptation and Metabolism of Enterobacteria, Department of Microbiology, Université de Paris, UMR CNRS 2001, Institut Pasteur, Paris, France
| | - Elena Fernández-Fueyo
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, Netherlands
| | - Pierre Simon Garcia
- Unit 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, France
| | - Helena Shomar
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, Netherlands
| | - Martin Pelosse
- Univ. Grenoble Alpes, CNRS, CEA, IRIG, Laboratoire de Chimie et Biologie des Métaux, Grenoble, France
| | - Rita Rebelo Manuel
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, Netherlands
| | - Ferhat Büke
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, Netherlands
| | - Siyi Liu
- Aix-Marseille Université-CNRS, Laboratoire de Chimie Bactérienne UMR 7283, Institut de Microbiologie de la Méditerranée, Institut Microbiologie Bioénergies Biotechnologie, Marseille, France
| | - Niels van den Broek
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, Netherlands
| | - Nicolas Duraffourg
- Univ. Grenoble Alpes, CNRS, CEA, IRIG, Laboratoire de Chimie et Biologie des Métaux, Grenoble, France
| | - Carol de Ram
- Department of Biotechnology, Delft University of Technology, Delft, Netherlands
| | - Martin Pabst
- Department of Biotechnology, Delft University of Technology, Delft, Netherlands
| | - Emmanuelle Bouveret
- Unit Stress Adaptation and Metabolism of Enterobacteria, Department of Microbiology, Université de Paris, UMR CNRS 2001, Institut Pasteur, Paris, France
| | - Simonetta Gribaldo
- Institut Pasteur, Université de Paris, CNRS UMR6047, Evolutionary Biology of the Microbial Cell, Department of Microbiology, Paris, France
| | - Béatrice Py
- Aix-Marseille Université-CNRS, Laboratoire de Chimie Bactérienne UMR 7283, Institut de Microbiologie de la Méditerranée, Institut Microbiologie Bioénergies Biotechnologie, Marseille, France
| | | | - Frédéric Barras
- Unit Stress Adaptation and Metabolism of Enterobacteria, Department of Microbiology, Université de Paris, UMR CNRS 2001, Institut Pasteur, Paris, France
| | - Gregory Bokinsky
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, Netherlands
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Shomar H, Bokinsky G. Towards a Synthetic Biology Toolset for Metallocluster Enzymes in Biosynthetic Pathways: What We Know and What We Need. Molecules 2021; 26:molecules26226930. [PMID: 34834021 PMCID: PMC8617995 DOI: 10.3390/molecules26226930] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 11/14/2021] [Accepted: 11/15/2021] [Indexed: 11/16/2022] Open
Abstract
Microbes are routinely engineered to synthesize high-value chemicals from renewable materials through synthetic biology and metabolic engineering. Microbial biosynthesis often relies on expression of heterologous biosynthetic pathways, i.e., enzymes transplanted from foreign organisms. Metallocluster enzymes are one of the most ubiquitous family of enzymes involved in natural product biosynthesis and are of great biotechnological importance. However, the functional expression of recombinant metallocluster enzymes in live cells is often challenging and represents a major bottleneck. The activity of metallocluster enzymes requires essential supporting pathways, involved in protein maturation, electron supply, and/or enzyme stability. Proper function of these supporting pathways involves specific protein-protein interactions that remain poorly characterized and are often overlooked by traditional synthetic biology approaches. Consequently, engineering approaches that focus on enzymatic expression and carbon flux alone often overlook the particular needs of metallocluster enzymes. This review highlights the biotechnological relevance of metallocluster enzymes and discusses novel synthetic biology strategies to advance their industrial application, with a particular focus on iron-sulfur cluster enzymes. Strategies to enable functional heterologous expression and enhance recombinant metallocluster enzyme activity in industrial hosts include: (1) optimizing specific maturation pathways; (2) improving catalytic stability; and (3) enhancing electron transfer. In addition, we suggest future directions for developing microbial cell factories that rely on metallocluster enzyme catalysis.
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Affiliation(s)
- Helena Shomar
- INSERM U722, Faculté de Médecine, Université de Paris, Site Xavier Bichat, 75018 Paris, France
- Correspondence: (H.S.); (G.B.)
| | - Gregory Bokinsky
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ Delft, The Netherlands
- Correspondence: (H.S.); (G.B.)
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Bernheim A, Millman A, Ofir G, Meitav G, Avraham C, Shomar H, Rosenberg MM, Tal N, Melamed S, Amitai G, Sorek R. Prokaryotic viperins produce diverse antiviral molecules. Nature 2021; 589:120-124. [PMID: 32937646 PMCID: PMC7610908 DOI: 10.1038/s41586-020-2762-2] [Citation(s) in RCA: 118] [Impact Index Per Article: 39.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 08/27/2020] [Indexed: 12/31/2022]
Abstract
Viperin is an interferon-induced cellular protein that is conserved in animals1. It has previously been shown to inhibit the replication of multiple viruses by producing the ribonucleotide 3'-deoxy-3',4'-didehydro (ddh)-cytidine triphosphate (ddhCTP), which acts as a chain terminator for viral RNA polymerase2. Here we show that eukaryotic viperin originated from a clade of bacterial and archaeal proteins that protect against phage infection. Prokaryotic viperins produce a set of modified ribonucleotides that include ddhCTP, ddh-guanosine triphosphate (ddhGTP) and ddh-uridine triphosphate (ddhUTP). We further show that prokaryotic viperins protect against T7 phage infection by inhibiting viral polymerase-dependent transcription, suggesting that it has an antiviral mechanism of action similar to that of animal viperin. Our results reveal a class of potential natural antiviral compounds produced by bacterial immune systems.
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Affiliation(s)
- Aude Bernheim
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Adi Millman
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Gal Ofir
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Gilad Meitav
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Carmel Avraham
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | | | | | - Nir Tal
- Pantheon Biosciences, Yavne, Israel
| | - Sarah Melamed
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Gil Amitai
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Rotem Sorek
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel.
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