Staphylococcus aureus FtsZ and PBP4 bind to the conformationally dynamic N-terminal domain of GpsB

Sacco, Michael D.; Hammond, Lauren R.; Noor, Radwan E.; Bhattacharya, Dipanwita; McKnight, Lily J.; Madsen, Jesper J.; Zhang, Xiujun; Butler, Shane G.; Kemp, M. Trent; Jaskolka-Brown, Aiden C.; Khan, Sebastian J.; Gelis, Ioannis; Eswara, Prahathees; Chen, Yu

doi:10.7554/elife.85579

Title: Staphylococcus aureus FtsZ and PBP4 bind to the conformationally dynamic N-terminal domain of GpsB

Journal Article · 18 April 2024 · eLife

DOI: https://doi.org/10.7554/elife.85579 · OSTI ID:2470217

^[1]; Hammond, Lauren R. ^[1]; Noor, Radwan E. ^[1];

^[1]; McKnight, Lily J. ^[1];

^[1]; Zhang, Xiujun ^[1]; Butler, Shane G. ^[1]; Kemp, M. Trent ^[1]; Jaskolka-Brown, Aiden C. ^[1]; Khan, Sebastian J. ^[1]; Gelis, Ioannis ^[1];

^[1];

^[1]

University of South Florida, Tampa, FL (United States)

In the Firmicutes phylum, GpsB is a membrane associated protein that coordinates peptidoglycan synthesis with cell growth and division. Although GpsB has been studied in several bacteria, the structure, function, and interactome of Staphylococcus aureus GpsB is largely uncharacterized. To address this knowledge gap, we solved the crystal structure of the N-terminal domain of S. aureus GpsB, which adopts an atypical, asymmetric dimer, and demonstrates major conformational flexibility that can be mapped to a hinge region formed by a three-residue insertion exclusive to Staphylococci. When this three-residue insertion is excised, its thermal stability increases, and the mutant no longer produces a previously reported lethal phenotype when overexpressed in Bacillus subtilis. In S. aureus, we show that these hinge mutants are less functional and speculate that the conformational flexibility imparted by the hinge region may serve as a dynamic switch to fine-tune the function of the GpsB complex and/or to promote interaction with its various partners. Furthermore, we provide the first biochemical, biophysical, and crystallographic evidence that the N-terminal domain of GpsB binds not only PBP4, but also FtsZ, through a conserved recognition motif located on their C-termini, thus coupling peptidoglycan synthesis to cell division. Taken together, the unique structure of S. aureus GpsB and its direct interaction with FtsZ/PBP4 provide deeper insight into the central role of GpsB in S. aureus cell division.

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

Sponsoring Organization:: National Institutes of Health (NIH); USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: AC02-06CH11357

OSTI ID:: 2470217

Journal Information:: eLife, Journal Name: eLife Vol. 13; ISSN 2050-084X

Publisher:: eLife Sciences Publications, Ltd.Copyright Statement

Country of Publication:: United States

Language:: English

References (63)

