1
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Pham C, Nasr MA, Skarina T, Di Leo R, Kwan DH, Martin VJJ, Stogios PJ, Mahadevan R, Savchenko A. Functional and structural characterization of an IclR family transcription factor for the development of dicarboxylic acid biosensors. FEBS J 2024. [PMID: 38696354 DOI: 10.1111/febs.17149] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 03/15/2024] [Accepted: 04/17/2024] [Indexed: 05/04/2024]
Abstract
Prokaryotic transcription factors (TFs) regulate gene expression in response to small molecules, thus representing promising candidates as versatile small molecule-detecting biosensors valuable for synthetic biology applications. The engineering of such biosensors requires thorough in vitro and in vivo characterization of TF ligand response as well as detailed molecular structure information. In this work, we functionally and structurally characterize the Pca regulon regulatory protein (PcaR) transcription factor belonging to the IclR transcription factor family. Here, we present in vitro functional analysis of the ligand profile of PcaR and the construction of genetic circuits for the characterization of PcaR as an in vivo biosensor in the model eukaryote Saccharomyces cerevisiae. We report the crystal structures of PcaR in the apo state and in complex with one of its ligands, succinate, which suggests the mechanism of dicarboxylic acid recognition by this transcription factor. This work contributes key structural and functional insights enabling the engineering of PcaR for dicarboxylic acid biosensors, in addition to providing more insights into the IclR family of regulators.
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Affiliation(s)
- Chester Pham
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Canada
| | - Mohamed A Nasr
- Centre for Applied Synthetic Biology, Concordia University, Montreal, Canada
- Department of Biology, Concordia University, Montreal, Canada
- PROTEO, Quebec Network for Research on Protein Function, Structure, and Engineering, Canada
| | - Tatiana Skarina
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Canada
| | - Rosa Di Leo
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Canada
| | - David H Kwan
- Centre for Applied Synthetic Biology, Concordia University, Montreal, Canada
- Department of Biology, Concordia University, Montreal, Canada
- PROTEO, Quebec Network for Research on Protein Function, Structure, and Engineering, Canada
- Department of Chemistry and Biochemistry, Concordia University, Montreal, Canada
| | - Vincent J J Martin
- Centre for Applied Synthetic Biology, Concordia University, Montreal, Canada
- Department of Biology, Concordia University, Montreal, Canada
| | - Peter J Stogios
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Canada
| | - Radhakrishnan Mahadevan
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Canada
- The Institute of Biomedical Engineering, University of Toronto, Canada
| | - Alexei Savchenko
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Canada
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Canada
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2
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Diep P, Stogios PJ, Evdokimova E, Savchenko A, Mahadevan R, Yakunin AF. Ni(II)-binding affinity of CcNikZ-II and its homologs: the role of the HH-prong and variable loop revealed by structural and mutational studies. FEBS J 2024. [PMID: 38555564 DOI: 10.1111/febs.17125] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 01/30/2024] [Accepted: 03/13/2024] [Indexed: 04/02/2024]
Abstract
Extracytoplasmic Ni(II)-binding proteins (NiBPs) are molecular shuttles involved in cellular nickel uptake. Here, we determined the crystal structure of apo CcNikZ-II at 2.38 Å, which revealed a Ni(II)-binding site comprised of the double His (HH-)prong (His511, His512) and a short variable (v-)loop nearby (Thr59-Thr64, TEDKYT). Mutagenesis of the site identified Glu60 and His511 as critical for high affinity Ni(II)-binding. Phylogenetic analysis showed 15 protein clusters with two groups containing the HH-prong. Metal-binding assays with 11 purified NiBPs containing this feature yielded higher Ni(II)-binding affinities. Replacement of the wild type v-loop with those from other NiBPs improved the affinity by up to an order of magnitude. This work provides molecular insights into the determinants for Ni(II) affinity and paves way for NiBP engineering.
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Affiliation(s)
- Patrick Diep
- Department of Chemical Engineering and Applied Chemistry, BioZone - Centre for Applied Bioscience and Bioengineering, University of Toronto, Toronto, Ontario, Canada
- Systems & Synthetic Biology Group, Biosciences and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Peter J Stogios
- Department of Chemical Engineering and Applied Chemistry, BioZone - Centre for Applied Bioscience and Bioengineering, University of Toronto, Toronto, Ontario, Canada
| | - Elena Evdokimova
- Department of Chemical Engineering and Applied Chemistry, BioZone - Centre for Applied Bioscience and Bioengineering, University of Toronto, Toronto, Ontario, Canada
| | - Alexei Savchenko
- Department of Chemical Engineering and Applied Chemistry, BioZone - Centre for Applied Bioscience and Bioengineering, University of Toronto, Toronto, Ontario, Canada
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
| | - Radhakrishnan Mahadevan
- Department of Chemical Engineering and Applied Chemistry, BioZone - Centre for Applied Bioscience and Bioengineering, University of Toronto, Toronto, Ontario, Canada
- Institute of Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada
| | - Alexander F Yakunin
- Department of Chemical Engineering and Applied Chemistry, BioZone - Centre for Applied Bioscience and Bioengineering, University of Toronto, Toronto, Ontario, Canada
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Bangor, Wales, UK
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3
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Syriste L, Patel DT, Stogios PJ, Skarina T, Patel D, Savchenko A. An acetyltransferase effector conserved across Legionella species targets the eukaryotic eIF3 complex to modulate protein translation. mBio 2024; 15:e0322123. [PMID: 38335095 PMCID: PMC10936415 DOI: 10.1128/mbio.03221-23] [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: 12/05/2023] [Accepted: 01/16/2024] [Indexed: 02/12/2024] Open
Abstract
The survival of Legionella spp. as intracellular pathogens relies on the combined action of protein effectors delivered inside their eukaryotic hosts by the Dot/Icm (defective in organelle trafficking/intracellular multiplication) type IVb secretion system. The specific repertoire of effector arsenals varies dramatically across over 60 known species of this genera with Legionella pneumophila responsible for most cases of Legionnaires' disease in humans encoding over 360 Dot/Icm effectors. However, a small subset of "core" effectors appears to be conserved across all Legionella species raising an intriguing question of their role in these bacteria's pathogenic strategy, which for most of these effectors remains unknown. L. pneumophila Lpg0103 effector, also known as VipF, represents one of the core effector families that features a tandem of Gcn5-related N-acetyltransferase (GNAT) domains. Here, we present the crystal structure of the Lha0223, the VipF representative from Legionella hackeliae in complex with acetyl-coenzyme A determined to 1.75 Å resolution. Our structural analysis suggested that this effector family shares a common fold with the two GNAT domains forming a deep groove occupied by residues conserved across VipF homologs. Further analysis suggested that only the C-terminal GNAT domain of VipF effectors retains the active site composition compatible with catalysis, whereas the N-terminal GNAT domain binds the ligand in a non-catalytical mode. We confirmed this by in vitro enzymatic assays which revealed VipF activity not only against generic small molecule substrates, such as chloramphenicol, but also against poly-L-lysine and histone-derived peptides. We identified the human eukaryotic translation initiation factor 3 (eIF3) complex co-precipitating with Lpg0103 and demonstrated the direct interaction between the several representatives of the VipF family, including Lpg0103 and Lha0223 with the K subunit of eIF3. According to our data, these interactions involve primarily the C-terminal tail of eIF3-K containing two lysine residues that are acetylated by VipF. VipF catalytic activity results in the suppression of eukaryotic protein translation in vitro, revealing the potential function of VipF "core" effectors in Legionella's pathogenic strategy.IMPORTANCEBy translocating effectors inside the eukaryotic host cell, bacteria can modulate host cellular processes in their favor. Legionella species, which includes the pneumonia-causing Legionella pneumophila, encode a widely diverse set of effectors with only a small subset that is conserved across this genus. Here, we demonstrate that one of these conserved effector families, represented by L. pneumophila VipF (Lpg0103), is a tandem Gcn5-related N-acetyltransferase interacting with the K subunit of human eukaryotic initiation factor 3 complex. VipF catalyzes the acetylation of lysine residues on the C-terminal tail of the K subunit, resulting in the suppression of eukaryotic translation initiation factor 3-mediated protein translation in vitro. These new data provide the first insight into the molecular function of this pathogenic factor family common across Legionellae.
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Affiliation(s)
- Lukas Syriste
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
| | - Deepak T. Patel
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
| | - Peter J. Stogios
- Department of Chemical Engineering and Applied Chemistry, Toronto University, Toronto, Ontario, Canada
| | - Tatiana Skarina
- Department of Chemical Engineering and Applied Chemistry, Toronto University, Toronto, Ontario, Canada
| | - Dhruvin Patel
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
| | - Alexei Savchenko
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
- Department of Chemical Engineering and Applied Chemistry, Toronto University, Toronto, Ontario, Canada
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4
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Penner TV, Lorente Cobo N, Patel DT, Patel DH, Savchenko A, Brassinga AKC, Prehna G. Structural characterization of the Sel1-like repeat protein LceB from Legionella pneumophila. Protein Sci 2024; 33:e4889. [PMID: 38160319 PMCID: PMC10868440 DOI: 10.1002/pro.4889] [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: 07/03/2023] [Revised: 12/21/2023] [Accepted: 12/22/2023] [Indexed: 01/03/2024]
Abstract
Legionella are freshwater Gram-negative bacteria that in their normal environment infect protozoa. However, this adaptation also allows Legionella to infect human alveolar macrophages and cause pneumonia. Central to Legionella pathogenesis are more than 330 secreted effectors, of which there are nine core effectors that are conserved in all pathogenic species. Despite their importance, the biochemical function of several core effectors remains unclear. To address this, we have taken a structural approach to characterize the core effector of unknown function LceB, or Lpg1356, from Legionella pneumophila. Here, we solve an X-ray crystal structure of LceB using an AlphaFold model for molecular replacement. The experimental structure shows that LceB adopts a Sel1-like repeat (SLR) fold as predicted. However, the crystal structure captured multiple conformations of LceB, all of which differed from the AlphaFold model. A comparison of the predicted model and the experimental models suggests that LceB is highly flexible in solution. Additionally, the molecular analysis of LceB using its close structural homologs reveals sequence and structural motifs of known biochemical function. Specifically, LceB harbors a repeated KAAEQG motif that both stabilizes the SLR fold and is known to participate in protein-protein interactions with eukaryotic host proteins. We also observe that LceB forms several higher-order oligomers in solution. Overall, our results have revealed that LceB has conformational flexibility, self-associates, and contains a molecular surface for binding a target host-cell protein. Additionally, our data provides structural insights into the SLR family of proteins that remain poorly studied.
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Affiliation(s)
- Tiffany V Penner
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Neil Lorente Cobo
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Deepak T Patel
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
| | - Dhruvin H Patel
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
| | - Alexei Savchenko
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
| | | | - Gerd Prehna
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
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5
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Bordeleau E, Stogios PJ, Evdokimova E, Koteva K, Savchenko A, Wright GD. Mechanistic plasticity in ApmA enables aminoglycoside promiscuity for resistance. Nat Chem Biol 2024; 20:234-242. [PMID: 37973888 DOI: 10.1038/s41589-023-01483-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 10/12/2023] [Indexed: 11/19/2023]
Abstract
The efficacy of aminoglycoside antibiotics is waning due to the acquisition of diverse resistance mechanisms by bacteria. Among the most prevalent are aminoglycoside acetyltransferases (AACs) that inactivate the antibiotics through acetyl coenzyme A-mediated modification. Most AACs are members of the GCN5 superfamily of acyltransferases which lack conserved active site residues that participate in catalysis. ApmA is the first reported AAC belonging to the left-handed β-helix superfamily. These enzymes are characterized by an essential active site histidine that acts as an active site base. Here we show that ApmA confers broad-spectrum aminoglycoside resistance with a molecular mechanism that diverges from other detoxifying left-handed β-helix superfamily enzymes and canonical GCN5 AACs. We find that the active site histidine plays different functions depending on the acetyl-accepting aminoglycoside substrate. This flexibility in the mechanism of a single enzyme underscores the plasticity of antibiotic resistance elements to co-opt protein catalysts in the evolution of drug detoxification.
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Affiliation(s)
- Emily Bordeleau
- David Braley Centre for Antibiotics Discovery, M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Peter J Stogios
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Elena Evdokimova
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Kalinka Koteva
- David Braley Centre for Antibiotics Discovery, M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Alexei Savchenko
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
- Center for Structural Genomics of Infectious Diseases (CSGID) University of Calgary, Calgary, Alberta, Canada
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
| | - Gerard D Wright
- David Braley Centre for Antibiotics Discovery, M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada.
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6
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Lin JD, Stogios PJ, Abe KT, Wang A, MacPherson J, Skarina T, Gingras AC, Savchenko A, Ensminger AW. Functional diversification despite structural congruence in the HipBST toxin-antitoxin system of Legionella pneumophila. mBio 2023; 14:e0151023. [PMID: 37819088 PMCID: PMC10653801 DOI: 10.1128/mbio.01510-23] [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: 06/16/2023] [Accepted: 08/29/2023] [Indexed: 10/13/2023] Open
Abstract
IMPORTANCE Toxin-antitoxin (TA) systems are parasitic genetic elements found in almost all bacterial genomes. They are exchanged horizontally between cells and are typically poorly conserved across closely related strains and species. Here, we report the characterization of a tripartite TA system in the bacterial pathogen Legionella pneumophila that is highly conserved across Legionella species genomes. This system (denoted HipBSTLp) is a distant homolog of the recently discovered split-HipA system in Escherichia coli (HipBSTEc). We present bioinformatic, molecular, and structural analyses of the divergence between these two systems and the functionality of this newly described TA system family. Furthermore, we provide evidence to refute previous claims that the toxin in this system (HipTLp) possesses bifunctionality as an L. pneumophila virulence protein. Overall, this work expands our understanding of the split-HipA system architecture and illustrates the potential for undiscovered biology in these abundant genetic elements.
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Affiliation(s)
- Jordan D. Lin
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Peter J. Stogios
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Kento T. Abe
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, Ontario, Canada
| | - Avril Wang
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - John MacPherson
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Tatiana Skarina
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Anne-Claude Gingras
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, Ontario, Canada
| | - Alexei Savchenko
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
- Center for Structural Genomics of Infectious Diseases (CSGID), University of Calgary, Calgary, Alberta, Canada
| | - Alexander W. Ensminger
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
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7
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Rosas-Lemus M, Dey S, Minasov G, Tan K, Anderson SM, Brunzelle J, Nocadello S, Shabalin I, Filippova E, Halavaty A, Kim Y, Maltseva N, Osipiuk J, Minor W, Joachimiak A, Savchenko A, Anderson WF, Satchell KJF. A high-throughput structural system biology approach to increase structure representation of proteins from Clostridioides difficile. Microbiol Resour Announc 2023; 12:e0050723. [PMID: 37747257 PMCID: PMC10586155 DOI: 10.1128/mra.00507-23] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 08/15/2023] [Indexed: 09/26/2023] Open
Abstract
Clostridioides difficile causes life-threatening gastrointestinal infections. It is a high-risk pathogen due to a lack of effective treatments, antimicrobial resistance, and a poorly conserved genomic core. Herein, we report 30 X-ray structures from a structure genomics pipeline spanning 13 years, representing 10.2% of the X-ray structures for this important pathogen.
