The Structural Basis of T4 Phage Lysis Control: DNA as the Signal for Lysis Inhibition

Krieger, Inna V.; Kuznetsov, Vladimir; Chang, Jeng-Yih; Zhang, Junjie; Moussa, Samir H.; Young, Ryland F.; Sacchettini, James C.

doi:10.1016/j.jmb.2020.06.013

The Structural Basis of T4 Phage Lysis Control: DNA as the Signal for Lysis Inhibition

Journal Article · Wed Jun 17 00:00:00 EDT 2020 · Journal of Molecular Biology

DOI:https://doi.org/10.1016/j.jmb.2020.06.013· OSTI ID:1671132

Krieger, Inna V. ^[1]; Kuznetsov, Vladimir ^[2]; Chang, Jeng-Yih ^[3]; Zhang, Junjie ^[3]; Moussa, Samir H. ^[4]; Young, Ryland F. ^[3]; Sacchettini, James C. ^[1]

Texas A & M Univ., College Station, TX (United States)
Texas A & M Univ., College Station, TX (United States); KBI Biopharma, Research Triangle, NC (United States)
Texas A & M Univ., College Station, TX (United States); Center for Phage Technology, College Station, TX (United States)
Texas A & M Univ., College Station, TX (United States); Center for Phage Technology, College Station, TX (United States); Boston BioHub, Waltham, MA (United States)

Optimal phage propagation depends on the regulation of the lysis of the infected host cell. In T4 phage infection, lysis occurs when the holin protein (T) forms lesions in the host membrane. However, the lethal function of T can be blocked by an antiholin (RI) during lysis inhibition (LIN). LIN sets if the infected cell undergoes superinfection, then the lysis is delayed until host/phage ratio becomes more favorable for the release of progeny. It has been thought that a signal derived from the superinfection is required to activate RI. Here we report structures that suggest a radically different model in which RI binds to T irrespective of superinfection, causing it to accumulate in a membrane as heterotetrameric 2RI–2T complex. Moreover, we show the complex binds non-specifically to DNA, suggesting that the gDNA from the superinfecting phage serves as the LIN signal and that stabilization of the complex by DNA binding is what defines LIN. Finally, we show that soluble domain of free RI crystallizes in a domain-swapped homotetramer, which likely works as a sink for RI molecules released from the RI–T complex to ensure efficient lysis. These results constitute the first structural basis and a new model not only for the historic LIN phenomenon but also for the temporal regulation of phage lysis in general.

View Accepted Manuscript (DOE)

Research Organization:: Advanced Photon Source (APS), Argonne National Laboratory (ANL), Argonne, IL (US)

Sponsoring Organization:: National Institutes of Health (NIH); USDOE; Welch Foundation

OSTI ID:: 1671132

Journal Information:: Journal of Molecular Biology, Journal Name: Journal of Molecular Biology Journal Issue: 16 Vol. 432; ISSN 0022-2836

Publisher:: ElsevierCopyright Statement

Country of Publication:: United States

Language:: ENGLISH

References (36)

