Biology subjects

Rice, P.

Publications and source records attributed to Rice, P..

4 recordsLinked to original sources

bioRxiv2025

Structural basis of directionality control in large serine integrases

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 SP{beta} integrase-DNA complexes along the integrative (-RDF) and excisive (+RDF) reaction pathways, at resolutions extending to 3.15 [A]. 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 integrases 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.

biochemistry↗

bioRxiv2024

Variable orthogonality of RDF-large serine integrase interactions within the phiC31 family

Large serine integrases are phage- (or mobile element-) encoded enzymes that catalyse site-specific recombination reactions between a short DNA sequence on the phage genome (attP) and a corresponding host genome sequence (attB), thereby integrating the phage DNA into the host genome. Each integrase has its unique pair of attP and attB sites, a feature that allows them to be used as orthogonal tools for genome modification applications. In the presence of a second protein, the Recombination Directionality Factor (RDF), integrase catalyses the reverse, excisive reaction, generating new recombination sites, attR and attL. In addition to promoting attR x attL reaction, the RDF inhibits attP x attB recombination. This feature makes the directionality of integrase reactions programmable, allowing them to be useful for building synthetic biology devices. In this report, we describe the degree of orthogonality of both integrative and excisive reactions for three related integrases ({phi}C31, {phi}BT1, and TG1) and their RDFs. Among these, TG1 integrase is the most active, showing near complete recombination in both attP x attB and attR x attL reactions, and the most directional in the presence of its RDF. Our findings show that there is varying orthogonality among these three integrases - RDF pairs: {phi}C31 integrase was the least selective, with all three RDFs activating it for attR x attL recombination. Similarly, {phi}C31 RDF was the least effective among the three RDFs in promoting the excisive activities of the integrases, including its cognate {phi}C31 integrase. {phi}BT1 and TG1 RDFs were noticeably more effective than {phi}C31 RDF at inhibiting attP x attB recombination by their respective integrases, making them more suitable for building reversible genetic switches. AlphaFold-Multimer predicts very similar structural interactions between each cognate integrase - RDF pair. The binding surface on RDF is much more conserved than the binding surface on integrase, an indication that specificity is determined more by the integrase than the RDF. Overall, the observed weak integrase/RDF orthogonality across the three enzymes emphasizes the need for identifying and characterizing more integrase - RDF pairs. Additionally, the ability of a particular integrases preferred reaction direction to be controlled to varying degrees by non-cognate RDFs provides a path to tunable, non-binary genetic switches.

molecular biology↗

bioRxiv2022

Mobile genetic element-encoded putative DNA primases composed of A-family polymerase - SSB pairs

1Mobile genetic elements can encode a wide variety of genes that support their own stability and mobility as well as genes that provide accessory functions to their hosts. Such genes can be adopted from host chromosomes and can be exchanged with other mobile elements. Due to their accessory nature, the evolutionary trajectories of these genes can differ from those of essential host genes. The mobilome therefore provides a rich source of genetic innovation. We previously described a new type of primase encoded by S. aureus SCCmec elements that is composed of an A-family polymerase catalytic domain in complex with a small second protein that confers single-stranded DNA binding. Here we use new structure prediction methods in conjunction with sequence database searches to show that related primases are widespread among putative mobile genetic elements in the Firmicutes. Structure predictions show that the second protein adopts an OB fold (common among single-stranded DNA binding (SSB) proteins) and these predictions were far more powerful than simple sequence comparisons in identifying its homologs. The protein-protein interaction surface varies among these polymerase - SSB complexes and appears to have arisen repeatedly by exploiting partial truncations of the polymerases N-terminal accessory domains.

biochemistry↗

bioRxiv2021

Single cell RNA Sequencing Identifies G-protein Coupled Receptor 87 as a Novel Basal Cell Marker of Distal Honeycomb Cysts in Idiopathic Pulmonary Fibrosis

Idiopathic Pulmonary Fibrosis (IPF) is a progressive and fatal lung disease with limited therapeutic options. Epithelial reprogramming and honeycomb cysts are key pathological features of IPF, however, the IPF distal bronchiole cell subtypes and their potential contribution to IPF development and progression still remain poorly characterized. Here, we utilized single-cell RNA sequencing on enriched EpCAM+ cells of the distal IPF and Donor lung. Using the 10x Genomics platform, we generated a dataset of 47,881 cells and found distinct cell clusters, including rare cell types, such as suprabasal cells recently reported in the healthy lung. We identified G-protein coupled receptor (GPR) 87 as a novel surface marker of distal Keratin (KRT)5+ basal cells. GPR87 expression was localized to distal bronchioles and honeycomb cysts in IPF in situ by RNA Scope and immunolabeling. Modulation of GPR87 in primary human bronchial epithelial cells cultures resulted in impaired airway differentiation and ciliogenesis. Thus, GPR87 is a novel marker and potentially druggable target of KRT5+ basal progenitor cells likely contributing to bronchiole remodeling and honeycomb cyst development in IPF.

cell biology↗