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Dennis JA, Johnson NW, Thorpe TW, Wallace S. Biocompatible α-Methylenation of Metabolic Butyraldehyde in Living Bacteria. Angew Chem Int Ed Engl 2023; 62:e202306347. [PMID: 37477977 PMCID: PMC10952924 DOI: 10.1002/anie.202306347] [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: 05/06/2023] [Revised: 07/19/2023] [Accepted: 07/20/2023] [Indexed: 07/22/2023]
Abstract
Small molecule organocatalysts are abundant in all living organisms. However, their use as organocatalysts in cells has been underexplored. Herein, we report that organocatalytic aldol chemistry can be interfaced with living Escherichia coli to enable the α-methylenation of cellular aldehydes using biogenic amines such as L-Pro or phosphate. The biocompatible reaction is mild and can be interfaced with butyraldehyde generated from D-glucose via engineered metabolism to enable the production of 2-methylenebutanal (2-MB) and 2-methylbutanal (2-MBA) by anaerobic fermentation, and 2-methylbutanol (2-MBO) by whole-cell catalysis. Overall, this study demonstrates the combination of non-enzymatic organocatalytic and metabolic reactions in vivo for the sustainable synthesis of valuable non-natural chemicals that cannot be accessed using enzymatic chemistry alone.
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Affiliation(s)
- Jonathan A. Dennis
- Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological SciencesUniversity of EdinburghEdinburghEH9 3FFUK
- EaStCHEM School of ChemistryUniversity of EdinburghEdinburghEH9 3FJUK
| | - Nick W. Johnson
- Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological SciencesUniversity of EdinburghEdinburghEH9 3FFUK
| | - Thomas W. Thorpe
- Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological SciencesUniversity of EdinburghEdinburghEH9 3FFUK
| | - Stephen Wallace
- Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological SciencesUniversity of EdinburghEdinburghEH9 3FFUK
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2
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Robinson MP, Jung J, Lopez-Barbosa N, Chang M, Li M, Jaroentomeechai T, Cox EC, Zheng X, Berkmen M, DeLisa MP. Isolation of full-length IgG antibodies from combinatorial libraries expressed in the cytoplasm of Escherichia coli. Nat Commun 2023; 14:3514. [PMID: 37316535 PMCID: PMC10267130 DOI: 10.1038/s41467-023-39178-x] [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: 05/09/2020] [Accepted: 06/01/2023] [Indexed: 06/16/2023] Open
Abstract
Here we describe a facile and robust genetic selection for isolating full-length IgG antibodies from combinatorial libraries expressed in the cytoplasm of redox-engineered Escherichia coli cells. The method is based on the transport of a bifunctional substrate comprised of an antigen fused to chloramphenicol acetyltransferase, which allows positive selection of bacterial cells co-expressing cytoplasmic IgGs called cyclonals that specifically capture the chimeric antigen and sequester the antibiotic resistance marker in the cytoplasm. The utility of this approach is first demonstrated by isolating affinity-matured cyclonal variants that specifically bind their cognate antigen, the leucine zipper domain of a yeast transcriptional activator, with subnanomolar affinities, which represent a ~20-fold improvement over the parental IgG. We then use the genetic assay to discover antigen-specific cyclonals from a naïve human antibody repertoire, leading to the identification of lead IgG candidates with affinity and specificity for an influenza hemagglutinin-derived peptide antigen.
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Affiliation(s)
- Michael-Paul Robinson
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, 14853, USA
| | - Jinjoo Jung
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, 14853, USA
| | - Natalia Lopez-Barbosa
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, 14853, USA
| | - Matthew Chang
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, 14853, USA
| | - Mingji Li
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, 14853, USA
| | - Thapakorn Jaroentomeechai
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, 14853, USA
| | - Emily C Cox
- Biomedical and Biological Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Xiaolu Zheng
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, 14853, USA
| | - Mehmet Berkmen
- New England Biolabs, 240 County Road, Ipswich, MA, 01938, USA
| | - Matthew P DeLisa
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, 14853, USA.
- Biomedical and Biological Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA.
- Cornell Institute of Biotechnology, Cornell University, Ithaca, NY, 14853, USA.
