Structural insight into the Staphylococcus aureus ATP-driven exporter of virulent peptide toxins

Zeytuni, N.; Dickey, S. W.; Hu, J.; Chou, H. T.; Worrall, L. J.; Alexander, J. N.; Carlson, M. L.; Nosella, M.; Duong, F.; Yu, Z.; Otto, M.; Strynadka, N. J.

doi:10.1126/sciadv.abb8219

Title: Structural insight into the Staphylococcus aureus ATP-driven exporter of virulent peptide toxins

Journal Article · Fri Oct 02 00:00:00 EDT 2020 · Science Advances

DOI:https://doi.org/10.1126/sciadv.abb8219· OSTI ID:1833677

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Univ. of British Columbia, Vancouver, BC (Canada). Centre for Blood Research
National Institutes of Health (NIH), Bethesda, MD (United States). National Inst. of Allergy and Infectious Diseases, Lab. of Bacteriology
Howard Hughes Medical Inst., Ashburn, VA (United States). CryoEM Shared Resources, Janelia Research Campus
Univ. of British Columbia, Vancouver, BC (Canada). Centre for Blood Research; Univ. of British Columbia, Vancouver, BC (Canada). High Resolution Macromolecular Cryo-Electron Microscopy Facility

Staphylococcus aureus is a major human pathogen that has acquired alarming broad-spectrum antibiotic resistance. One group of secreted toxins with key roles during infection is the phenol-soluble modulins (PSMs). PSMs are amphipathic, membrane-destructive cytolytic peptides that are exported to the host-cell environment by a designated adenosine 5'-triphosphate (ATP)–binding cassette (ABC) transporter, the PSM transporter (PmtABCD). Here, we demonstrate that the minimal Pmt unit necessary for PSM export is PmtCD and provide its first atomic characterization by single-particle cryo-EM and x-ray crystallography. We have captured the transporter in the ATP-bound state at near atomic resolution, revealing a type II ABC exporter fold, with an additional cytosolic domain. Comparison to a lower-resolution nucleotide-free map displaying an “open” conformation and putative hydrophobic inner chamber of a size able to accommodate the binding of two PSM peptides provides mechanistic insight and sets the foundation for therapeutic design.

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

Sponsoring Organization:: USDOE Office of Science (SC); National Institutes of Health (NIH)

Grant/Contract Number:: AC02-06CH11357; FI2GM11999101

OSTI ID:: 1833677

Journal Information:: Science Advances, Vol. 6, Issue 40; ISSN 2375-2548

Publisher:: AAASCopyright Statement

Country of Publication:: United States

Language:: ENGLISH

References (51)

