A monomeric mycobacteriophage immunity repressor utilizes two domains to recognize an asymmetric DNA sequence

McGinnis, Reliza J.; Brambley, Chad A.; Stamey, Brandon; Green, William C.; Gragg, Kimberly N.; Cafferty, Erin R.; Terwilliger, Thomas C.; Hammel, Michal; Hollis, Thomas J.; Miller, Justin M.; Gainey, Maria D.; Wallen, Jamie R.

doi:10.1038/s41467-022-31678-6

A monomeric mycobacteriophage immunity repressor utilizes two domains to recognize an asymmetric DNA sequence

Journal Article · Thu Jul 14 00:00:00 EDT 2022 · Nature Communications

DOI:https://doi.org/10.1038/s41467-022-31678-6· OSTI ID:1881826

^[1]; ^[2]; Stamey, Brandon ^[3]; Green, William C. ^[3]; Gragg, Kimberly N. ^[3]; ^[4]; ^[5]; ^[6]; ^[7]; ^[2]; ^[3]; ^[3]

Univ. of Michigan, Ann Arbor, MI (United States); Western Carolina University, Cullowhee, NC (United States)
Middle Tennessee State Univ., Murfreesboro, TN (United States)
Western Carolina University, Cullowhee, NC (United States)
Univ. of Utah, Salt Lake City, UT (United States); Western Carolina University, Cullowhee, NC (United States)
New Mexico Consortium, Los Alamos, NM (United States)
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Wake Forest Univ., Winston-Salem, NC (United States)

Regulation of bacteriophage gene expression involves repressor proteins that bind and downregulate early lytic promoters. A large group of mycobacteriophages code for repressors that are unusual in also terminating transcription elongation at numerous binding sites (stoperators) distributed across the phage genome. Here we provide the X-ray crystal structure of a mycobacteriophage immunity repressor bound to DNA, which reveals the binding of a monomer to an asymmetric DNA sequence using two independent DNA binding domains. The structure is supported by small-angle X-ray scattering, DNA binding, molecular dynamics, and in vivo immunity assays. We propose a model for how dual DNA binding domains facilitate regulation of both transcription initiation and elongation, while enabling evolution of other superinfection immune specificities.

View Accepted Manuscript (DOE)

Research Organization:: Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Advanced Light Source (ALS); Los Alamos National Laboratory (LANL), Los Alamos, NM (United States)

Sponsoring Organization:: Howard Hughes Medical Institute; National Institutes of Health (NIH); USDOE Office of Science (SC), Basic Energy Sciences (BES); USDOE Office of Science (SC), Biological and Environmental Research (BER); Western Carolina University

Grant/Contract Number:: 89233218CNA000001; AC02-05CH11231

OSTI ID:: 1881826

Report Number(s):: LA-UR-22-22632

Journal Information:: Nature Communications, Journal Name: Nature Communications Journal Issue: 1 Vol. 13; ISSN 2041-1723

Publisher:: Nature Publishing GroupCopyright Statement

Country of Publication:: United States

Language:: English

References (63)