Comparative Protein Structure Modeling Using Modeller Eswar, Narayanan; Webb, Ben; Marti-Renom, Marc A. Current Protocols in Bioinformatics, Vol. 15, Issue 1 https://doi.org/10.1002/0471250953.bi0506s15	journal	September 2006
Bacterial cytokinesis: From Z ring to divisome Lutkenhaus, Joe; Pichoff, Sebastien; Du, Shishen Cytoskeleton, Vol. 69, Issue 10 https://doi.org/10.1002/cm.21054	journal	August 2012
CHARMM-GUI: A web-based graphical user interface for CHARMM Jo, Sunhwan; Kim, Taehoon; Iyer, Vidyashankara G. Journal of Computational Chemistry, Vol. 29, Issue 11 https://doi.org/10.1002/jcc.20945	journal	March 2008
CHARMM: The biomolecular simulation program Brooks, B. R.; Brooks, C. L.; Mackerell, A. D. Journal of Computational Chemistry, Vol. 30, Issue 10 https://doi.org/10.1002/jcc.21287	journal	July 2009
NMRPipe: A multidimensional spectral processing system based on UNIX pipes Delaglio, Frank; Grzesiek, Stephan; Vuister, GeertenW. Journal of Biomolecular NMR, Vol. 6, Issue 3 https://doi.org/10.1007/BF00197809	journal	November 1995
GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers Abraham, Mark James; Murtola, Teemu; Schulz, Roland SoftwareX, Vol. 1-2 https://doi.org/10.1016/j.softx.2015.06.001	journal	September 2015
The bacterial two-hybrid system based on adenylate cyclase reconstitution in Escherichia coli Battesti, Aurélia; Bouveret, Emmanuelle Methods, Vol. 58, Issue 4 https://doi.org/10.1016/j.ymeth.2012.07.018	journal	December 2012
CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field Lee, Jumin; Cheng, Xi; Swails, Jason M. Journal of Chemical Theory and Computation, Vol. 12, Issue 1 https://doi.org/10.1021/acs.jctc.5b00935	journal	December 2015
A Membrane Protein, EzrA, Regulates Assembly Dynamics of FtsZ by Interacting with the C-Terminal Tail of FtsZ Singh, Jay Kumar; Makde, Ravindra D.; Kumar, Vinay Biochemistry, Vol. 46, Issue 38 https://doi.org/10.1021/bi700710j	journal	August 2007
Inhibition of WTA Synthesis Blocks the Cooperative Action of PBPs and Sensitizes MRSA to β-Lactams Farha, Maya A.; Leung, Alexander; Sewell, Edward W. ACS Chemical Biology, Vol. 8, Issue 1 https://doi.org/10.1021/cb300413m	journal	October 2012
Rapid and Efficient Genome Editing in Staphylococcus aureus by Using an Engineered CRISPR/Cas9 System Chen, Weizhong; Zhang, Yifei; Yeo, Won-Sik Journal of the American Chemical Society, Vol. 139, Issue 10 https://doi.org/10.1021/jacs.6b13317	journal	March 2017
The complete genome sequence of the Gram-positive bacterium Bacillus subtilis Kunst, F.; Ogasawara, N.; Moszer, I. Nature, Vol. 390, Issue 6657 https://doi.org/10.1038/36786	journal	November 1997
Features critical for membrane binding revealed by DivIVA crystal structure Oliva, Maria A.; Halbedel, Sven; Freund, Stefan M. The EMBO Journal, Vol. 29, Issue 12 https://doi.org/10.1038/emboj.2010.99	journal	May 2010
MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets Steinegger, Martin; Söding, Johannes Nature Biotechnology, Vol. 35, Issue 11 https://doi.org/10.1038/nbt.3988	journal	October 2017
CHARMM36m: an improved force field for folded and intrinsically disordered proteins Huang, Jing; Rauscher, Sarah; Nawrocki, Grzegorz Nature Methods, Vol. 14, Issue 1 https://doi.org/10.1038/nmeth.4067	journal	November 2016
The cell cycle regulator GpsB functions as cytosolic adaptor for multiple cell wall enzymes Cleverley, Robert M.; Rutter, Zoe J.; Rismondo, Jeanine Nature Communications, Vol. 10, Issue 1 https://doi.org/10.1038/s41467-018-08056-2	journal	January 2019
SEDS–bPBP pairs direct lateral and septal peptidoglycan synthesis in Staphylococcus aureus Reichmann, Nathalie T.; Tavares, Andreia C.; Saraiva, Bruno M. Nature Microbiology, Vol. 4, Issue 8 https://doi.org/10.1038/s41564-019-0437-2	journal	May 2019
