About

Phoebe A. Rice, PhD, is a Professor of Biochemistry and Molecular Biology at the University of Chicago. Her research focuses on understanding how mobile genetic elements jump, utilizing biochemistry, structural biology, and microbiology to obtain mechanistic insights. Her projects include studying the SCCmec element of MRSA and the Mu transposase, contributing to the understanding of DNA recombination and transposition mechanisms. Dr. Rice's academic background includes a PhD in Molecular Biophysics & Biochemistry from Yale University, a post-doctoral fellowship in Transposition Biochemistry at NIH/NIDDK, and a BA in Biochemistry from Brandeis University. She has been recognized as a Distinguished Educator in the Basic Sciences at the University of Chicago and has received an NSF fellowship. Her work has significant implications for microbiology and infectious disease research, particularly in the context of antibiotic resistance and genetic mobility.

Research topics

• Machine Learning
• Computer Science
• Genetics
• Computational biology
• Biology

Selected publications

• Structural Determinants of SCCmec Recombination in <i>Staphylococcus aureus</i>

  Knowledge@UChicago (University of Chicago) · 2026-01-01

  otherOpen accessSenior author

  Methicillin resistance in Staphylococcus aureus emerges through acquisition of a mobile genetic element named staphylococcal cassette chromosome mec (SCCmec). SCCmec contains the mecA gene, which confers resistance, and the ccrA/ccrB or ccrC operons encoding large serine recombinases that integrate and excise the element. CcrA and B catalyze recombination between phage (attP) DNA and bacterial (attB) DNA attachment sites by introducing a double-stranded break, rotating the DNA strands 180 degrees, and re-ligating them. CcrA and B are unique among serine recombinases in that they lack clear directionality, form a tetramer from two proteins instead of one, and are structurally asymmetrical. This project investigates how attachment site architecture influences SCCmec recombination efficiency. Although attP and attB sites consist of inverted repeats and are expected to be symmetrical, attP contains a one-nucleotide deletion in one half-site, producing a 36° rotational offset in DNA alignment compared to the other half. The deletion enables plasmid integration into attB without disrupting the reading frame of conserved host gene rlmH, which attB contains the C-terminal end of. However, the functional impact of the deletion on recombination remains unclear. To address this question, I used fluorescence-based recombination assays in E. coli to test recombination across different attachment site configurations. These assays demonstrated, consistent with prior SCCmec studies, that recombination requires the half-site containing the C-terminal end of the rlmH gene. I then used in vitro biochemical recombination assays to evaluate synthetic attachment site variants that alter site symmetry. Preliminary results suggest that reducing native attP asymmetry increases recombination efficiency, indicating a tradeoff between optimal recombination and preservation of rlmH expression. Further work is needed to determine how specific attachment site features regulate SCCmec recombination. Understanding these constraints may ultimately inform strategies to disrupt SCCmec mobility and limit the spread of methicillin resistance in S. aureus.

  PublisherOA PDFDOI

• Antagonism by the type VI secretion system of <i>Bacteroides fragilis</i> is controlled by a TetR family regulator and released small molecule

  Proceedings of the National Academy of Sciences · 2026-04-07

  articleOpen access

  Antagonistic systems of bacteria are often tightly regulated. The human gut Bacteroidales harbor three distinct antagonistic type VI secretion systems (T6SS), one of which is present only in Bacteroides fragilis , known as the GA3 T6SS. Although this is the best studied of the three T6SSs, little is known about how it is regulated. The gene upstream of the GA3 T6SS locus encodes a TetR family transcriptional regulator (TetR GA3 ), which we show represses expression of the GA3 T6SS locus. The gene immediately upstream and divergently transcribed from tetR GA3 , designated here as lgs GA3 , encodes a product of the α-oxoamine synthase family of pyridoxal phosphate-dependent enzymes with structural homology to the CqsA autoinducer synthase of the CAI-1 quorum sensing system of Vibrio spp . When lgs GA3 is deleted, transcription of the GA3 T6SS locus is repressed in a TetR-dependent manner. Strains synthesizing Lgs GA3 produce a molecule released into the supernatant that likely serves as the TetR GA3 ligand, overcoming TetR transcriptional repression of the GA3 T6SS. We show that GA3 T6SS-specific immunity genes present on two acquired immunity defense islands are also regulated by Lgs GA3 coordinating expression of GA3 T6SS antagonism with protection from competitor’s GA3 T6SS toxins. Production and firing of the GA3 T6SS and subsequent antagonism occurs in bacteria deleted for lgs GA3 when growing with bacteria containing this gene or their supernatants or when cocolonizing gnotobiotic mice. These data show that the GA3 T6SS is regulated by a small molecule acting through TetR GA3 allowing the bacteria to coordinate antagonistic and protective systems.

