Structural and Functional Survey of Environmental Aminoglycoside Acetyltransferases Reveals Functionality of Resistance Enzymes

Xu, Zhiyu; Stogios, Peter J.; Quaile, Andrew T.; Forsberg, Kevin J.; Patel, Sanket; Skarina, Tatiana; Houliston, Scott; Arrowsmith, Cheryl; Dantas, Gautam; Savchenko, Alexei

doi:10.1021/acsinfecdis.7b00068

Structural and Functional Survey of Environmental Aminoglycoside Acetyltransferases Reveals Functionality of Resistance Enzymes

Journal Article · Sun Jul 30 00:00:00 EDT 2017 · ACS Infectious Diseases

DOI:https://doi.org/10.1021/acsinfecdis.7b00068· OSTI ID:1544871

Xu, Zhiyu ^[1]; Stogios, Peter J. ^[2]; Quaile, Andrew T. ^[1]; Forsberg, Kevin J. ^[3]; Patel, Sanket ^[3]; Skarina, Tatiana ^[2]; Houliston, Scott ^[1]; Arrowsmith, Cheryl ^[1]; Dantas, Gautam ^[4]; ^[2]

Univ. of Toronto, ON (Canada)
Univ. of Toronto, ON (Canada); Health Research Innovation Center, Calgary, AB (Canada)
Washington Univ. School of Medicine, St. Louis, MO (United States)
Washington Univ. School of Medicine, St. Louis, MO (United States); Washington Univ., St. Louis, MO (United States)

Aminoglycoside N-acetyltransferases (AACs) confer resistance against the clinical use of aminoglycoside antibiotics. The origin of AACs can be traced to environmental microbial species representing a vast reservoir for new and emerging resistance enzymes, which are currently undercharacterized. In this work, we performed detailed structural characterization and functional analyses of four metagenomic AAC (meta-AACs) enzymes recently identified in a survey of agricultural and grassland soil microbiomes (Forsberg et al. Nature 2014, 509, 612). These enzymes are new members of the Gcn5-Related-N-Acetyltransferase superfamily and confer resistance to the aminoglycosides gentamicin C, sisomicin, and tobramycin. Moreover, the meta-AAC0020 enzyme demonstrated activity comparable with an AAC(3)-I enzyme that serves as a model AAC enzyme identified in a clinical bacterial isolate. The crystal structure of meta-AAC0020 in complex with sisomicin confirmed an unexpected AAC(6') regiospecificity of this enzyme and revealed a drug binding mechanism distinct from previously characterized AAC(6') enzymes. Together, our data highlights the presence of highly active antibiotic-modifying enzymes in the environmental microbiome and reveals unexpected diversity in substrate specificity. These observations of additional AAC enzymes must be considered in the search for novel aminoglycosides less prone to resistance.

View Accepted Manuscript (DOE)

Research Organization:: Argonne National Laboratory (ANL), Argonne, IL (United States). Advanced Photon Source (APS)

Sponsoring Organization:: National Human Genome Research Institute (NHGRI); National Institute of Allergy and Infectious Diseases (NIAID); National Institute of General Medical Sciences (NIGMS); National Institutes of Health (NIH)

OSTI ID:: 1544871

Journal Information:: ACS Infectious Diseases, Journal Name: ACS Infectious Diseases Journal Issue: 9 Vol. 3; ISSN 2373-8227

Publisher:: American Chemical Society (ACS)Copyright Statement

Country of Publication:: United States

Language:: ENGLISH

References (26)