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Affiliation(s)
- Monica Rosas-Lemus
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
- Center for Structural Biology of Infectious Diseases, Chicago, Illinois, USA
| | - Supratim Dey
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
- Center for Structural Biology of Infectious Diseases, Chicago, Illinois, USA
| | - George Minasov
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
- Center for Structural Biology of Infectious Diseases, Chicago, Illinois, USA
| | - Kemin Tan
- Center for Structural Biology of Infectious Diseases, Chicago, Illinois, USA
- Consortium for Advanced Science and Engineering, University of Chicago, Chicago, Illinois, USA
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, Illinois, USA
| | - Spencer M. Anderson
- Northwestern Synchrotron Research Center, Life Sciences Collaborative Access Team, Northwestern University, Argonne, Illinois, USA
| | - Joseph Brunzelle
- Northwestern Synchrotron Research Center, Life Sciences Collaborative Access Team, Northwestern University, Argonne, Illinois, USA
| | - Salvatore Nocadello
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
- Center for Structural Biology of Infectious Diseases, Chicago, Illinois, USA
| | - Ivan Shabalin
- Center for Structural Biology of Infectious Diseases, Chicago, Illinois, USA
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
| | - Ekaterina Filippova
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
- Center for Structural Biology of Infectious Diseases, Chicago, Illinois, USA
| | - Andrei Halavaty
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
- Center for Structural Biology of Infectious Diseases, Chicago, Illinois, USA
| | - Youngchang Kim
- Center for Structural Biology of Infectious Diseases, Chicago, Illinois, USA
- Consortium for Advanced Science and Engineering, University of Chicago, Chicago, Illinois, USA
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, Illinois, USA
| | - Natalia Maltseva
- Center for Structural Biology of Infectious Diseases, Chicago, Illinois, USA
- Consortium for Advanced Science and Engineering, University of Chicago, Chicago, Illinois, USA
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, Illinois, USA
| | - Jerzy Osipiuk
- Center for Structural Biology of Infectious Diseases, Chicago, Illinois, USA
- Consortium for Advanced Science and Engineering, University of Chicago, Chicago, Illinois, USA
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, Illinois, USA
| | - Wladek Minor
- Center for Structural Biology of Infectious Diseases, Chicago, Illinois, USA
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
| | - Andrzej Joachimiak
- Center for Structural Biology of Infectious Diseases, Chicago, Illinois, USA
- Consortium for Advanced Science and Engineering, University of Chicago, Chicago, Illinois, USA
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, Illinois, USA
| | - Alexei Savchenko
- Center for Structural Biology of Infectious Diseases, Chicago, Illinois, USA
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
| | - Wayne F. Anderson
- Center for Structural Biology of Infectious Diseases, Chicago, Illinois, USA
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Karla J. F. Satchell
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
- Center for Structural Biology of Infectious Diseases, Chicago, Illinois, USA
| | - Center for Structural Biology of Infectious Diseases team members
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
- Center for Structural Biology of Infectious Diseases, Chicago, Illinois, USA
- Consortium for Advanced Science and Engineering, University of Chicago, Chicago, Illinois, USA
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, Illinois, USA
- Northwestern Synchrotron Research Center, Life Sciences Collaborative Access Team, Northwestern University, Argonne, Illinois, USA
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
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8
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Skrivergaard S, Young JF, Sahebekhtiari N, Semper C, Venkatesan M, Savchenko A, Stogios PJ, Therkildsen M, Rasmussen MK. A simple and robust serum-free media for the proliferation of muscle cells. Food Res Int 2023; 172:113194. [PMID: 37689947 DOI: 10.1016/j.foodres.2023.113194] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 06/23/2023] [Accepted: 06/27/2023] [Indexed: 09/11/2023]
Abstract
Cultivated meat production requires an efficient, robust and highly optimized serum-free cell culture media for the needed upscaling of muscle cell expansion. Existing formulations of serum-free media are complex, expensive and have not been optimized for muscle cells. Thus, we undertook this work to develop a simple and robust serum-free media for the proliferation of bovine satellite cells (SCs) through Design of Experiment (DOE) and Response Surface Methodology (RSM) using precise and high-throughput image-based cytometry. Proliferative attributes were investigated with transcriptomics and long-term performance was validated using multiple live assays. Here we formulated a media based on three highly optimized components; FGF2 (2 ng/mL), fetuin (600 µg/mL) and BSA (75 µg/mL) which together with an insulin-transferrin-selenium (1x) supplement, sustained the proliferation of bovine SCs, porcine SCs and murine C2C12 muscle cells. Remarkably, cells cultured in our media named Tri-basal 2.0+ performed better than cell cultured in 10% FBS, with respect to proliferation. Hence, the optimized Tri-basal 2.0+ enhanced serum-free cell attachment and long-term proliferation, providing an alternative solution to the use of FBS in the production of cultivated meat.
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Affiliation(s)
| | | | | | - Cameron Semper
- Department of Microbiology, Immunology, and Infectious Disease. University of Calgary, Calgary, Canada
| | - Meenakshi Venkatesan
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Canada
| | - Alexei Savchenko
- Department of Microbiology, Immunology, and Infectious Disease. University of Calgary, Calgary, Canada; Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Canada
| | - Peter J Stogios
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Canada
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9
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Khusnutdinova AN, Batyrova KA, Brown G, Fedorchuk T, Chai YS, Skarina T, Flick R, Petit AP, Savchenko A, Stogios P, Yakunin AF. Structural insights into hydrolytic defluorination of difluoroacetate by microbial fluoroacetate dehalogenases. FEBS J 2023; 290:4966-4983. [PMID: 37437000 DOI: 10.1111/febs.16903] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 06/19/2023] [Accepted: 07/10/2023] [Indexed: 07/14/2023]
Abstract
Fluorine forms the strongest single bond to carbon with the highest bond dissociation energy among natural products. However, fluoroacetate dehalogenases (FADs) have been shown to hydrolyze this bond in fluoroacetate under mild reaction conditions. Furthermore, two recent studies demonstrated that the FAD RPA1163 from Rhodopseudomonas palustris can also accept bulkier substrates. In this study, we explored the substrate promiscuity of microbial FADs and their ability to defluorinate polyfluorinated organic acids. Enzymatic screening of eight purified dehalogenases with reported fluoroacetate defluorination activity revealed significant hydrolytic activity against difluoroacetate in three proteins. Product analysis using liquid chromatography-mass spectrometry identified glyoxylic acid as the final product of enzymatic DFA defluorination. The crystal structures of DAR3835 from Dechloromonas aromatica and NOS0089 from Nostoc sp. were determined in the apo-state along with the DAR3835 H274N glycolyl intermediate. Structure-based site-directed mutagenesis of DAR3835 demonstrated a key role for the catalytic triad and other active site residues in the defluorination of both fluoroacetate and difluoroacetate. Computational analysis of the dimer structures of DAR3835, NOS0089, and RPA1163 indicated the presence of one substrate access tunnel in each protomer. Moreover, protein-ligand docking simulations suggested similar catalytic mechanisms for the defluorination of both fluoroacetate and difluoroacetate, with difluoroacetate being defluorinated via two consecutive defluorination reactions producing glyoxylate as the final product. Thus, our findings provide molecular insights into substrate promiscuity and catalytic mechanism of FADs, which are promising biocatalysts for applications in synthetic chemistry and bioremediation of fluorochemicals.
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Affiliation(s)
- Anna N Khusnutdinova
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, ON, Canada
- Institute of Basic Biological Problems, Russian Academy of Sciences, Pushchino, Russia
- Biological Chemistry and Drug Discovery Division, School of Life Sciences, University of Dundee, UK
| | - Khorcheska A Batyrova
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, ON, Canada
- Institute of Basic Biological Problems, Russian Academy of Sciences, Pushchino, Russia
| | - Greg Brown
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, ON, Canada
| | - Tatiana Fedorchuk
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, ON, Canada
- Institute of Basic Biological Problems, Russian Academy of Sciences, Pushchino, Russia
| | - Yao Sheng Chai
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, ON, Canada
| | - Tatiana Skarina
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, ON, Canada
| | - Robert Flick
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, ON, Canada
| | - Alain-Pierre Petit
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, ON, Canada
- Biological Chemistry and Drug Discovery Division, School of Life Sciences, University of Dundee, UK
| | - Alexei Savchenko
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, ON, Canada
- Department of Microbiology, Immunology & Infectious Diseases, Health Research Innovation Centre, University of Calgary, AB, Canada
| | - Peter Stogios
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, ON, Canada
| | - Alexander F Yakunin
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, ON, Canada
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, UK
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10
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Semper C, Savchenko A. Protein expression and purification of bioactive growth factors for use in cell culture and cellular agriculture. STAR Protoc 2023; 4:102351. [PMID: 37314918 PMCID: PMC10277608 DOI: 10.1016/j.xpro.2023.102351] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 02/28/2023] [Accepted: 05/11/2023] [Indexed: 06/16/2023] Open
Abstract
Mitogenic growth factors are major cost drivers in serum-free media, contributing up to 95% of the total cost. Here, we present a streamlined workflow detailing cloning, expression testing, protein purification, and bioactivity screening that allows for low-cost production of bioactive growth factors including basic fibroblast growth factor and transforming growth factor β1. This generalized procedure can be used for multiple families of growth factors with minor modification, and the outputs are bioactive and suitable for cell culture applications. For complete details on the use and execution of this protocol, please refer to Venkatesan, et al.1.
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Affiliation(s)
- Cameron Semper
- Department of Microbiology, Immunology and Infectious Disease, University of Calgary, 3330 Hospital Drive NW, Calgary, AB T2N 4N1, Canada.
| | - Alexei Savchenko
- Department of Microbiology, Immunology and Infectious Disease, University of Calgary, 3330 Hospital Drive NW, Calgary, AB T2N 4N1, Canada; Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON M5S 3E8, Canada.
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11
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Venkatesan M, Fruci M, Verellen LA, Skarina T, Mesa N, Flick R, Pham C, Mahadevan R, Stogios PJ, Savchenko A. Molecular mechanism of plasmid-borne resistance to sulfonamide antibiotics. Nat Commun 2023; 14:4031. [PMID: 37419898 PMCID: PMC10328974 DOI: 10.1038/s41467-023-39778-7] [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: 01/16/2023] [Accepted: 06/21/2023] [Indexed: 07/09/2023] Open
Abstract
The sulfonamides (sulfas) are the oldest class of antibacterial drugs and inhibit the bacterial dihydropteroate synthase (DHPS, encoded by folP), through chemical mimicry of its co-substrate p-aminobenzoic acid (pABA). Resistance to sulfa drugs is mediated either by mutations in folP or acquisition of sul genes, which code for sulfa-insensitive, divergent DHPS enzymes. While the molecular basis of resistance through folP mutations is well understood, the mechanisms mediating sul-based resistance have not been investigated in detail. Here, we determine crystal structures of the most common Sul enzyme types (Sul1, Sul2 and Sul3) in multiple ligand-bound states, revealing a substantial reorganization of their pABA-interaction region relative to the corresponding region of DHPS. We use biochemical and biophysical assays, mutational analysis, and in trans complementation of E. coli ΔfolP to show that a Phe-Gly sequence enables the Sul enzymes to discriminate against sulfas while retaining pABA binding and is necessary for broad resistance to sulfonamides. Experimental evolution of E. coli results in a strain harboring a sulfa-resistant DHPS variant that carries a Phe-Gly insertion in its active site, recapitulating this molecular mechanism. We also show that Sul enzymes possess increased active site conformational dynamics relative to DHPS, which could contribute to substrate discrimination. Our results reveal the molecular foundation for Sul-mediated drug resistance and facilitate the potential development of new sulfas less prone to resistance.
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Affiliation(s)
- Meenakshi Venkatesan
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, M5S 1A4, Canada
| | - Michael Fruci
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, N5V 4T3, Canada
- Department of Microbiology and Immunology, Western University, London, ON, N6A 3K7, Canada
| | - Lou Ann Verellen
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, N5V 4T3, Canada
- Department of Microbiology and Immunology, Western University, London, ON, N6A 3K7, Canada
| | - Tatiana Skarina
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, M5S 1A4, Canada
| | - Nathalie Mesa
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, M5S 1A4, Canada
| | - Robert Flick
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, M5S 1A4, Canada
| | - Chester Pham
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, M5S 1A4, Canada
| | - Radhakrishnan Mahadevan
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, M5S 1A4, Canada
- Institute of Biomedical Engineering, University of Toronto, Toronto, ON, M5S 3E2, Canada
| | - Peter J Stogios
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, M5S 1A4, Canada.
- Center for Structural Biology of Infectious Diseases (CSBID), Calgary, AB, Canada.
| | - Alexei Savchenko
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, M5S 1A4, Canada.
- Center for Structural Biology of Infectious Diseases (CSBID), Calgary, AB, Canada.
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, AB, T2N 4N1, Canada.
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12
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Arellano-Saab A, Skarina T, Xu Z, McErlean CSP, Savchenko A, Lumba S, Stogios PJ, McCourt P. Structural analysis of a hormone-bound Striga strigolactone receptor. Nat Plants 2023; 9:883-888. [PMID: 37264151 DOI: 10.1038/s41477-023-01423-y] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 04/25/2023] [Indexed: 06/03/2023]
Abstract
Strigolactones (SLs) regulate many aspects of plant development, but ambiguities remain about how this hormone is perceived because SL-complexed receptor structures do not exist. We find that when SL binds the Striga receptor, ShHTL5, a series of conformational changes relative to the unbound state occur, but these events are not sufficient for signalling. Ligand-complexed receptors, however, form internal tunnels that posit an explanation for how SL exits its receptor after hydrolysis.
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Affiliation(s)
- Amir Arellano-Saab
- Department of Cell and Systems Biology, University of Toronto, Toronto, Canada
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Tatiana Skarina
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Zhenhua Xu
- Department of Cell and Systems Biology, University of Toronto, Toronto, Canada
| | | | - Alexei Savchenko
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
| | - Shelley Lumba
- Department of Cell and Systems Biology, University of Toronto, Toronto, Canada
| | - Peter J Stogios
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada.
| | - Peter McCourt
- Department of Cell and Systems Biology, University of Toronto, Toronto, Canada.
