Structural basis of Acinetobacter type IV pili targeting by an RNA virus.


Journal

Nature communications
ISSN: 2041-1723
Titre abrégé: Nat Commun
Pays: England
ID NLM: 101528555

Informations de publication

Date de publication:
29 Mar 2024
Historique:
received: 26 10 2023
accepted: 20 03 2024
medline: 30 3 2024
pubmed: 30 3 2024
entrez: 30 3 2024
Statut: epublish

Résumé

Acinetobacters pose a significant threat to human health, especially those with weakened immune systems. Type IV pili of acinetobacters play crucial roles in virulence and antibiotic resistance. Single-stranded RNA bacteriophages target the bacterial retractile pili, including type IV. Our study delves into the interaction between Acinetobacter phage AP205 and type IV pili. Using cryo-electron microscopy, we solve structures of the AP205 virion with an asymmetric dimer of maturation proteins, the native Acinetobacter type IV pili bearing a distinct post-translational pilin cleavage, and the pili-bound AP205 showing its maturation proteins adapted to pilin modifications, allowing each phage to bind to one or two pili. Leveraging these results, we develop a 20-kilodalton AP205-derived protein scaffold targeting type IV pili in situ, with potential for research and diagnostics.

Identifiants

pubmed: 38553443
doi: 10.1038/s41467-024-47119-5
pii: 10.1038/s41467-024-47119-5
doi:

Types de publication

Journal Article

Langues

eng

Sous-ensembles de citation

IM

Pagination

2746

Subventions

Organisme : Foundation for the National Institutes of Health (Foundation for the National Institutes of Health, Inc.)
ID : R21AI156846
Organisme : Foundation for the National Institutes of Health (Foundation for the National Institutes of Health, Inc.)
ID : U24GM1167
Organisme : National Science Foundation (NSF)
ID : MCB-1902392

Informations de copyright

© 2024. The Author(s).

