Phoebe A. Rice

Research Summary
How do mobile genetic elements jump? We use biochemistry, structural biology, and microbiology to get mechanistic answers. Projects include the SCCmec element of MRSA and the paradigmatic Mu transposase.
Mobile Genetic Elements, Biochemistry, Xray Crystallography, DNA recombination, Cryo electron Microscopy, Staphylococcus aureus, MRSA
  • NIH / NIDDK, Bethesda, MD, post-doctoral Transposition Biochemistry 1997
  • Yale University, New Haven, CT, PhD Molecular Biophysics & Biochemistry 1992
  • Brandeis University, Waltham, MA, BA Biochemistry 1986
Biosciences Graduate Program Association
Awards & Honors
  • 1982 - 1986 Gannett Newspaper Carrier Scholarship
  • 1987 - NSF fellowship
  • 2015 - Distinguished Educator in the Basic Sciences University of Chicago, Biological Sciences Division
  1. First full views of a CRISPR-guided system for gene insertion. Nature. 2023 Jan 11. View in: PubMed

  2. Structural basis for topological regulation of Tn3 resolvase. Nucleic Acids Res. 2023 02 22; 51(3):1001-1018. View in: PubMed

  3. The protein-protein interactions required for assembly of the Tn3 resolution synapse. Mol Microbiol. 2020 12; 114(6):952-965. View in: PubMed

  4. A novel DNA primase-helicase pair encoded by SCCmec elements. Elife. 2020 09 18; 9. View in: PubMed

  5. Comment on "RNA-guided DNA insertion with CRISPR-associated transposases". Science. 2020 06 05; 368(6495). View in: PubMed

  6. ABHD10 is an S-depalmitoylase affecting redox homeostasis through peroxiredoxin-5. Nat Chem Biol. 2019 12; 15(12):1232-1240. View in: PubMed

  7. Structure of the P element transpososome reveals new twists on the DD(E/D) theme. Nat Struct Mol Biol. 2019 11; 26(11):989-990. View in: PubMed

  8. Target highlights in CASP13: Experimental target structures through the eyes of their authors. Proteins. 2019 12; 87(12):1037-1057. View in: PubMed

  9. A conserved RNA structural motif for organizing topology within picornaviral internal ribosome entry sites. Nat Commun. 2019 08 09; 10(1):3629. View in: PubMed

  10. Characterizing Watson-Crick versus Hoogsteen Base Pairing in a DNA-Protein Complex Using Nuclear Magnetic Resonance and Site-Specifically 13C- and 15N-Labeled DNA. Biochemistry. 2019 04 16; 58(15):1963-1974. View in: PubMed

  11. Static Kinks or Flexible Hinges: Multiple Conformations of Bent DNA Bound to Integration Host Factor Revealed by Fluorescence Lifetime Measurements. J Phys Chem B. 2018 12 13; 122(49):11519-11534. View in: PubMed

  12. A new twist on V(D)J recombination. Nat Struct Mol Biol. 2018 08; 25(8):648-649. View in: PubMed

  13. Crystal Structure of an Unusual Single-Stranded DNA-Binding Protein Encoded by Staphylococcal Cassette Chromosome Elements. Structure. 2018 08 07; 26(8):1144-1150.e3. View in: PubMed

  14. Snapshots of a molecular swivel in action. Nucleic Acids Res. 2018 06 01; 46(10):5286-5296. View in: PubMed

  15. Mu transpososome activity-profiling yields hyperactive MuA variants for highly efficient genetic and genome engineering. Nucleic Acids Res. 2018 05 18; 46(9):4649-4661. View in: PubMed

  16. Two-step interrogation then recognition of DNA binding site by Integration Host Factor: an architectural DNA-bending protein. Nucleic Acids Res. 2018 02 28; 46(4):1741-1755. View in: PubMed