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13
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Popov G, Fiebig-Comyn A, Syriste L, Little DJ, Skarina T, Stogios PJ, Birstonas S, Coombes BK, Savchenko A. Correction for Popov et al., "Distinct Molecular Features of NleG Type 3 Secreted Effectors Allow for Different Roles during Citrobacter rodentium Infection in Mice". Infect Immun 2023; 91:e0009423. [PMID: 36946756 PMCID: PMC10112251 DOI: 10.1128/iai.00094-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2023] Open
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14
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Guo Y, Karimullina E, Emde T, Otwinowski Z, Borek D, Savchenko A. Monomer and dimer structures of cytochrome bo 3 ubiquinol oxidase from Escherichia coli. Protein Sci 2023; 32:e4616. [PMID: 36880269 PMCID: PMC10037687 DOI: 10.1002/pro.4616] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 02/28/2023] [Accepted: 03/01/2023] [Indexed: 03/08/2023]
Abstract
The E. coli cytochrome bo3 ubiquinol oxidase is a four-subunit heme-copper oxidase that serves as a proton pump in the E. coli aerobic respiratory chain. Despite many mechanistic studies, it is unclear whether this ubiquinol oxidase functions as a monomer, or as a dimer in a manner similar to its eukaryotic counterparts - the mitochondrial electron transport complexes. In this study, we determined the monomeric and dimeric structures of the E. coli cytochrome bo3 ubiquinol oxidase reconstituted in amphipol by cryogenic electron microscopy single particle reconstruction (cryo-EM SPR) to a resolution of 3.15 Å and 3.46 Å, respectively. We have discovered that the protein can form a dimer with C2 symmetry, with the dimerization interface maintained by interactions between the subunit II of one monomer and the subunit IV of the other monomer. Moreover, the dimerization does not induce significant structural changes in the monomers, except the movement of a loop in subunit IV (residues 67-74). This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Yirui Guo
- Department of Biophysics, The University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, Texas, US
- Ligo Analytics, 2207 Chunk Ct, Dallas, Texas, United States
| | - Elina Karimullina
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
- Center for Structural Genomics of Infectious Diseases (CSGID), Chicago, Illinois, USA
- Centers for Research on Structural Biology of Infectious Diseases (CSBID), Chicago, Illinois, USA
| | - Tabitha Emde
- Department of Biophysics, The University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, Texas, US
- Center for Structural Genomics of Infectious Diseases (CSGID), Chicago, Illinois, USA
- Centers for Research on Structural Biology of Infectious Diseases (CSBID), Chicago, Illinois, USA
| | - Zbyszek Otwinowski
- Department of Biophysics, The University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, Texas, US
- Center for Structural Genomics of Infectious Diseases (CSGID), Chicago, Illinois, USA
- Centers for Research on Structural Biology of Infectious Diseases (CSBID), Chicago, Illinois, USA
- Department of Biochemistry, The University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, Texas, US
| | - Dominika Borek
- Department of Biophysics, The University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, Texas, US
- Center for Structural Genomics of Infectious Diseases (CSGID), Chicago, Illinois, USA
- Centers for Research on Structural Biology of Infectious Diseases (CSBID), Chicago, Illinois, USA
- Department of Biochemistry, The University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, Texas, US
| | - Alexei Savchenko
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
- Center for Structural Genomics of Infectious Diseases (CSGID), Chicago, Illinois, USA
- Centers for Research on Structural Biology of Infectious Diseases (CSBID), Chicago, Illinois, USA
- BioZone, Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
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15
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Popov G, Fiebig-Comyn A, Syriste L, Little DJ, Skarina T, Stogios PJ, Birstonas S, Coombes BK, Savchenko A. Distinct Molecular Features of NleG Type 3 Secreted Effectors Allow for Different Roles during Citrobacter rodentium Infection in Mice. Infect Immun 2023; 91:e0050522. [PMID: 36511702 PMCID: PMC9872709 DOI: 10.1128/iai.00505-22] [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: 11/17/2022] [Accepted: 11/19/2022] [Indexed: 12/15/2022] Open
Abstract
The NleGs are the largest family of type 3 secreted effectors in attaching and effacing (A/E) pathogens, such as enterohemorrhagic Escherichia coli (EHEC), enteropathogenic E. coli, and Citrobacter rodentium. NleG effectors contain a conserved C-terminal U-box domain acting as a ubiquitin protein ligase and target host proteins via a variable N-terminal portion. The specific roles of these effectors during infection remain uncertain. Here, we demonstrate that the three NleG effectors-NleG1Cr, NleG7Cr, and NleG8Cr-encoded by C. rodentium DBS100 play distinct roles during infection in mice. Using individual nleGCr knockout strains, we show that NleG7Cr contributes to bacterial survival during enteric infection while NleG1Cr promotes the expression of diarrheal symptoms and NleG8Cr contributes to accelerated lethality in susceptible mice. Furthermore, the NleG8Cr effector contains a C-terminal PDZ domain binding motif that enables interaction with the host protein GOPC. Both the PDZ domain binding motif and the ability to engage with host ubiquitination machinery via the intact U-box domain proved to be necessary for NleG8Cr function, contributing to the observed phenotype during infection. We also establish that the PTZ binding motif in the EHEC NleG8 (NleG8Ec) effector, which shares 60% identity with NleG8Cr, is engaged in interactions with human GOPC. The crystal structure of the NleG8Ec C-terminal peptide in complex with the GOPC PDZ domain, determined to 1.85 Å, revealed a conserved interaction mode similar to that observed between GOPC and eukaryotic PDZ domain binding motifs. Despite these common features, nleG8Ec does not complement the ΔnleG8Cr phenotype during infection, revealing functional diversification between these NleG effectors.
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Affiliation(s)
- Georgy Popov
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
| | - Aline Fiebig-Comyn
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
| | - Lukas Syriste
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
| | - Dustin J. Little
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
- Department of Chemistry and Biology, Toronto Metropolitan University, Toronto, Ontario, Canada
| | - Tatiana Skarina
- Department of Chemical Engineering and Applied Chemistry, Toronto University, Toronto, Ontario, Canada
| | - Peter J. Stogios
- Department of Chemical Engineering and Applied Chemistry, Toronto University, Toronto, Ontario, Canada
| | - Sarah Birstonas
- Department of Chemistry and Biology, Toronto Metropolitan University, Toronto, Ontario, Canada
| | - Brian K. Coombes
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
| | - Alexei Savchenko
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
- Department of Chemical Engineering and Applied Chemistry, Toronto University, Toronto, Ontario, Canada
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16
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Savchenko A, Zamora J, Alvarenga R, Kõljalg U, Miettinen O. Additions to Dendrodacrys and outline of taxa with branched hyphidia in Dacrymycetes ( Basidiomycota). Fungal Syst Evol 2022; 10:103-126. [PMID: 36789282 PMCID: PMC9903345 DOI: 10.3114/fuse.2022.10.04] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 09/28/2022] [Indexed: 01/07/2023] Open
Abstract
The genus Dendrodacrys is a monophyletic group that belongs to Dacrymycetes (Agaricomycotina, Basidiomycota) and accommodates species distinguished by strongly branched hyphidia in combination with 3-septate basidiospores. While the original circumscription mainly treated European taxa, here we shift the focus to tropical and sub-tropical material and uncover wider variation in morphology within Dendrodacrys. Still united by hyphidia shape and basidiospore septation, the genus is expanded with 10 taxa having pustulate, cerebriform, or stipitate basidiocarps of yellow to dark brown colours, cylindrical to ovoid basidiospores, and hyphal septa with or without clamps. Monophyly of the amended Dendrodacrys is confirmed with a phylogeny based on six markers (SSU, ITS, LSU, TEF1-α, RPB1, and RPB2). As a result, we describe two new species (De. laetum and De. rigoratum), transfer three existing species to Dendrodacrys (De. brasiliense, De. dendrocalami, and De. pezizoideum), and raise one variety to the species level (De. kennedyae ≡ Dacrymyces enatus var. macrosporus). In addition, we provide descriptions for the earlier combined De. paraphysatum and four new informal taxa. Lastly, we present illustrations, a character table, and an identification key that addresses all known dacrymycetes with branched hyphidia. Citation: Savchenko A, Zamora JC, Alvarenga R, Kõljalg U, Miettinen O (2022). Additions to Dendrodacrys and outline of taxa with branched hyphidia in Dacrymycetes (Basidiomycota). Fungal Systematics and Evolution 10: 103-126. doi: 10.3114/fuse.2022.10.04.
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Affiliation(s)
- A. Savchenko
- Institute of Ecology and Earth Sciences, University of Tartu, J. Liivi 2, 50409, Tartu, Estonia,*Corresponding author:
| | - J.C. Zamora
- Museum of Evolution, Uppsala University, Norbyvägen 16, SE-75236, Uppsala, Sweden,Conservatoire et Jardin Botaniques de la Ville de Genève, Chemin de l’Impératrice 1, 1292 Chambésy-Genève, Switzerland
| | - R. Alvarenga
- Departamento de Micologia, Centro de Biociências, Universidade Federal de Pernambuco, Avenida da Engenharia, S/N 50740-600 – Cidade Universitária, Recife, Pernambuco, Brazil
| | - U. Kõljalg
- Institute of Ecology and Earth Sciences, University of Tartu, J. Liivi 2, 50409, Tartu, Estonia,Natural History Museum, University of Tartu, Vanemuise 46, 51003, Tartu, Estonia
| | - O. Miettinen
- Finnish Museum of Natural History, University of Helsinki, P.O. Box 7, FI-00014, Helsinki, Finland
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17
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Mok T, Pujol JL, Tsuboi M, Lee J, Kim E, Leonov O, Zhang J, Duan J, Lobetti-Bodoni C, Brase J, Savchenko A, Garrido Lopez P. LBA4 CANOPY-N: A phase II study of canakinumab (CAN) or pembrolizumab (PEM), alone or in combination, as neoadjuvant therapy in patients (pts) with resectable stage Ib–IIIa non-small cell lung cancer (NSCLC). Ann Oncol 2022. [DOI: 10.1016/j.annonc.2022.10.322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2022] Open
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18
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Venkatesan M, Semper C, Skrivergaard S, Di Leo R, Mesa N, Rasmussen MK, Young JF, Therkildsen M, Stogios PJ, Savchenko A. Recombinant production of growth factors for application in cell culture. iScience 2022; 25:105054. [PMID: 36157583 PMCID: PMC9489951 DOI: 10.1016/j.isci.2022.105054] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [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: 02/10/2022] [Revised: 06/07/2022] [Accepted: 08/26/2022] [Indexed: 11/04/2022] Open
Abstract
Culturing eukaryotic cells has widespread applications in research and industry, including the emerging field of cell-cultured meat production colloquially referred to as “cellular agriculture”. These applications are often restricted by the high cost of growth medium necessary for cell growth. Mitogenic protein growth factors (GFs) are essential components of growth medium and account for upwards of 90% of the total costs. Here, we present a set of expression constructs and a simplified protocol for recombinant production of functionally active GFs, including FGF2, IGF1, PDGF-BB, and TGF-β1 in Escherichia coli. Using this E. coli expression system, we produced soluble GF orthologs from species including bovine, chicken, and salmon. Bioactivity analysis revealed orthologs with improved performance compared to commercially available alternatives. We estimated that the production cost of GFs using our methodology will significantly reduce the cost of cell culture medium, facilitating low-cost protocols tailored for cultured meat production and tissue engineering. Developed methodology for low-cost production of soluble, bioactive GFs Purified GFs were active on NIH-3T3 and bovine satellite cells Some GF orthologs outperformed commercially sourced GFs Production of GFs using these methods can foster significant cost savings
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Affiliation(s)
- Meenakshi Venkatesan
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON M5S 3E8, Canada
| | - Cameron Semper
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, AB T2N 4N1, Canada
| | | | - Rosa Di Leo
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON M5S 3E8, Canada
| | - Nathalie Mesa
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON M5S 3E8, Canada
| | | | | | | | - Peter J Stogios
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON M5S 3E8, Canada
| | - Alexei Savchenko
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON M5S 3E8, Canada.,Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, AB T2N 4N1, Canada
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19
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Cruz MR, Cristy S, Guha S, De Cesare GB, Evdokimova E, Sanchez H, Borek D, Miramón P, Yano J, Fidel PL, Savchenko A, Andes DR, Stogios PJ, Lorenz MC, Garsin DA. Structural and functional analysis of EntV reveals a 12 amino acid fragment protective against fungal infections. Nat Commun 2022; 13:6047. [PMID: 36229448 PMCID: PMC9562342 DOI: 10.1038/s41467-022-33613-1] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 09/23/2022] [Indexed: 01/25/2023] Open
Abstract
Fungal pathogens are a continuing challenge due to few effective antifungals and a rise in resistance. In previous work, we described the inhibition of Candida albicans virulence following exposure to the 68 amino acid bacteriocin, EntV, secreted by Enterococcus faecalis. Here, to optimize EntV as a potential therapeutic and better understand its antifungal features, an X-ray structure is obtained. The structure consists of six alpha helices enclosing a seventh 16 amino acid helix (α7). The individual helices are tested for antifungal activity using in vitro and nematode infection assays. Interestingly, α7 retains antifungal, but not antibacterial activity and is also effective against Candida auris and Cryptococcus neoformans. Further reduction of α7 to 12 amino acids retains full antifungal activity, and excellent efficacy is observed in rodent models of C. albicans oropharyngeal, systemic, and venous catheter infections. Together, these results showcase EntV-derived peptides as promising candidates for antifungal therapeutic development.
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Affiliation(s)
- Melissa R. Cruz
- grid.267308.80000 0000 9206 2401Department of Microbiology and Molecular Genetics, The University of Texas Health Science Center at Houston, Houston, TX 77030 USA
| | - Shane Cristy
- grid.267308.80000 0000 9206 2401Department of Microbiology and Molecular Genetics, The University of Texas Health Science Center at Houston, Houston, TX 77030 USA
| | - Shantanu Guha
- grid.267308.80000 0000 9206 2401Department of Microbiology and Molecular Genetics, The University of Texas Health Science Center at Houston, Houston, TX 77030 USA
| | - Giuseppe Buda De Cesare
- grid.267308.80000 0000 9206 2401Department of Microbiology and Molecular Genetics, The University of Texas Health Science Center at Houston, Houston, TX 77030 USA
| | - Elena Evdokimova
- grid.17063.330000 0001 2157 2938BioZone, Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON M5S 3E5 Canada
| | - Hiram Sanchez
- grid.28803.310000 0001 0701 8607Department of Medicine, University of Wisconsin, Madison, WI 53705 USA ,grid.28803.310000 0001 0701 8607Department of Medical Microbiology and Immunology, University of Wisconsin, Madison, WI 53705 USA
| | - Dominika Borek
- grid.267313.20000 0000 9482 7121Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, TX 75390 USA ,grid.267313.20000 0000 9482 7121Department of Biochemistry, The University of Texas Southwestern Medical Center, Dallas, TX 75390 USA
| | - Pedro Miramón
- grid.267308.80000 0000 9206 2401Department of Microbiology and Molecular Genetics, The University of Texas Health Science Center at Houston, Houston, TX 77030 USA
| | - Junko Yano
- grid.279863.10000 0000 8954 1233Department of Oral and Craniofacial Biology, Louisiana State University Health School of Dentistry, New Orleans, LA 70119 USA
| | - Paul L. Fidel
- grid.279863.10000 0000 8954 1233Department of Oral and Craniofacial Biology, Louisiana State University Health School of Dentistry, New Orleans, LA 70119 USA
| | - Alexei Savchenko
- grid.17063.330000 0001 2157 2938BioZone, Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON M5S 3E5 Canada ,grid.22072.350000 0004 1936 7697Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, AB T2N 4N1 Canada ,Center for Structural Genomics of Infectious Diseases (CSGID), Chicago, IL USA
| | - David R. Andes
- grid.28803.310000 0001 0701 8607Department of Medicine, University of Wisconsin, Madison, WI 53705 USA ,grid.28803.310000 0001 0701 8607Department of Medical Microbiology and Immunology, University of Wisconsin, Madison, WI 53705 USA
| | - Peter J. Stogios
- grid.17063.330000 0001 2157 2938BioZone, Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON M5S 3E5 Canada
| | - Michael C. Lorenz
- grid.267308.80000 0000 9206 2401Department of Microbiology and Molecular Genetics, The University of Texas Health Science Center at Houston, Houston, TX 77030 USA
| | - Danielle A. Garsin
- grid.267308.80000 0000 9206 2401Department of Microbiology and Molecular Genetics, The University of Texas Health Science Center at Houston, Houston, TX 77030 USA
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20
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Stogios PJ, Liston SD, Semper C, Quade B, Michalska K, Evdokimova E, Ram S, Otwinowski Z, Borek D, Cowen LE, Savchenko A. Molecular analysis and essentiality of Aro1 shikimate biosynthesis multi-enzyme in Candida albicans. Life Sci Alliance 2022; 5:e202101358. [PMID: 35512834 PMCID: PMC9074039 DOI: 10.26508/lsa.202101358] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 04/10/2022] [Accepted: 04/13/2022] [Indexed: 11/24/2022] Open
Abstract
In the human fungal pathogen Candida albicans, ARO1 encodes an essential multi-enzyme that catalyses consecutive steps in the shikimate pathway for biosynthesis of chorismate, a precursor to folate and the aromatic amino acids. We obtained the first molecular image of C. albicans Aro1 that reveals the architecture of all five enzymatic domains and their arrangement in the context of the full-length protein. Aro1 forms a flexible dimer allowing relative autonomy of enzymatic function of the individual domains. Our activity and in cellulo data suggest that only four of Aro1's enzymatic domains are functional and essential for viability of C. albicans, whereas the 3-dehydroquinate dehydratase (DHQase) domain is inactive because of active site substitutions. We further demonstrate that in C. albicans, the type II DHQase Dqd1 can compensate for the inactive DHQase domain of Aro1, suggesting an unrecognized essential role for this enzyme in shikimate biosynthesis. In contrast, in Candida glabrata and Candida parapsilosis, which do not encode a Dqd1 homolog, Aro1 DHQase domains are enzymatically active, highlighting diversity across Candida species.
