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.
Keywords
Mobile Genetic Elements, Biochemistry, Xray Crystallography, DNA recombination, Cryo electron Microscopy, Staphylococcus aureus, MRSA
Education
  • 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
Publications
  1. Rice PA, Craig NL, Dyda F. Comment on "RNA-guided DNA insertion with CRISPR-associated transposases". Science. 2020 06 05; 368(6495). View in: PubMed

  2. Cao Y, Qiu T, Kathayat RS, Azizi SA, Thorne AK, Ahn D, Fukata Y, Fukata M, Rice PA, Dickinson BC. ABHD10 is an S-depalmitoylase affecting redox homeostasis through peroxiredoxin-5. Nat Chem Biol. 2019 12; 15(12):1232-1240. View in: PubMed

  3. Rice PA. 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

  4. Lepore R, Kryshtafovych A, Alahuhta M, Veraszto HA, Bomble YJ, Bufton JC, Bullock AN, Caba C, Cao H, Davies OR, Desfosses A, Dunne M, Fidelis K, Goulding CW, Gurusaran M, Gutsche I, Harding CJ, Hartmann MD, Hayes CS, Joachimiak A, Leiman PG, Loppnau P, Lovering AL, Lunin VV, Michalska K, Mir-Sanchis I, Mitra AK, Moult J, Phillips GN, Pinkas DM, Rice PA, Tong Y, Topf M, Walton JD, Schwede T. Target highlights in CASP13: Experimental target structures through the eyes of their authors. Proteins. 2019 12; 87(12):1037-1057. View in: PubMed

  5. Koirala D, Shao Y, Koldobskaya Y, Fuller JR, Watkins AM, Shelke SA, Pilipenko EV, Das R, Rice PA, Piccirilli JA. 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

  6. Zhou H, Sathyamoorthy B, Stelling A, Xu Y, Xue Y, Pigli YZ, Case DA, Rice PA, Al-Hashimi HM. 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

  7. Connolly M, Arra A, Zvoda V, Steinbach PJ, Rice PA, Ansari A. 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

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

  9. Mir-Sanchis I, Pigli YZ, Rice PA. 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

  10. Trejo CS, Rock RS, Stark WM, Boocock MR, Rice PA. Snapshots of a molecular swivel in action. Nucleic Acids Res. 2018 06 01; 46(10):5286-5296. View in: PubMed

  11. Rasila TS, Pulkkinen E, Kiljunen S, Haapa-Paananen S, Pajunen MI, Salminen A, Paulin L, Vihinen M, Rice PA, Savilahti H. 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

  12. Velmurugu Y, Vivas P, Connolly M, Kuznetsov SV, Rice PA, Ansari A. 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

  13. Toussaint A, Rice PA. Transposable phages, DNA reorganization and transfer. Curr Opin Microbiol. 2017 Aug; 38:88-94. View in: PubMed

  14. Fuller JR, Rice PA. Target DNA bending by the Mu transpososome promotes careful transposition and prevents its reversal. Elife. 2017 02 13; 6. View in: PubMed

  15. Mir-Sanchis I, Roman CA, Misiura A, Pigli YZ, Boyle-Vavra S, Rice PA. 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

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

  17. Suslov NB, DasGupta S, Huang H, Fuller JR, Lilley DM, Rice PA, Piccirilli JA. Crystal structure of the Varkud satellite ribozyme. Nat Chem Biol. 2015 Nov; 11(11):840-6. View in: PubMed

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

  19. Ling L, Montaño SP, Sauer RT, Rice PA, Baker TA. 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

  20. Huang H, Suslov NB, Li NS, Shelke SA, Evans ME, Koldobskaya Y, Rice PA, Piccirilli JA. A G-quadruplex-containing RNA activates fluorescence in a GFP-like fluorophore. Nat Chem Biol. 2014 Aug; 10(8):686-91. View in: PubMed

  21. Boocock MR, Rice PA. A proposed mechanism for IS607-family serine transposases. Mob DNA. 2013 Nov 06; 4(1):24. View in: PubMed

  22. Vivas P, Velmurugu Y, Kuznetsov SV, Rice PA, Ansari A. 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

  23. Keenholtz RA, Mouw KW, Boocock MR, Li NS, Piccirilli JA, Rice PA. 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

  24. Misiura A, Pigli YZ, Boyle-Vavra S, Daum RS, Boocock MR, Rice PA. Roles of two large serine recombinases in mobilizing the methicillin-resistance cassette SCCmec. Mol Microbiol. 2013 Jun; 88(6):1218-29. View in: PubMed