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Zhong Q, Kobe B, Kappler U. Molybdenum Enzymes and How They Support Virulence in Pathogenic Bacteria. Front Microbiol 2020; 11:615860. [PMID: 33362753 PMCID: PMC7759655 DOI: 10.3389/fmicb.2020.615860] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Accepted: 11/23/2020] [Indexed: 12/11/2022] Open
Abstract
Mononuclear molybdoenzymes are highly versatile catalysts that occur in organisms in all domains of life, where they mediate essential cellular functions such as energy generation and detoxification reactions. Molybdoenzymes are particularly abundant in bacteria, where over 50 distinct types of enzymes have been identified to date. In bacterial pathogens, all aspects of molybdoenzyme biology such as molybdate uptake, cofactor biosynthesis, and function of the enzymes themselves, have been shown to affect fitness in the host as well as virulence. Although current studies are mostly focused on a few key pathogens such as Escherichia coli, Salmonella enterica, Campylobacter jejuni, and Mycobacterium tuberculosis, some common themes for the function and adaptation of the molybdoenzymes to pathogen environmental niches are emerging. Firstly, for many of these enzymes, their role is in supporting bacterial energy generation; and the corresponding pathogen fitness and virulence defects appear to arise from a suboptimally poised metabolic network. Secondly, all substrates converted by virulence-relevant bacterial Mo enzymes belong to classes known to be generated in the host either during inflammation or as part of the host signaling network, with some enzyme groups showing adaptation to the increased conversion of such substrates. Lastly, a specific adaptation to bacterial in-host survival is an emerging link between the regulation of molybdoenzyme expression in bacterial pathogens and the presence of immune system-generated reactive oxygen species. The prevalence of molybdoenzymes in key bacterial pathogens including ESKAPE pathogens, paired with the mounting evidence of their central roles in bacterial fitness during infection, suggest that they could be important future drug targets.
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Affiliation(s)
- Qifeng Zhong
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, Australia
| | - Bostjan Kobe
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, Australia.,Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD, Australia
| | - Ulrike Kappler
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, Australia
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4
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Gonzalez E, Pitre FE, Pagé AP, Marleau J, Guidi Nissim W, St-Arnaud M, Labrecque M, Joly S, Yergeau E, Brereton NJB. Trees, fungi and bacteria: tripartite metatranscriptomics of a root microbiome responding to soil contamination. MICROBIOME 2018; 6:53. [PMID: 29562928 PMCID: PMC5863371 DOI: 10.1186/s40168-018-0432-5] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 03/02/2018] [Indexed: 05/05/2023]
Abstract
BACKGROUND One method for rejuvenating land polluted with anthropogenic contaminants is through phytoremediation, the reclamation of land through the cultivation of specific crops. The capacity for phytoremediation crops, such as Salix spp., to tolerate and even flourish in contaminated soils relies on a highly complex and predominantly cryptic interacting community of microbial life. METHODS Here, Illumina HiSeq 2500 sequencing and de novo transcriptome assembly were used to observe gene expression in washed Salix purpurea cv. 'Fish Creek' roots from trees pot grown in petroleum hydrocarbon-contaminated or non-contaminated soil. All 189,849 assembled contigs were annotated without a priori assumption as to sequence origin and differential expression was assessed. RESULTS The 839 contigs differentially expressed (DE) and annotated from S. purpurea revealed substantial increases in transcripts encoding abiotic stress response equipment, such as glutathione S-transferases, in roots of contaminated trees as well as the hallmarks of fungal interaction, such as SWEET2 (Sugars Will Eventually Be Exported Transporter). A total of 8252 DE transcripts were fungal in origin, with contamination conditions resulting in a community shift from Ascomycota to Basidiomycota genera. In response to contamination, 1745 Basidiomycota transcripts increased in abundance (the majority uniquely expressed in contaminated soil) including major monosaccharide transporter MST1, primary cell wall and lamella CAZy enzymes, and an ectomycorrhiza-upregulated exo-β-1,3-glucanase (GH5). Additionally, 639 DE polycistronic transcripts from an uncharacterised Enterobacteriaceae species were uniformly in higher abundance in contamination conditions and comprised a wide spectrum of genes cryptic under laboratory conditions but considered putatively involved in eukaryotic interaction, biofilm formation and dioxygenase hydrocarbon degradation. CONCLUSIONS Fungal gene expression, representing the majority of contigs assembled, suggests out-competition of white rot Ascomycota genera (dominated by Pyronema), a sometimes ectomycorrhizal (ECM) Ascomycota (Tuber) and ECM Basidiomycota (Hebeloma) by a poorly characterised putative ECM Basidiomycota due to contamination. Root and fungal expression involved transcripts encoding carbohydrate/amino acid (C/N) dialogue whereas bacterial gene expression included the apparatus necessary for biofilm interaction and direct reduction of contamination stress, a potential bacterial currency for a role in tripartite mutualism. Unmistakable within the metatranscriptome is the degree to which the landscape of rhizospheric biology, particularly the important but predominantly uncharacterised fungal genetics, is yet to be discovered.