ColabFold: making protein folding accessible to all Mirdita, Milot; Schütze, Konstantin; Moriwaki, Yoshitaka Nature Methods, Vol. 19, Issue 6 https://doi.org/10.1038/s41592-022-01488-1	journal	May 2022
Narrow-spectrum antibacterial agents Melander, Roberta J.; Zurawski, Daniel V.; Melander, Christian MedChemComm, Vol. 9, Issue 1 https://doi.org/10.1039/C7MD00528H	journal	January 2018
Polymorphic transitions in single crystals: A new molecular dynamics method Parrinello, M.; Rahman, A. Journal of Applied Physics, Vol. 52, Issue 12 https://doi.org/10.1063/1.328693	journal	December 1981
Comparison of simple potential functions for simulating liquid water Jorgensen, William L.; Chandrasekhar, Jayaraman; Madura, Jeffry D. The Journal of Chemical Physics, Vol. 79, Issue 2 https://doi.org/10.1063/1.445869	journal	July 1983
A unified formulation of the constant temperature molecular dynamics methods Nosé, Shuichi The Journal of Chemical Physics, Vol. 81, Issue 1 https://doi.org/10.1063/1.447334	journal	July 1984
Particle mesh Ewald: An N ⋅log( N ) method for Ewald sums in large systems Darden, Tom; York, Darrin; Pedersen, Lee The Journal of Chemical Physics, Vol. 98, Issue 12 https://doi.org/10.1063/1.464397	journal	June 1993
Teichoic acids are temporal and spatial regulators of peptidoglycan cross-linking in Staphylococcus aureus Atilano, M. L.; Pereira, P. M.; Yates, J. Proceedings of the National Academy of Sciences, Vol. 107, Issue 44 https://doi.org/10.1073/pnas.1004304107	journal	October 2010
Extreme C Terminus of Bacterial Cytoskeletal Protein FtsZ Plays Fundamental Role in Assembly Independent of Modulatory Proteins Buske, Paul J.; Levin, Petra Anne Journal of Biological Chemistry, Vol. 287, Issue 14 https://doi.org/10.1074/jbc.M111.330324	journal	March 2012
Constant pressure molecular dynamics for molecular systems Nosé, Shuichi; Klein, M. L. Molecular Physics, Vol. 50, Issue 5 https://doi.org/10.1080/00268978300102851	journal	December 1983
A molecular dynamics method for simulations in the canonical ensemble Nosé, Shūichi Molecular Physics, Vol. 52, Issue 2 https://doi.org/10.1080/00268978400101201	journal	June 1984
Subunit Arrangement in GpsB, a Regulator of Cell Wall Biosynthesis Cleverley, Robert M.; Rismondo, Jeanine; Lockhart-Cairns, Michael P. Microbial Drug Resistance, Vol. 22, Issue 6 https://doi.org/10.1089/mdr.2016.0050	journal	September 2016
AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models Varadi, Mihaly; Anyango, Stephen; Deshpande, Mandar Nucleic Acids Research, Vol. 50, Issue D1 https://doi.org/10.1093/nar/gkab1061	journal	November 2021
Protein complex prediction with AlphaFold-Multimer Evans, Richard; O???Neill, Michael; Pritzel, Alexander https://doi.org/10.1101/2021.10.04.463034	preprint	March 2022
Canonical dynamics: Equilibrium phase-space distributions Hoover, William G. Physical Review A, Vol. 31, Issue 3 https://doi.org/10.1103/PhysRevA.31.1695	journal	March 1985
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
iMOSFLM : a new graphical interface for diffraction-image processing with MOSFLM Battye, T. Geoff G.; Kontogiannis, Luke; Johnson, Owen Acta Crystallographica Section D Biological Crystallography, Vol. 67, Issue 4 https://doi.org/10.1107/S0907444910048675	journal	March 2011
How good are my data and what is the resolution? Evans, Philip R.; Murshudov, Garib N. Acta Crystallographica Section D Biological Crystallography, Vol. 69, Issue 7 https://doi.org/10.1107/S0907444913000061	journal	June 2013