  17. Transposable phages, DNA reorganization and transfer. Curr Opin Microbiol. 2017 Aug; 38:88-94. View in: PubMed

  18. Target DNA bending by the Mu transpososome promotes careful transposition and prevents its reversal. Elife. 2017 02 13; 6. View in: PubMed

  19. Staphylococcal SCCmec elements encode an active MCM-like helicase and thus may be replicative. Nat Struct Mol Biol. 2016 Oct; 23(10):891-898. View in: PubMed

  20. Mobile genetic elements: in silico, in vitro, in vivo. Mol Ecol. 2016 Mar; 25(5):1027-31. View in: PubMed

  21. Crystal structure of the Varkud satellite ribozyme. Nat Chem Biol. 2015 Nov; 11(11):840-6. View in: PubMed

  22. Serine Resolvases. Microbiol Spectr. 2015 Apr; 3(2):MDNA3-0045-2014. View in: PubMed

  23. Deciphering the Roles of Multicomponent Recognition Signals by the AAA+ Unfoldase ClpX. J Mol Biol. 2015 Sep 11; 427(18):2966-82. View in: PubMed

  24. A G-quadruplex-containing RNA activates fluorescence in a GFP-like fluorophore. Nat Chem Biol. 2014 Aug; 10(8):686-91. View in: PubMed

  25. A proposed mechanism for IS607-family serine transposases. Mob DNA. 2013 Nov 06; 4(1):24. View in: PubMed

  26. Global analysis of ion dependence unveils hidden steps in DNA binding and bending by integration host factor. J Chem Phys. 2013 Sep 28; 139(12):121927. View in: PubMed

  27. Arginine as a general acid catalyst in serine recombinase-mediated DNA cleavage. J Biol Chem. 2013 Oct 04; 288(40):29206-14. View in: PubMed

  28. Roles of two large serine recombinases in mobilizing the methicillin-resistance cassette SCCmec. Mol Microbiol. 2013 Jun; 88(6):1218-29. View in: PubMed

  29. The ? transpososome structure sheds light on DDE recombinase evolution. Nature. 2012 Nov 15; 491(7424):413-7. View in: PubMed

  30. Mapping the transition state for DNA bending by IHF. J Mol Biol. 2012 May 18; 418(5):300-15. View in: PubMed

  31. Automated real-space refinement of protein structures using a realistic backbone move set. Biophys J. 2011 Aug 17; 101(4):899-909. View in: PubMed

  32. Regulation of Rad51 function by phosphorylation. EMBO Rep. 2011 Jul 08; 12(8):833-9. View in: PubMed

  33. Structural basis for catalytic activation of a serine recombinase. Structure. 2011 Jun 08; 19(6):799-809. View in: PubMed

  34. Moving DNA around: DNA transposition and retroviral integration. Curr Opin Struct Biol. 2011 Jun; 21(3):370-8. View in: PubMed

  35. Sin resolvase catalytic activity and oligomerization state are tightly coupled. J Mol Biol. 2010 Nov 19; 404(1):16-33. View in: PubMed

  36. Meeting report for mobile DNA 2010. Mob DNA. 2010 Aug 24; 1(1):20. View in: PubMed

  37. Structure of the LexA-DNA complex and implications for SOS box measurement. Nature. 2010 Aug 12; 466(7308):883-6. View in: PubMed

  38. Orchestrating serine resolvases. Biochem Soc Trans. 2010 Apr; 38(2):384-7. View in: PubMed

  39. Crystal structures of the reduced, sulfenic acid, and mixed disulfide forms of SarZ, a redox active global regulator in Staphylococcus aureus. J Biol Chem. 2009 Aug 28; 284(35):23517-24. View in: PubMed

  40. Regulatory mutations in Sin recombinase support a structure-based model of the synaptosome. Mol Microbiol. 2009 Oct; 74(2):282-98. View in: PubMed

  41. Inter-subunit interactions that coordinate Rad51's activities. Nucleic Acids Res. 2009 Feb; 37(2):557-67. View in: PubMed