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Affiliation(s)
- E Gonzalez
- Canadian Center for Computational Genomics, McGill University and Genome Quebec Innovation Center, Montréal, H3A 1A4, Canada
- Department of Human Genetics, McGill University, Montreal, H3A 1B1, Canada
| | - F E Pitre
- Institut de recherche en biologie végétale, University of Montreal, Montreal, QC, H1X 2B2, Canada
- Montreal Botanical Garden, Montreal, QC, H1X 2B2, Canada
| | - A P Pagé
- Aquatic and Crop Resource Development (ACRD), National Research Council Canada, Montréal, QC, H4P 2R2, Canada
| | - J Marleau
- Institut de recherche en biologie végétale, University of Montreal, Montreal, QC, H1X 2B2, Canada
| | - W Guidi Nissim
- Department of Agri-food and Environmental Science, University of Florence, Viale delle Idee, Sesto Fiorentino, FI, Italy
| | - M St-Arnaud
- Institut de recherche en biologie végétale, University of Montreal, Montreal, QC, H1X 2B2, Canada
- Montreal Botanical Garden, Montreal, QC, H1X 2B2, Canada
| | - M Labrecque
- Institut de recherche en biologie végétale, University of Montreal, Montreal, QC, H1X 2B2, Canada
- Montreal Botanical Garden, Montreal, QC, H1X 2B2, Canada
| | - S Joly
- Institut de recherche en biologie végétale, University of Montreal, Montreal, QC, H1X 2B2, Canada
- Montreal Botanical Garden, Montreal, QC, H1X 2B2, Canada
| | - E Yergeau
- Institut National de la Recherche Scientifique, Centre INRS-Institut Armand-Frappier, Laval, QC, Canada
| | - N J B Brereton
- Institut de recherche en biologie végétale, University of Montreal, Montreal, QC, H1X 2B2, Canada.
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Structure and electrochemistry of proteins harboring iron-sulfur clusters of different nuclearities. Part I. [4Fe-4S] + [2Fe-2S] iron-sulfur proteins. J Struct Biol 2017; 200:1-19. [DOI: 10.1016/j.jsb.2017.05.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 05/25/2017] [Indexed: 01/08/2023]
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Correia MAS, Otrelo-Cardoso AR, Schwuchow V, Sigfridsson Clauss KGV, Haumann M, Romão MJ, Leimkühler S, Santos-Silva T. The Escherichia coli Periplasmic Aldehyde Oxidoreductase Is an Exceptional Member of the Xanthine Oxidase Family of Molybdoenzymes. ACS Chem Biol 2016; 11:2923-2935. [PMID: 27622978 DOI: 10.1021/acschembio.6b00572] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The xanthine oxidase (XO) family comprises molybdenum-dependent enzymes that usually form homodimers (or dimers of heterodimers/trimers) organized in three domains that harbor two [2Fe-2S] clusters, one FAD, and a Mo cofactor. In this work, we crystallized an unusual member of the family, the periplasmic aldehyde oxidoreductase PaoABC from Escherichia coli. This is the first example of an E. coli protein containing a molybdopterin-cytosine-dinucleotide cofactor and is the only heterotrimer of the XO family so far structurally characterized. The crystal structure revealed the presence of an unexpected [4Fe-4S] cluster, anchored to an additional 40 residues subdomain. According to phylogenetic analysis, proteins containing this cluster are widely spread in many bacteria phyla, putatively through repeated gene transfer events. The active site of PaoABC is highly exposed to the surface with no aromatic residues and an arginine (PaoC-R440) making a direct interaction with PaoC-E692, which acts as a base catalyst. In order to understand the importance of R440, kinetic assays were carried out, and the crystal structure of the PaoC-R440H variant was also determined.