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Affiliation(s)
- Peter J Stogios
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Canada
| | - Sean D Liston
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Cameron Semper
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Canada
| | - Bradley Quade
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Karolina Michalska
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, IL, USA
| | - Elena Evdokimova
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Canada
| | - Shane Ram
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Canada
| | - Zbyszek Otwinowski
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Dominika Borek
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Leah E Cowen
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Alexei Savchenko
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Canada
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Canada
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21
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Pham C, Stogios PJ, Savchenko A, Mahadevan R. Advances in engineering and optimization of transcription factor-based biosensors for plug-and-play small molecule detection. Curr Opin Biotechnol 2022; 76:102753. [PMID: 35872379 DOI: 10.1016/j.copbio.2022.102753] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 05/31/2022] [Accepted: 06/06/2022] [Indexed: 11/30/2022]
Abstract
Transcription factor (TF)-based biosensors have been applied in biotechnology for a variety of functions, including protein engineering, dynamic control, environmental detection, and point-of-care diagnostics. Such biosensors are promising analytical tools due to their wide range of detectable ligands and modular nature. However, designing biosensors tailored for applications of interest with the desired performance parameters, including ligand specificity, remains challenging. Biosensors often require significant engineering and tuning to meet desired specificity, sensitivity, dynamic range, and operating range parameters. Another limitation is the orthogonality of biosensors across hosts, given the role of the cellular context. Here, we describe recent advances and examples in the engineering and optimization of TF-based biosensors for plug-and-play small molecule detection. We highlight novel developments in TF discovery and biosensor design, TF specificity engineering, and biosensor tuning, with emphasis on emerging computational methods.
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Affiliation(s)
- Chester Pham
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, ON, Canada
| | - Peter J Stogios
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, ON, Canada
| | - Alexei Savchenko
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, ON, Canada; Department of Microbiology, Immunology and Infectious Disease, University of Calgary, AB, Canada
| | - Radhakrishnan Mahadevan
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, ON, Canada; The Institute of Biomedical Engineering, University of Toronto, ON, Canada.
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22
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Arellano-Saab A, McErlean CSP, Lumba S, Savchenko A, Stogios PJ, McCourt P. A novel strigolactone receptor antagonist provides insights into the structural inhibition, conditioning, and germination of the crop parasite Striga. J Biol Chem 2022; 298:101734. [PMID: 35181340 PMCID: PMC9035408 DOI: 10.1016/j.jbc.2022.101734] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 11/30/2021] [Revised: 02/12/2022] [Accepted: 02/14/2022] [Indexed: 01/14/2023] Open
Abstract
Crop parasites of the Striga genera are a major biological deterrent to food security in Africa and are one of the largest obstacles to poverty alleviation on the continent. Striga seeds germinate by sensing small-molecule hormones, strigolactones (SLs), that emanate from host roots. Although SL receptors (Striga hermonthica HYPOSENSITIVE TO LIGHT [ShHTL]) have been identified, discerning their function has been difficult because these parasites cannot be easily grown under laboratory conditions. Moreover, many Striga species are obligate outcrossers that are not transformable, hence not amenable to genetic analysis. By combining phenotypic screening with ShHTL structural information and hybrid drug discovery methods, we discovered a potent SL perception inhibitor for Striga, dormirazine (DOZ). Structural analysis of this piperazine-based antagonist reveals a novel binding mechanism, distinct from that of known SLs, blocking access of the hormone to its receptor. Furthermore, DOZ reduces the flexibility of protein–protein interaction domains important for receptor signaling to downstream partners. In planta, we show, via temporal additions of DOZ, that SL receptors are required at a specific time during seed conditioning. This conditioning is essential to prime seed germination at the right time; thus, this SL-sensitive stage appears to be critical for adequate receptor signaling. Aside from uncovering a function for ShHTL during seed conditioning, these results suggest that future Ag-Biotech Solutions to Striga infestations will need to carefully time the application of antagonists to exploit receptor availability and outcompete natural SLs, critical elements for successful parasitic plant invasions.
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Affiliation(s)
- Amir Arellano-Saab
- Department of Cell and Systems Biology, University of Toronto, 25 Willcocks Street, Toronto M5S 3B2, Canada; Department of Chemical Engineering and Applied Chemistry, University of Toronto. Toronto, ON. M5S 3E5, Canada
| | | | - Shelley Lumba
- Department of Cell and Systems Biology, University of Toronto, 25 Willcocks Street, Toronto M5S 3B2, Canada
| | - Alexei Savchenko
- Department of Chemical Engineering and Applied Chemistry, University of Toronto. Toronto, ON. M5S 3E5, Canada; Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
| | - Peter J Stogios
- Department of Chemical Engineering and Applied Chemistry, University of Toronto. Toronto, ON. M5S 3E5, Canada
| | - Peter McCourt
- Department of Cell and Systems Biology, University of Toronto, 25 Willcocks Street, Toronto M5S 3B2, Canada
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23
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Zamora J, Savchenko A, González-Cruz Á, Prieto-García F, Olariaga I, Ekman S. Dendrodacrys: a new genus for species with branched hyphidia in Dacrymyces s.l., with the description of four new species. Fungal Syst Evol 2022; 9:27-42. [PMID: 35978985 PMCID: PMC9355100 DOI: 10.3114/fuse.2022.09.04] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 02/18/2022] [Indexed: 12/04/2022] Open
Abstract
A new genus named Dendrodacrys is proposed for a monophyletic group in Dacrymycetaceae, containing species with pulvinate to depressed basidiocarps, distinctly branched hymenial hyphidia, and up to 3-septate mature basidiospores. Four taxa in this group, occurring in Europe, are proposed as new species, viz. De. ciprense, De. concrescens, De. ellipsosporum, and De. oblongisporum, based both on morphological and DNA data (nrDNA, RPB1, RPB2, TEF-1α, 12S). These new species are all described in detail, illustrated, and compared with other published taxa that with which they can be confounded. The new combination De. paraphysatum is proposed after revising the type material of Dacrymyces paraphysatus, but other combinations or potentially new non-European species descriptions are postponed pending further studies of additional specimens. Citation: Zamora JC, Savchenko A, González-Cruz Á, Prieto-García F, Olariaga I, Ekman S (2022). Dendrodacrys: a new genus for species with branched hyphidia in Dacrymyces s.l., with the description of four new species. Fungal Systematics and Evolution9: 27–42. doi: 10.3114/fuse.2022.09.04
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Affiliation(s)
- J.C. Zamora
- Museum of Evolution, Uppsala University, Norbyvägen 16, 752 36 Uppsala, Sweden
- Conservatoire et Jardin Botaniques de la Ville de Genève, Chemin de l’Impératrice 1, 1292 Chambésy-Genève, Switzerland
| | - A. Savchenko
- Institute of Ecology & Earth Sciences, University of Tartu, 51014 Tartu, Estonia
| | | | | | - I. Olariaga
- Departamento de Biología y Geología, Física y Química Inorgánica, Universidad Rey Juan Carlos, Tulipán s/n, 28933 Móstoles, Madrid, Spain
| | - S. Ekman
- Museum of Evolution, Uppsala University, Norbyvägen 16, 752 36 Uppsala, Sweden
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24
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Savchenko A, Zamora J, Shirouzu T, Spirin V, Malysheva V, Kõljalg U, Miettinen O. Revision of Cerinomyces ( Dacrymycetes, Basidiomycota) with notes on morphologically and historically related taxa. Stud Mycol 2021; 99:100117. [PMID: 34934464 PMCID: PMC8645972 DOI: 10.1016/j.simyco.2021.100117] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Cerinomyces (Dacrymycetes, Basidiomycota) is a genus traditionally defined by corticioid basidiocarps, in contrast to the rest of the class, which is characterized by gelatinous ones. In the traditional circumscription the genus is polyphyletic, and the monotypic family Cerinomycetaceae is paraphyletic. Aiming for a more concise delimitation, we revise Cerinomyces s.l. with a novel phylogeny based on sequences of nrDNA (SSU, ITS, LSU) and protein-coding genes (RPB1, RPB2, TEF1-α). We establish that monophyletic Cerinomyces s.s. is best characterized not by the corticioid morphology, but by a combination of traits: hyphal clamps, predominantly aseptate thin-walled basidiospores, and low content of carotenoid pigments. In our updated definition, Cerinomyces s.s. encompasses five well-supported phylogenetic clades divided into two morphological groups: (i-iii) taxa with arid corticioid basidiocarps, including the generic type C. pallidus; and (iv-v) newly introduced members with gelatinous basidiocarps, like Dacrymyces enatus and D. tortus. The remaining corticioid species of Cerinomyces s.l. are morphologically distinct and belong to the Dacrymycetaceae: our analysis places the carotenoid-rich Cerinomyces canadensis close to Femsjonia, and we transfer the clamps-lacking C. grandinioides group to Dacrymyces. In addition, we address genera related to Cerinomyces s.l. historically and morphologically, such as Ceracea, Dacryonaema and Unilacryma. Overall, we describe twenty-four new species and propose nine new combinations in both Cerinomycetaceae and Dacrymycetaceae.
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Affiliation(s)
- A. Savchenko
- Institute of Ecology and Earth Sciences, University of Tartu, 14a Ravila, 50411, Tartu, Estonia
- Natural History Museum, University of Tartu, Vanemuise 46, 51003, Tartu, Estonia
- Correspondence: A. Savchenko
| | - J.C. Zamora
- Museum of Evolution, Uppsala University, Norbyvägen 16, SE-75236, Uppsala, Sweden
| | - T. Shirouzu
- Graduate School of Bioresources, Mie University, 1577 Kurima-machiya, Tsu, Mie, 514-8507, Japan
| | - V. Spirin
- Finnish Museum of Natural History, University of Helsinki, P.O. Box 7, FI-00014, Helsinki, Finland
| | - V. Malysheva
- Komarov Botanical Institute, Russian Academy of Sciences, Prof. Popova str. 2, RU-197376, St. Petersburg, Russia
| | - U. Kõljalg
- Institute of Ecology and Earth Sciences, University of Tartu, 14a Ravila, 50411, Tartu, Estonia
- Natural History Museum, University of Tartu, Vanemuise 46, 51003, Tartu, Estonia
| | - O. Miettinen
- Finnish Museum of Natural History, University of Helsinki, P.O. Box 7, FI-00014, Helsinki, Finland
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25
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MacAlpine J, Daniel-Ivad M, Liu Z, Yano J, Revie NM, Todd RT, Stogios PJ, Sanchez H, O'Meara TR, Tompkins TA, Savchenko A, Selmecki A, Veri AO, Andes DR, Fidel PL, Robbins N, Nodwell J, Whitesell L, Cowen LE. A small molecule produced by Lactobacillus species blocks Candida albicans filamentation by inhibiting a DYRK1-family kinase. Nat Commun 2021; 12:6151. [PMID: 34686660 PMCID: PMC8536679 DOI: 10.1038/s41467-021-26390-w] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 10/01/2021] [Indexed: 11/23/2022] Open
Abstract
The fungus Candida albicans is an opportunistic pathogen that can exploit imbalances in microbiome composition to invade its human host, causing pathologies ranging from vaginal candidiasis to fungal sepsis. Bacteria of the genus Lactobacillus are colonizers of human mucosa and can produce compounds with bioactivity against C. albicans. Here, we show that some Lactobacillus species produce a small molecule under laboratory conditions that blocks the C. albicans yeast-to-filament transition, an important virulence trait. It remains unexplored whether the compound is produced in the context of the human host. Bioassay-guided fractionation of Lactobacillus-conditioned medium linked this activity to 1-acetyl-β-carboline (1-ABC). We use genetic approaches to show that filamentation inhibition by 1-ABC requires Yak1, a DYRK1-family kinase. Additional biochemical characterization of structurally related 1-ethoxycarbonyl-β-carboline confirms that it inhibits Yak1 and blocks C. albicans biofilm formation. Thus, our findings reveal Lactobacillus-produced 1-ABC can prevent the yeast-to-filament transition in C. albicans through inhibition of Yak1.
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Affiliation(s)
- Jessie MacAlpine
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | | | - Zhongle Liu
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Junko Yano
- Center of Excellence in Oral and Craniofacial Biology, Louisiana State University Health Sciences Center School of Dentistry, New Orleans, LA, USA
| | - Nicole M Revie
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Robert T Todd
- Department of Microbiology and Immunology, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Peter J Stogios
- BioZone, Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, Canada
- Center for Structural Genomics of Infectious Diseases (CSGID), Chicago, IL, USA
| | - Hiram Sanchez
- Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
- Department of Medical Microbiology and Immunology, University of Wisconsin, Madison, WI, USA
| | - Teresa R O'Meara
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Thomas A Tompkins
- Rosell Institute for Microbiome and Probiotics, 6100 Avenue Royalmount, Montreal, QC, Canada
| | - Alexei Savchenko
- BioZone, Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, Canada
- Center for Structural Genomics of Infectious Diseases (CSGID), Chicago, IL, USA
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, AB, Canada
| | - Anna Selmecki
- Department of Microbiology and Immunology, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Amanda O Veri
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - David R Andes
- Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
- Department of Medical Microbiology and Immunology, University of Wisconsin, Madison, WI, USA
| | - Paul L Fidel
- Center of Excellence in Oral and Craniofacial Biology, Louisiana State University Health Sciences Center School of Dentistry, New Orleans, LA, USA
| | - Nicole Robbins
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Justin Nodwell
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Luke Whitesell
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Leah E Cowen
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
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26
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Kosinova A, Grinshtein Y, Savchenko A, Goncharov M. The influence of metabolic activity of platelets on sensitivity to Acetylsalicylic acid in patients with coronary heart disease. Eur Heart J 2021. [DOI: 10.1093/eurheartj/ehab724.3225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Abstract
Background
Acetylsalicylic acid (ASA) is used to reduce the risk of shunt occlusion after coronary artery bypass grafting (CABG). From 5% to 60% of CHD patients do not respond to ASA. This phenomenon was defined as ASA resistance. The functional activity of platelets is largely determined by the state of their metabolism.
Methods
The venous blood samples were acquired from 66 patients with CHD before CABG, on the first day after surgery, and on the 8–10th day after surgery. The aggregometry was carried out for all participants by an optical aggregometer with 1 mM of arachidonic acid (AA) and 5 mM Adenosinediphosphate (ADP). Resistance to ASA was determined at the level of platelet aggregation with AA over 20% on ASA therapy or over 20% after platelet incubation with ASA in vitro before CABG. Patients were divided into ASA sensitive (sASA) and ASA resistant (rASA) groups. The level of synthesis of primary and secondary reactive oxygen species (ROS) by platelets was determined using chemiluminescent analysis. We investigated the overall level of radical synthesis from the values of Imax and S (area under the chemiluminescence curve), which, respectively, characterizes the maximum synthesis per unit time and the total amount of radical. The kinetics of ROS synthesis was characterized by Tmax (time to reach the maximum for the chemiluminescent curve). The activity of NAD- and NADP-dependent dehydrogenases in platelets was determined by the bioluminescent method.
Results
It was found that the aggregation activity of platelets depended on the sensitivity of CHD patients to ASA and decreased during postoperative ASA therapy. The most pronounced differences in metabolic parameters of platelets in sASA and rASA patients were detected by Nox2 activity. Platelet aggregation activity was correlated with platelet Nox2 activity only in sASA patients and only before CABG. The level of AA-induced platelet aggregation with the addition of ASA in sASA patients before CABG was negatively correlated with the Imax of ADP-induced lucigenin-enhanced (r=−0.27, p=0.046) and S of spontaneous luminol-enhanced (r=−0.31, p=0.022) platelet chemiluminescence. Patients with rASA before CABG had positive correlations of AA-induced aggregation with S of spontaneous (r=0.63, p=0.029) as well as Imax (r=0.85, p<0.001) and S (r=0.87, p<0.001) of ADP-induced luminol-enhanced chemiluminescence of platelets. Therefore, the absence of correlations between platelet aggregation activity and Nox2 activity was determined by ASA resistance and postoperative ASA therapy. The synthesis of secondary ROS (Table) by platelets of CHD patients did not depend on the sensitivity of patients to ASA but increased during postoperative treatment with ASA. The activity of NAD(P)-dependent dehydrogenases in platelets did not differ in sASA and rASA patients with CHD.