  42. Protein binding has a large effect on radical mediated DNA damage. J Am Chem Soc. 2008 Oct 01; 130(39):12890-1. View in: PubMed

  43. Architecture of a serine recombinase-DNA regulatory complex. Mol Cell. 2008 Apr 25; 30(2):145-55. View in: PubMed

  44. Crystal structures of DNA/RNA repair enzymes AlkB and ABH2 bound to dsDNA. Nature. 2008 Apr 24; 452(7190):961-5. View in: PubMed

  45. Binding and catalytic contributions to site recognition by flp recombinase. J Biol Chem. 2008 Apr 25; 283(17):11414-23. View in: PubMed

  46. Control of transposase activity within a transpososome by the configuration of the flanking DNA segment of the transposon. Proc Natl Acad Sci U S A. 2007 Sep 11; 104(37):14622-7. View in: PubMed

  47. Identification of a potential general acid/base in the reversible phosphoryl transfer reactions catalyzed by tyrosine recombinases: Flp H305. Chem Biol. 2007 Feb; 14(2):121-9. View in: PubMed

  48. Shaping the Borrelia burgdorferi genome: crystal structure and binding properties of the DNA-bending protein Hbb. Mol Microbiol. 2007 Mar; 63(5):1319-30. View in: PubMed

  49. Binding then bending: a mechanism for wrapping DNA. Proc Natl Acad Sci U S A. 2006 Dec 19; 103(51):19217-8. View in: PubMed

  50. Structure-based analysis of HU-DNA binding. J Mol Biol. 2007 Jan 26; 365(4):1005-16. View in: PubMed

  51. Amino acid residues in Rag1 crucial for DNA hairpin formation. Nat Struct Mol Biol. 2006 Nov; 13(11):1010-5. View in: PubMed

  52. An oxidation-sensing mechanism is used by the global regulator MgrA in Staphylococcus aureus. Nat Chem Biol. 2006 Nov; 2(11):591-5. View in: PubMed

  53. Mechanisms of site-specific recombination. Annu Rev Biochem. 2006; 75:567-605. View in: PubMed

  54. Resolving integral questions in site-specific recombination. Nat Struct Mol Biol. 2005 Aug; 12(8):641-3. View in: PubMed

  55. The structure of the human AGT protein bound to DNA and its implications for damage detection. J Mol Biol. 2005 Jul 22; 350(4):657-66. View in: PubMed

  56. Visualizing Mu transposition: assembling the puzzle pieces. Genes Dev. 2005 Apr 01; 19(7):773-5. View in: PubMed

  57. Crystal structure of a Rad51 filament. Nat Struct Mol Biol. 2004 Aug; 11(8):791-6. View in: PubMed

  58. IHF and HU: flexible architects of bent DNA. Curr Opin Struct Biol. 2004 Feb; 14(1):28-35. View in: PubMed

  59. Flexible DNA bending in HU-DNA cocrystal structures. EMBO J. 2003 Jul 15; 22(14):3749-60. View in: PubMed

  60. Integration host factor: putting a twist on protein-DNA recognition. J Mol Biol. 2003 Jul 11; 330(3):493-502. View in: PubMed

  61. The role of the conserved Trp330 in Flp-mediated recombination. Functional and structural analysis. J Biol Chem. 2003 Jul 04; 278(27):24800-7. View in: PubMed

  62. New insight into site-specific recombination from Flp recombinase-DNA structures. Annu Rev Biophys Biomol Struct. 2003; 32:135-59. View in: PubMed

  63. Structural plasticity of the Flp-Holliday junction complex. J Mol Biol. 2003 Feb 14; 326(2):425-34. View in: PubMed

  64. Comparative architecture of transposase and integrase complexes. Nat Struct Biol. 2001 May; 8(5):302-7. View in: PubMed

  65. Crystallization and preliminary X-ray study of the edema factor exotoxin adenylyl cyclase domain from Bacillus anthracis in the presence of its activator, calmodulin. Acta Crystallogr D Biol Crystallogr. 2001 Dec; 57(Pt 12):1881-4. View in: PubMed

