Department of Diagnostic and Biological Sciences
Biology, BA, St. Olaf College, 1984
Genetics, Ph.D., University of Minnesota, 1989
Postdoctoral Associate, Cytogam Inc. (Phoenix, Ariz), 1989-1990
18-242 Moos Tower
515 Delaware St. SE
Minneapolis, MN 55455
My research interest is in viral assembly, using the Bacillus subtilis bacteriophage ø29 as a model system. ø29 is a member of the tailed double-stranded DNA (dsDNA) bacteriophages that includes lambda, SPP1 and T4. Bacteriophages are excellent model systems for discerning the mechanisms of assembly and serve as model systems for similar processes in the medically relevant dsDNA animal viruses, such as herpesvirus and adenovirus. ø29 morphogenesis includes assembly of a precursor capsid (prohead), packaging of the viral genomic DNA into the head, followed by the sequential addition of tail proteins to yield the mature infectious virion. The cascade of conformational changes that drive assembly uncover basic principles of protein-protein, protein-DNA, protein-RNA interactions, and DNA transport. ø29 is a premier model system for mechanistic studies of assembly due to the highly efficient in vitro assembly assays and its relative compositional simplicity.
Recent emphasis has been on determining the molecular mechanism of DNA packaging. During this process, the viral genome is packaged into a prohead, thereby compacting the DNA to near-crystalline density. This remarkable process is driven by a transiently assembled molecular motor that converts energy from ATP hydrolysis into the translocation of DNA. Since they must work against the large entropic and electrostatic forces that resist DNA compaction, these packaging motors are among the most powerful biological motors known. The motor is assembled at a unique vertex of the head and, in ø29, is comprised of the dodecameric head-tail connector, a pentameric ring of viral-encoded prohead RNA (pRNA), and a pentameric ring of the viral packaging ATPase. We employ a highly integrated, multi-disciplinary approach to dissect the mechanism of packaging: in my lab, genetic and biochemical studies of motor components provides functional analysis and are combined with collaborations in structural biology (X-ray crystallography, cryo-EM, and NMR) to provide atomic pictures of the motor and the motor-in-action, and single-molecule laser tweezers analysis to dissect motor dynamics. Recent high-resolution tweezers studies have revealed that the ø29 DNA packaging motor operates via a complex, highly coordinated two-phase mechanism. During the “dwell” phase, DNA is stationary; the five ATPase subunits release ADP from the previous cycle, and bind ATP to re-load the motor. During the “burst” phase, ATP hydrolysis and subsequent Pi release are coupled to a rapid translocation of 10bp of DNA into the viral head. This 10bp “burst” is comprised of four 2.5bp sub-steps, with the “fifth” subunit playing a regulatory role to align the motor each cycle. The strict, sequential order of operation demands significant communication in the motor to achieve this level of coordination.
A particular interest of mine is the role of the novel pentameric pRNA ring in the packaging motor. While the head-tail connector and ATPase protein motor components are common to the dsDNA phages, ø29 and its relatives are distinct in that RNA is an essential part of the DNA packaging motor. Given that the phage motors are carrying out the same essential task, it is likely that the functions provided by pRNA are encoded in sub-domains of the larger motor proteins in the other phages. pRNA is a viral-encoded 174-base transcript that forms a pentameric ring through intermolecular base-pairing between complementary loops of adjacent pRNAs in the ring. Visualization of pRNA in the motor by cryo-EM 3-D reconstruction reveals a ring form with five protruding spokes; it is to these “spokes” that the ATPase assembles into its functional ring form. Recent progress has included the first atomic structures of functional sub-domains of pRNA and assignment of function to the essential loops and bulges of pRNA. Of note was the visualization of RNA superhelices in the crystal structure of a pRNA ring that show this suprastructure is formed by alignment of helical elements from adjacent pRNAs via the intermolecular base-pairing. Functionally, these supehelices would serve to connect all the protein components of the motor (capsid, connector and ATPase), suggesting a potential role in motor communication/coordination. The ultimate goal of this research is to determine the atomic structures and dissect the roles of the individual motor components in the packaging process and understand how they work together and communicate and coordinate with each other to create this elegant motor.
NIH / GMS RNA in Viral DNA Packaging
NIH / GMS The DNA Packaging Motor of Bacteriophage phi29
NIH / GMS Mechanisms of Viral DNA Packaging
Liu, S., G. Chistol, C. L. Hetherington, S. Tafoya, K. Aathavan, J. Schnitzbauer, S. Grimes, P.J. Jardine, and C. Bustamante. 2014. A viral packaging motor varies its DNA rotation and step size to preserve subunit coordination as the capsid fills. Cell 157:702-713.
Cao, S., M. Saha, W. Zhao, P. J. Jardine, W. Zhang, S. Grimes** and M. Morais**. 2014. Insight into the structure and assembly of the bacteriophage ø29 double-stranded DNA packaging motor. J. Virol 88:3986-3996.
Berndsen, Z.T., N. Keller, S. Grimes, P.J. Jardine and D.E. Smith. 2014. Nonequilibrium dynamics and ultraslow relaxation of confined DNA during viral packaging. Proc Natl Acad Sci USA 111:8345-8350.
Keller, N., D. delToro, S. Grimes, P.J. Jardine and D.E. Smith. 2014. Repulsive DNA-DNA interactions accelerate viral DNA packaging in phage phi29. Phys Rev Lett. 112:248101.
Chistol, G, S. Liu, C. L. Hetherington, J. R. Moffitt, S. Grimes, P. J. Jardine and C. Bustamante. 2012. High degree of coordination and division of labor among subunits in a homomeric ring ATPase. Cell 151:1017-1028.