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
GROMACS: Fast, flexible, and free Van Der Spoel, David; Lindahl, Erik; Hess, Berk Journal of Computational Chemistry, Vol. 26, Issue 16 https://doi.org/10.1002/jcc.20291	journal	January 2005
CHARMM36 all-atom additive protein force field: Validation based on comparison to NMR data Huang, Jing; MacKerell, Alexander D. Journal of Computational Chemistry, Vol. 34, Issue 25 https://doi.org/10.1002/jcc.23354	journal	July 2013
The Bio3D packages for structural bioinformatics Grant, Barry J.; Skjærven, Lars; Yao, Xin‐Qiu Protein Science, Vol. 30, Issue 1 https://doi.org/10.1002/pro.3923	journal	August 2020
Generalized correlation for biomolecular dynamics Lange, Oliver F.; Grubmüller, Helmut Proteins: Structure, Function, and Bioinformatics, Vol. 62, Issue 4 https://doi.org/10.1002/prot.20784	journal	December 2005
Essential dynamics of proteins Amadei, Andrea; Linssen, Antonius B. M.; Berendsen, Herman J. C. Proteins: Structure, Function, and Genetics, Vol. 17, Issue 4 https://doi.org/10.1002/prot.340170408	journal	December 1993
Comparative Protein Modelling by Satisfaction of Spatial Restraints Šali, Andrej; Blundell, Tom L. Journal of Molecular Biology, Vol. 234, Issue 3 https://doi.org/10.1006/jmbi.1993.1626	journal	December 1993
Homeodomain proteins: an update Bürglin, Thomas R.; Affolter, Markus Chromosoma, Vol. 125, Issue 3 https://doi.org/10.1007/s00412-015-0543-8	journal	October 2015
GROMACS: A message-passing parallel molecular dynamics implementation Berendsen, H. J. C.; van der Spoel, D.; van Drunen, R. Computer Physics Communications, Vol. 91, Issue 1-3 https://doi.org/10.1016/0010-4655(95)00042-E	journal	September 1995
VMD: Visual molecular dynamics Humphrey, William; Dalke, Andrew; Schulten, Klaus Journal of Molecular Graphics, Vol. 14, Issue 1 https://doi.org/10.1016/0263-7855(96)00018-5	journal	February 1996
Cleavage of the lambda and P22 repressors by recA protein. Sauer, R. T.; Ross, M. J.; Ptashne, M. Journal of Biological Chemistry, Vol. 257, Issue 8 https://doi.org/10.1016/S0021-9258(18)34744-6	journal	April 1982
Preparation of selenomethionyl proteins for phase determination Doublié, Sylvie Methods in Enzymology https://doi.org/10.1016/S0076-6879(97)76075-0 p. 523-530	book	January 1997
Dali: a network tool for protein structure comparison Holm, Liisa; Sander, Chris Trends in Biochemical Sciences, Vol. 20, Issue 11 https://doi.org/10.1016/S0968-0004(00)89105-7	journal	November 1995
Structure of a Ternary Transcription Activation Complex Jain, Deepti; Nickels, Bryce E.; Sun, Li Molecular Cell, Vol. 13, Issue 1 https://doi.org/10.1016/S1097-2765(03)00483-0	journal	January 2004
Accurate SAXS Profile Computation and its Assessment by Contrast Variation Experiments Schneidman-Duhovny, Dina; Hammel, Michal; Tainer, John A. Biophysical Journal, Vol. 105, Issue 4 https://doi.org/10.1016/j.bpj.2013.07.020	journal	August 2013
The many faces of the helix-turn-helix domain: Transcription regulation and beyond Aravind, L.; Anantharaman, V.; Balaji, S. FEMS Microbiology Reviews, Vol. 29, Issue 2 https://doi.org/10.1016/j.femsre.2004.12.008	journal	April 2005
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
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
Crank Ness, Steven R.; de Graaff, Rudolf A. G.; Abrahams, Jan Pieter Structure, Vol. 12, Issue 10 https://doi.org/10.1016/j.str.2004.07.018	journal	October 2004
X-ray solution scattering (SAXS) combined with crystallography and computation: defining accurate macromolecular structures, conformations and assemblies in solution Putnam, Christopher D.; Hammel, Michal; Hura, Greg L. Quarterly Reviews of Biophysics, Vol. 40, Issue 3 https://doi.org/10.1017/S0033583507004635	journal	August 2007
All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins ^† MacKerell, A. D.; Bashford, D.; Bellott, M. The Journal of Physical Chemistry B, Vol. 102, Issue 18 https://doi.org/10.1021/jp973084f	journal	April 1998
Lysogeny in nature: mechanisms, impact and ecology of temperate phages Howard-Varona, Cristina; Hargreaves, Katherine R.; Abedon, Stephen T. The ISME Journal, Vol. 11, Issue 7 https://doi.org/10.1038/ismej.2017.16	journal	March 2017