  PublisherDOI

• Functional Relevance of <scp>CASP16</scp> Nucleic Acid Predictions as Evaluated by Structure Providers

  Proteins Structure Function and Bioinformatics · 2025-09-04 · 11 citations

  articleOpen access

  Accurate biomolecular structure prediction enables the prediction of mutational effects, the speculation of function based on predicted structural homology, the analysis of ligand binding modes, experimental model building, and many other applications. Such algorithms to predict essential functional and structural features remain out of reach for biomolecular complexes containing nucleic acids. Here, we report a quantitative and qualitative evaluation of nucleic acid structures for the CASP16 blind prediction challenge by 12 of the experimental groups who provided nucleic acid targets. Blind predictions accurately model secondary structure and some aspects of tertiary structure, including reasonable global folds for some complex RNAs; however, predictions often lack accuracy in the regions of highest functional importance. All models have inaccuracies in non-canonical regions where, for example, the nucleic-acid backbone bends, deviating from an A-form helix geometry, or a base forms a non-standard hydrogen bond (not a Watson-Crick base pair). These bends and non-canonical interactions are integral to forming functionally important regions such as RNA enzymatic active sites. Additionally, the modeling of conserved and functional interfaces between nucleic acids and ligands, proteins, or other nucleic acids remains poor. For some targets, the experimental structures may not represent the only structure the biomolecular complex occupies in solution or in its functional life cycle, posing a future challenge for the community.

  PublisherOA PDFDOI

• Author response for "Functional Relevance of CASP16 Nucleic Acid Predictions as Evaluated by Structure Providers"

  2025-08-04 · 2 citations

  peer-review
  PublisherDOI

• Flagellar switch inverted repeats impact heterogeneity in flagellar gene expression and thus C. difficile RT027/MLST1 virulence

  Cell Reports · 2025-06-01 · 4 citations

  articleOpen access

  Clostridioides difficile (C. difficile) RT027 strains cause infections that vary in severity from asymptomatic to lethal, but the molecular basis for this variability is poorly understood. Through comparative analyses of RT027 clinical isolates, we determine that isolates that exhibit greater heterogeneity in their flagellar gene expression exhibit greater virulence in vivo. C. difficile flagellar genes are phase-variably expressed due to the site-specific inversion of the flgB 5' UTR region, which reversibly generates ON vs. OFF orientations for the flagellar switch. We find that longer inverted repeat (IR) sequences in this switch region correlate with greater disease severity, with RT027 strains carrying 6A/6T IR sequences exhibiting greater phenotypic heterogeneity in flagellar gene expression (60%-75% ON) and causing more severe disease than those with shorter IRs (>99% ON or OFF). Our results reveal that phenotypic heterogeneity in flagellar gene expression may contribute to the variable disease severity observed in C. difficile patients.

  PublisherOA PDFDOI

• Structure of TnsABCD transpososome reveals mechanisms of targeted DNA transposition

  Structural Dynamics · 2025-09-01

  articleOpen access

  Tn7-like transposons are characterized by their ability to insert specifically into host chromosomes. Recognition of the attachment (att) site by TnsD recruits the TnsABC proteins to form the transpososome and facilitate transposition. Although this pathway is well established, atomic-level structural insights of this process remain largely elusive. Here, we present the cryo- electron microscopy (cryo-EM) structures of the TnsC-TnsD- att DNA complex and the TnsABCD transpososome from the Tn7-like transposon in Peltigera membranacea cyanobiont 210A, a type I-B CRISPR-associated transposon. Our structures reveal a striking bending of the att DNA, featured by the intercalation of an arginine side chain of TnsD into a CC/GG dinucleotide step. The TnsABCD transpososome structure reveals TnsA-TnsB interactions and demonstrates that TnsC not only recruits TnsAB but also directly participates in the transpososome assembly. These findings provide mechanistic insights into targeted DNA insertion by Tn7- like transposons, with implications for improving the precision and efficiency of their genome-editing applications.

  PublisherOA PDFDOI

• Abstract 2425 Large serine integrases: how do they know which way to go?

  Journal of Biological Chemistry · 2025-05-01

  articleOpen access1st authorCorresponding

  Site-specific DNA recombinases catalyze DNA insertions, inversions, and deletions in an extremely tidy fashion, leaving no broken phosphodiester bonds. However, the mechanism by which they do so leaves them with an interesting thermodynamic problem: the net number of high-energy bonds in the product is the same as that in the substrate. How do these enzymes drive their reactions to near completion? Furthermore, how do they “decide” which pairs of sites to pair as substrates and in what relative orientation? I will describe our progress on answering these questions for the serine-family group of site-specific recombinases termed the large serine integrases.