  25. Montaño SP, Pigli YZ, Rice PA. The µ transpososome structure sheds light on DDE recombinase evolution. Nature. 2012 Nov 15; 491(7424):413-7. View in: PubMed

  26. Vivas P, Velmurugu Y, Kuznetsov SV, Rice PA, Ansari A. Mapping the transition state for DNA bending by IHF. J Mol Biol. 2012 May 18; 418(5):300-15. View in: PubMed

  27. Haddadian EJ, Gong H, Jha AK, Yang X, Debartolo J, Hinshaw JR, Rice PA, Sosnick TR, Freed KF. 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

  28. Flott S, Kwon Y, Pigli YZ, Rice PA, Sung P, Jackson SP. Regulation of Rad51 function by phosphorylation. EMBO Rep. 2011 Jul 08; 12(8):833-9. View in: PubMed

  29. Keenholtz RA, Rowland SJ, Boocock MR, Stark WM, Rice PA. Structural basis for catalytic activation of a serine recombinase. Structure. 2011 Jun 08; 19(6):799-809. View in: PubMed

  30. Montaño SP, Rice PA. Moving DNA around: DNA transposition and retroviral integration. Curr Opin Struct Biol. 2011 Jun; 21(3):370-8. View in: PubMed

  31. Mouw KW, Steiner AM, Ghirlando R, Li NS, Rowland SJ, Boocock MR, Stark WM, Piccirilli JA, Rice PA. Sin resolvase catalytic activity and oligomerization state are tightly coupled. J Mol Biol. 2010 Nov 19; 404(1):16-33. View in: PubMed

  32. Chaconas G, Craig N, Curcio MJ, Deininger P, Feschotte C, Levin H, Rice PA, Voytas DF. Meeting report for mobile DNA 2010. Mob DNA. 2010 Aug 24; 1(1):20. View in: PubMed

  33. Zhang AP, Pigli YZ, Rice PA. Structure of the LexA-DNA complex and implications for SOS box measurement. Nature. 2010 Aug 12; 466(7308):883-6. View in: PubMed

  34. Rice PA, Mouw KW, Montaño SP, Boocock MR, Rowland SJ, Stark WM. Orchestrating serine resolvases. Biochem Soc Trans. 2010 Apr; 38(2):384-7. View in: PubMed

  35. Poor CB, Chen PR, Duguid E, Rice PA, He C. 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

  36. Rowland SJ, Boocock MR, McPherson AL, Mouw KW, Rice PA, Stark WM. Regulatory mutations in Sin recombinase support a structure-based model of the synaptosome. Mol Microbiol. 2009 Oct; 74(2):282-98. View in: PubMed

  37. Grigorescu AA, Vissers JH, Ristic D, Pigli YZ, Lynch TW, Wyman C, Rice PA. Inter-subunit interactions that coordinate Rad51's activities. Nucleic Acids Res. 2009 Feb; 37(2):557-67. View in: PubMed

  38. Peng X, Pigli YZ, Rice PA, Greenberg MM. 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

  39. Mouw KW, Rowland SJ, Gajjar MM, Boocock MR, Stark WM, Rice PA. Architecture of a serine recombinase-DNA regulatory complex. Mol Cell. 2008 Apr 25; 30(2):145-55. View in: PubMed

  40. Yang CG, Yi C, Duguid EM, Sullivan CT, Jian X, Rice PA, He C. Crystal structures of DNA/RNA repair enzymes AlkB and ABH2 bound to dsDNA. Nature. 2008 Apr 24; 452(7190):961-5. View in: PubMed

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

  42. Mizuuchi M, Rice PA, Wardle SJ, Haniford DB, Mizuuchi K. 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

  43. Whiteson KL, Chen Y, Chopra N, Raymond AC, Rice PA. 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

  44. Mouw KW, Rice PA. 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

  45. Khrapunov S, Brenowitz M, Rice PA, Catalano CE. 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

  46. Swinger KK, Rice PA. Structure-based analysis of HU-DNA binding. J Mol Biol. 2007 Jan 26; 365(4):1005-16. View in: PubMed

  47. Lu CP, Sandoval H, Brandt VL, Rice PA, Roth DB. Amino acid residues in Rag1 crucial for DNA hairpin formation. Nat Struct Mol Biol. 2006 Nov; 13(11):1010-5. View in: PubMed

  48. Chen PR, Bae T, Williams WA, Duguid EM, Rice PA, Schneewind O, He C. 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

  49. Grindley ND, Whiteson KL, Rice PA. Mechanisms of site-specific recombination. Annu Rev Biochem. 2006; 75:567-605. View in: PubMed

