Structural basis of template strand deoxyuridine promoter recognition by a viral RNA polymerase

Fraser, Alec; Sokolova, Maria L.; Drobysheva, Arina V.; Gordeeva, Julia V.; Borukhov, Sergei; Jumper, John; Severinov, Konstantin V.; Leiman, Petr G.

doi:10.1038/s41467-022-31214-6

Structural basis of template strand deoxyuridine promoter recognition by a viral RNA polymerase

Journal Article · Mon Jun 20 00:00:00 EDT 2022 · Nature Communications

DOI:https://doi.org/10.1038/s41467-022-31214-6· OSTI ID:1875162

Fraser, Alec ^[1]; ^[2]; Drobysheva, Arina V. ^[3]; Gordeeva, Julia V. ^[3]; ^[4]; ^[5]; ^[6]; ^[1]

University of Texas Medical Branch, Galveston, TX (United States)
University of Texas Medical Branch, Galveston, TX (United States); Skolkovo Institute of Science and Technology (Russian Federation)
Skolkovo Institute of Science and Technology (Russian Federation)
Rowan University School of Osteopathic Medicine, Stratford, NJ (United States)
DeepMind Technologies Limited, London (United Kingdom)
Skolkovo Institute of Science and Technology (Russian Federation); Russian Academy of Sciences (RAS), Moscow (Russian Federation); State University of New Jersey, Piscataway, NJ (United States)

Recognition of promoters in bacterial RNA polymerases (RNAPs) is controlled by sigma subunits. The key sequence motif recognized by the sigma, the -10 promoter element, is located in the non-template strand of the double-stranded DNA molecule ~10 nucleotides upstream of the transcription start site. Here, we explain the mechanism by which the phage AR9 non-virion RNAP (nvRNAP), a bacterial RNAP homolog, recognizes the -10 element of its deoxyuridine-containing promoter in the template strand. The AR9 sigma-like subunit, the nvRNAP enzyme core, and the template strand together form two nucleotide base-accepting pockets whose shapes dictate the requirement for the conserved deoxyuridines. A single amino acid substitution in the AR9 sigma-like subunit allows one of these pockets to accept a thymine thus expanding the promoter consensus. Our work demonstrates the extent to which viruses can evolve host-derived multisubunit enzymes to make transcription of their own genes independent of the host.

View Accepted Manuscript (DOE)

Research Organization:: Argonne National Laboratory (ANL), Argonne, IL (United States). Advanced Photon Source (APS); Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: Michigan Economic Development Corporation; Michigan Technology Tri-Corridor; Ministry of Science and Higher Education of Russian Federation; Russian Foundation for Basic Research; Russian Science Foundation; USDOE Office of Science (SC)

Grant/Contract Number:: AC02-05CH11231; AC02-06CH11357

OSTI ID:: 1875162

Alternate ID(s):: OSTI ID: 1876079

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 (74)