New LIC vectors for production of proteins from genes containing rare codons Eschenfeldt, William H.; Makowska-Grzyska, Magdalena; Stols, Lucy Journal of Structural and Functional Genomics, Vol. 14, Issue 4 https://doi.org/10.1007/s10969-013-9163-9	journal	September 2013
Crystal Structure of a GCN5-Related N-acetyltransferase Wolf, Eva; Vassilev, Alex; Makino, Yasutaka Cell, Vol. 94, Issue 4 https://doi.org/10.1016/S0092-8674(00)81585-8	journal	August 1998
Aminoglycoside modifying enzymes Ramirez, Maria S.; Tolmasky, Marcelo E. Drug Resistance Updates, Vol. 13, Issue 6 https://doi.org/10.1016/j.drup.2010.08.003	journal	December 2010
Inference of Macromolecular Assemblies from Crystalline State Krissinel, Evgeny; Henrick, Kim Journal of Molecular Biology, Vol. 372, Issue 3 https://doi.org/10.1016/j.jmb.2007.05.022	journal	September 2007
Bacterial GCN5-Related N -Acetyltransferases: From Resistance to Regulation Favrot, Lorenza; Blanchard, John S.; Vergnolle, Olivia Biochemistry, Vol. 55, Issue 7 https://doi.org/10.1021/acs.biochem.5b01269	journal	February 2016
Structural and Biochemical Characterization of Acinetobacter spp. Aminoglycoside Acetyltransferases Highlights Functional and Evolutionary Variation among Antibiotic Resistance Enzymes Stogios, Peter J.; Kuhn, Misty L.; Evdokimova, Elena ACS Infectious Diseases, Vol. 3, Issue 2 https://doi.org/10.1021/acsinfecdis.6b00058	journal	November 2016
Kinetic and Mutagenic Characterization of the Chromosomally Encoded Salmonella enterica AAC(6‘)-Iy Aminoglycoside N -Acetyltransferase ^† Magnet, Sophie; Lambert, Thierry; Courvalin, Patrice Biochemistry, Vol. 40, Issue 12 https://doi.org/10.1021/bi002736e	journal	March 2001
Mechanistic and Structural Analysis of Aminoglycoside N -Acetyltransferase AAC(6′)-Ib and Its Bifunctional, Fluoroquinolone-Active AAC(6′)-Ib-cr Variant ^† ^‡ Vetting, Matthew W.; Park, Chi Hye; Hegde, Subray S. Biochemistry, Vol. 47, Issue 37 https://doi.org/10.1021/bi800664x	journal	September 2008
Aminoglycoside Antibiotics in the 21st Century Becker, Bernd; Cooper, Matthew A. ACS Chemical Biology, Vol. 8, Issue 1 https://doi.org/10.1021/cb3005116	journal	November 2012
Bacterial phylogeny structures soil resistomes across habitats Forsberg, Kevin J.; Patel, Sanket; Gibson, Molly K. Nature, Vol. 509, Issue 7502 https://doi.org/10.1038/nature13377	journal	May 2014
Fungal Rtt109 histone acetyltransferase is an unexpected structural homolog of metazoan p300/CBP Tang, Yong; Holbert, Marc A.; Wurtele, Hugo Nature Structural & Molecular Biology, Vol. 15, Issue 7 https://doi.org/10.1038/nsmb.1448	journal	June 2008
Structure-guided optimization of protein kinase inhibitors reverses aminoglycoside antibiotic resistance Stogios, Peter J.; Spanogiannopoulos, Peter; Evdokimova, Elena Biochemical Journal, Vol. 454, Issue 2 https://doi.org/10.1042/BJ20130317	journal	August 2013
Complete ¹ H and ¹³ C NMR Chemical Shift Assignments for Some N-Polyformylated Aminoglycoside Antibiotics Eneva, Galya I.; Spassov, Stefan L.; Haimova, Marietta A. Spectroscopy Letters, Vol. 28, Issue 1 https://doi.org/10.1080/00387019508011655	journal	January 1995
Antibiotic Susceptibility Testing by a Standardized Single Disk Method Bauer, A. W.; Kirby, W. M. M.; Sherris, J. C. American Journal of Clinical Pathology, Vol. 45, Issue 4_ts https://doi.org/10.1093/ajcp/45.4_ts.493	journal	April 1966
MrBayes 3: Bayesian phylogenetic inference under mixed models Ronquist, Fredrik; Huelsenbeck, John P. Bioinformatics, Vol. 19, Issue 12, p. 1572-1574 https://doi.org/10.1093/bioinformatics/btg180	journal	August 2003