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

  51. Duguid EM, Rice PA, He C. 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

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

  53. Conway AB, Lynch TW, Zhang Y, Fortin GS, Fung CW, Symington LS, Rice PA. Crystal structure of a Rad51 filament. Nat Struct Mol Biol. 2004 Aug; 11(8):791-6. View in: PubMed

  54. Swinger KK, Rice PA. IHF and HU: flexible architects of bent DNA. Curr Opin Struct Biol. 2004 Feb; 14(1):28-35. View in: PubMed

  55. Swinger KK, Lemberg KM, Zhang Y, Rice PA. Flexible DNA bending in HU-DNA cocrystal structures. EMBO J. 2003 Jul 15; 22(14):3749-60. View in: PubMed

  56. Lynch TW, Read EK, Mattis AN, Gardner JF, Rice PA. Integration host factor: putting a twist on protein-DNA recognition. J Mol Biol. 2003 Jul 11; 330(3):493-502. View in: PubMed

  57. Chen Y, Rice PA. 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

  58. Chen Y, Rice PA. New insight into site-specific recombination from Flp recombinase-DNA structures. Annu Rev Biophys Biomol Struct. 2003; 32:135-59. View in: PubMed

  59. Conway AB, Chen Y, Rice PA. Structural plasticity of the Flp-Holliday junction complex. J Mol Biol. 2003 Feb 14; 326(2):425-34. View in: PubMed

  60. Rice PA, Baker TA. Comparative architecture of transposase and integrase complexes. Nat Struct Biol. 2001 May; 8(5):302-7. View in: PubMed

  61. Drum CL, Shen Y, Rice PA, Bohm A, Tang WJ. 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

  62. Chen Y, Narendra U, Iype LE, Cox MM, Rice PA. 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

  63. Ram S, Mackinnon FG, Gulati S, McQuillen DP, Vogel U, Frosch M, Elkins C, Guttormsen HK, Wetzler LM, Oppermann M, Pangburn MK, Rice PA. 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

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

  65. Mühlecker W, Gulati S, McQuillen DP, Ram S, Rice PA, Reinhold VN. 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

  66. McQuillen DP, Gulati S, Ram S, Turner AK, Jani DB, Heeren TC, Rice PA. 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

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

  68. Rice PA, Yang S, Mizuuchi K, Nash HA. Crystal structure of an IHF-DNA complex: a protein-induced DNA U-turn. Cell. 1996 Dec 27; 87(7):1295-306. View in: PubMed

  69. Rice P, Craigie R, Davies DR. Retroviral integrases and their cousins. Curr Opin Struct Biol. 1996 Feb; 6(1):76-83. View in: PubMed

  70. Hughes RE, Rice PA, Steitz TA, Grindley ND. Protein-protein interactions directing resolvase site-specific recombination: a structure-function analysis. EMBO J. 1993 Apr; 12(4):1447-58. View in: PubMed

  71. Rice PA, Steitz TA. 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

  72. Rice PA, Steitz TA. Refinement of gamma delta resolvase reveals a strikingly flexible molecule. Structure. 1994 May 15; 2(5):371-84. View in: PubMed

  73. Rice P, Mizuuchi K. 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

  74. Savilahti H, Rice PA, Mizuuchi K. The phage Mu transpososome core: DNA requirements for assembly and function. EMBO J. 1995 Oct 02; 14(19):4893-903. View in: PubMed

  75. Steitz TA, Smerdon S, Jäger J, Wang J, Kohlstaedt LA, Friedman JM, Beese LS, Rice PA. 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

  76. Wang J, Smerdon SJ, Jäger J, Kohlstaedt LA, Rice PA, Friedman JM, Steitz TA. 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

  77. Smerdon SJ, Jäger J, Wang J, Kohlstaedt LA, Chirino AJ, Friedman JM, Rice PA, Steitz TA. 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

  78. Rice PA, Steitz TA. 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

  79. Hughes RE, Hatfull GF, Rice P, Steitz TA, Grindley ND. Cooperativity mutants of the gamma delta resolvase identify an essential interdimer interaction. Cell. 1990 Dec 21; 63(6):1331-8. View in: PubMed

  80. Sanderson MR, Freemont PS, Rice PA, Goldman A, Hatfull GF, Grindley ND, Steitz TA. 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

  81. Rice PA, Goldman A, Steitz TA. A helix-turn-strand structural motif common in alpha-beta proteins. Proteins. 1990; 8(4):334-40. View in: PubMed

  82. Kohlstaedt LA, Wang J, Friedman JM, Rice PA, Steitz TA. 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