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
Scalable molecular dynamics with NAMD Phillips, James C.; Braun, Rosemary; Wang, Wei Journal of Computational Chemistry, Vol. 26, Issue 16, p. 1781-1802 https://doi.org/10.1002/jcc.20289	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
UCSF ChimeraX: Meeting modern challenges in visualization and analysis: UCSF ChimeraX Visualization System Goddard, Thomas D.; Huang, Conrad C.; Meng, Elaine C. Protein Science, Vol. 27, Issue 1 https://doi.org/10.1002/pro.3235	journal	September 2017
Improvements to the APBS biomolecular solvation software suite: Improvements to the APBS Software Suite Jurrus, Elizabeth; Engel, Dave; Star, Keith Protein Science, Vol. 27, Issue 1 https://doi.org/10.1002/pro.3280	journal	October 2017
The genome of bacteriophage φKZ of Pseudomonas aeruginosa Mesyanzhinov, Vadim V.; Robben, Johan; Grymonprez, Barbara Journal of Molecular Biology, Vol. 317, Issue 1 https://doi.org/10.1006/jmbi.2001.5396	journal	March 2002
Avoiding singularities and numerical instabilities in free energy calculations based on molecular simulations Beutler, Thomas C.; Mark, Alan E.; van Schaik, René C. Chemical Physics Letters, Vol. 222, Issue 6 https://doi.org/10.1016/0009-2614(94)00397-1	journal	June 1994
Efficient estimation of free energy differences from Monte Carlo data Bennett, Charles H. Journal of Computational Physics, Vol. 22, Issue 2 https://doi.org/10.1016/0021-9991(76)90078-4	journal	October 1976
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
The helix-turn-helix DNA binding motif Brennan, R. G.; Matthews, B. W. Journal of Biological Chemistry, Vol. 264, Issue 4 https://doi.org/10.1016/S0021-9258(18)94115-3	journal	February 1989
Basic local alignment search tool Altschul, Stephen F.; Gish, Warren; Miller, Webb Journal of Molecular Biology, Vol. 215, Issue 3, p. 403-410 https://doi.org/10.1016/S0022-2836(05)80360-2	journal	October 1990
Structure of the Bacterial RNA Polymerase Promoter Specificity σ Subunit Campbell, Elizabeth A.; Muzzin, Oriana; Chlenov, Mark Molecular Cell, Vol. 9, Issue 3 https://doi.org/10.1016/S1097-2765(02)00470-7	journal	March 2002
Structural Basis for Promoter −10 Element Recognition by the Bacterial RNA Polymerase σ Subunit Feklistov, Andrey; Darst, Seth A. Cell, Vol. 147, Issue 6 https://doi.org/10.1016/j.cell.2011.10.041	journal	December 2011
The Phage Nucleus and Tubulin Spindle Are Conserved among Large Pseudomonas Phages Chaikeeratisak, Vorrapon; Nguyen, Katrina; Egan, MacKennon E. Cell Reports, Vol. 20, Issue 7 https://doi.org/10.1016/j.celrep.2017.07.064	journal	August 2017
Structure and Function of Lineage-specific Sequence Insertions in the Bacterial RNA Polymerase β′ Subunit Chlenov, Mark; Masuda, Shoko; Murakami, Katsuhiko S. Journal of Molecular Biology, Vol. 353, Issue 1 https://doi.org/10.1016/j.jmb.2005.07.073	journal	October 2005
Molecular Evolution of Multisubunit RNA Polymerases: Structural Analysis Lane, William J.; Darst, Seth A. Journal of Molecular Biology, Vol. 395, Issue 4 https://doi.org/10.1016/j.jmb.2009.10.063	journal	January 2010
A Completely Reimplemented MPI Bioinformatics Toolkit with a New HHpred Server at its Core Zimmermann, Lukas; Stephens, Andrew; Nam, Seung-Zin Journal of Molecular Biology, Vol. 430, Issue 15 https://doi.org/10.1016/j.jmb.2017.12.007	journal	July 2018
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
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
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
The genome of AR9, a giant transducing Bacillus phage encoding two multisubunit RNA polymerases Lavysh, Daria; Sokolova, Maria; Minakhin, Leonid Virology, Vol. 495 https://doi.org/10.1016/j.virol.2016.04.030	journal	August 2016
