The Faculty


Structural biochemistry of DNA recombination


B.A., Biochemistry Brandeis University, 1986

Ph.D., Molecular Biophysics and Biochemistry Yale University, 1992

Post-doctoral fellow at LMB/NIDDK/NIH 1993-1997

Research Summary

We combine biochemistry and x-ray crystallography to study protein-DNA interactions and DNA recombination.

Site-specific DNA recombinases: These cut and paste DNA at defined sequences, and are useful genetic tools. They exchange DNA partners via a remarkable molecular swivel. Two favorites are:
(1) Sin, which aids stable maintenance of multi-resistance plasmids of S. aureus. Sin is regulated by the global topology of its plasmid substrate. In collaboration with the Stark group in Glasgow, we are using kinetics, crystallography, and molecular modeling to understand this enzyme at the molecular level.
(2) CcrA/B/C, which mobilize the methicillin-resistance encoding element that turns garden-variety S. aureus into MRSA. Their catalytic domain is related to Sin’s, but their regulation is very different and rather mysterious. This is a local collaboration with Drs. Daum and Boyle- Vavra, who study the epidemiology of MRSA.

“classical” DNA transposases: members of this family are closely related to retroviral integrases. They catalyze the mobility of numerous DNA transposons, contributing to horizontal gene transfer and antibiotic resistance in bacteria.
Rad51 and its prokaryotic counterpart RecA , repair dsDNA breaks and rescue stalled replication forks. They bind a single strand of DNA, then play molecular matchmaker to align it with a homologous sequence in duplex DNA. We determined the first structure of a filament of yeast Rad51, and are examining the details of the protein-protein interactions that activate its ATPase.

LexA, the master regulator of the bacterial DNA damage response and a potential antibiotic target. LexA is a transcriptional repressor that cleaves itself when it contacts active RecA filaments. We recently determined the structure of LexA bound to an SOS box, and are working to understand its interactions with RecA, and the surprising variety of SOS systems found in diverse bacteria.

Selected Publications

A novel DNA primase-helicase pair encoded by SCCmec elements.
Bebel A, Walsh MA, Mir-Sanchis I, Rice PA.Elife. 2020 Sep 18;9:e55478. doi: 10.7554/eLife.55478.PMID: 32945259 Free PMC article.

Comment on "RNA-guided DNA insertion with CRISPR-associated transposases".
Rice PA, Craig NL, Dyda F.Science. 2020 Jun 5;368(6495):eabb2022. doi: 10.1126/science.abb2022.PMID: 32499410

Structure of the P element transpososome reveals new twists on the DD(E/D) theme.
Rice PA.Nat Struct Mol Biol. 2019 Nov;26(11):989-990. doi: 10.1038/s41594-019-0329-4.PMID: 31659331 No abstract available.

Target highlights in CASP13: Experimental target structures through the eyes of their authors.
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 Jr, Pinkas DM, Rice PA, Tong Y, Topf M, Walton JD, Schwede T.Proteins. 2019 Dec;87(12):1037-1057. doi: 10.1002/prot.25805. Epub 2019 Sep 9.PMID: 31442339 Free PMC article.

A conserved RNA structural motif for organizing topology within picornaviral internal ribosome entry sites.
Koirala D, Shao Y, Koldobskaya Y, Fuller JR, Watkins AM, Shelke SA, Pilipenko EV, Das R, Rice PA, Piccirilli JA.Nat Commun. 2019 Aug 9;10(1):3629. doi: 10.1038/s41467-019-11585-z.PMID: 31399592 Free PMC article.

Characterizing Watson-Crick versus Hoogsteen Base Pairing in a DNA-Protein Complex Using Nuclear Magnetic Resonance and Site-Specifically 13C- and 15N-Labeled DNA.
Zhou H, Sathyamoorthy B, Stelling A, Xu Y, Xue Y, Pigli YZ, Case DA, Rice PA, Al-Hashimi HM.Biochemistry. 2019 Apr 16;58(15):1963-1974. doi: 10.1021/acs.biochem.9b00027. Epub 2019 Apr 5.PMID: 30950607 Free PMC article.

Static Kinks or Flexible Hinges: Multiple Conformations of Bent DNA Bound to Integration Host Factor Revealed by Fluorescence Lifetime Measurements.
Connolly M, Arra A, Zvoda V, Steinbach PJ, Rice PA, Ansari A.J Phys Chem B. 2018 Dec 13;122(49):11519-11534. doi: 10.1021/acs.jpcb.8b07405. Epub 2018 Nov 7.PMID: 30336035

A new twist on V(D)J recombination.
Dyda F, Rice PA.Nat Struct Mol Biol. 2018 Aug;25(8):648-649. doi: 10.1038/s41594-018-0107-8.PMID: 30061601 Free PMC article.

Crystal Structure of an Unusual Single-Stranded DNA-Binding Protein Encoded by Staphylococcal Cassette Chromosome Elements.
Mir-Sanchis I, Pigli YZ, Rice PA.Structure. 2018 Aug 7;26(8):1144-1150.e3. doi: 10.1016/j.str.2018.05.016. Epub 2018 Jul 12.PMID: 30017563 Free PMC article.

Snapshots of a molecular swivel in action.
Trejo CS, Rock RS, Stark WM, Boocock MR, Rice PA.Nucleic Acids Res. 2018 Jun 1;46(10):5286-5296. doi: 10.1093/nar/gkx1309.PMID: 29315406 Free PMC article.

Mu transpososome activity-profiling yields hyperactive MuA variants for highly efficient genetic and genome engineering.
Rasila TS, Pulkkinen E, Kiljunen S, Haapa-Paananen S, Pajunen MI, Salminen A, Paulin L, Vihinen M, Rice PA, Savilahti H.Nucleic Acids Res. 2018 May 18;46(9):4649-4661. doi: 10.1093/nar/gkx1281.PMID: 29294068 Free PMC article.

Two-step interrogation then recognition of DNA binding site by Integration Host Factor: an architectural DNA-bending protein.
Velmurugu Y, Vivas P, Connolly M, Kuznetsov SV, Rice PA, Ansari A.Nucleic Acids Res. 2018 Feb 28;46(4):1741-1755. doi: 10.1093/nar/gkx1215.PMID: 29267885 Free PMC article.