Genomic polymorphism in the T-even bacteriophages. Repoila, F.; Tétart, F.; Bouet, J. Y. The EMBO Journal, Vol. 13, Issue 17 https://doi.org/10.1002/j.1460-2075.1994.tb06736.x	journal	September 1994
Protein determinants of phage T4 lysis inhibition: Characterization of the T4 Lysis Inhibition Proteins Moussa, Samir H.; Kuznetsov, Vladimir; Tran, Tram Anh T. Protein Science, Vol. 21, Issue 4 https://doi.org/10.1002/pro.2042	journal	March 2012
Energetics of the loop-to-helix transition leading to the coiled-coil structure of influenza virus hemagglutinin HA2 subunits Huang, Qiang; Korte, Thomas; Rachakonda, P. Sivaramakrishna Proteins: Structure, Function, and Bioinformatics, Vol. 74, Issue 2 https://doi.org/10.1002/prot.22157	journal	February 2009
Intracellular localization of deoxyribonucleases in Escherichia coli Obinata, Masuwo; Mizuno, Den'ichi Biochimica et Biophysica Acta (BBA) - Nucleic Acids and Protein Synthesis, Vol. 155, Issue 1 https://doi.org/10.1016/0005-2787(68)90339-0	journal	January 1968
Internal proteins of bacteriophage T4D: Their characterization and relation to head structure and assembly Black, Lindsay W.; Ahmad-Zadeh, C. Journal of Molecular Biology, Vol. 57, Issue 1 https://doi.org/10.1016/0022-2836(71)90120-3	journal	April 1971
[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
Genetic analysis of the T4 holin: timing and topology Ramanculov, Erlan; Young, Ry Gene, Vol. 265, Issue 1-2 https://doi.org/10.1016/S0378-1119(01)00365-1	journal	March 2001
Surprising similarities in structure comparison Gibrat, Jean-Francois; Madej, Thomas; Bryant, Stephen H. Current Opinion in Structural Biology, Vol. 6, Issue 3 https://doi.org/10.1016/S0959-440X(96)80058-3	journal	June 1996
Phage Therapy: A Renewed Approach to Combat Antibiotic-Resistant Bacteria Kortright, Kaitlyn E.; Chan, Benjamin K.; Koff, Jonathan L. Cell Host & Microbe, Vol. 25, Issue 2 https://doi.org/10.1016/j.chom.2019.01.014	journal	February 2019
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
EMAN2: An extensible image processing suite for electron microscopy Tang, Guang; Peng, Liwei; Baldwin, Philip R. Journal of Structural Biology, Vol. 157, Issue 1 https://doi.org/10.1016/j.jsb.2006.05.009	journal	January 2007
Gctf: Real-time CTF determination and correction Zhang, Kai Journal of Structural Biology, Vol. 193, Issue 1 https://doi.org/10.1016/j.jsb.2015.11.003	journal	January 2016
Flexible Fitting of Atomic Structures into Electron Microscopy Maps Using Molecular Dynamics Trabuco, Leonardo G.; Villa, Elizabeth; Mitra, Kakoli Structure, Vol. 16, Issue 5 https://doi.org/10.1016/j.str.2008.03.005	journal	May 2008
Regulation of a muralytic enzyme by dynamic membrane topology Sun, Qingan; Kuty, Gabriel F.; Arockiasamy, Arulandu Nature Structural & Molecular Biology, Vol. 16, Issue 11 https://doi.org/10.1038/nsmb.1681	journal	November 2009
An ancient player unmasked: T4 rI encodes a t-specific antiholin: T4 rI encodes an antiholin Ramanculov, Erlan; Young, Ry Molecular Microbiology, Vol. 41, Issue 3 https://doi.org/10.1046/j.1365-2958.2001.02491.x	journal	August 2001
A signal-arrest-release sequence mediates export and control of the phage P1 endolysin Xu, M.; Struck, D. K.; Deaton, J. Proceedings of the National Academy of Sciences, Vol. 101, Issue 17 https://doi.org/10.1073/pnas.0400957101	journal	April 2004
Holin triggering in real time White, R.; Chiba, S.; Pang, T. Proceedings of the National Academy of Sciences, Vol. 108, Issue 2 https://doi.org/10.1073/pnas.1011921108	journal	December 2010
Domain swapping: entangling alliances between proteins. Bennett, M. J.; Choe, S.; Eisenberg, D. Proceedings of the National Academy of Sciences, Vol. 91, Issue 8 https://doi.org/10.1073/pnas.91.8.3127	journal	April 1994
Structural and functional analysis of cystatin E reveals enzymologically relevant dimer and amyloid fibril states Dall, Elfriede; Hollerweger, Julia C.; Dahms, Sven O. Journal of Biological Chemistry, Vol. 293, Issue 34 https://doi.org/10.1074/jbc.RA118.002154	journal	August 2018
Dali server: conservation mapping in 3D Holm, Liisa; Rosenstrï¿½m, Pï¿½ivi Nucleic Acids Research, Vol. 38, Issue suppl_2 https://doi.org/10.1093/nar/gkq366	journal	May 2010
MOLREP an Automated Program for Molecular Replacement Vagin, A.; Teplyakov, A. Journal of Applied Crystallography, Vol. 30, Issue 6, p. 1022-1025 https://doi.org/10.1107/S0021889897006766	journal	December 1997
Generation, representation and flow of phase information in structure determination: recent developments in and around SHARP 2.0 Bricogne, G.; Vonrhein, C.; Flensburg, C. Acta Crystallographica Section D Biological Crystallography, Vol. 59, Issue 11 https://doi.org/10.1107/S0907444903017694	journal	October 2003
Experimental phasing with SHELXC / D / E : combining chain tracing with density modification Sheldrick, George M. Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 4 https://doi.org/10.1107/S0907444909038360	journal	March 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
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
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
The Last r Locus Unveiled: T4 RIII Is a Cytoplasmic Antiholin Chen, Yi; Young, Ry Journal of Bacteriology, Vol. 198, Issue 18 https://doi.org/10.1128/JB.00294-16	journal	July 2016
The T4 RI Antiholin Has an N-Terminal Signal Anchor Release Domain That Targets It for Degradation by DegP Tran, Tram Anh T.; Struck, Douglas K.; Young, Ry Journal of Bacteriology, Vol. 189, Issue 21 https://doi.org/10.1128/JB.00854-07	journal	August 2007
Genetic Dissection of T4 Lysis Moussa, S. H.; Lawler, J. L.; Young, R. Journal of Bacteriology, Vol. 196, Issue 12 https://doi.org/10.1128/JB.01548-14	journal	April 2014
Probing the Structure of the S105 Hole To, K. H.; Young, R. Journal of Bacteriology, Vol. 196, Issue 21 https://doi.org/10.1128/JB.01673-14	journal	August 2014
Periplasmic Domains Define Holin-Antiholin Interactions in T4 Lysis Inhibition Tran, Tram Anh T.; Struck, Douglas K.; Young, Ry Journal of Bacteriology, Vol. 187, Issue 19 https://doi.org/10.1128/JB.187.19.6631-6640.2005	journal	October 2005
Lysis and Lysis Inhibition with Escherichia coli Bacteriophage Doermann, A. H. Journal of Bacteriology, Vol. 55, Issue 2 https://doi.org/10.1128/JB.55.2.257-276.1948	journal	January 1948
Role of Superinfecting Phage in Lysis Inhibition with Phage T4 in Escherichia coli Rutberg, Blanka; Rutberg, Lars Journal of Bacteriology, Vol. 90, Issue 4 https://doi.org/10.1128/JB.90.4.891-894.1965	journal	January 1965
Lysis Inhibition in Escherichia coli Infected with Bacteriophage T4 Bode, Werner Journal of Virology, Vol. 1, Issue 5 https://doi.org/10.1128/JVI.1.5.948-955.1967	journal	January 1967
Breakdown and Exclusion of Superinfecting T-Even Bacteriophage in Escherichia coli Anderson, Carl W.; Eigner, Joseph Journal of Virology, Vol. 8, Issue 6 https://doi.org/10.1128/JVI.8.6.869-886.1971	journal	January 1971
Look Who’s Talking: T-Even Phage Lysis Inhibition, the Granddaddy of Virus-Virus Intercellular Communication Research Abedon, Stephen Viruses, Vol. 11, Issue 10 https://doi.org/10.3390/v11100951	journal	October 2019

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