Conclusions
Metabolic Activity of Platelets could influence on resistance to ASA in Patients with CHD.
Funding Acknowledgement
Type of funding sources: Public grant(s) – National budget only. Main funding source(s): The reported study was funded by Russian Foundation for Basic Research, Government of Krasno-yarsk Territory, Krasnoyarsk Regional Fund of Science to the research project: “Antiplatelet therapy personification in patients with coronary heart disease (CHD) depending on the level of P-selectin gene expression, the intensity of intercellular interaction and inflammation”
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Affiliation(s)
- A Kosinova
- Krasnoyarsk State Medical University, Krasnoyarsk, Russian Federation
| | - Y Grinshtein
- Krasnoyarsk State Medical University, Krasnoyarsk, Russian Federation
| | - A Savchenko
- Medical Research Institute for Northern Problems, Krasnoyarsk, Russian Federation
| | - M Goncharov
- Krasnoyarsk State Medical University, Krasnoyarsk, Russian Federation
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27
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Chan PWY, Chakrabarti N, Ing C, Halgas O, To TKW, Wälti M, Petit AP, Tran C, Savchenko A, Yakunin AF, Edwards EA, Pomès R, Pai EF. Defluorination Capability of l-2-Haloacid Dehalogenases in the HAD-Like Hydrolase Superfamily Correlates with Active Site Compactness. Chembiochem 2021; 23:e202100414. [PMID: 34643018 DOI: 10.1002/cbic.202100414] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 10/07/2021] [Indexed: 11/11/2022]
Abstract
l-2-Haloacid dehalogenases, industrially and environmentally important enzymes that catalyse cleavage of the carbon-halogen bond in S-2-halocarboxylic acids, were known to hydrolyse chlorinated, brominated and iodinated substrates but no activity towards fluorinated compounds had been reported. A screen for novel dehalogenase activities revealed four l-2-haloacid dehalogenases capable of defluorination. We now report crystal structures for two of these enzymes, Bpro0530 and Rha0230, as well as for the related proteins PA0810 and RSc1362, which hydrolyse chloroacetate but not fluoroacetate, all at ∼2.2 Å resolution. Overall structure and active sites of these enzymes are highly similar. In molecular dynamics (MD) calculations, only the defluorinating enzymes sample more compact conformations, which in turn allow more effective interactions with the small fluorine atom. Structural constraints, based on X-ray structures and MD calculations, correctly predict the defluorination activity of the homologous enzyme ST2570.
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Affiliation(s)
- Peter W Y Chan
- Department of Biochemistry, University of Toronto, Toronto, Ontario, M5S 1A8, Canada.,Zymeworks, Inc., 1385 West 8th Avenue Suite 540, Vancouver, British Columbia, V6H 3 V9, Canada.,Princess Margaret Cancer Centre, The Campbell Family Cancer Research Institute, University Health Network, Toronto, Ontario, M5G 1L7, Canada
| | | | - Chris Ing
- Department of Biochemistry, University of Toronto, Toronto, Ontario, M5S 1A8, Canada.,Molecular Medicine, Hospital for Sick Children, Toronto, Ontario, M5G 1X8, Canada.,ProteinQure, Inc., 119 Spadina Avenue suite 304, Toronto, Ontario, M5V 2L1, Canada
| | - Ondrej Halgas
- Department of Biochemistry, University of Toronto, Toronto, Ontario, M5S 1A8, Canada
| | - Terence K W To
- Princess Margaret Cancer Centre, The Campbell Family Cancer Research Institute, University Health Network, Toronto, Ontario, M5G 1L7, Canada.,International Point of Care, Inc., 135 The West Mall, Unit 9, Toronto, Ontario, M9C 1C2, Canada
| | - Marielle Wälti
- Princess Margaret Cancer Centre, The Campbell Family Cancer Research Institute, University Health Network, Toronto, Ontario, M5G 1L7, Canada.,Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0510, USA
| | - Alain-Pierre Petit
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, M5S 3E5, Canada.,Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Christopher Tran
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, M5S 3E5, Canada.,Ramboll Environment & Health, 2400 Meadowpine Boulevard, Suite 100, Mississauga, Ontario, L5N 6S2, Canada
| | - Alexei Savchenko
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, M5S 3E5, Canada.,Department of Microbiology, Immunology & Infectious Diseases, University of Calgary, Health Research Innovation Centre, 3330 Hospital Drive NW, Calgary, Alberta, T2N 4N1, Canada
| | - Alexander F Yakunin
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, M5S 3E5, Canada.,Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Bangor, Gwynedd, LL57 2UW, UK
| | - Elizabeth A Edwards
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, M5S 3E5, Canada.,Department of Cell & Systems Biology, University of Toronto, Toronto, Ontario, M5S 3G5, Canada
| | - Régis Pomès
- Department of Biochemistry, University of Toronto, Toronto, Ontario, M5S 1A8, Canada.,Molecular Medicine, Hospital for Sick Children, Toronto, Ontario, M5G 1X8, Canada
| | - Emil F Pai
- Department of Biochemistry, University of Toronto, Toronto, Ontario, M5S 1A8, Canada.,Princess Margaret Cancer Centre, The Campbell Family Cancer Research Institute, University Health Network, Toronto, Ontario, M5G 1L7, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, M5G 1L7, Canada
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28
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Lemak S, Serbanescu MA, Khusnutdinova AN, Ruszkowski M, Beloglazova N, Xu X, Brown G, Cui H, Tan K, Joachimiak A, Cvitkovitch DG, Savchenko A, Yakunin AF. Structural and biochemical insights into CRISPR RNA processing by the Cas5c ribonuclease SMU1763 from Streptococcus mutans. J Biol Chem 2021; 297:101251. [PMID: 34592310 PMCID: PMC8524198 DOI: 10.1016/j.jbc.2021.101251] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 09/13/2021] [Accepted: 09/24/2021] [Indexed: 12/01/2022] Open
Abstract
The cariogenic pathogen Streptococcus mutans contains two CRISPR systems (type I-C and type II-A) with the Cas5c protein (SmuCas5c) involved in processing of long CRISPR RNA transcripts (pre-crRNA) containing repeats and spacers to mature crRNA guides. In this study, we determined the crystal structure of SmuCas5c at a resolution of 1.72 Å, which revealed the presence of an N-terminal modified RNA recognition motif and a C-terminal twisted β-sheet domain with four bound sulphate molecules. Analysis of surface charge and residue conservation of the SmuCas5c structure suggested the location of an RNA-binding site in a shallow groove formed by the RNA recognition motif domain with several conserved positively charged residues (Arg39, Lys52, Arg109, Arg127, and Arg134). Purified SmuCas5c exhibited metal-independent ribonuclease activity against single-stranded pre-CRISPR RNAs containing a stem-loop structure with a seven-nucleotide stem and a pentaloop. We found SmuCas5c cleaves substrate RNA within the repeat sequence at a single cleavage site located at the 3'-base of the stem but shows significant tolerance to substrate sequence variations downstream of the cleavage site. Structure-based mutational analysis revealed that the conserved residues Tyr50, Lys120, and His121 comprise the SmuCas5c catalytic residues. In addition, site-directed mutagenesis of positively charged residues Lys52, Arg109, and Arg134 located near the catalytic triad had strong negative effects on the RNase activity of this protein, suggesting that these residues are involved in RNA binding. Taken together, our results reveal functional diversity of Cas5c ribonucleases and provide further insight into the molecular mechanisms of substrate selectivity and activity of these enzymes.
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Affiliation(s)
- Sofia Lemak
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - M Anca Serbanescu
- Faculty of Dentistry, Dental Research Institute, University of Toronto, Toronto, Ontario, Canada
| | - Anna N Khusnutdinova
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Milosz Ruszkowski
- Synchrotron Radiation Research Section of MCL, National Cancer Institute, Argonne, Illinois, USA
| | - Natalia Beloglazova
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Xiaohui Xu
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Greg Brown
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Hong Cui
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Kemin Tan
- X-Ray Science Division, Midwest Center for Structural Genomics and Structural Biology Center, Argonne National Laboratory, Argonne, Illinois, USA
| | - Andrzej Joachimiak
- X-Ray Science Division, Midwest Center for Structural Genomics and Structural Biology Center, Argonne National Laboratory, Argonne, Illinois, USA
| | - Dennis G Cvitkovitch
- Faculty of Dentistry, Dental Research Institute, University of Toronto, Toronto, Ontario, Canada
| | - Alexei Savchenko
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Alexander F Yakunin
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada; Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Bangor, Gwynedd, UK.
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Evdokias G, Semper C, Mora-Ochomogo M, Di Falco M, Nguyen TTM, Savchenko A, Tsang A, Benoit-Gelber I. Identification of a Novel Biosynthetic Gene Cluster in Aspergillus niger Using Comparative Genomics. J Fungi (Basel) 2021; 7:374. [PMID: 34064722 PMCID: PMC8151901 DOI: 10.3390/jof7050374] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Revised: 05/05/2021] [Accepted: 05/07/2021] [Indexed: 11/17/2022] Open
Abstract
Previously, DNA microarrays analysis showed that, in co-culture with Bacillus subtilis, a biosynthetic gene cluster anchored with a nonribosomal peptides synthetase of Aspergillus niger is downregulated. Based on phylogenetic and synteny analyses, we show here that this gene cluster, NRRL3_00036-NRRL3_00042, comprises genes predicted to encode a nonribosomal peptides synthetase, a FAD-binding domain-containing protein, an uncharacterized protein, a transporter, a cytochrome P450 protein, a NAD(P)-binding domain-containing protein and a transcription factor. We overexpressed the in-cluster transcription factor gene NRRL3_00042. The overexpression strain, NRRL3_00042OE, displays reduced growth rate and production of a yellow pigment, which by mass spectrometric analysis corresponds to two compounds with masses of 409.1384 and 425.1331. We deleted the gene encoding the NRRL3_00036 nonribosomal peptides synthetase in the NRRL3_00042OE strain. The resulting strain reverted to the wild-type phenotype. These results suggest that the biosynthetic gene cluster anchored by the NRRL3_00036 nonribosomal peptides synthetase gene is regulated by the in-cluster transcriptional regulator gene NRRL3_00042, and that it is involved in the production of two previously uncharacterized compounds.
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Affiliation(s)
- Gregory Evdokias
- Centre for Structural and Functional Genomics, Department of Biology, Concordia University, 7141 Rue Sherbrooke Ouest, Montréal, QC H4B 1R6, Canada; (G.E.); (M.M.-O.); (M.D.F.); (T.T.M.N.); (A.T.)
| | - Cameron Semper
- Department of Microbiology, Immunology and Infectious Disease, University of Calgary, 3330 Hospital Drive, Calgary, AB T2N 4N1, Canada; (C.S.); (A.S.)
| | - Montserrat Mora-Ochomogo
- Centre for Structural and Functional Genomics, Department of Biology, Concordia University, 7141 Rue Sherbrooke Ouest, Montréal, QC H4B 1R6, Canada; (G.E.); (M.M.-O.); (M.D.F.); (T.T.M.N.); (A.T.)
| | - Marcos Di Falco
- Centre for Structural and Functional Genomics, Department of Biology, Concordia University, 7141 Rue Sherbrooke Ouest, Montréal, QC H4B 1R6, Canada; (G.E.); (M.M.-O.); (M.D.F.); (T.T.M.N.); (A.T.)
| | - Thi Truc Minh Nguyen
- Centre for Structural and Functional Genomics, Department of Biology, Concordia University, 7141 Rue Sherbrooke Ouest, Montréal, QC H4B 1R6, Canada; (G.E.); (M.M.-O.); (M.D.F.); (T.T.M.N.); (A.T.)
| | - Alexei Savchenko
- Department of Microbiology, Immunology and Infectious Disease, University of Calgary, 3330 Hospital Drive, Calgary, AB T2N 4N1, Canada; (C.S.); (A.S.)
| | - Adrian Tsang
- Centre for Structural and Functional Genomics, Department of Biology, Concordia University, 7141 Rue Sherbrooke Ouest, Montréal, QC H4B 1R6, Canada; (G.E.); (M.M.-O.); (M.D.F.); (T.T.M.N.); (A.T.)
| | - Isabelle Benoit-Gelber
- Centre for Structural and Functional Genomics, Department of Biology, Concordia University, 7141 Rue Sherbrooke Ouest, Montréal, QC H4B 1R6, Canada; (G.E.); (M.M.-O.); (M.D.F.); (T.T.M.N.); (A.T.)
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Korniienko V, Husak Y, Yanovska A, Banasiuk R, Yusupova A, Savchenko A, Holubnycha V, Pogorielov M. Functional and biological characterization of chitosan electrospun nanofibrous membrane nucleated with silver nanoparticles. Appl Nanosci 2021. [DOI: 10.1007/s13204-021-01808-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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31
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Semper C, Watanabe N, Savchenko A. Structural characterization of nonstructural protein 1 from SARS-CoV-2. iScience 2020; 24:101903. [PMID: 33319167 PMCID: PMC7721355 DOI: 10.1016/j.isci.2020.101903] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [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: 10/08/2020] [Revised: 10/21/2020] [Accepted: 12/03/2020] [Indexed: 12/12/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is a single-stranded, enveloped RNA virus and the etiological agent of the current coronavirus disease 2019 pandemic. Efficient replication of the virus relies on the activity of nonstructural protein 1 (Nsp1), a major virulence factor shown to facilitate suppression of host gene expression through promotion of host mRNA degradation and interaction with the 40S ribosomal subunit. Here, we report the crystal structure of the globular domain of SARS-CoV-2 Nsp1, encompassing residues 13 to 127, at a resolution of 1.65 Å. Our structure features a six-stranded, capped β-barrel motif similar to Nsp1 from SARS-CoV and reveals how variations in amino acid sequence manifest as distinct structural features. Combining our high-resolution crystal structure with existing data on the C-terminus of Nsp1 from SARS-CoV-2, we propose a model of the full-length protein. Our results provide insight into the molecular structure of a major pathogenic determinant of SARS-CoV-2. SARS-CoV-2 Nsp1 features a capped β-barrel structure, similar to that of SARS-CoV Distinct structural features distinguish SARS-CoV-2 Nsp1 from its SARS-CoV ortholog The plasticity of the Nsp1 protein fold is evident through comparison with homologs
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Affiliation(s)
- Cameron Semper
- Department of Microbiology, Immunology and Infectious Disease, University of Calgary, HSC B724 3330 Hospital Drive NW, Calgary, Alberta, T2N 4N1, Canada
| | - Nobuhiko Watanabe
- Department of Microbiology, Immunology and Infectious Disease, University of Calgary, HSC B724 3330 Hospital Drive NW, Calgary, Alberta, T2N 4N1, Canada.,Center for Structural Genomics of Infectious Diseases (CSGID)
| | - Alexei Savchenko
- Department of Microbiology, Immunology and Infectious Disease, University of Calgary, HSC B724 3330 Hospital Drive NW, Calgary, Alberta, T2N 4N1, Canada.,Center for Structural Genomics of Infectious Diseases (CSGID)
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32
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Batyrova KA, Khusnutdinova AN, Wang PH, Di Leo R, Flick R, Edwards EA, Savchenko A, Yakunin AF. Biocatalytic in Vitro and in Vivo FMN Prenylation and (De)carboxylase Activation. ACS Chem Biol 2020; 15:1874-1882. [PMID: 32579338 DOI: 10.1021/acschembio.0c00136] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Reversible UbiD-like (de)carboxylases represent a large family of mostly uncharacterized enzymes, which require the recently discovered prenylated FMN (prFMN) cofactor for activity. Functional characterization of novel UbiDs is hampered by a lack of robust protocols for prFMN generation and UbiD activation. Here, we report two systems for in vitro and in vivo FMN prenylation and UbiD activation under aerobic conditions. The in vitro one-pot prFMN cascade includes five enzymes: FMN prenyltransferase (UbiX), prenol kinase, polyphosphate kinase, formate dehydrogenase, and FMN reductase, which use prenol, polyphosphate, formate, ATP, NAD+, and FMN as substrates and cofactors. Under aerobic conditions, this cascade produced prFMN from FMN with over 98% conversion and activated purified ferulic acid decarboxylase Fdc1 from Aspergillus niger and protocatechuic acid decarboxylase ENC0058 from Enterobacter cloaceae. The in vivo system for FMN prenylation and UbiD activation is based on the coexpression of Fdc1 and UbiX in Escherichia coli cells under aerobic conditions in the presence of prenol. The in vitro and in vivo FMN prenylation cascades will facilitate functional characterization of novel UbiDs and their applications.