CASTp: computed atlas of surface topography of proteins with structural and topographical mapping of functionally annotated residues Dundas, J.; Ouyang, Z.; Tseng, J. Nucleic Acids Research, Vol. 34, Issue Web Server https://doi.org/10.1093/nar/gkl282	journal	July 2006
Coot model-building tools for molecular graphics Emsley, Paul; Cowtan, Kevin Acta Crystallographica Section D Biological Crystallography, Vol. 60, Issue 12, p. 2126-2132 https://doi.org/10.1107/S0907444904019158	journal	November 2004
HKL -3000: the integration of data reduction and structure solution – from diffraction images to an initial model in minutes Minor, Wladek; Cymborowski, Marcin; Otwinowski, Zbyszek Acta Crystallographica Section D Biological Crystallography, Vol. 62, Issue 8 https://doi.org/10.1107/S0907444906019949	journal	July 2006
XDS Kabsch, Wolfgang Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2 https://doi.org/10.1107/S0907444909047337	journal	January 2010
PHENIX: a comprehensive Python-based system for macromolecular structure solution Adams, Paul D.; Afonine, Pavel V.; Bunkóczi, Gábor Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2, p. 213-221 https://doi.org/10.1107/S0907444909052925	journal	January 2010
Overview of the CCP 4 suite and current developments Winn, Martyn D.; Ballard, Charles C.; Cowtan, Kevin D. Acta Crystallographica Section D Biological Crystallography, Vol. 67, Issue 4 https://doi.org/10.1107/S0907444910045749	journal	March 2011
Characterization of the chromosomal aac(6')-Ii gene specific for Enterococcus faecium. Costa, Y.; Galimand, M.; Leclercq, R. Antimicrobial Agents and Chemotherapy, Vol. 37, Issue 9 https://doi.org/10.1128/AAC.37.9.1896	journal	September 1993
Cloning and characterization of a 3-N-aminoglycoside acetyltransferase gene, aac(3)-Ib, from Pseudomonas aeruginosa Schwocho, L. R.; Schaffner, C. P.; Miller, G. H. Antimicrobial Agents and Chemotherapy, Vol. 39, Issue 8 https://doi.org/10.1128/AAC.39.8.1790	journal	August 1995
Aminoglycoside therapy in infectious diseases Poulikakos, Panagiotis; Falagas, Matthew E. Expert Opinion on Pharmacotherapy, Vol. 14, Issue 12 https://doi.org/10.1517/14656566.2013.806486	journal	May 2013
Novel resistance functions uncovered using functional metagenomic investigations of resistance reservoirs Pehrsson, Erica C.; Forsberg, Kevin J.; Gibson, Molly K. Frontiers in Microbiology, Vol. 4 https://doi.org/10.3389/fmicb.2013.00145	journal	January 2013
Dissemination of Antimicrobial Resistance in Microbial Ecosystems through Horizontal Gene Transfer von Wintersdorff, Christian J. H.; Penders, John; van Niekerk, Julius M. Frontiers in Microbiology, Vol. 7 https://doi.org/10.3389/fmicb.2016.00173	journal	February 2016

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Structure of the full‐length Serratia marcescens acetyltransferase AAC(3)‐Ia in complex with coenzyme A Popov, Georgy; Evdokimova, Elena; Stogios, Peter J. Protein Science, Vol. 29, Issue 3 https://doi.org/10.1002/pro.3811	journal	January 2020

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60 APPLIED LIFE SCIENCES
acetyltransferase
aminoglycosides
antibiotic resistance
crystal structure
environmental
resistome

Structural and Functional Survey of Environmental Aminoglycoside Acetyltransferases Reveals Functionality of Resistance Enzymes

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References (26)

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