Different drugs for bad bugs: antivirulence strategies in the age of antibiotic resistance Dickey, Seth W.; Cheung, Gordon Y. C.; Otto, Michael Nature Reviews Drug Discovery, Vol. 16, Issue 7 https://doi.org/10.1038/nrd.2017.23	journal	March 2017
Architecture of a channel-forming O-antigen polysaccharide ABC transporter Bi, Yunchen; Mann, Evan; Whitfield, Chris Nature, Vol. 553, Issue 7688 https://doi.org/10.1038/nature25190	journal	January 2018
Lipid Composition of Staphylococcus aureus and Its Derived L-forms Hayami, Masaaki; Okabe, Akinobu; Kariyama, Reiko Microbiology and Immunology, Vol. 23, Issue 6 https://doi.org/10.1111/j.1348-0421.1979.tb00483.x	journal	June 1979
Genetic Classification and Distinguishing of Staphylococcus Species Based on Different Partial gap, 16S rRNA, hsp60, rpoB, sodA, and tuf Gene Sequences Ghebremedhin, B.; Layer, F.; Konig, W. Journal of Clinical Microbiology, Vol. 46, Issue 3 https://doi.org/10.1128/JCM.02058-07	journal	January 2008
Structure and mechanism of ABC transporters Wilkens, Stephan F1000Prime Reports, Vol. 7 https://doi.org/10.12703/P7-14	journal	February 2015
Structure of a bacterial multidrug ABC transporter Dawson, Roger J. P.; Locher, Kaspar P. Nature, Vol. 443, Issue 7108 https://doi.org/10.1038/nature05155	journal	August 2006
cisTEM, user-friendly software for single-particle image processing Grant, Timothy; Rohou, Alexis; Grigorieff, Nikolaus eLife, Vol. 7 https://doi.org/10.7554/eLife.35383	journal	March 2018
Allosteric ACTion: the varied ACT domains regulating enzymes of amino-acid metabolism Lang, Eric JM; Cross, Penelope J.; Mittelstädt, Gerd Current Opinion in Structural Biology, Vol. 29 https://doi.org/10.1016/j.sbi.2014.10.007	journal	December 2014
Conformation space of a heterodimeric ABC exporter under turnover conditions Hofmann, Susanne; Januliene, Dovile; Mehdipour, Ahmad R. Nature, Vol. 571, Issue 7766 https://doi.org/10.1038/s41586-019-1391-0	journal	July 2019
CTFFIND4: Fast and accurate defocus estimation from electron micrographs Rohou, Alexis; Grigorieff, Nikolaus Journal of Structural Biology, Vol. 192, Issue 2 https://doi.org/10.1016/j.jsb.2015.08.008	journal	November 2015
Impact of methionine oxidation on calmodulin structural dynamics McCarthy, Megan R.; Thompson, Andrew R.; Nitu, Florentin Biochemical and Biophysical Research Communications, Vol. 456, Issue 2 https://doi.org/10.1016/j.bbrc.2014.11.091	journal	January 2015
ABC Transporters: From Microorganisms to Man Higgins, C. F. Annual Review of Cell Biology, Vol. 8, Issue 1 https://doi.org/10.1146/annurev.cb.08.110192.000435	journal	November 1992
Structural Basis for the Lipopolysaccharide Export Activity of the Bacterial Lipopolysaccharide Transport System Hicks, Greg; Jia, Zongchao International Journal of Molecular Sciences, Vol. 19, Issue 9 https://doi.org/10.3390/ijms19092680	journal	September 2018
Crystal structures of a polypeptide processing and secretion transporter Lin, David Yin-wei; Huang, Shuo; Chen, Jue Nature, Vol. 523, Issue 7561 https://doi.org/10.1038/nature14623	journal	July 2015
New tools for automated high-resolution cryo-EM structure determination in RELION-3 Zivanov, Jasenko; Nakane, Takanori; Forsberg, Björn O. eLife, Vol. 7 https://doi.org/10.7554/eLife.42166	journal	November 2018
Staphylococcus aureus α-Toxin: Nearly a Century of Intrigue Berube, Bryan; Wardenburg, Juliane Toxins, Vol. 5, Issue 6 https://doi.org/10.3390/toxins5061140	journal	June 2013
Insight into structure-function relationship in phenol-soluble modulins using an alanine screen of the phenol-soluble modulin (PSM) α3 peptide Cheung, Gordon Y. C.; Kretschmer, Dorothee; Queck, Shu Y. The FASEB Journal, Vol. 28, Issue 1 https://doi.org/10.1096/fj.13-232041	journal	January 2014