Zhao, W., M. Saha, A. Ke, M.C. Morais, P. J. Jardine and S. Grimes. 2012. Three-helix junction is the interface between two functional domains of prohead RNA in ø29 DNA packaging. J. Virol 86:11625-11632.
Harjes, E., A. Kitamura, W. Zhao, M. C. Morais, P. J. Jardine, S. Grimes** and H. Matsuo** Structure of the RNA claw of the DNA packaging motor of bacteriophage ø29. 2012. Nucleic Acids Res. 40:9953-9963.
Grimes, S., Ma, S., Gao, J., Atz, R., and Jardine, P.J. 2011. Role of ø29 Connector Channel Loops in Late-Stage DNA-gp3 Packaging. J. Mol. Biol. 410:50-59.
Ding, F., Lu, C., Zhao, W., Rajashankar, K.R, Anderson D. L., Jardine, P. J., Grimes, S., and A. Ke. 2011. Structure and assembly of the essential RNA ring component of a viral DNA packaging motor. Proc. Natl. Acad. Sci. USA 108:7357-7362.
Aathavan, K., A.T. Politzer, A. Kaplan, J.R. Moffitt, Y.R. Chemla, S. Grimes, P.J. Jardine, D.L. Anderson and C. Bustamante. 2009. Substrate Interactions and Promiscuity in a Viral DNA Packaging Motor. Nature 461:669-673.
Xiang, Y., P. G. Leiman, L. Li, S. Grimes, D. L. Anderson, and M. G. Rossmann. 2009. Crystallographic insights into the autocatalytic assembly mechanism of a bacteriophage tail spike. Mol. Cell 34:375-386.
Moffitt, J. R., Y. R. Chemla, K. Aathavan, S. Grimes, P. J. Jardine, D. L Anderson, and C. Bustamante. 2009. Intersubunit coordination in a homomeric ring ATPase. Nature 457:446-450.
Zhao, W., M. C. Morais, D. L. Anderson, P. J. Jardine, and S. Grimes. 2008. Role of the CCA bulge of prohead RNA of bacteriophage ø29 in DNA packaging. J. Mol. Biol. 383:520-528.
Kitamura, A., P. J. Jardine, D. L. Anderson, S. Grimes, and H. Matsuo. 2008. Analysis of intermolecular base pair formation of prohead RNA of the phage ø29 DNA packaging motor using NMR spectroscopy. Nucleic Acids Res. 36:839-848.
Tang, J., N. Olson, P. J. Jardine, S. Grimes, D. L. Anderson, and T. S. Baker. 2008. DNA poised for release in bacteriophage ø29. Structure 6:935-943.
Comolli, L. R., A. J. Spakowitz, C. E. Siegerist, P. J. Jardine, S. Grimes, D. L. Anderson, C. Bustamante, and K. H. Downing. 2008. Three-dimensional architecture of the bacteriophage ø29 packaged genome and elucidation of its packaging process. Virology 371:267-277.
Rickgauer, J. P., D. N. Fuller, S. Grimes, P. J. Jardine, D. L. Anderson, and D. E. Smith. 2008. Portal motor velocity and internal force resisting viral DNA packaging in bacteriophage ø29. Biophys. J. 94:159-167.
Fuller, D. N., D. M. Raymer, J. P. Rickgauer, R. M. Robertson, C. E. Catalano, D. L. Anderson, S. Grimes, and D. E. Smith. 2007. Measurements of single DNA molecule packaging dynamics in bacteriophage lambda reveal high forces, high motor processivity, and capsid transformations. J. Mol. Biol. 373:1113-1122.
Fuller, D., J. P. Rickgauer, P. J. Jardine, S. Grimes, D. L. Anderson, and D. E. Smith. 2007. Ionic effects on viral DNA packaging and portal motor function in bacteriophage ø29. Proc. Natl. Acad. Sci. U. S. A. 104:11245-11250.
Atz, R., S. Ma, J. Gao, D. L. Anderson, and S. Grimes. 2007. Alanine scanning and Fe-BABE probing of the bacteriophage ø29 prohead RNA-connector interaction. J. Mol. Biol. 369:239-248.
Hugel, T., J. Michaelis, C. L. Hetherington, P. J. Jardine, S. Grimes, J. M. Walter, W. Falk, D. L. Anderson, and C. Bustamante. 2007. Experimental test of connector rotation during DNA packaging into bacteriophage phi29 capsids. PLoS Biol. 5(3):e59.
Xiang, Y., M. C. Morais, A. J. Battisti, S. Grimes, P. J. Jardine, D. L. Anderson, and M. G. Rossmann. 2006. Structural changes of bacteriophage ø29 upon DNA packaging and release. EMBO J. 25:5229-5239.
Chemla, Y., R. K. Aathavan, J. Michaelis, S. Grimes, P. J. Jardine, D. L. Anderson, and C. Bustamante. 2005. Mechanism of force generation of a viral DNA packaging motor. Cell 122:683-692.
Smith, D. E., S. J. Tans, S. B. Smith, S. Grimes, D. L. Anderson, and C. Bustamante. 2001. The bacteriophage ø29 portal motor can package DNA against a large internal force. Nature 413:748-752.
Morais, M., C., Y. Tao, N. H. Olson, S. Grimes, P. J. Jardine, D. L. Anderson, T. S. Baker, and M. G. Rossmann. 2001. Cryoelectron-microscopy image reconstruction of symmetry mismatches in bacteriophage ø29. J. Struct. Biol. 135:38-46.
Simpson, A. A., Y. Tao, P. G. Leiman, M. O. Badasso, Y. He, P. J. Jardine, N. H. Olson, M. C. Morais, S. Grimes, D. L. Anderson, T. S. Baker, and M. G. Rossmann. 2000. Structure of the bacteriophage ø29 DNA packaging motor. Nature 408:745-750.