The Phenix software for automated determination of macromolecular structures Adams, Paul D.; Afonine, Pavel V.; Bunkóczi, Gábor Methods, Vol. 55, Issue 1 https://doi.org/10.1016/j.ymeth.2011.07.005	journal	September 2011
Standard Binding Free Energies from Computer Simulations: What Is the Best Strategy? Gumbart, James C.; Roux, Benoît; Chipot, Christophe Journal of Chemical Theory and Computation, Vol. 9, Issue 1 https://doi.org/10.1021/ct3008099	journal	November 2012
Good Practices in Free-Energy Calculations Pohorille, Andrew; Jarzynski, Christopher; Chipot, Christophe The Journal of Physical Chemistry B, Vol. 114, Issue 32 https://doi.org/10.1021/jp102971x	journal	August 2010
A mechanism for all polymerases Steitz, Thomas A. Nature, Vol. 391, Issue 6664 https://doi.org/10.1038/34542	journal	January 1998
Quantifying the local resolution of cryo-EM density maps Kucukelbir, Alp; Sigworth, Fred J.; Tagare, Hemant D. Nature Methods, Vol. 11, Issue 1 https://doi.org/10.1038/nmeth.2727	journal	November 2013
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
MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy Zheng, Shawn Q.; Palovcak, Eugene; Armache, Jean-Paul Nature Methods, Vol. 14, Issue 4 https://doi.org/10.1038/nmeth.4193	journal	February 2017
Structural basis for transcription initiation by bacterial ECF σ factors Li, Lingting; Fang, Chengli; Zhuang, Ningning Nature Communications, Vol. 10, Issue 1 https://doi.org/10.1038/s41467-019-09096-y	journal	March 2019
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
Non-uniform refinement: adaptive regularization improves single-particle cryo-EM reconstruction Punjani, Ali; Zhang, Haowei; Fleet, David J. Nature Methods, Vol. 17, Issue 12 https://doi.org/10.1038/s41592-020-00990-8	journal	November 2020
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
Constant pressure molecular dynamics simulation: The Langevin piston method Feller, Scott E.; Zhang, Yuhong; Pastor, Richard W. The Journal of Chemical Physics, Vol. 103, Issue 11 https://doi.org/10.1063/1.470648	journal	September 1995
Structure and dynamics of TIP3P, TIP4P, and TIP5P water near smooth and atomistic walls of different hydroaffinity Harrach, Michael F.; Drossel, Barbara The Journal of Chemical Physics, Vol. 140, Issue 17 https://doi.org/10.1063/1.4872239	journal	May 2014
Calculation of absolute protein-ligand binding free energy from computer simulations Woo, H. -J.; Roux, B. Proceedings of the National Academy of Sciences, Vol. 102, Issue 19 https://doi.org/10.1073/pnas.0409005102	journal	May 2005
Structures of E . coli σ ^S -transcription initiation complexes provide new insights into polymerase mechanism Liu, Bin; Zuo, Yuhong; Steitz, Thomas A. Proceedings of the National Academy of Sciences, Vol. 113, Issue 15 https://doi.org/10.1073/pnas.1520555113	journal	March 2016
Obligate movements of an active site–linked surface domain control RNA polymerase elongation and pausing via a Phe pocket anchor Bao, Yu; Landick, Robert Proceedings of the National Academy of Sciences, Vol. 118, Issue 36 https://doi.org/10.1073/pnas.2101805118	journal	September 2021
Bacterial RNA polymerase subunit and eukaryotic RNA polymerase subunit RPB6 are sequence, structural, and functional homologs and promote RNA polymerase assembly Minakhin, L.; Bhagat, S.; Brunning, A. Proceedings of the National Academy of Sciences, Vol. 98, Issue 3 https://doi.org/10.1073/pnas.98.3.892	journal	January 2001
X-ray Crystal Structure of Escherichia coli RNA Polymerase σ ⁷⁰ Holoenzyme Murakami, Katsuhiko S. Journal of Biological Chemistry, Vol. 288, Issue 13 https://doi.org/10.1074/jbc.M112.430900	journal	February 2013
Cryo-EM structure of Escherichia coli σ70 RNA polymerase and promoter DNA complex revealed a role of σ non-conserved region during the open complex formation Narayanan, Anoop; Vago, Frank S.; Li, Kunpeng Journal of Biological Chemistry, Vol. 293, Issue 19 https://doi.org/10.1074/jbc.RA118.002161	journal	May 2018
