Biology subjects

Sullivan, A. E.

Publications and source records attributed to Sullivan, A. E..

4 recordsLinked to original sources

bioRxiv2026

Minimal diadenylate cyclases have been co-opted to detect phage immune evasion

Many bacterial immune defenses transmit recognition of phage infection via the generation of diverse cyclic nucleotide second messengers. Phage have evolved to subvert this kind of immunity by sequestering, degrading, or inhibiting synthesis of these signaling molecules. Consequently, bacteria have evolved counter-mechanisms to detect disruption of cyclic nucleotide signaling and induce another layer of immune protection. Here we detail our discovery of the PanDA defense system (Panoptes-like DisA), an antiphage defense which detects sequestration of 3'3'-c-di-AMP by phage sponge proteins. PanDA consists of two proteins, PanS and PanE, which are both necessary for defense. PanS contains a minimal diadenylate cyclase (DAC) domain that constitutively generates the cyclic dinucleotide 3'3'-c-di-AMP which binds to and represses a toxic effector, the 2TM-{beta} family protein PanE. When a cell is infected by a phage encoding the sponge protein Acb4 (anti-CBASS protein 4), PanE is activated and induces membrane permeability. This work represents the first confirmed use of 3'3'-c-di-AMP as an immune second messenger in bacteria, facilitated by the exaptation of a DAC domain which has thus far only been best understood for its non-immune signaling roles.

microbiology↗

bioRxiv2025

A minimal CRISPR polymerase produces decoy cyclic nucleotides to detect phage anti-defense proteins

Bacteria use antiphage systems to combat phages, their ubiquitous competitors, and evolve new defenses through repeated reshuffling of basic functional units into novel reformulations. A common theme is generating a nucleotide-derived second messenger in response to phage that activates an effector protein to halt virion production. Phages respond with counter-defenses that deplete these second messengers, leading to an escalating arms race with the host. Here we discover a novel antiphage system we call Panoptes that detects phage infection by surveying the cytosol for phage proteins that antagonize the nucleotide-derived second messenger pool. Panoptes is a two-gene operon, optSE. OptS is predicted to synthesize a second messenger using a minimal CRISPR polymerase (mCpol) domain, a version of the polymerase domain found in Type III CRISPR systems (Cas10) that is distantly related to GGDEF and Thg1 tRNA repair polymerase domains. OptE is predicted to be a transmembrane effector protein that binds cyclic nucleotides. optSE potently restricted phage replication but mutant phages that had loss-of-function mutations in anti-CBASS protein 2 (Acb2) escaped defense. These findings were unexpected because Acb2 is a nucleotide "sponge" that antagonizes second messenger signaling. Using genetic and biochemical assays, we found that Acb2 bound the OptS-synthesized nucleotide, 2',3'-cyclic adenosine monophosphate (2',3'-c-di-AMP); however, 2',3'-c-di-AMP was synthesized constitutively by OptS and inhibited OptE. Nucleotide depletion by Acb2 released OptE toxicity thereby initiating abortive infection to halt phage replication. These data demonstrate a sophisticated immune strategy that hosts use to guard their second messenger pool and turn immune evasion against the virus.

microbiology↗

bioRxiv2022

Core and Flanking bHLH-PAS:DNA interactions mediate specificity and drive obesity

The basic-Helix-Loop-Helix Per-Arnt-Sim (PAS) homology domain (bHLH-PAS) transcription factor (TF) family comprises critical biological sensors of physiological (hypoxia, tryptophan metabolites, neuronal activity, and appetite) and environmental (diet derived metabolites and environmental pollutants) stimuli to regulate genes involved in signal adaptation and homeostasis1. bHLH TFs bind DNA as homo or heterodimers via E-box (CANNTG) response elements, however the DNA binding specificity of the PAS domain-containing bHLH subfamily remains unresolved1. We systematically analysed cognate DNA binding hierarchies of prototypical bHLH-PAS family members (ARNT, ARNT2, HIF1, HIF2, AhR, NPAS4, SIM1) and demonstrate distinct core (NNCGTG) specificities for different heterodimer classes. The results also show that bHLH-PAS TFs bind over a large footprint 12-15bp and recognise preferential DNA sequences flanking the core. For example, specificity beyond otherwise identical core binding by SIM1 and the HIFs is mediated through N-terminal HIF-DNA interactions. We also reveal an intimate relationship between DNA shape and both core and flanking TF binding allowing motif sequence flexibility and underpinning TF binding specificity. Furthermore, DNA-shape affinity relationships revealed that novel downstream PAS-A-loop DNA interactions are associated with AT-rich sequences that lead to high-affinity binding, and that loss of this function underpins a monogenic cause of human hyperphagic obesity in a recapitulated SIM1.R171H knock-in mouse model. Importantly, models of protein-DNA binding accurately predict in vivo occupancy, while response element methylation blocks DNA binding and predicts cell type specific chromatin occupancy. These data provide a definitive and accurate map of bHLH-PAS TF specificity and target selectivity through novel flanking protein-DNA interactions that are crucial for in vivo biological function.

molecular biology↗

bioRxiv2020

A comprehensive, FAIR file format for neuroanatomical structure modeling

With advances in microscopy and computer science, the technique of digitally reconstructing, modeling, and quantifying microscopic anatomies has become central to many fields of biological research. MBF Bioscience has chosen to openly document their digital reconstruction file format, Neuromorphological File Specification (4.0), available at www.mbfbioscience.com/filespecification (Angstman et al. 2020). One of such technologies, the format created and maintained by MBF Bioscience is broadly utilized by the neuroscience community. The data formats structure and capabilities have evolved since its inception, with modifications made to keep pace with advancements in microscopy and the scientific questions raised by worldwide experts in the field. More recent modifications to the neuromorphological data format ensure it abides by the Findable, Accessible, Interoperable, and Reusable (FAIR) data standards promoted by the International Neuroinformatics Coordinating Facility (INCF; Wilkinson et al. 2016). The incorporated metadata make it easy to identify and repurpose these data types for downstream application and investigation. This publication describes key elements of the file format and details their relevant structural advantages in an effort to encourage the reuse of these rich data files for alternative analysis or reproduction of derived conclusions.

neuroscience↗