Rigidity versus flexibility: the dilemma of understanding protein thermal stability Karshikoff, Andrey; Nilsson, Lennart; Ladenstein, Rudolf FEBS Journal, Vol. 282, Issue 20 https://doi.org/10.1111/febs.13343	journal	July 2015
Control of the cell elongation–division cycle by shuttling of PBP1 protein in Bacillus subtilis Claessen, Dennis; Emmins, Robyn; Hamoen, Leendert W. Molecular Microbiology, Vol. 68, Issue 4 https://doi.org/10.1111/j.1365-2958.2008.06210.x	journal	March 2008
Multiple essential roles for EzrA in cell division of Staphylococcus aureus Steele, Victoria R.; Bottomley, Amy L.; Garcia‐Lara, Jorge Molecular Microbiology, Vol. 80, Issue 2 https://doi.org/10.1111/j.1365-2958.2011.07591.x	journal	March 2011
A Role in vivo for Penicillin-Binding Protein-4 of Staphylococcus aureus Wyke, Anne W.; Ward, J. Barrie; Hayes, Michael V. European Journal of Biochemistry, Vol. 119, Issue 2 https://doi.org/10.1111/j.1432-1033.1981.tb05620.x	journal	October 1981
Peptidoglycan cross‐linking in Staphylococcus aureus Snowden, Michael A.; Perkins, Harold R. European Journal of Biochemistry, Vol. 191, Issue 2 https://doi.org/10.1111/j.1432-1033.1990.tb19132.x	journal	July 1990
Structure of the bacterial cell division determinant GpsB and its interaction with penicillin‐binding proteins Rismondo, Jeanine; Cleverley, Robert M.; Lane, Harriet V. Molecular Microbiology, Vol. 99, Issue 5 https://doi.org/10.1111/mmi.13279	journal	December 2015
Structural basis for interaction of DivIVA/GpsB proteins with their ligands Halbedel, Sven; Lewis, Richard J. Molecular Microbiology, Vol. 111, Issue 6 https://doi.org/10.1111/mmi.14244	journal	April 2019
Gram-Positive Pathogens Fischetti, Vincent A.; Novick, Richard P.; Ferretti, Joseph J. https://doi.org/10.1128/9781555816513	book	March 2006
PBP4 Mediates β-Lactam Resistance by Altered Function Chatterjee, Som S.; Chen, Liang; Gilbert, Aubre Antimicrobial Agents and Chemotherapy, Vol. 61, Issue 11 https://doi.org/10.1128/AAC.00932-17	journal	August 2017
Profiling of β-Lactam Selectivity for Penicillin-Binding Proteins in Streptococcus pneumoniae D39 Kocaoglu, Ozden; Tsui, Ho-Ching T.; Winkler, Malcolm E. Antimicrobial Agents and Chemotherapy, Vol. 59, Issue 6 https://doi.org/10.1128/AAC.05142-14	journal	April 2015
Staphylococcus aureus penicillin-binding protein 4 and intrinsic beta-lactam resistance Henze, U. U.; Berger-Bächi, B. Antimicrobial Agents and Chemotherapy, Vol. 39, Issue 11 https://doi.org/10.1128/AAC.39.11.2415	journal	November 1995
Role of Penicillin-Binding Protein 4 in Expression of Vancomycin Resistance among Clinical Isolates of Oxacillin-Resistant Staphylococcus aureus Finan, J. E.; Archer, Gordon L.; Pucci, Michael J. Antimicrobial Agents and Chemotherapy, Vol. 45, Issue 11 https://doi.org/10.1128/AAC.45.11.3070-3075.2001	journal	November 2001
Cytological Characterization of YpsB, a Novel Component of the Bacillus subtilis Divisome Tavares, José Roberto; de Souza, Robson F.; Meira, Guilherme Louzada Silva Journal of Bacteriology, Vol. 190, Issue 21 https://doi.org/10.1128/JB.00064-08	journal	November 2008
¡vIVA la DivIVA! Hammond, Lauren R.; White, Maria L.; Eswara, Prahathees J. Journal of Bacteriology, Vol. 201, Issue 21 https://doi.org/10.1128/JB.00245-19	journal	November 2019
Molecular Basis for the Role of Staphylococcus aureus Penicillin Binding Protein 4 in Antimicrobial Resistance Navratna, Vikas; Nadig, Savitha; Sood, Varun Journal of Bacteriology, Vol. 192, Issue 1 https://doi.org/10.1128/JB.00822-09	journal	January 2010
Two-Step Assembly Dynamics of theBacillussubtilisDivisome Gamba, Pamela; Veening, Jan-Willem; Saunders, Nigel J. Journal of Bacteriology, Vol. 191, Issue 13 https://doi.org/10.1128/JB.01758-08	journal	July 2009