UCSF Chimera?A visualization system for exploratory research and analysis Pettersen, Eric F.; Goddard, Thomas D.; Huang, Conrad C. Journal of Computational Chemistry, Vol. 25, Issue 13 https://doi.org/10.1002/jcc.20084	journal	January 2004
Essential Staphylococcus aureus toxin export system Chatterjee, Som S.; Joo, Hwang-Soo; Duong, Anthony C. Nature Medicine, Vol. 19, Issue 3 https://doi.org/10.1038/nm.3047	journal	February 2013
Identification of novel cytolytic peptides as key virulence determinants for community-associated MRSA Wang, Rong; Braughton, Kevin R.; Kretschmer, Dorothee Nature Medicine, Vol. 13, Issue 12 https://doi.org/10.1038/nm1656	journal	November 2007
Cryo-EM structures of a human ABCG2 mutant trapped in ATP-bound and substrate-bound states Manolaridis, Ioannis; Jackson, Scott M.; Taylor, Nicholas M. I. Nature, Vol. 563, Issue 7731 https://doi.org/10.1038/s41586-018-0680-3	journal	November 2018
Inducible production and cellular location of the epidermin biosynthetic enzyme EpiB using an improved staphylococcal expression system Peschel, Andreas; OttenwÃ¤lder, Birgit; GÃ¶tz, Friedrich FEMS Microbiology Letters, Vol. 137, Issue 2-3 https://doi.org/10.1111/j.1574-6968.1996.tb08119.x	journal	April 1996
Nanodiscs for structural and functional studies of membrane proteins Denisov, Ilia G.; Sligar, Stephen G. Nature Structural & Molecular Biology, Vol. 23, Issue 6 https://doi.org/10.1038/nsmb.3195	journal	June 2016
Phenol-soluble modulins – critical determinants of staphylococcal virulence Cheung, Gordon Y. C.; Joo, Hwang-Soo; Chatterjee, Som S. FEMS Microbiology Reviews, Vol. 38, Issue 4 https://doi.org/10.1111/1574-6976.12057	journal	July 2014
Structural basis of lipopolysaccharide extraction by the LptB2FGC complex Li, Yanyan; Orlando, Benjamin J.; Liao, Maofu Nature, Vol. 567, Issue 7749 https://doi.org/10.1038/s41586-019-1025-6	journal	March 2019
Inward facing conformations of the MetNI methionine ABC transporter: Implications for the mechanism of transinhibition: Inward Facing Conformations of the MetNI ABC Transporter Johnson, Eric; Nguyen, Phong T.; Yeates, Todd O. Protein Science, Vol. 21, Issue 1 https://doi.org/10.1002/pro.765	journal	December 2011
Membrane reconstitution of ABC transporters and assays of translocator function Geertsma, Eric R.; Nik Mahmood, N. A. B.; Schuurman-Wolters, Gea K. Nature Protocols, Vol. 3, Issue 2 https://doi.org/10.1038/nprot.2007.519	journal	January 2008
Invasive Methicillin-Resistant <EMPH TYPE="ITAL">Staphylococcus aureus</EMPH> Infections in the United States Klevens, R. Monina JAMA, Vol. 298, Issue 15 https://doi.org/10.1001/jama.298.15.1763	journal	October 2007
Mechanism of Gene Regulation by a Staphylococcus aureus Toxin Joo, Hwang-Soo; Chatterjee, Som S.; Villaruz, Amer E. mBio, Vol. 7, Issue 5 https://doi.org/10.1128/mBio.01579-16	journal	November 2016
A lipid gating mechanism for the channel-forming O antigen ABC transporter Caffalette, Christopher A.; Corey, Robin A.; Sansom, Mark S. P. Nature Communications, Vol. 10, Issue 1 https://doi.org/10.1038/s41467-019-08646-8	journal	February 2019
Antimicrobial Peptide Resistance Mechanism Contributes to Staphylococcus aureus Infection Cheung, Gordon Y. C.; Fisher, Emilie L.; McCausland, Joshua W. The Journal of Infectious Diseases, Vol. 217, Issue 7 https://doi.org/10.1093/infdis/jiy024	journal	January 2018
Noncanonical role for the binding protein in substrate uptake by the MetNI methionine ATP Binding Cassette (ABC) transporter Nguyen, Phong T.; Lai, Jeffrey Y.; Lee, Allen T. Proceedings of the National Academy of Sciences, Vol. 115, Issue 45 https://doi.org/10.1073/pnas.1811003115	journal	October 2018
Crystal structure of the human sterol transporter ABCG5/ABCG8 Lee, Jyh-Yeuan; Kinch, Lisa N.; Borek, Dominika M. Nature, Vol. 533, Issue 7604 https://doi.org/10.1038/nature17666	journal	May 2016