Using collective variables to drive molecular dynamics simulations Fiorin, Giacomo; Klein, Michael L.; Hénin, Jérôme Molecular Physics, Vol. 111, Issue 22-23 https://doi.org/10.1080/00268976.2013.813594	journal	December 2013
Clustal W and Clustal X version 2.0 Larkin, M. A.; Blackshields, G.; Brown, N. P. Bioinformatics, Vol. 23, Issue 21, p. 2947-2948 https://doi.org/10.1093/bioinformatics/btm404	journal	September 2007
lDDT: a local superposition-free score for comparing protein structures and models using distance difference tests Mariani, Valerio; Biasini, Marco; Barbato, Alessandro Bioinformatics, Vol. 29, Issue 21 https://doi.org/10.1093/bioinformatics/btt473	journal	August 2013
Structure-based analysis of RNA polymerase function: the largest subunit's rudder contributes critically to elongation complex stability and is not involved in the maintenance of RNA-DNA hybrid length Kuznedelov, Konstantin; Korzheva, Nataliya; Mustaev, Arkady The EMBO Journal, Vol. 21, Issue 6 https://doi.org/10.1093/emboj/21.6.1369	journal	March 2002
Structure of the bacteriophage PhiKZ non-virion RNA polymerase de Martín Garrido, Natàlia; Orekhova, Mariia; Lai Wan Loong, Yuen Ting Emilie Nucleic Acids Research, Vol. 49, Issue 13 https://doi.org/10.1093/nar/gkab539	journal	June 2021
Structural and functional analyses of the interaction of archaeal RNA polymerase with DNA Wojtas, Magdalena N.; Mogni, Maria; Millet, Oscar Nucleic Acids Research, Vol. 40, Issue 19 https://doi.org/10.1093/nar/gks692	journal	July 2012
Deciphering key features in protein structures with the new ENDscript server Robert, Xavier; Gouet, Patrice Nucleic Acids Research, Vol. 42, Issue W1 https://doi.org/10.1093/nar/gku316	journal	April 2014
Dali server update Holm, Liisa; Laakso, Laura M. Nucleic Acids Research, Vol. 44, Issue W1 https://doi.org/10.1093/nar/gkw357	journal	April 2016
A non-canonical multisubunit RNA polymerase encoded by the AR9 phage recognizes the template strand of its uracil-containing promoters Sokolova, Maria; Borukhov, Sergei; Lavysh, Daria Nucleic Acids Research, Vol. 45, Issue 10 https://doi.org/10.1093/nar/gkx264	journal	April 2017
Structures and mechanism of transcription initiation by bacterial ECF factors Fang, Chengli; Li, Lingting; Shen, Liqiang Nucleic Acids Research, Vol. 47, Issue 13 https://doi.org/10.1093/nar/gkz470	journal	May 2019
WebLogo: A Sequence Logo Generator Crooks, Gavin E.; Hon, Gary; Chandonia, John-Marc Genome Research, Vol. 14, Issue 6, p. 1188-1190 https://doi.org/10.1101/gr.849004	journal	May 2004
HKL2MAP : a graphical user interface for macromolecular phasing with SHELX programs Pape, Thomas; Schneider, Thomas R. Journal of Applied Crystallography, Vol. 37, Issue 5 https://doi.org/10.1107/S0021889804018047	journal	September 2004
Phaser crystallographic software McCoy, Airlie J.; Grosse-Kunstleve, Ralf W.; Adams, Paul D. Journal of Applied Crystallography, Vol. 40, Issue 4 https://doi.org/10.1107/S0021889807021206	journal	July 2007
The Buccaneer software for automated model building. 1. Tracing protein chains Cowtan, Kevin Acta Crystallographica Section D Biological Crystallography, Vol. 62, Issue 9 https://doi.org/10.1107/S0907444906022116	journal	August 2006
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
Recent developments in classical density modification Cowtan, Kevin Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 4 https://doi.org/10.1107/S090744490903947X	journal	March 2010
XDS Kabsch, Wolfgang Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2 https://doi.org/10.1107/S0907444909047337	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