Références

Wong, D. et al. Clinical and pathophysiological overview of acinetobacter infections: a century of challenges. Clin. Microbiol. Rev. 30, 409–447 (2017).
pubmed: 27974412 doi: 10.1128/CMR.00058-16
Strathdee, S. A., Hatfull, G. F., Mutalik, V. K. & Schooley, R. T. Phage therapy: from biological mechanisms to future directions. Cell 186, 17–31 (2023).
pubmed: 36608652 pmcid: 9827498 doi: 10.1016/j.cell.2022.11.017
Craig, L., Pique, M. E. & Tainer, J. A. Type IV pilus structure and bacterial pathogenicity. Nat. Rev. Microbiol. 2, 363–378 (2004).
pubmed: 15100690 doi: 10.1038/nrmicro885
Vesel, N. & Blokesch, M. Pilus production in acinetobacter baumannii is growth phase dependent and essential for natural transformation. J. Bacteriol. 203, e00034–21 (2021).
pubmed: 33495250 pmcid: 8088505 doi: 10.1128/JB.00034-21
Korotkov, K. V., Gonen, T. & Hol, W. G. J. Secretins: dynamic channels for protein transport across membranes. Trends Biochem. Sci. 36, 433–443 (2011).
pubmed: 21565514 pmcid: 3155655 doi: 10.1016/j.tibs.2011.04.002
Thongchol, J., Lill, Z., Hoover, Z. & Zhang, J. Recent advances in structural studies of single-stranded rna bacteriophages. Viruses 15, 10 (2023).
doi: 10.3390/v15101985
Chamakura, K. R. et al. Rapid de novo evolution of lysis genes in single-stranded RNA phages. Nat. Commun. 11, 6009 (2020).
pubmed: 33243984 pmcid: 7693330 doi: 10.1038/s41467-020-19860-0
Neri, U. et al. Expansion of the global RNA virome reveals diverse clades of bacteriophages. Cell 185, 4023–4037.e18 (2022).
pubmed: 36174579 doi: 10.1016/j.cell.2022.08.023
Dai, X. et al. In situ structures of the genome and genome-delivery apparatus in an ssRNA virus. Nature 541, 112–116 (2017).
pubmed: 27992877 doi: 10.1038/nature20589
Zhong, Q. et al. Genetic, structural, and phenotypic properties of ms2 coliphage with resistance to clo2 disinfection. Environ. Sci. Technol. 50, 13520–13528 (2016).
pubmed: 27709908 doi: 10.1021/acs.est.6b04170
Koning, R. I. et al. Asymmetric cryo-EM reconstruction of phage MS2 reveals genome structure in situ. Nat. Commun. 7, 12524 (2016).
pubmed: 27561669 pmcid: 5007439 doi: 10.1038/ncomms12524
Gorzelnik, K. V. et al. Asymmetric cryo-EM structure of the canonical Allolevivirus Qbeta reveals a single maturation protein and the genomic ssRNA in situ. Proc. Natl Acad. Sci. USA 113, 11519–11524 (2016).
pubmed: 27671640 pmcid: 5068298 doi: 10.1073/pnas.1609482113
Clarke, M., Maddera, L., Harris, R. L. & Silverman, P. M. F-pili dynamics by live-cell imaging. Proc. Natl. Acad. Sci. USA 105, 17978–17981 (2008).
pubmed: 19004777 pmcid: 2582581 doi: 10.1073/pnas.0806786105
Harb, L. et al. ssRNA phage penetration triggers detachment of the F-pilus. Proc. Natl Acad. Sci. USA 117, 25751–25758 (2020).
pubmed: 32989140 pmcid: 7568308 doi: 10.1073/pnas.2011901117
Meng, R. et al. Structural basis for the adsorption of a single-stranded RNA bacteriophage. Nat. Commun. 10, 3130 (2019).
pubmed: 31311931 pmcid: 6635492 doi: 10.1038/s41467-019-11126-8
Shishovs, M. et al. Structure of AP205 coat protein reveals circular permutation in ssrna bacteriophages. J. Mol. Biol. 428, 4267–4279 (2016).
pubmed: 27591890 doi: 10.1016/j.jmb.2016.08.025
Ronish, L. A., Lillehoj, E., Fields, J. K., Sundberg, E. J. & Piepenbrink, K. H. The structure of PilA from Acinetobacter baumannii AB5075 suggests a mechanism for functional specialization in Acinetobacter type IV pili. J. Biol. Chem. 294, 218–230 (2019).
pubmed: 30413536 doi: 10.1074/jbc.RA118.005814
Chang, J. Y. et al. Hierarchical natural move Monte Carlo refines flexible RNA structures into cryo-EM densities. Rna 26, 1755–1766 (2020).
pubmed: 32826323 pmcid: 7668250 doi: 10.1261/rna.071100.119
Cui, Z. et al. Structures of Qbeta virions, virus-like particles, and the Qbeta-MurA complex reveal internal coat proteins and the mechanism of host lysis. Proc. Natl Acad. Sci. USA 114, 11697–11702 (2017).
pubmed: 29078304 pmcid: 5676892 doi: 10.1073/pnas.1707102114
Chang, J.-Y., Gorzelnik, K. V., Thongchol, J. & Zhang, J. Structural Assembly of Qβ Virion and Its Diverse Forms of Virus-like Particles. Viruses 14, 225 (2022).
pubmed: 35215818 pmcid: 8880383 doi: 10.3390/v14020225
Rumnieks, J. & Tars, K. Crystal Structure of the Maturation Protein from Bacteriophage Qβ. J. Mol. Biol. 429, 688–696 (2017).
pubmed: 28111107 doi: 10.1016/j.jmb.2017.01.012
Valegård, K., Murray, J. B., Stockley, P. G., Stonehouse, N. J. & Liljas, L. Crystal structure of an RNA bacteriophage coat protein–operator complex. Nature 371, 623–626 (1994).
pubmed: 7523953 doi: 10.1038/371623a0
Klovins, J., Tsareva, N. A., de Smit, M. H., Berzins, V. & van Duin, J. Rapid evolution of translational control mechanisms in RNA genomes. J. Mol. Biol. 265, 372–384 (1997).
pubmed: 9034357 doi: 10.1006/jmbi.1996.0745
Stockley, P. G. et al. Packaging signals in single-stranded RNA viruses: nature’s alternative to a purely electrostatic assembly mechanism. J. Biol. Phys. 39, 277–287 (2013).
pubmed: 23704797 pmcid: 3662417 doi: 10.1007/s10867-013-9313-0
Strom, M. S., Nunn, D. N. & Lory, S. Posttranslational processing of type IV prepilin and homologs by PilD of Pseudomonas aeruginosa. Methods Enzym 235, 527–540 (1994).
doi: 10.1016/0076-6879(94)35168-6
