Biology subjects

Duggan, G.

Publications and source records attributed to Duggan, G..

3 recordsLinked to original sources

bioRxiv2024

Models trained to predict differential expression across plant organs identify distal and proximal regulatory regions

AO_SCPLOWBSTRACTC_SCPLOWA large proportion of standing phenotypic variation is explained by genetic variation in noncoding regulatory regions. However, tools for the automated identification and characterization of noncoding regulatory sequences in genomes have lagged far behind those employed to annotate and predict the functions of protein coding sequences. We developed a modified transformer model and trained it to predict relative patterns of expression across a diverse set of tissues given a large sequence window for each gene of interest in the maize (Zea mays) genome. Nucleotides in the input DNA sequence with high saliency in gene expression pattern prediction overlapped with regions identified via comparative genomic or chromatin-based approaches as potential regulatory sequences. High saliency regions identified in a second species, sorghum (Sorghum bicolor), without species-specific training were also associated with potential regulatory sequences in noncoding regions upstream and downstream of each gene of interest. The potential impact of a scaleable and transferable approach to identifying regulatory sequences using saliency calculated from large context window models spans multiple applications. Specific use cases could include genome annotation, interpretation of natural genetic variation, and targeted editing in noncoding regions to alter patterns of levels of gene expression.

plant biology↗

bioRxiv2022

Transcriptional profiling of zebrafish identifies host factors controlling susceptibility to Shigella flexneri

Shigella flexneri is a human adapted pathovar of Escherichia coli that can invade the intestinal epithelium, causing inflammation and bacillary dysentery. Although an important human pathogen, the host response to S. flexneri is poorly understood. Zebrafish larvae, highly innovative for genomics, transcriptomics and genetic tractability, represent a valuable animal model to study human infections in vivo. Here we use a S. flexneri-zebrafish infection model to generate mRNA expression profiles of host response to S. flexneri infection at the whole animal level. The signature of early S. flexneri infection (detected at 6 hours post-infection) is dominated by immune response-related processes. Consistent with its clearance from the host, the signature of late S. flexneri infection (detected at 24 hours post-infection) is significantly changed, where only a small set of immune-related genes remain differentially expressed, including gpr84 which encodes a putative G-protein coupled receptor. Using mutant zebrafish lines generated by ENU, CRISPR mutagenesis and the F0 CRISPR knockout method, we show that gpr84-deficient larvae are more susceptible to S. flexneri infection. Together, these results highlight the power of zebrafish to model infection by bacterial pathogens and provide a community resource to investigate host response to S. flexneri infection.

microbiology↗

bioRxiv2018

A membrane-depolarising toxin substrate of the Staphylococcus aureus Type VII protein secretion system targets eukaryotes and bacteria

The type VII protein secretion system (T7SS) is conserved across Staphylococcus aureus strains and plays important roles in virulence and interbacterial competition. To date only one T7SS substrate protein, encoded in a subset of S. aureus genomes, has been functionally characterized. Here, using an unbiased proteomic approach, we identify TspA as a further T7SS substrate. TspA is encoded distantly from the T7SS gene cluster and is found across all S. aureus strains as well as in Listeria and Enterococci. Heterologous expression of TspA from S. aureus strain RN6390 indicates its C-terminal domain is toxic when targeted to the Escherichia coli periplasm and that it depolarizes the cytoplasmic membrane. The membrane depolarizing activity is alleviated by co-production of the membrane-bound TsaI immunity protein, which is encoded adjacent to tspA on the S. aureus chromosome. Using a zebrafish hindbrain ventricle infection model, we demonstrate that the T7SS of strain RN6390 promotes bacterial replication in vivo, and deletion of tspA leads to increased bacterial clearance. The toxin domain of TspA is highly polymorphic and S. aureus strains encode multiple tsaI homologues at the tspA locus, suggestive of additional roles in intra-species competition. In agreement, we demonstrate TspA-dependent growth inhibition of RN6390 by strain COL in the zebrafish infection model that is alleviated by the presence of TsaI homologues. Significance statementStaphylococcus aureus, a human commensal organism that asymptomatically colonizes the nares, is capable of causing serious disease following breach of the mucosal barrier. S. aureus strains encode a Type VII secretion system (T7SS) that is required for virulence in mouse infection models, and some strains also secrete a nuclease toxin by this route that has antibacterial activity. Here we identify TspA, widely found in Staphylococci and other pathogenic bacteria, as a T7 substrate. We show that TspA has membrane-depolarizing activity and that S. aureus uses TspA to inhibit the growth of a bacterial competitor in vivo.

microbiology↗