  66. Crystal structure of a Flp recombinase-Holliday junction complex: assembly of an active oligomer by helix swapping. Mol Cell. 2000 Oct; 6(4):885-97. View in: PubMed

  67. The contrasting mechanisms of serum resistance of Neisseria gonorrhoeae and group B Neisseria meningitidis. Mol Immunol. 1999 Sep-Oct; 36(13-14):915-28. View in: PubMed

  68. Holding damaged DNA together. Nat Struct Biol. 1999 Sep; 6(9):805-6. View in: PubMed

  69. An essential saccharide binding domain for the mAb 2C7 established for Neisseria gonorrhoeae LOS by ES-MS and MSn. Glycobiology. 1999 Feb; 9(2):157-71. View in: PubMed

  70. Complement processing and immunoglobulin binding to Neisseria gonorrhoeae determined in vitro simulates in vivo effects. J Infect Dis. 1999 Jan; 179(1):124-35. View in: PubMed

  71. Making DNA do a U-turn: IHF and related proteins. Curr Opin Struct Biol. 1997 Feb; 7(1):86-93. View in: PubMed

  72. Crystal structure of an IHF-DNA complex: a protein-induced DNA U-turn. Cell. 1996 Dec 27; 87(7):1295-306. View in: PubMed

  73. Retroviral integrases and their cousins. Curr Opin Struct Biol. 1996 Feb; 6(1):76-83. View in: PubMed

  74. Protein-protein interactions directing resolvase site-specific recombination: a structure-function analysis. EMBO J. 1993 Apr; 12(4):1447-58. View in: PubMed

  75. Model for a DNA-mediated synaptic complex suggested by crystal packing of gamma delta resolvase subunits. EMBO J. 1994 Apr 01; 13(7):1514-24. View in: PubMed

  76. Refinement of gamma delta resolvase reveals a strikingly flexible molecule. Structure. 1994 May 15; 2(5):371-84. View in: PubMed

  77. Structure of the bacteriophage Mu transposase core: a common structural motif for DNA transposition and retroviral integration. Cell. 1995 Jul 28; 82(2):209-20. View in: PubMed

  78. The phage Mu transpososome core: DNA requirements for assembly and function. EMBO J. 1995 Oct 02; 14(19):4893-903. View in: PubMed

  79. Two DNA polymerases: HIV reverse transcriptase and the Klenow fragment of Escherichia coli DNA polymerase I. Cold Spring Harb Symp Quant Biol. 1993; 58:495-504. View in: PubMed

  80. Structural basis of asymmetry in the human immunodeficiency virus type 1 reverse transcriptase heterodimer. Proc Natl Acad Sci U S A. 1994 Jul 19; 91(15):7242-6. View in: PubMed

  81. Structure of the binding site for nonnucleoside inhibitors of the reverse transcriptase of human immunodeficiency virus type 1. Proc Natl Acad Sci U S A. 1994 Apr 26; 91(9):3911-5. View in: PubMed

  82. Ribosomal protein L7/L12 has a helix-turn-helix motif similar to that found in DNA-binding regulatory proteins. Nucleic Acids Res. 1989 May 25; 17(10):3757-62. View in: PubMed

  83. Cooperativity mutants of the gamma delta resolvase identify an essential interdimer interaction. Cell. 1990 Dec 21; 63(6):1331-8. View in: PubMed

  84. The crystal structure of the catalytic domain of the site-specific recombination enzyme gamma delta resolvase at 2.7 A resolution. Cell. 1990 Dec 21; 63(6):1323-9. View in: PubMed

  85. A helix-turn-strand structural motif common in alpha-beta proteins. Proteins. 1990; 8(4):334-40. View in: PubMed

  86. Crystal structure at 3.5 A resolution of HIV-1 reverse transcriptase complexed with an inhibitor. Science. 1992 Jun 26; 256(5065):1783-90. View in: PubMed