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Affiliation(s)
- Márcia A. S. Correia
- UCIBIO/Requimte,
Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Ana Rita Otrelo-Cardoso
- UCIBIO/Requimte,
Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Viola Schwuchow
- Institut
für Biologie und Biochemie, Universität Potsdam, Am Neuen Palais
10, 14469 Potsdam, Deutschland
| | | | - Michael Haumann
- Freie Universität Berlin, Fachbereich Physik, 14195 Berlin, Germany
| | - Maria João Romão
- UCIBIO/Requimte,
Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Silke Leimkühler
- Institut
für Biologie und Biochemie, Universität Potsdam, Am Neuen Palais
10, 14469 Potsdam, Deutschland
| | - Teresa Santos-Silva
- UCIBIO/Requimte,
Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
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7
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Hu L, Chen H. Assessment of DFT Methods for Computing Activation Energies of Mo/W-Mediated Reactions. J Chem Theory Comput 2015; 11:4601-14. [DOI: 10.1021/acs.jctc.5b00373] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Lianrui Hu
- Beijing National Laboratory
for Molecular Sciences (BNLMS), CAS Key Laboratory of Photochemistry,
Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Hui Chen
- Beijing National Laboratory
for Molecular Sciences (BNLMS), CAS Key Laboratory of Photochemistry,
Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
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8
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An engineered genetic selection for ternary protein complexes inspired by a natural three-component hitchhiker mechanism. Sci Rep 2014; 4:7570. [PMID: 25531212 PMCID: PMC4273604 DOI: 10.1038/srep07570] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Accepted: 12/02/2014] [Indexed: 12/29/2022] Open
Abstract
The bacterial twin-arginine translocation (Tat) pathway is well known to translocate correctly folded monomeric and dimeric proteins across the tightly sealed cytoplasmic membrane. We identified a naturally occurring heterotrimer, the Escherichia coli aldehyde oxidoreductase PaoABC, that is co-translocated by the Tat translocase according to a ternary “hitchhiker” mechanism. Specifically, the PaoB and PaoC subunits, each devoid of export signals, are escorted to the periplasm in a piggyback fashion by the Tat signal peptide-containing subunit PaoA. Moreover, export of PaoA was blocked when either PaoB or PaoC was absent, revealing a surprising interdependence for export that is not seen for classical secretory proteins. Inspired by this observation, we created a bacterial three-hybrid selection system that links the formation of ternary protein complexes with antibiotic resistance. As proof-of-concept, a bispecific antibody was employed as an adaptor that physically crosslinked one antigen fused to a Tat export signal with a second antigen fused to TEM-1 β-lactamase (Bla). The resulting non-covalent heterotrimer was exported in a Tat-dependent manner, delivering Bla to the periplasm where it hydrolyzed β-lactam antibiotics. Collectively, these results highlight the remarkable flexibility of the Tat system and its potential for studying and engineering ternary protein interactions in living bacteria.
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Yokoyama K, Leimkühler S. The role of FeS clusters for molybdenum cofactor biosynthesis and molybdoenzymes in bacteria. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2014; 1853:1335-49. [PMID: 25268953 DOI: 10.1016/j.bbamcr.2014.09.021] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Revised: 09/19/2014] [Accepted: 09/22/2014] [Indexed: 11/29/2022]
Abstract
The biosynthesis of the molybdenum cofactor (Moco) has been intensively studied, in addition to its insertion into molybdoenzymes. In particular, a link between the assembly of molybdoenzymes and the biosynthesis of FeS clusters has been identified in the recent years: 1) the synthesis of the first intermediate in Moco biosynthesis requires an FeS-cluster containing protein, 2) the sulfurtransferase for the dithiolene group in Moco is also involved in the synthesis of FeS clusters, thiamin and thiolated tRNAs, 3) the addition of a sulfido-ligand to the molybdenum atom in the active site additionally involves a sulfurtransferase, and 4) most molybdoenzymes in bacteria require FeS clusters as redox active cofactors. In this review we will focus on the biosynthesis of the molybdenum cofactor in bacteria, its modification and insertion into molybdoenzymes, with an emphasis to its link to FeS cluster biosynthesis and sulfur transfer.
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Affiliation(s)
- Kenichi Yokoyama
- Department of Biochemistry, Duke University Medical Center, Durham, NC, USA
| | - Silke Leimkühler
- Department of Molecular Enzymology, Institute of Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany.
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