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
Opening and Closing of the Bacterial RNA Polymerase Clamp Chakraborty, A.; Wang, D.; Ebright, Y. W. Science, Vol. 337, Issue 6094 https://doi.org/10.1126/science.1218716	journal	August 2012
Development of Giant Bacteriophage KZ Is Independent of the Host Transcription Apparatus Ceyssens, P. -J.; Minakhin, L.; Van den Bossche, A. Journal of Virology, Vol. 88, Issue 18 https://doi.org/10.1128/JVI.01347-14	journal	June 2014
Characterization of the Genome, Proteome, and Structure of Yersiniophage ϕR1-37 Skurnik, Mikael; Hyytiäinen, Heidi J.; Happonen, Lotta J. Journal of Virology, Vol. 86, Issue 23 https://doi.org/10.1128/JVI.01783-12	journal	December 2012
Comparative Genomics of Three Novel Jumbo Bacteriophages Infecting Staphylococcus aureus Korn, Abby M.; Hillhouse, Andrew E.; Sun, Lichang Journal of Virology, Vol. 95, Issue 19 https://doi.org/10.1128/JVI.02391-20	journal	September 2021
Transcription Profiling of Bacillus subtilis Cells Infected with AR9, a Giant Phage Encoding Two Multisubunit RNA Polymerases Lavysh, Daria; Sokolova, Maria; Slashcheva, Marina mBio, Vol. 8, Issue 1 https://doi.org/10.1128/mBio.02041-16	journal	March 2017
Origins of Specificity in Protein-DNA Recognition Rohs, Remo; Jin, Xiangshu; West, Sean M. Annual Review of Biochemistry, Vol. 79, Issue 1 https://doi.org/10.1146/annurev-biochem-060408-091030	journal	June 2010
Bacterial Sigma Factors: A Historical, Structural, and Genomic Perspective Feklístov, Andrey; Sharon, Brian D.; Darst, Seth A. Annual Review of Microbiology, Vol. 68, Issue 1 https://doi.org/10.1146/annurev-micro-092412-155737	journal	September 2014
Free Energy Via Molecular Simulation: Applications to Chemical and Biomolecular Systems Beveridge, D. L.; DiCapua, F. M. Annual Review of Biophysics and Biophysical Chemistry, Vol. 18, Issue 1 https://doi.org/10.1146/annurev.bb.18.060189.002243	journal	June 1989
Bacterial RNA Polymerase-DNA Interaction—The Driving Force of Gene Expression and the Target for Drug Action Lee, Jookyung; Borukhov, Sergei Frontiers in Molecular Biosciences, Vol. 3 https://doi.org/10.3389/fmolb.2016.00073	journal	November 2016
Bacterial Sigma Factors and Anti-Sigma Factors: Structure, Function and Distribution Paget, Mark Biomolecules, Vol. 5, Issue 3 https://doi.org/10.3390/biom5031245	journal	June 2015
Multisubunit RNA Polymerases of Jumbo Bacteriophages Sokolova, Maria L.; Misovetc, Inna; V. Severinov, Konstantin Viruses, Vol. 12, Issue 10 https://doi.org/10.3390/v12101064	journal	September 2020
Jumbo Phages: A Comparative Genomic Overview of Core Functions and Adaptions for Biological Conflicts M. Iyer, Lakshminarayan; Anantharaman, Vivek; Krishnan, Arunkumar Viruses, Vol. 13, Issue 1 https://doi.org/10.3390/v13010063	journal	January 2021
Structure of a bacterial RNA polymerase holoenzyme open promoter complex Bae, Brian; Feklistov, Andrey; Lass-Napiorkowska, Agnieszka eLife, Vol. 4 https://doi.org/10.7554/eLife.08504	journal	September 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

Similar Records

Site-specific aptamer inhibitors of Thermus RNA polymerase

Journal Article · Sun Jan 14 23:00:00 EST 2018 · Biochemical and Biophysical Research Communications · OSTI ID:23134089

Catching RNA Polymerase in the act of Binding: Intermediates in Transcription Illuminated by Synchrotron Footprinting

Journal Article · Fri Dec 31 23:00:00 EST 2004 · Proc Natl Acad Sci USA · OSTI ID:913907

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
RNA-binding proteins
bacteriophages
computational biophysics
cryoelectron microscopy
transcription

Structural basis of template strand deoxyuridine promoter recognition by a viral RNA polymerase

Citation Formats

References (74)

Similar Records

Related Subjects