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Affiliation(s)
- Khorcheska A. Batyrova
- Department of Chemical Engineering and Applied Sciences, University of Toronto, Toronto, Ontario M5S 3E5, Canada
- Institute of Basic Biological Problems of the Russian Academy of Sciences, a Separate Subdivision of PSCBR RAS (IBP RAS), Pushchino, 142290, Russia
| | - Anna N. Khusnutdinova
- Department of Chemical Engineering and Applied Sciences, University of Toronto, Toronto, Ontario M5S 3E5, Canada
- Institute of Basic Biological Problems of the Russian Academy of Sciences, a Separate Subdivision of PSCBR RAS (IBP RAS), Pushchino, 142290, Russia
| | - Po-Hsiang Wang
- Department of Chemical Engineering and Applied Sciences, University of Toronto, Toronto, Ontario M5S 3E5, Canada
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, 152-8550, Japan
- Graduate Institute of Environmental Engineering, National Central University, Taoyuan, Taiwan
| | - Rosa Di Leo
- Department of Chemical Engineering and Applied Sciences, University of Toronto, Toronto, Ontario M5S 3E5, Canada
| | - Robert Flick
- Department of Chemical Engineering and Applied Sciences, University of Toronto, Toronto, Ontario M5S 3E5, Canada
| | - Elizabeth A. Edwards
- Department of Chemical Engineering and Applied Sciences, University of Toronto, Toronto, Ontario M5S 3E5, Canada
| | - Alexei Savchenko
- Department of Chemical Engineering and Applied Sciences, University of Toronto, Toronto, Ontario M5S 3E5, Canada
- Department of Microbiology, Immunology and Infectious Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta T2N 4N1, Canada
| | - Alexander F. Yakunin
- Department of Chemical Engineering and Applied Sciences, University of Toronto, Toronto, Ontario M5S 3E5, Canada
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Bangor, LL57 2UW, United Kingdom
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Hersch SJ, Watanabe N, Stietz MS, Manera K, Kamal F, Burkinshaw B, Lam L, Pun A, Li M, Savchenko A, Dong TG. Envelope stress responses defend against type six secretion system attacks independently of immunity proteins. Nat Microbiol 2020; 5:706-714. [PMID: 32094588 PMCID: PMC7190449 DOI: 10.1038/s41564-020-0672-6] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 01/16/2020] [Indexed: 11/23/2022]
Abstract
The arms race among microbes is a key driver in the evolution of not only the weapons but also defence mechanisms. Many gram-negative bacteria use the type six secretion system (T6SS) to deliver toxic effectors directly into neighbouring cells. Defence against effectors requires cognate immunity proteins. However, here we show immunity-independent protection mediated by envelope stress responses in Escherichia coli and Vibrio cholerae against a V. cholerae T6SS effector, TseH. We demonstrate that TseH is a PAAR-dependent species-specific effector highly potent against Aeromonas species but not against its V. cholerae immunity mutant or E. coli. Structural analysis reveals TseH is likely a NlpC/P60 family cysteine endopeptidase. We determine that two envelope stress response pathways, Rcs and BaeSR, protect E. coli from TseH toxicity by mechanisms including capsule synthesis. The two-component system WigKR (VxrAB) is critical for protecting V. cholerae from its own T6SS despite expressing immunity genes. WigR also regulates T6SS expression, suggesting a dual role in attack and defence. This deepens our understanding of how bacteria survive T6SS attacks and suggests that defending against the T6SS represents a major selective pressure driving the evolution of species-specific effectors and protective mechanisms mediated by envelope stress responses and capsule synthesis.
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Affiliation(s)
- Steven J Hersch
- Department of Ecosystem and Public Health, University of Calgary, Calgary, Canada
| | - Nobuhiko Watanabe
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Canada
| | - Maria Silvina Stietz
- Department of Ecosystem and Public Health, University of Calgary, Calgary, Canada
| | - Kevin Manera
- Department of Ecosystem and Public Health, University of Calgary, Calgary, Canada
| | - Fatima Kamal
- Department of Ecosystem and Public Health, University of Calgary, Calgary, Canada
| | - Brianne Burkinshaw
- Department of Ecosystem and Public Health, University of Calgary, Calgary, Canada
| | - Linh Lam
- Department of Ecosystem and Public Health, University of Calgary, Calgary, Canada
| | - Alexander Pun
- Department of Ecosystem and Public Health, University of Calgary, Calgary, Canada
| | - Meixin Li
- Department of Ecosystem and Public Health, University of Calgary, Calgary, Canada
| | - Alexei Savchenko
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Canada
| | - Tao G Dong
- Department of Ecosystem and Public Health, University of Calgary, Calgary, Canada. .,State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
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34
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Popov G, Evdokimova E, Stogios PJ, Savchenko A. Structure of the full-length Serratia marcescens acetyltransferase AAC(3)-Ia in complex with coenzyme A. Protein Sci 2020; 29:803-808. [PMID: 31876342 DOI: 10.1002/pro.3811] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 12/20/2019] [Accepted: 12/23/2019] [Indexed: 12/21/2022]
Abstract
Acyl-coenzyme A-dependent N-acetyltransferases (AACs) catalyze the modification of aminoglycosides rendering the bacteria carrying such enzymes resistant to this class of antibiotics. Here we present the crystal structure of AAC(3)-Ia enzyme from Serratia marcescens in complex with coenzyme A determined to 1.8 Å resolution. This enzyme served as an architype for the AAC enzymes targeting the amino group at Position 3 of aminoglycoside main aminocyclitol ring. The structure of this enzyme has been previously determined only in truncated form and was interpreted as distinct from subsequently characterized AACs. The reason for the unusual arrangement of secondary structure elements of AAC(3)-Ia was not further investigated. By determining the full-length structure of AAC(3)-Ia we establish that this enzyme adopts the canonical AAC fold conserved across this family and it does not undergo through significant rearrangement of secondary structure elements upon ligand binding as was proposed previously. In addition, our results suggest that the C-terminal tail in AAC(3)-Ia monomer forms intramolecular hydrogen bonds that contributes to formation of stable dimer, representing the predominant oligomeric state for this enzyme.
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Affiliation(s)
- Georgy Popov
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
| | - Elena Evdokimova
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada.,Center for Structural Genomics for Infectious Diseases, University of Calgary, Calgary, Canada
| | - Peter J Stogios
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada.,Center for Structural Genomics for Infectious Diseases, University of Calgary, Calgary, Canada
| | - Alexei Savchenko
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada.,Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada.,Center for Structural Genomics for Infectious Diseases, University of Calgary, Calgary, Canada
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35
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Semper C, Stogios P, Meziane-Cherif D, Evdokimova E, Courvalin P, Savchenko A. Structural characterization of aminoglycoside 4'-O-adenylyltransferase ANT(4')-IIb from Pseudomonas aeruginosa. Protein Sci 2020; 29:758-767. [PMID: 31891426 DOI: 10.1002/pro.3815] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2019] [Revised: 12/23/2019] [Accepted: 12/27/2019] [Indexed: 12/23/2022]
Abstract
Aminoglycosides were one of the first classes of broad-spectrum antibacterial drugs clinically used to effectively combat infections. The rise of resistance to these drugs, mediated by enzymatic modification, has since compromised their utility as a treatment option, prompting intensive research into the molecular function of resistance enzymes. Here, we report the crystal structure of aminoglycoside nucleotidyltransferase ANT(4')-IIb in apo and tobramycin-bound forms at a resolution of 1.6 and 2.15 Å, respectively. ANT(4')-IIb was discovered in the opportunistic pathogen Pseudomonas aeruginosa and conferred resistance to amikacin and tobramycin. Analysis of the ANT(4')-IIb structures revealed a two-domain organization featuring a mixed β-sheet and an α-helical bundle. ANT(4')-IIb monomers form a dimer required for its enzymatic activity, as coordination of the aminoglycoside substrate relies on residues contributed by both monomers. Despite harbouring appreciable primary sequence diversity compared to previously characterized homologues, the ANT(4')-IIb structure demonstrates a surprising level of structural conservation highlighting the high plasticity of this general protein fold. Site-directed mutagenesis of active site residues and kinetic analysis provides support for a catalytic mechanism similar to those of other nucleotidyltransferases. Using the molecular insights provided into this ANT(4')-IIb-represented enzymatic group, we provide a hypothesis for the potential evolutionary origin of these aminoglycoside resistance determinants.
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Affiliation(s)
- Cameron Semper
- Department of Microbiology, Immunology and Infectious Disease, University of Calgary, Calgary, Alberta, Canada
| | - Peter Stogios
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada.,Center for Structural Genomics of Infectious Diseases (CSGID)
| | | | - Elena Evdokimova
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada.,Center for Structural Genomics of Infectious Diseases (CSGID)
| | - Patrice Courvalin
- Institut Pasteur, Unité des Agents Anitbactériens, Paris Cedex, France
| | - Alexei Savchenko
- Department of Microbiology, Immunology and Infectious Disease, University of Calgary, Calgary, Alberta, Canada.,Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada.,Center for Structural Genomics of Infectious Diseases (CSGID)
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36
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Stogios PJ, Savchenko A. Molecular mechanisms of vancomycin resistance. Protein Sci 2020; 29:654-669. [PMID: 31899563 DOI: 10.1002/pro.3819] [Citation(s) in RCA: 106] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 12/30/2019] [Accepted: 01/02/2020] [Indexed: 12/18/2022]
Abstract
Vancomycin and related glycopeptides are drugs of last resort for the treatment of severe infections caused by Gram-positive bacteria such as Enterococcus species, Staphylococcus aureus, and Clostridium difficile. Vancomycin was long considered immune to resistance due to its bactericidal activity based on binding to the bacterial cell envelope rather than to a protein target as is the case for most antibiotics. However, two types of complex resistance mechanisms, each comprised of a multi-enzyme pathway, emerged and are now widely disseminated in pathogenic species, thus threatening the clinical efficiency of vancomycin. Vancomycin forms an intricate network of hydrogen bonds with the d-Ala-d-Ala region of Lipid II, interfering with the peptidoglycan layer maturation process. Resistance to vancomycin involves degradation of this natural precursor and its replacement with d-Ala-d-lac or d-Ala-d-Ser alternatives to which vancomycin has low affinity. Through extensive research over 30 years after the initial discovery of vancomycin resistance, remarkable progress has been made in molecular understanding of the enzymatic cascades responsible. Progress has been driven by structural studies of the key components of the resistance mechanisms which provided important molecular understanding such as, for example, the ability of this cascade to discriminate between vancomycin sensitive and resistant peptidoglycan precursors. Important structural insights have been also made into the molecular evolution of vancomycin resistance enzymes. Altogether this molecular data can accelerate inhibitor discovery and optimization efforts to reverse vancomycin resistance. Here, we overview our current understanding of this complex resistance mechanism with a focus on the structural and molecular aspects.
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Affiliation(s)
- Peter J Stogios
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada.,Center for Structural Genomics of Infectious Diseases (CSGID)
| | - Alexei Savchenko
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada.,Center for Structural Genomics of Infectious Diseases (CSGID).,Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
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37
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Lau CHF, DeJong EN, Dussault F, Carrillo C, Stogios PJ, Savchenko A, Topp E. A penicillin-binding protein that can promote advanced-generation cephalosporin resistance and genome adaptation in the opportunistic pathogen Pseudomonas aeruginosa. Int J Antimicrob Agents 2020; 55:105896. [PMID: 31927042 DOI: 10.1016/j.ijantimicag.2020.105896] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 12/16/2019] [Accepted: 01/04/2020] [Indexed: 11/28/2022]
Abstract
A previous soil metagenomics study recovered a novel cephalosporin resistance determinant, pbpTET A6, for which the exact resistance mechanism was unclear. This study used a three-dimensional structure-guided mutagenesis approach to demonstrate that PBPTET A6 is likely to be a class A penicillin-binding protein (PBP), and that its ability to confer cephalosporin resistance is directly linked to the functional integrity of its transpeptidase (TP) catalytic core. Screening of a library of PBPTET A6 variants carrying randomly introduced point mutations revealed additional residue modifications that compromised resistance, all of which were proximal to the TP active site except one which was found in a 29-amino-acid-long superstructure (α6-α7 loop) absent in other class A PBP homologues. Based on the site-specific mutagenesis results, it is hypothesized that residue arginine-400 plays an important role in limiting the access of certain cephalosporin compounds to the enzymatic core of the TP domain of PBPTET A6. Using a combination of adaptive evolution assays and whole-genome sequencing, the potential impact of PBPTET A6 on promoting the development of resistance in the clinically significant opportunistic pathogen Pseudomonas aeruginosa was investigated. Under the selective pressure of serial ceftazidime exposures, the pbpTET A6-expressing P. aeruginosa population readily evolved by excluding a ~400-kbp chromosomal element to acquire additional resistance against cephalosporins, suggesting that PBPTET A6 has a catalytic effect on facilitating antibiotic-resistance-associated genome adaptation. Overall, the soil environment contains genes conferring resistance to critically important antibiotics by cryptic mechanisms. Understanding what impact anthropogenic activities might have on the abundance and evolution of these genes should be a priority.
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Affiliation(s)
- Calvin Ho-Fung Lau
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, Ontario, Canada; Ottawa Laboratory (Carling), Canadian Food Inspection Agency, Ottawa, Ontario, Canada.
| | - Erica N DeJong
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, Ontario, Canada
| | - Forest Dussault
- Ottawa Laboratory (Carling), Canadian Food Inspection Agency, Ottawa, Ontario, Canada
| | - Catherine Carrillo
- Ottawa Laboratory (Carling), Canadian Food Inspection Agency, Ottawa, Ontario, Canada
| | - Peter J Stogios
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada; Center for Structural Genomics of Infectious Diseases
| | - Alexei Savchenko
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada; Center for Structural Genomics of Infectious Diseases; Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
| | - Edward Topp
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, Ontario, Canada; Department of Biology, University of Western Ontario, London, Ontario, Canada.
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38
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Fedorchuk TP, Khusnutdinova AN, Evdokimova E, Flick R, Di Leo R, Stogios P, Savchenko A, Yakunin AF. One-Pot Biocatalytic Transformation of Adipic Acid to 6-Aminocaproic Acid and 1,6-Hexamethylenediamine Using Carboxylic Acid Reductases and Transaminases. J Am Chem Soc 2020; 142:1038-1048. [PMID: 31886667 DOI: 10.1021/jacs.9b11761] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Production of platform chemicals from renewable feedstocks is becoming increasingly important due to concerns on environmental contamination, climate change, and depletion of fossil fuels. Adipic acid (AA), 6-aminocaproic acid (6-ACA) and 1,6-hexamethylenediamine (HMD) are key precursors for nylon synthesis, which are currently produced primarily from petroleum-based feedstocks. In recent years, the biosynthesis of adipic acid from renewable feedstocks has been demonstrated using both bacterial and yeast cells. Here we report the biocatalytic conversion/transformation of AA to 6-ACA and HMD by carboxylic acid reductases (CARs) and transaminases (TAs), which involves two rounds (cascades) of reduction/amination reactions (AA → 6-ACA → HMD). Using purified wild type CARs and TAs supplemented with cofactor regenerating systems for ATP, NADPH, and amine donor, we established a one-pot enzyme cascade catalyzing up to 95% conversion of AA to 6-ACA. To increase the cascade activity for the transformation of 6-ACA to HMD, we determined the crystal structure of the CAR substrate-binding domain in complex with AMP and succinate and engineered three mutant CARs with enhanced activity against 6-ACA. In combination with TAs, the CAR L342E protein showed 50-75% conversion of 6-ACA to HMD. For the transformation of AA to HMD (via 6-ACA), the wild type CAR was combined with the L342E variant and two different TAs resulting in up to 30% conversion to HMD and 70% to 6-ACA. Our results highlight the suitability of CARs and TAs for several rounds of reduction/amination reactions in one-pot cascade systems and their potential for the biobased synthesis of terminal amines.