MolProbity : all-atom structure validation for macromolecular crystallography Chen, Vincent B.; Arendall, W. Bryan; Headd, Jeffrey J. Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 1 https://doi.org/10.1107/S0907444909042073	journal	December 2009
Automatic protein structure solution from weak X-ray data Skubák, Pavol; Pannu, Navraj S. Nature Communications, Vol. 4, Issue 1 https://doi.org/10.1038/ncomms3777	journal	November 2013
Features and development of Coot Emsley, P.; Lohkamp, B.; Scott, W. G. Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 4 https://doi.org/10.1107/S0907444910007493	journal	March 2010
The toxic shock syndrome exotoxin structural gene is not detectably transmitted by a prophage Kreiswirth, Barry N.; Löfdahl, Sven; Betley, Marsha J. Nature, Vol. 305, Issue 5936 https://doi.org/10.1038/305709a0	journal	October 1983
EMRinger: side chain–directed model and map validation for 3D cryo-electron microscopy Barad, Benjamin A.; Echols, Nathaniel; Wang, Ray Yu-Ruei Nature Methods, Vol. 12, Issue 10 https://doi.org/10.1038/nmeth.3541	journal	August 2015
Staphylococcus epidermidis surfactant peptides promote biofilm maturation and dissemination of biofilm-associated infection in mice Wang, Rong; Khan, Burhan A.; Cheung, Gordon Y. C. Journal of Clinical Investigation, Vol. 121, Issue 1 https://doi.org/10.1172/JCI42520	journal	January 2011
Structural and Mutational Analysis of the SBDS Protein Family Shammas, Camille; Menne, Tobias F.; Hilcenko, Christine Journal of Biological Chemistry, Vol. 280, Issue 19 https://doi.org/10.1074/jbc.M414656200	journal	May 2005
Structure of the Human Lipid Exporter ABCA1 Qian, Hongwu; Zhao, Xin; Cao, Pingping Cell, Vol. 169, Issue 7 https://doi.org/10.1016/j.cell.2017.05.020	journal	June 2017
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
Refinement of Protein Structures into Low-Resolution Density Maps Using Rosetta DiMaio, Frank; Tyka, Michael D.; Baker, Matthew L. Journal of Molecular Biology, Vol. 392, Issue 1 https://doi.org/10.1016/j.jmb.2009.07.008	journal	September 2009
Diversity in ABC transporters: Type I, II and III importers Rice, Austin J.; Park, Aekyung; Pinkett, Heather W. Critical Reviews in Biochemistry and Molecular Biology, Vol. 49, Issue 5 https://doi.org/10.3109/10409238.2014.953626	journal	June 2014
Phenol-soluble modulins and staphylococcal infection Peschel, Andreas; Otto, Michael Nature Reviews Microbiology, Vol. 11, Issue 10 https://doi.org/10.1038/nrmicro3110	journal	September 2013
Staphylococcus epidermidis — the 'accidental' pathogen Otto, Michael Nature Reviews Microbiology, Vol. 7, Issue 8 https://doi.org/10.1038/nrmicro2182	journal	August 2009
Automated electron microscope tomography using robust prediction of specimen movements Mastronarde, David N. Journal of Structural Biology, Vol. 152, Issue 1 https://doi.org/10.1016/j.jsb.2005.07.007	journal	October 2005
cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination Punjani, Ali; Rubinstein, John L.; Fleet, David J. Nature Methods, Vol. 14, Issue 3 https://doi.org/10.1038/nmeth.4169	journal	February 2017
[20] Processing of X-ray diffraction data collected in oscillation mode Otwinowski, Zbyszek; Minor, Wladek Macromolecular Crystallography Part A, 307-326 https://doi.org/10.1016/S0076-6879(97)76066-X	book	January 1997
The cytotoxic Staphylococcus aureus PSMα3 reveals a cross-α amyloid-like fibril Tayeb-Fligelman, Einav; Tabachnikov, Orly; Moshe, Asher Science, Vol. 355, Issue 6327 https://doi.org/10.1126/science.aaf4901	journal	February 2017
The Peptidisc, a simple method for stabilizing membrane proteins in detergent-free solution Carlson, Michael Luke; Young, John William; Zhao, Zhiyu eLife, Vol. 7 https://doi.org/10.7554/eLife.34085	journal	August 2018

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