Crystal structure of the λ repressor and a model for pairwise cooperative operator binding Stayrook, Steven; Jaru-Ampornpan, Peera; Ni, Jenny Nature, Vol. 452, Issue 7190 https://doi.org/10.1038/nature06831	journal	April 2008
Structural insights into the mycobacteria transcription initiation complex from analysis of X-ray crystal structures Hubin, Elizabeth A.; Lilic, Mirjana; Darst, Seth A. Nature Communications, Vol. 8, Issue 1 https://doi.org/10.1038/ncomms16072	journal	July 2017
Highly accurate protein structure prediction with AlphaFold Jumper, John; Evans, Richard; Pritzel, Alexander Nature https://doi.org/10.1038/s41586-021-03819-2	journal	July 2021
Engineered bacteriophages for treatment of a patient with a disseminated drug-resistant Mycobacterium abscessus Dedrick, Rebekah M.; Guerrero-Bustamante, Carlos A.; Garlena, Rebecca A. Nature Medicine, Vol. 25, Issue 5 https://doi.org/10.1038/s41591-019-0437-z	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
Transcriptional regulation and immunity in mycobacteriophage Bxb1 Jain, Shruti; Hatfull, Graham F. Molecular Microbiology, Vol. 38, Issue 5 https://doi.org/10.1046/j.1365-2958.2000.02184.x	journal	January 2002
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
Identification of slow molecular order parameters for Markov model construction Pérez-Hernández, Guillermo; Paul, Fabian; Giorgino, Toni The Journal of Chemical Physics, Vol. 139, Issue 1 https://doi.org/10.1063/1.4811489	journal	July 2013
Low-dimensional, free-energy landscapes of protein-folding reactions by nonlinear dimensionality reduction Das, P.; Moll, M.; Stamati, H. Proceedings of the National Academy of Sciences, Vol. 103, Issue 26 https://doi.org/10.1073/pnas.0603553103	journal	June 2006
Site-specific integration of mycobacteriophage L5: integration-proficient vectors for Mycobacterium smegmatis, Mycobacterium tuberculosis, and bacille Calmette-Guerin. Lee, M. H.; Pascopella, L.; Jacobs, W. R. Proceedings of the National Academy of Sciences, Vol. 88, Issue 8 https://doi.org/10.1073/pnas.88.8.3111	journal	April 1991
Bio3d: an R package for the comparative analysis of protein structures Grant, B. J.; Rodrigues, A. P. C.; ElSawy, K. M. Bioinformatics, Vol. 22, Issue 21 https://doi.org/10.1093/bioinformatics/btl461	journal	August 2006
Transcriptional silencing by the mycobacteriophage L5 repressor Brown, Kelly L.; Sarkis, Gary J.; Wadsworth, Curtis The EMBO Journal, Vol. 16, Issue 19 https://doi.org/10.1093/emboj/16.19.5914	journal	October 1997
MEME SUITE: tools for motif discovery and searching Bailey, T. L.; Boden, M.; Buske, F. A. Nucleic Acids Research, Vol. 37, Issue Web Server https://doi.org/10.1093/nar/gkp335	journal	May 2009
FoXS: a web server for rapid computation and fitting of SAXS profiles Schneidman-Duhovny, D.; Hammel, M.; Sali, A. Nucleic Acids Research, Vol. 38, Issue Web Server https://doi.org/10.1093/nar/gkq461	journal	May 2010
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
Crystal Structure and Pair Potentials: A Molecular-Dynamics Study Parrinello, M.; Rahman, A. Physical Review Letters, Vol. 45, Issue 14 https://doi.org/10.1103/PhysRevLett.45.1196	journal	October 1980
Implementation and performance of SIBYLS: a dual endstation small-angle X-ray scattering and macromolecular crystallography beamline at the Advanced Light Source Classen, Scott; Hura, Greg L.; Holton, James M. Journal of Applied Crystallography, Vol. 46, Issue 1 https://doi.org/10.1107/S0021889812048698	journal	January 2013
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
Iterative model building, structure refinement and density modification with the PHENIX AutoBuild wizard Terwilliger, Thomas C.; Grosse-Kunstleve, Ralf W.; Afonine, Pavel V. Acta Crystallographica Section D Biological Crystallography, Vol. 64, Issue 1 https://doi.org/10.1107/S090744490705024X	journal	December 2007
Decision-making in structure solution using Bayesian estimates of map quality: the PHENIX AutoSol wizard Terwilliger, Thomas C.; Adams, Paul D.; Read, Randy J. Acta Crystallographica Section D Biological Crystallography, Vol. 65, Issue 6 https://doi.org/10.1107/S0907444909012098	journal	May 2009
XDS Kabsch, Wolfgang Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2 https://doi.org/10.1107/S0907444909047337	journal	January 2010