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Affiliation(s)
- Tatiana P Fedorchuk
- Department of Chemical Engineering and Applied Chemistry , University of Toronto , Toronto , Ontario M5S 3E5 , Canada.,Institute of Basic Biological Problems , Russian Academy of Sciences , Pushchino , Moscow Region 142290 , Russia
| | - Anna N Khusnutdinova
- Department of Chemical Engineering and Applied Chemistry , University of Toronto , Toronto , Ontario M5S 3E5 , Canada.,Institute of Basic Biological Problems , Russian Academy of Sciences , Pushchino , Moscow Region 142290 , Russia
| | - Elena Evdokimova
- Department of Chemical Engineering and Applied Chemistry , University of Toronto , Toronto , Ontario M5S 3E5 , Canada
| | - Robert Flick
- Department of Chemical Engineering and Applied Chemistry , University of Toronto , Toronto , Ontario M5S 3E5 , Canada
| | - Rosa Di Leo
- Department of Chemical Engineering and Applied Chemistry , University of Toronto , Toronto , Ontario M5S 3E5 , Canada
| | - Peter Stogios
- Department of Chemical Engineering and Applied Chemistry , University of Toronto , Toronto , Ontario M5S 3E5 , Canada
| | - Alexei Savchenko
- Department of Chemical Engineering and Applied Chemistry , University of Toronto , Toronto , Ontario M5S 3E5 , Canada.,Department of Microbiology, Immunology and Infectious Diseases , University of Calgary , Calgary , Alberta T2N 4N1 , Canada
| | - Alexander F Yakunin
- Department of Chemical Engineering and Applied Chemistry , University of Toronto , Toronto , Ontario M5S 3E5 , Canada.,Centre for Environmental Biotechnology, School of Natural Sciences , Bangor University , Gwynedd LL57 2UW , U.K
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Caplan T, Lorente-Macías Á, Stogios PJ, Evdokimova E, Hyde S, Wellington MA, Liston S, Iyer KR, Puumala E, Shekhar-Guturja T, Robbins N, Savchenko A, Krysan DJ, Whitesell L, Zuercher WJ, Cowen LE. Overcoming Fungal Echinocandin Resistance through Inhibition of the Non-essential Stress Kinase Yck2. Cell Chem Biol 2020; 27:269-282.e5. [PMID: 31924499 DOI: 10.1016/j.chembiol.2019.12.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 11/20/2019] [Accepted: 12/17/2019] [Indexed: 01/12/2023]
Abstract
New strategies are urgently needed to counter the threat to human health posed by drug-resistant fungi. To explore an as-yet unexploited target space for antifungals, we screened a library of protein kinase inhibitors for the ability to reverse resistance of the most common human fungal pathogen, Candida albicans, to caspofungin, a widely used antifungal. This screen identified multiple 2,3-aryl-pyrazolopyridine scaffold compounds capable of restoring caspofungin sensitivity. Using chemical genomic, biochemical, and structural approaches, we established the target for our most potent compound as Yck2, a casein kinase 1 family member. Combination of this compound with caspofungin eradicated drug-resistant C. albicans infection while sparing co-cultured human cells. In mice, genetic depletion of YCK2 caused an ∼3-log10 decline in fungal burden in a model of systemic caspofungin-resistant C. albicans infection. Structural insights and our tool compound's profile in culture support targeting the Yck2 kinase function as a broadly active antifungal strategy.
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Affiliation(s)
- Tavia Caplan
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1M1, Canada
| | - Álvaro Lorente-Macías
- Structural Genomics Consortium, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Medicinal & Organic Chemistry and Excellence Research Unit of "Chemistry Applied to Biomedicine and the Environment", Faculty of Pharmacy, University of Granada, Campus de Cartuja s/n, 18071 Granada, Spain
| | - Peter J Stogios
- Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON M5G 1M1, Canada; Center for Structural Genomics of Infectious Diseases (CSGID), Toronto, ON, M5G 1M1, Canada
| | - Elena Evdokimova
- Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON M5G 1M1, Canada; Center for Structural Genomics of Infectious Diseases (CSGID), Toronto, ON, M5G 1M1, Canada
| | - Sabrina Hyde
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1M1, Canada
| | - Melanie A Wellington
- Departments of Pediatrics and Microbiology/Immunology, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Sean Liston
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1M1, Canada
| | - Kali R Iyer
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1M1, Canada
| | - Emily Puumala
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1M1, Canada
| | - Tanvi Shekhar-Guturja
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1M1, Canada
| | - Nicole Robbins
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1M1, Canada
| | - Alexei Savchenko
- Center for Structural Genomics of Infectious Diseases (CSGID), Toronto, ON, M5G 1M1, Canada; Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Damian J Krysan
- Departments of Pediatrics and Microbiology/Immunology, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Luke Whitesell
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1M1, Canada
| | - William J Zuercher
- Structural Genomics Consortium, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Leah E Cowen
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1M1, Canada.
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Kim T, Stogios PJ, Khusnutdinova AN, Nemr K, Skarina T, Flick R, Joo JC, Mahadevan R, Savchenko A, Yakunin AF. Rational engineering of 2-deoxyribose-5-phosphate aldolases for the biosynthesis of ( R)-1,3-butanediol. J Biol Chem 2019; 295:597-609. [PMID: 31806708 DOI: 10.1074/jbc.ra119.011363] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 12/04/2019] [Indexed: 12/14/2022] Open
Abstract
Carbon-carbon bond formation is one of the most important reactions in biocatalysis and organic chemistry. In nature, aldolases catalyze the reversible stereoselective aldol addition between two carbonyl compounds, making them attractive catalysts for the synthesis of various chemicals. In this work, we identified several 2-deoxyribose-5-phosphate aldolases (DERAs) having acetaldehyde condensation activity, which can be used for the biosynthesis of (R)-1,3-butanediol (1,3BDO) in combination with aldo-keto reductases (AKRs). Enzymatic screening of 20 purified DERAs revealed the presence of significant acetaldehyde condensation activity in 12 of the enzymes, with the highest activities in BH1352 from Bacillus halodurans, TM1559 from Thermotoga maritima, and DeoC from Escherichia coli The crystal structures of BH1352 and TM1559 at 1.40-2.50 Å resolution are the first full-length DERA structures revealing the presence of the C-terminal Tyr (Tyr224 in BH1352). The results from structure-based site-directed mutagenesis of BH1352 indicated a key role for the catalytic Lys155 and other active-site residues in the 2-deoxyribose-5-phosphate cleavage and acetaldehyde condensation reactions. These experiments also revealed a 2.5-fold increase in acetaldehyde transformation to 1,3BDO (in combination with AKR) in the BH1352 F160Y and F160Y/M173I variants. The replacement of the WT BH1352 by the F160Y or F160Y/M173I variants in E. coli cells expressing the DERA + AKR pathway increased the production of 1,3BDO from glucose five and six times, respectively. Thus, our work provides detailed insights into the molecular mechanisms of substrate selectivity and activity of DERAs and identifies two DERA variants with enhanced activity for in vitro and in vivo 1,3BDO biosynthesis.
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Affiliation(s)
- Taeho Kim
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3E5, Canada; Future Technology Center, LG Chem, Gangseo-gu, Seoul 150-721, Korea
| | - Peter J Stogios
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3E5, Canada
| | - Anna N Khusnutdinova
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3E5, Canada
| | - Kayla Nemr
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3E5, Canada
| | - Tatiana Skarina
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3E5, Canada
| | - Robert Flick
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3E5, Canada
| | - Jeong Chan Joo
- Center for Bio-Based Chemistry, Division of Convergence Chemistry, Korea Research Institute of Chemical Technology, Yuseong-gu, Daejeon 34114, Korea
| | - Radhakrishnan Mahadevan
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3E5, Canada
| | - Alexei Savchenko
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3E5, Canada; Department of Microbiology, Immunology, and Infectious Diseases, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - Alexander F Yakunin
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3E5, Canada; Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Bangor LL57 2UW, United Kingdom.
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Valleau D, Quaile AT, Cui H, Xu X, Evdokimova E, Chang C, Cuff ME, Urbanus ML, Houliston S, Arrowsmith CH, Ensminger AW, Savchenko A. Discovery of Ubiquitin Deamidases in the Pathogenic Arsenal of Legionella pneumophila. Cell Rep 2019; 23:568-583. [PMID: 29642013 DOI: 10.1016/j.celrep.2018.03.060] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 08/31/2017] [Accepted: 03/14/2018] [Indexed: 12/31/2022] Open
Abstract
Legionella pneumophila translocates the largest known arsenal of over 330 pathogenic factors, called "effectors," into host cells during infection, enabling L. pneumophila to establish a replicative niche inside diverse amebas and human macrophages. Here, we reveal that the L. pneumophila effectors MavC (Lpg2147) and MvcA (Lpg2148) are structural homologs of cycle inhibiting factor (Cif) effectors and that the adjacent gene, lpg2149, produces a protein that directly inhibits their activity. In contrast to canonical Cifs, both MavC and MvcA contain an insertion domain and deamidate the residue Gln40 of ubiquitin but not Gln40 of NEDD8. MavC and MvcA are functionally diverse, with only MavC interacting with the human E2-conjugating enzyme UBE2N (Ubc13). MavC deamidates the UBE2N∼Ub conjugate, disrupting Lys63 ubiquitination and dampening NF-κB signaling. Combined, our data reveal a molecular mechanism of host manipulation by pathogenic bacteria and highlight the complex regulatory mechanisms integral to L. pneumophila's pathogenic strategy.
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Affiliation(s)
- Dylan Valleau
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, Canada
| | - Andrew T Quaile
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, Canada
| | - Hong Cui
- The Hospital for Sick Children Research Institute and Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Xiaohui Xu
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, Canada
| | - Elena Evdokimova
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, Canada
| | - Changsoo Chang
- Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, IL, USA
| | - Marianne E Cuff
- Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, IL, USA
| | - Malene L Urbanus
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Scott Houliston
- Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada; Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Cheryl H Arrowsmith
- Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada; Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Alexander W Ensminger
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Alexei Savchenko
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, Canada; Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, AB, Canada.
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42
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Chan C, Ng D, Shah M, Watanabe N, Lai C, Savchenko A, Moraes T, Schryvers A. Structural basis of FbpA-mediated periplasmic iron transport in Moraxella catarrhalis. Acta Crystallogr A Found Adv 2019. [DOI: 10.1107/s0108767319099896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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43
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Arnal G, Stogios PJ, Asohan J, Attia MA, Skarina T, Viborg AH, Henrissat B, Savchenko A, Brumer H. Substrate specificity, regiospecificity, and processivity in glycoside hydrolase family 74. J Biol Chem 2019; 294:13233-13247. [PMID: 31324716 DOI: 10.1074/jbc.ra119.009861] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 07/16/2019] [Indexed: 12/11/2022] Open
Abstract
Glycoside hydrolase family 74 (GH74) is a historically important family of endo-β-glucanases. On the basis of early reports of detectable activity on cellulose and soluble cellulose derivatives, GH74 was originally considered to be a "cellulase" family, although more recent studies have generally indicated a high specificity toward the ubiquitous plant cell wall matrix glycan xyloglucan. Previous studies have indicated that GH74 xyloglucanases differ in backbone cleavage regiospecificities and can adopt three distinct hydrolytic modes of action: exo, endo-dissociative, and endo-processive. To improve functional predictions within GH74, here we coupled in-depth biochemical characterization of 17 recombinant proteins with structural biology-based investigations in the context of a comprehensive molecular phylogeny, including all previously characterized family members. Elucidation of four new GH74 tertiary structures, as well as one distantly related dual seven-bladed β-propeller protein from a marine bacterium, highlighted key structure-function relationships along protein evolutionary trajectories. We could define five phylogenetic groups, which delineated the mode of action and the regiospecificity of GH74 members. At the extremes, a major group of enzymes diverged to hydrolyze the backbone of xyloglucan nonspecifically with a dissociative mode of action and relaxed backbone regiospecificity. In contrast, a sister group of GH74 enzymes has evolved a large hydrophobic platform comprising 10 subsites, which facilitates processivity. Overall, the findings of our study refine our understanding of catalysis in GH74, providing a framework for future experimentation as well as for bioinformatics predictions of sequences emerging from (meta)genomic studies.
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Affiliation(s)
- Gregory Arnal
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, British Columbia V6T 1Z4, Canada
| | - Peter J Stogios
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3E5, Canada
| | - Jathavan Asohan
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, British Columbia V6T 1Z4, Canada
| | - Mohamed A Attia
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, British Columbia V6T 1Z4, Canada; Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
| | - Tatiana Skarina
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3E5, Canada
| | - Alexander Holm Viborg
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, British Columbia V6T 1Z4, Canada
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques (AFMB), CNRS, Aix-Marseille University, 13007 Marseille, France; INRA, USC1408 Architecture et Fonction des Macromolécules Biologiques (AFMB), 13007 Marseille, France
| | - Alexei Savchenko
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3E5, Canada; Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta T2N 4N1, Canada.
| | - Harry Brumer
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, British Columbia V6T 1Z4, Canada; Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada; Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada; Department of Botany, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada.
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44
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Spirin V, Malysheva V, Trichies G, Savchenko A, Põldmaa K, Nordén J, Miettinen O, Larsson KH. A preliminary overview of the corticioid Atractiellomycetes ( Pucciniomycotina, Basidiomycetes). Fungal Syst Evol 2018; 2:311-340. [PMID: 32467892 PMCID: PMC7225582 DOI: 10.3114/fuse.2018.02.09] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [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] [Indexed: 11/12/2022] Open
Abstract
The taxonomy of the corticioid fungi from the class Atractiellomycetes (Pucciniomycotina, Basidiomycetes) currently addressed to the genus Helicogloea, is revised based on morphological and nuclear ribosomal DNA (ITS and LSU) data. The genus is restricted to 25 species with semitranslucent, gelatinous basidiocarps lacking differentiated cystidia and clamps on hyphae, of which 11 are described as new to science. The asexual genus Leucogloea is placed as a synonym of Helicogloea s. str. Since the type species of Saccoblastia, S. ovispora, is combined to Helicogloea, a new genus, Saccosoma, is introduced to encompass Saccoblastia farinacea and six related species, one of which is described as new. In contrast to Helicogloea in the strict sense, the basidiocarps of Saccosoma are arid, not gelatinized, and hyphae are clamped. The third lineage of the corticioid Atractiellomycetes is represented by the Bourdotigloea vestita complex. Species of Bourdotigloea are devoid of clamps but often possess well-differentiated cystidia, as well as long, cylindrical-fusiform basidiospores. Bourdotigloea encompasses nine species, of which six are described here as new.