  PublisherOA PDFDOI

• Structural basis of directionality control in large serine integrases

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-01-03 · 4 citations

  preprintOpen accessSenior authorCorresponding

  Summary Large serine integrases (LSIs) catalyze unidirectional site-specific insertion of large DNA payloads, and in the presence of a cognate recombination directionality factor (RDF), catalyze unidirectional excision. Because neither reaction changes the net number of covalent bonds, the preferred direction must be controlled by the energetics of the changing protein-DNA complexes along these reaction pathways. However, a detailed understanding has been hampered by a lack of structural information. Here, we report 8 structures of SPβ integrase-DNA complexes along the integrative (-RDF) and excisive (+RDF) reaction pathways, at resolutions extending to 3.15 Å. These complexes include tetrameric intermediates before and after strand exchange and product-bound dimers for both pathways. Our findings reveal that both recombination-induced conformational changes and RDF-mediated repositioning of the integrase’s coiled-coil subdomain (1) dictate which pairs of DNA sites can be assembled into a synaptic complex to initiate recombination and (2) dictate which product complexes will be conformationally locked, preventing back reactions. Critically, we find that the synaptic complex in which excision occurs is fundamentally different from that in which integration occurs. These mechanistic insights provide a conceptual framework for engineering efficient and versatile genome editing tools.

  PublisherDOI

• Large serine integrases utilise scavenged phage proteins as directionality cofactors

  Nucleic Acids Research · 2025-01-21 · 2 citations

  articleOpen access

  Recombination directionality factors (RDFs) for large serine integrases (LSIs) are cofactor proteins that control the directionality of recombination to favour excision over insertion. Although RDFs are predicted to bind their cognate LSIs in similar ways, there is no overall common structural theme across LSI RDFs, leading to the suggestion that some of them may be moonlighting proteins with other primary functions. To test this hypothesis, we searched for characterized proteins with structures similar to the predicted structures of known RDFs. Our search shows that the RDFs for two LSIs, TG1 integrase and Bxb1 integrase, show high similarities to a single-stranded DNA binding (SSB) protein and an editing exonuclease, respectively. We present experimental data to show that Bxb1 RDF is probably an exonuclease and TG1 RDF is a functional SSB protein. We used mutational analysis to validate the integrase-RDF interface predicted by AlphaFold2 multimer for TG1 integrase and its RDF, and establish that control of recombination directionality is mediated via protein-protein interaction at the junction of recombinase's second DNA binding domain and the base of the coiled-coil domain.

  PublisherOA PDFDOI

• Identification of cognate recombination directionality factors for large serine recombinases by virtual pulldown

  Nucleic Acids Research · 2025-07-19

  articleOpen accessSenior author

  Integrases from the "large serine" family are simple, highly directional site-specific DNA recombinases that have great promise as synthetic biology and genome editing tools. Integrative recombination (mimicking phage or mobile element insertion) requires only integrase and two short (∼40-50) DNA sites. The reverse reaction, excisive recombination, does not occur until it is triggered by the presence of a second protein termed a recombination directionality factor (RDF), which binds specifically to its cognate integrase. Identification of RDFs has been hampered due to their lack of sequence conservation and lack of synteny with the phage integrase gene. Here we use AlphaFold2-multimer to identify putative RDFs for more than half of a test set of 98 large serine recombinases, and experimental methods to verify predicted RDFs for 6 of 9 integrases chosen as test cases. We find no universally conserved structural motifs among known and predicted RDFs, yet they are all predicted to bind a similar location on their cognate integrase, suggesting convergent evolution of function. Our methodology greatly expands the available genetic toolkit of cognate integrase-RDF pairs.

  PublisherOA PDFDOI

Recent grants

• Molecular and Cellular Biology Training

  NIH · $34.0M · 1975–2023

• Lifestyle of the SCCmec element and mechanisms of self-loading helicases

  NIH · $1.7M · 2017–2021

• NIH Grant R01GM086826

  NIH · $1.3M · 2013

• NIH Grant R56GM066011

  NIH · $261k · 2009

• NIH Grant R21AI117593

  NIH · $435k · 2018

Frequent coauthors

• J. Kenneth Baillie

  Roslin Institute

  100 shared

• James Scriven

  60 shared

• Julie Camsooksai

  Intensive Care National Audit & Research Centre

  40 shared

• Kathryn Simpson

  40 shared

• Joanna L. Birch

  University of Glasgow

  40 shared

• Jessica Jones

  40 shared

• Erola Pairo‐Castineira

  Roslin Institute

  32 shared

• Thomas A. Steitz

  Yale University

  31 shared

Labs

• Phoebe A. Rice's LabPI

Education

• B.A., Biochemistry

  Brandeis University

  1986

• Ph.D., Molecular Biophysics & Biochemistry

  Yale University

  1992

• Other, Transposition Biochemistry

  NIH / NIDDK

  1997

Awards & honors

• Distinguished Educator in the Basic Sciences University of C…
• NSF fellowship (1987)
• Gannett Newspaper Carrier Scholarship (1982 - 1986)