FtsZ Ring Stability: of Bundles, Tubules, Crosslinks, and Curves Huang, Kuo-Hsiang; Durand-Heredia, Jorge; Janakiraman, Anuradha Journal of Bacteriology, Vol. 195, Issue 9 https://doi.org/10.1128/JB.02157-12	journal	May 2013
Role of Penicillin-Binding Protein 2 (PBP2) in the Antibiotic Susceptibility and Cell Wall Cross-Linking of Staphylococcus aureus: Evidence for the Cooperative Functioning of PBP2, PBP4, and PBP2A Łęski, Tomasz A.; Tomasz, Alexander Journal of Bacteriology, Vol. 187, Issue 5 https://doi.org/10.1128/JB.187.5.1815-1824.2005	journal	March 2005
Low-affinity penicillin-binding protein associated with beta-lactam resistance in Staphylococcus aureus Hartman, B. J.; Tomasz, A. Journal of Bacteriology, Vol. 158, Issue 2 https://doi.org/10.1128/jb.158.2.513-516.1984	journal	May 1984
GpsB Coordinates Cell Division and Cell Surface Decoration by Wall Teichoic Acids in Staphylococcus aureus Hammond, Lauren R.; Sacco, Michael D.; Khan, Sebastian J. Microbiology Spectrum, Vol. 10, Issue 3 https://doi.org/10.1128/spectrum.01413-22	journal	June 2022
Identification of the full set of Listeria monocytogenes penicillin-binding proteins and characterization of PBPD2 (Lmo2812) Korsak, Dorota; Markiewicz, Zdzislaw; Gutkind, Gabriel O. BMC Microbiology, Vol. 10, Issue 1 https://doi.org/10.1186/1471-2180-10-239	journal	January 2010
A new platform for ultra-high density Staphylococcus aureus transposon libraries Santiago, Marina; Matano, Leigh M.; Moussa, Samir H. BMC Genomics, Vol. 16, Issue 1 https://doi.org/10.1186/s12864-015-1361-3	journal	March 2015
Bacterial cell division at a glance Mahone, Christopher R.; Goley, Erin D. Journal of Cell Science, Vol. 133, Issue 7 https://doi.org/10.1242/jcs.237057	journal	April 2020
Interplay of the Serine/Threonine-Kinase StkP and the Paralogs DivIVA and GpsB in Pneumococcal Cell Elongation and Division Fleurie, Aurore; Manuse, Sylvie; Zhao, Chao PLoS Genetics, Vol. 10, Issue 4 https://doi.org/10.1371/journal.pgen.1004275	journal	April 2014
Coordination of Chromosome Segregation and Cell Division in Staphylococcus aureus Bottomley, Amy L.; Liew, Andrew T. F.; Kusuma, Kennardy D. Frontiers in Microbiology, Vol. 8 https://doi.org/10.3389/fmicb.2017.01575	journal	August 2017
Recognition of Peptidoglycan Fragments by the Transpeptidase PBP4 From Staphylococcus aureus Maya-Martinez, Roberto; Alexander, J. Andrew N.; Otten, Christian F. Frontiers in Microbiology, Vol. 9 https://doi.org/10.3389/fmicb.2018.03223	journal	January 2019
The roles of GpsB and DivIVA in Staphylococcus aureus growth and division Sutton, Joshua A. F.; Cooke, Mark; Tinajero-Trejo, Mariana Frontiers in Microbiology, Vol. 14 https://doi.org/10.3389/fmicb.2023.1241249	journal	August 2023
Live-Cell Fluorescence Microscopy to Investigate Subcellular Protein Localization and Cell Morphology Changes in Bacteria Brzozowski, Robert S.; White, Maria L.; Eswara, Prahathees J. Journal of Visualized Experiments, Issue 153 https://doi.org/10.3791/59905	journal	November 2019
An essential Staphylococcus aureus cell division protein directly regulates FtsZ dynamics Eswara, Prahathees J.; Brzozowski, Robert S.; Viola, Marissa G. eLife, Vol. 7 https://doi.org/10.7554/eLife.38856	journal	October 2018

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59 BASIC BIOLOGICAL SCIENCES
B. subtilis
DivIVA
EzrA
GpsB recognition motif
Life Sciences & Biomedicine
Microbiology and Infectious Disease
Research Article
S. aureus
Staphylococcus aureus
cell division
cell wall
penicillin-binding protein

Title: Staphylococcus aureus FtsZ and PBP4 bind to the conformationally dynamic N-terminal domain of GpsB

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