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Affiliation(s)
- V. Spirin
- Botany Unit (Mycology), Finnish Museum of Natural History, P.O. Box 7, FI-00014 University of Helsinki, Finland
- Natural History Museum, University of Oslo, P.O. Box 1172, Blindern, 0318 Oslo, Norway
| | - V. Malysheva
- Komarov Botanical Institute, Russian Academy of Sciences, Prof. Popova str. 2, 197376 St. Petersburg, Russia
| | - G. Trichies
- 5, Empasse des Écoles, F-57700 Neufchef, France
| | - A. Savchenko
- Institute of Ecology and Earth Sciences, University of Tartu, Lai 40, EE-51005 Tartu, Estonia
| | - K. Põldmaa
- Institute of Ecology and Earth Sciences, University of Tartu, Lai 40, EE-51005 Tartu, Estonia
| | - J. Nordén
- Norwegian Institute for Nature Research, Gaustadalléen 21, 0349 Oslo, Norway
| | - O. Miettinen
- Botany Unit (Mycology), Finnish Museum of Natural History, P.O. Box 7, FI-00014 University of Helsinki, Finland
| | - K.-H. Larsson
- Natural History Museum, University of Oslo, P.O. Box 1172, Blindern, 0318 Oslo, Norway
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Hajighasemi M, Tchigvintsev A, Nocek B, Flick R, Popovic A, Hai T, Khusnutdinova AN, Brown G, Xu X, Cui H, Anstett J, Chernikova TN, Brüls T, Le Paslier D, Yakimov MM, Joachimiak A, Golyshina OV, Savchenko A, Golyshin PN, Edwards EA, Yakunin AF. Screening and Characterization of Novel Polyesterases from Environmental Metagenomes with High Hydrolytic Activity against Synthetic Polyesters. Environ Sci Technol 2018; 52:12388-12401. [PMID: 30284819 DOI: 10.1021/acs.est.8b04252] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
The continuous growth of global plastics production, including polyesters, has resulted in increasing plastic pollution and subsequent negative environmental impacts. Therefore, enzyme-catalyzed depolymerization of synthetic polyesters as a plastics recycling approach has become a focus of research. In this study, we screened over 200 purified uncharacterized hydrolases from environmental metagenomes and sequenced microbial genomes and identified at least 10 proteins with high hydrolytic activity against synthetic polyesters. These include the metagenomic esterases MGS0156 and GEN0105, which hydrolyzed polylactic acid (PLA), polycaprolactone, as well as bis(benzoyloxyethyl)-terephthalate. With solid PLA as a substrate, both enzymes produced a mixture of lactic acid monomers, dimers, and higher oligomers as products. The crystal structure of MGS0156 was determined at 1.95 Å resolution and revealed a modified α/β hydrolase fold, with a lid domain and highly hydrophobic active site. Mutational studies of MGS0156 identified the residues critical for hydrolytic activity against both polyester and monoester substrates, with two-times higher polyesterase activity in the MGS0156 L169A mutant protein. Thus, our work identified novel, highly active polyesterases in environmental metagenomes and provided molecular insights into their activity, thereby augmenting our understanding of enzymatic polyester hydrolysis.
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Affiliation(s)
- Mahbod Hajighasemi
- Department of Chemical Engineering and Applied Chemistry , University of Toronto , Toronto , ON M5S 3E5 , Canada
| | - Anatoli Tchigvintsev
- Department of Chemical Engineering and Applied Chemistry , University of Toronto , Toronto , ON M5S 3E5 , Canada
| | - Boguslaw Nocek
- Midwest Center for Structural Genomics and Structural Biology Center, Biosciences Division , Argonne National Laboratory , Argonne , Illinois 60439 , United States
| | - Robert Flick
- Department of Chemical Engineering and Applied Chemistry , University of Toronto , Toronto , ON M5S 3E5 , Canada
| | - Ana Popovic
- Department of Chemical Engineering and Applied Chemistry , University of Toronto , Toronto , ON M5S 3E5 , Canada
| | - Tran Hai
- School of Biological Sciences , Bangor University , Gwynedd LL57 2UW , U.K
| | - Anna N Khusnutdinova
- Department of Chemical Engineering and Applied Chemistry , University of Toronto , Toronto , ON M5S 3E5 , Canada
| | - Greg Brown
- Department of Chemical Engineering and Applied Chemistry , University of Toronto , Toronto , ON M5S 3E5 , Canada
| | - Xiaohui Xu
- Department of Chemical Engineering and Applied Chemistry , University of Toronto , Toronto , ON M5S 3E5 , Canada
| | - Hong Cui
- Department of Chemical Engineering and Applied Chemistry , University of Toronto , Toronto , ON M5S 3E5 , Canada
| | - Julia Anstett
- Department of Chemical Engineering and Applied Chemistry , University of Toronto , Toronto , ON M5S 3E5 , Canada
| | | | - Thomas Brüls
- Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Direction de la Recherche Fondamentale, Institut de Génomique , Université de d'Evry Val d'Essonne (UEVE), Centre National de la Recherche Scientifique (CNRS), UMR8030, Génomique métabolique , Evry , France
| | - Denis Le Paslier
- Université de d'Evry Val d'Essonne (UEVE), Centre National de la Recherche Scientifique (CNRS) , UMR8030, Génomique métabolique, Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Direction de la Recherche Fondamentale, Institut de Génomique , Evry , France
| | - Michail M Yakimov
- Institute for Coastal Marine Environment , CNR , 98122 Messina , Italy
| | - Andrzej Joachimiak
- Midwest Center for Structural Genomics and Structural Biology Center, Biosciences Division , Argonne National Laboratory , Argonne , Illinois 60439 , United States
| | - Olga V Golyshina
- School of Biological Sciences , Bangor University , Gwynedd LL57 2UW , U.K
| | - Alexei Savchenko
- Department of Chemical Engineering and Applied Chemistry , University of Toronto , Toronto , ON M5S 3E5 , Canada
| | - Peter N Golyshin
- School of Biological Sciences , Bangor University , Gwynedd LL57 2UW , U.K
| | - Elizabeth A Edwards
- Department of Chemical Engineering and Applied Chemistry , University of Toronto , Toronto , ON M5S 3E5 , Canada
| | - Alexander F Yakunin
- Department of Chemical Engineering and Applied Chemistry , University of Toronto , Toronto , ON M5S 3E5 , Canada
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46
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Goncharik D, Goncharik D, Mrochek A, Chasnoits A, Kovalenko O, Golenischa V, Barsukevich V, Plaschinskaya L, Persidskih YU, Savchenko A. P66408 years of experience of idiopathic VA endocardial ablation in real practice. Eur Heart J 2018. [DOI: 10.1093/eurheartj/ehy566.p6640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- D Goncharik
- Republican Scientific and Practical Centre of Cardiology, Minsk, Belarus
| | - D Goncharik
- Republican Scientific and Practical Centre of Cardiology, Minsk, Belarus
| | - A Mrochek
- Republican Scientific and Practical Centre of Cardiology, Minsk, Belarus
| | - A Chasnoits
- Republican Scientific and Practical Centre of Cardiology, Minsk, Belarus
| | - O Kovalenko
- Republican Scientific and Practical Centre of Cardiology, Minsk, Belarus
| | | | - V Barsukevich
- Republican Scientific and Practical Centre of Cardiology, Minsk, Belarus
| | - L Plaschinskaya
- Republican Scientific and Practical Centre of Cardiology, Minsk, Belarus
| | - Y U Persidskih
- Republican Scientific and Practical Centre of Cardiology, Minsk, Belarus
| | - A Savchenko
- Republican Scientific and Practical Centre of Cardiology, Minsk, Belarus
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Plashchinskaya L, Goncharik D, Chasnoits A, Barsukevich V, Savchenko A, Persidskikh Y, Mrochek A. P1490Renal denervation as antiarrhythmic strategy in recurrent ventricular arrhythmias in patients with implanted cardioverter-defibrillators. Eur Heart J 2018. [DOI: 10.1093/eurheartj/ehy565.p1490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- L Plashchinskaya
- Republican Scientific and Practical Centre of Cardiology, Minsk, Belarus
| | - D Goncharik
- Republican Scientific and Practical Centre of Cardiology, Minsk, Belarus
| | - A Chasnoits
- Republican Scientific and Practical Centre of Cardiology, Minsk, Belarus
| | - V Barsukevich
- Republican Scientific and Practical Centre of Cardiology, Minsk, Belarus
| | - A Savchenko
- Republican Scientific and Practical Centre of Cardiology, Minsk, Belarus
| | - Y Persidskikh
- Republican Scientific and Practical Centre of Cardiology, Minsk, Belarus
| | - A Mrochek
- Republican Scientific and Practical Centre of Cardiology, Minsk, Belarus
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48
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Persidskikh Y, Mrochek A, Ustinova I, Sevruk T, Goncharik D, Chasnoits A, Plashchinskaya L, Barsukevich V, Rebeko E, Savchenko A. P6463Association of left atrial strain with arrhythmia recurrences in patients with persistent atrial fibrillation undergoing cardioversion. Eur Heart J 2018. [DOI: 10.1093/eurheartj/ehy566.p6463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
| | | | | | - T Sevruk
- RSPC “Cardiology”, Minsk, Belarus
| | | | | | | | | | - E Rebeko
- RSPC “Cardiology”, Minsk, Belarus
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Idrisova L, Solopova A, Savchenko A, Makacarya A, Chukanova E, Alipov V, Kapanadze D. [CERVICAL CANCER REHABILITATION: A PROSPECTIVE STUDY]. Georgian Med News 2018:17-23. [PMID: 30204088] [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] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Aim - to evaluate the rehabilitation program impact on the quality of life of оncogynecological patients and to introduce this approach in clinical practice. The study included93 reproductive-aged women, who underwent the cervical cancer treatment. Patients were divided into two groups: the experimental group, which received rehabilitation, and the control group. The thrombotic complications risk, lymphatic system condition, cognitive functions and anxiety level were assessed in all patients using special questionnaires, physical examination, and laboratory assessment. The lower limbs lymphedema was observed in 19.1% of cases in the control group and in 2.1% in the experimental group (p <0.05). According to the Moka test data, cognitive impairment level at the end of the study was 24.02 (17-30, CI: = 22.5-25.54) in the control group and 26.85 (19-30, CI: = 26.0 - 27.64) in the experimental group (p <0.05). The cognitive impairment subjective signs were significantly higher in the control group (p <0.05) as well. The anxiety level at the end of the study was 7.022 (1-19, CI: = 5.91-8.13) in the experimental group and 11.02 (4-22, CI: = 9.83-12.22) in the control group (p <0.05). At the end of the study, the following depression levels were obtained: 12.43 (5 - 21; CI: = 11.23 - 13.64) and 7.69 (1 -14; CI: = 6.77 - 8.62) in the control and the experimental group respectively (p <0.05). At the end of the study, deep vein thrombosis was observed in 21 patients in the control group (44.7%) and 7 patients in the experimental group (15.22%) (p <0.05). One patient from the control group had PATE. According to EORTC QLQ-C30, the quality of life and socialization level was significantly higher in the experimental group, while fatigue level was lower. At the end of the study, 36.2% and 76.0% of patients in the control and the experimental group respectively were employed. The rehabilitation program improves the emotional and cognitive functioning, induced menopause associated somatic disorders, quality of life, and work capacity.
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Affiliation(s)
- L Idrisova
- Federal State Autonomous Educational Institution of Higher Education I.M. Sechenov First Moscow State Medical University; Oncological Clinical Health center №1 of Moscow Department of Health, Russia
| | - A Solopova
- Federal State Autonomous Educational Institution of Higher Education I.M. Sechenov First Moscow State Medical University; Oncological Clinical Health center №1 of Moscow Department of Health, Russia
| | - A Savchenko
- Federal State Autonomous Educational Institution of Higher Education I.M. Sechenov First Moscow State Medical University; Oncological Clinical Health center №1 of Moscow Department of Health, Russia
| | - A Makacarya
- Federal State Autonomous Educational Institution of Higher Education I.M. Sechenov First Moscow State Medical University; Oncological Clinical Health center №1 of Moscow Department of Health, Russia
| | - E Chukanova
- Federal State Autonomous Educational Institution of Higher Education I.M. Sechenov First Moscow State Medical University; Oncological Clinical Health center №1 of Moscow Department of Health, Russia
| | - V Alipov
- Federal State Autonomous Educational Institution of Higher Education I.M. Sechenov First Moscow State Medical University; Oncological Clinical Health center №1 of Moscow Department of Health, Russia
| | - D Kapanadze
- Federal State Autonomous Educational Institution of Higher Education I.M. Sechenov First Moscow State Medical University; Oncological Clinical Health center №1 of Moscow Department of Health, Russia
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Cox G, Ejim L, Stogios PJ, Koteva K, Bordeleau E, Evdokimova E, Sieron AO, Savchenko A, Serio AW, Krause KM, Wright GD. Plazomicin Retains Antibiotic Activity against Most Aminoglycoside Modifying Enzymes. ACS Infect Dis 2018; 4:980-987. [PMID: 29634241 DOI: 10.1021/acsinfecdis.8b00001] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Plazomicin is a next-generation, semisynthetic aminoglycoside antibiotic currently under development for the treatment of infections due to multidrug-resistant Enterobacteriaceae. The compound was designed by chemical modification of the natural product sisomicin to provide protection from common aminoglycoside modifying enzymes that chemically alter these drugs via N-acetylation, O-adenylylation, or O-phosphorylation. In this study, plazomicin was profiled against a panel of isogenic strains of Escherichia coli individually expressing twenty-one aminoglycoside resistance enzymes. Plazomicin retained antibacterial activity against 15 of the 17 modifying enzyme-expressing strains tested. Expression of only two of the modifying enzymes, aac(2')-Ia and aph(2″)-IVa, decreased plazomicin potency. On the other hand, expression of 16S rRNA ribosomal methyltransferases results in a complete lack of plazomicin potency. In vitro enzymatic assessment confirmed that AAC(2')-Ia and APH(2'')-IVa (aminoglycoside acetyltransferase, AAC; aminoglycoside phosphotransferase, APH) were able to utilize plazomicin as a substrate. AAC(2')-Ia and APH(2'')-IVa are limited in their distribution to Providencia stuartii and Enterococci, respectively. These data demonstrate that plazomicin is not modified by a broad spectrum of common aminoglycoside modifying enzymes including those commonly found in Enterobacteriaceae. However, plazomicin is inactive in the presence of 16S rRNA ribosomal methyltransferases, which should be monitored in future surveillance programs.
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Affiliation(s)
- Georgina Cox
- M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, DeGroote School of Medicine, McMaster University, 1280 Main Street West, Hamilton, Ontario L8N 4K1, Canada
| | - Linda Ejim
- M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, DeGroote School of Medicine, McMaster University, 1280 Main Street West, Hamilton, Ontario L8N 4K1, Canada
| | - Peter J. Stogios
- Center for Structural Genomics of Infectious Diseases (CSGID) and Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5G 1L6, Canada
| | - Kalinka Koteva
- M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, DeGroote School of Medicine, McMaster University, 1280 Main Street West, Hamilton, Ontario L8N 4K1, Canada
| | - Emily Bordeleau
- M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, DeGroote School of Medicine, McMaster University, 1280 Main Street West, Hamilton, Ontario L8N 4K1, Canada
| | - Elena Evdokimova
- Center for Structural Genomics of Infectious Diseases (CSGID) and Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5G 1L6, Canada
| | - Arthur O. Sieron
- M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, DeGroote School of Medicine, McMaster University, 1280 Main Street West, Hamilton, Ontario L8N 4K1, Canada
| | - Alexei Savchenko
- Center for Structural Genomics of Infectious Diseases (CSGID) and Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5G 1L6, Canada
- Department of Microbiology, Immunology and Infectious Diseases, Health Research Innovation Centre, University of Calgary, 3330 Hospital Drive NW, HRIC-2C66, Calgary, Alberta T2N 4N1, Canada
| | - Alisa W. Serio
- Achaogen, One Tower Place, Suite 300, South San Francisco, California 94080, United States
| | - Kevin M. Krause
- Achaogen, One Tower Place, Suite 300, South San Francisco, California 94080, United States
| | - Gerard D. Wright
- M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, DeGroote School of Medicine, McMaster University, 1280 Main Street West, Hamilton, Ontario L8N 4K1, Canada
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