REFMAC 5 for the refinement of macromolecular crystal structures Murshudov, Garib N.; Skubák, Pavol; Lebedev, Andrey A. Acta Crystallographica Section D Biological Crystallography, Vol. 67, Issue 4 https://doi.org/10.1107/S0907444911001314	journal	March 2011
The PDB_REDO server for macromolecular structure model optimization Joosten, Robbie P.; Long, Fei; Murshudov, Garib N. IUCrJ, Vol. 1, Issue 4 https://doi.org/10.1107/S2052252514009324	journal	May 2014
Superinfection immunity of mycobacteriophage L5: applications for genetic transformation of mycobacteria Donnelly-Wu, Mary K.; Jacobs, William R.; Hatfull, Graham F. Molecular Microbiology, Vol. 7, Issue 3 https://doi.org/10.1111/j.1365-2958.1993.tb01132.x	journal	February 1993
Dark Matter of the Biosphere: the Amazing World of Bacteriophage Diversity Hatfull, Graham F. Journal of Virology, Vol. 89, Issue 16 https://doi.org/10.1128/JVI.01340-15	journal	May 2015
Evolution of Superinfection Immunity in Cluster A Mycobacteriophages Mavrich, Travis N.; Hatfull, Graham F. mBio, Vol. 10, Issue 3 https://doi.org/10.1128/mBio.00971-19	journal	June 2019
Toward a Phage Cocktail for Tuberculosis: Susceptibility and Tuberculocidal Action of Mycobacteriophages against Diverse Mycobacterium tuberculosis Strains Guerrero-Bustamante, Carlos A.; Dedrick, Rebekah M.; Garlena, Rebecca A. mBio, Vol. 12, Issue 3 https://doi.org/10.1128/mBio.00973-21	journal	June 2021
A Broadly Implementable Research Course in Phage Discovery and Genomics for First-Year Undergraduate Students Jordan, Tuajuanda C.; Burnett, Sandra H.; Carson, Susan mBio, Vol. 5, Issue 1 https://doi.org/10.1128/mBio.01051-13	journal	February 2014
Molecular Basis of Lysis–Lysogeny Decisions in Gram-Positive Phages Brady, Aisling; Felipe-Ruiz, Alonso; Gallego del Sol, Francisca Annual Review of Microbiology, Vol. 75, Issue 1 https://doi.org/10.1146/annurev-micro-033121-020757	journal	October 2021
Mycobacteriophages: Genes and Genomes Hatfull, Graham F. Annual Review of Microbiology, Vol. 64, Issue 1 https://doi.org/10.1146/annurev.micro.112408.134233	journal	October 2010
Repressor of temperate mycobacteriophage L1 harbors a stable C-terminal domain and binds to different asymmetric operator DNAs with variable affinity Ganguly, Tridib; Bandhu, Amitava; Chattoraj, Partho Virology Journal, Vol. 4, Issue 1 https://doi.org/10.1186/1743-422X-4-64	journal	June 2007
Detection of Functional Modes in Protein Dynamics Hub, Jochen S.; de Groot, Bert L. PLoS Computational Biology, Vol. 5, Issue 8 https://doi.org/10.1371/journal.pcbi.1000480	journal	August 2009
Conformational Dynamics and Ligand Binding in the Multi-Domain Protein PDC109 Kim, Hyun Jin; Choi, Moo Young; Kim, Hyung J. PLoS ONE, Vol. 5, Issue 2 https://doi.org/10.1371/journal.pone.0009180	journal	February 2010
An Unusual Phage Repressor Encoded by Mycobacteriophage BPs Villanueva, Valerie M.; Oldfield, Lauren M.; Hatfull, Graham F. PLOS ONE, Vol. 10, Issue 9 https://doi.org/10.1371/journal.pone.0137187	journal	September 2015
The Hinge Region Strengthens the Nonspecific Interaction between Lac-Repressor and DNA: A Computer Simulation Study Sun, Lili; Tabaka, Marcin; Hou, Sen PLOS ONE, Vol. 11, Issue 3 https://doi.org/10.1371/journal.pone.0152002	journal	March 2016
Structure and flexibility within proteins as identified through small angle X-ray scattering Pelikan, M.; Hura, G.; Hammel, M. General Physiology and Biophysics, Vol. 28, Issue 2 https://doi.org/10.4149/gpb_2009_02_174	journal	January 2009
Potential of Mean Force Simulation by Pulling a DNA Aptamer in Complex with Thrombin Yang, Changwon; Kim, Eunae; Pak, Youngshang Bulletin of the Korean Chemical Society, Vol. 33, Issue 11 https://doi.org/10.5012/bkcs.2012.33.11.3597	journal	November 2012
A Monomeric Mycobacteriophage Immunity Repressor Utilizes Two Domains to Recognize an Asymmetric DNA Sequence McGinnis, Reliza J.; Brambley, Chad A.; Stamey, Brandon Zenodo https://doi.org/10.5281/zenodo.6604543	dataset	January 2022
Whole genome comparison of a large collection of mycobacteriophages reveals a continuum of phage genetic diversity Pope, Welkin H.; Bowman, Charles A.; Russell, Daniel A. eLife, Vol. 4 https://doi.org/10.7554/eLife.06416	journal	April 2015

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A monomeric mycobacteriophage immunity repressor utilizes two domains to recognize an asymmetric DNA sequence

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