Piepenbrink, K. H. et al. Structural Diversity in the Type IV Pili of Multidrug-resistant Acinetobacter *. J. Biol. Chem. 291, 22924–22935 (2016).
pubmed: 27634041 pmcid: 5087714 doi: 10.1074/jbc.M116.751099
Iwashkiw, J. A. et al. Identification of a General O-linked Protein Glycosylation System in Acinetobacter baumannii and Its Role in Virulence and Biofilm Formation. Plos Pathog. 8, e1002758 (2012).
pubmed: 22685409 pmcid: 3369928 doi: 10.1371/journal.ppat.1002758
Craig, L., Forest, K. T. & Maier, B. Type IV pili: dynamics, biophysics and functional consequences. Nat. Rev. Microbiol. 17, 429–440 (2019).
pubmed: 30988511 doi: 10.1038/s41579-019-0195-4
Sanjuán, R. From Molecular Genetics to Phylodynamics: Evolutionary Relevance of Mutation Rates Across Viruses. PLoS Pathog 8, e1002685 (2012).
pubmed: 22570614 pmcid: 3342999 doi: 10.1371/journal.ppat.1002685
Zheng, S. Q. et al. MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy. Nat Methods 14, 331–332 (2017).
pubmed: 28250466 pmcid: 5494038 doi: 10.1038/nmeth.4193
Tang, G. et al. EMAN2: An extensible image processing suite for electron microscopy. J. Struct. Biol. 157, 38–46 (2007).
pubmed: 16859925 doi: 10.1016/j.jsb.2006.05.009
Zhang, K. Gctf: Real-time CTF determination and correction. J. Struct. Biology 193, 1–12 (2016).
doi: 10.1016/j.jsb.2015.11.003
Scheres, S. H. W. RELION: Implementation of a Bayesian approach to cryo-EM structure determination. J. Struct. Biol. 180, 519–530 (2012).
pubmed: 23000701 pmcid: 3690530 doi: 10.1016/j.jsb.2012.09.006
Punjani, A., Rubinstein, J. L., Fleet, D. J. & Brubaker, M. A. cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination. Nat Methods 14, 290–296 (2017).
pubmed: 28165473 doi: 10.1038/nmeth.4169
Tan, Y. Z. et al. Addressing preferred specimen orientation in single-particle cryo-EM through tilting. Nat. Methods 14, 793–796 (2017).
pubmed: 28671674 pmcid: 5533649 doi: 10.1038/nmeth.4347
Roy, A., Kucukural, A. & Zhang, Y. I-TASSER: a unified platform for automated protein structure and function prediction. Nat. Protoc. 5, 725–738 (2010).
pubmed: 20360767 pmcid: 2849174 doi: 10.1038/nprot.2010.5
Chai, L. et al. AlphaFold Protein Structure Database for Sequence-Independent Molecular Replacement. Crystals 11, 1227 (2021).
doi: 10.3390/cryst11101227
Emsley, P. & Cowtan, K. Coot: model‐building tools for molecular graphics. Acta Crystallogr Sect. D. 60, 2126–2132 (2004).
doi: 10.1107/S0907444904019158
Croll, T. I. ISOLDE: a physically realistic environment for model building into low-resolution electron-density maps. Acta Crystallogr Sect. D. Struct. Biol.74, 519–530 (2018).
doi: 10.1107/S2059798318002425
Goddard, T. D. et al. UCSF ChimeraX: Meeting modern challenges in visualization and analysis. Protein Sci. 27, 14–25 (2018).
pubmed: 28710774 doi: 10.1002/pro.3235
Song, Y. et al. High-Resolution Comparative Modeling with RosettaCM. Structure 21, 1735–1742 (2013).
pubmed: 24035711 doi: 10.1016/j.str.2013.08.005
Afonine, P. V. et al. Real‐space refinement in PHENIX for cryo‐EM and crystallography. Acta Crystallogr. Sect. D 74, 531–544 (2018).
doi: 10.1107/S2059798318006551
Pettersen, E. F. et al. UCSF Chimera—A visualization system for exploratory research and analysis. J. Comput. Chem. 25, 1605–1612 (2004).
pubmed: 15264254 doi: 10.1002/jcc.20084
Kappel, K. et al. De novo computational RNA modeling into cryo-EM maps of large ribonucleoprotein complexes. Nat. Methods 15, 947–954 (2018).
pubmed: 30377372 pmcid: 6636682 doi: 10.1038/s41592-018-0172-2
Trabuco, L. G., Villa, E., Schreiner, E., Harrison, C. B. & Schulten, K. Molecular dynamics flexible fitting: A practical guide to combine cryo-electron microscopy and X-ray crystallography. Methods 49, 174–180 (2009).
pubmed: 19398010 pmcid: 2753685 doi: 10.1016/j.ymeth.2009.04.005

Auteurs

Ran Meng (R)

Center for Phage Technology, Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA.
Yale University, New Haven, CT, 06520, USA.

Zhongliang Xing (Z)

Center for Phage Technology, Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA.

Jeng-Yih Chang (JY)

Center for Phage Technology, Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA.
UMass Chan Medical School, Worcester, MA, 01655, USA.

Zihao Yu (Z)

Center for Phage Technology, Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA.

Jirapat Thongchol (J)

Center for Phage Technology, Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA.

Wen Xiao (W)

Center for Phage Technology, Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA.

Yuhang Wang (Y)

Center for Phage Technology, Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA.

Karthik Chamakura (K)

Center for Phage Technology, Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA.
Armata Pharmaceuticals, Inc., Marina del Rey, CA, 90292, USA.

Zhiqi Zeng (Z)

Center for Phage Technology, Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA.

Fengbin Wang (F)

Department of Biochemistry and Molecular Genetics, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, 35294, USA.

Ry Young (R)

Center for Phage Technology, Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA.

Lanying Zeng (L)

Center for Phage Technology, Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA.

Junjie Zhang (J)

Center for Phage Technology, Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA. junjiez@tamu.edu.

Classifications MeSH