Biology subjects

de Moraes, M. H.

Publications and source records attributed to de Moraes, M. H..

4 recordsLinked to original sources

bioRxiv2026

An endonuclease V protects Bacillus subtilis against a deaminase toxin and a uracil-containing phage

Bacteria deploy polymorphic toxins to inhibit competitors and rely on cognate immunity proteins to prevent self-intoxication. Immunity determinants act by binding and neutralizing incoming toxins, and in the rare cases where toxin-induced damage is also reversed, that activity resides within the immunity protein itself. Whether a conflict system can instead dedicate a separate gene to repairing the damage is unknown. Here we report that an operon in Bacillus subtilis encodes the toxin YwqJ, its cognate immunity protein YwqK, and EndoV an endonuclease that incises DNA at the lesion the toxin creates. YwqJ is a single-stranded DNA cytidine deaminase translocated by the type VIIb secretion system (T7SSb) to mediate contact-dependent interbacterial antagonism. Unexpectedly, EndoV exhibits a preference for uracil over the canonical hypoxanthine, processing genomic uracil in cells and protecting against YwqJ when immunity is absent. Because EndoV acts on the chemical lesion rather than the effector, its protection is indifferent to the source of deamination. EndoVBs accordingly restricts replication of PBS1, a bacteriophage whose genome naturally substitutes uracil for thymine. These findings establish DNA repair as a novel layer of defense within toxin-immunity loci and reveal a DNA repair mechanism that unifies interbacterial antagonism and antiviral immunity.

microbiology↗

bioRxiv2025

Pandoomain, a scalable pipeline for genomic and protein domain context analysis, reveals widespread PT-TG domain architectural diversity and novel polymorphic toxins

The rapid expansion of bacterial genome databases presents significant opportunities for functional discovery, yet a large fraction of genes and protein domains remain uncharacterized. Analyzing genomic context and domain architecture are powerful approaches for functional inference, but existing tools often lack the scalability and integrated workflow required for high-throughput analysis. To address this, we developed Pandoomain, a Snakemake pipeline that automates the acquisition of genomes from NCBI, identifies proteins of interest using Hidden Markov Models (HMMs), and performs systematic domain annotation and gene neighborhood analysis. We demonstrate the utility of Pandoomain through a comprehensive analysis of the poorly characterized pre-toxin TG (PT-TG) domain across 347,289 bacterial genomes. Our analysis revealed 10,226 PT-TG-containing proteins organized into 312 unique domain architectures, highlighting their association with diverse interbacterial antagonistic systems, including the Type VI, Type VII, and CDI systems. By leveraging genomic context, we identified a novel variant of the WXG trafficking domain, termed W10XG, and subsequently discovered 24 new families of associated toxin domains. We experimentally validated six of these toxins, confirming that five are neutralized by their cognate immunity proteins. Furthermore, our analysis revealed a significant enrichment of mobile genetic elements near W10XG and WXG domains compared to other trafficking domains, suggesting these loci are hotspots for genomic diversification. Pandoomain is an accessible tool that enables systematic, large-scale exploration of protein domains, and our analysis of the PT-TG domain provides a rich resource for future investigations into the mechanisms and evolution of bacterial antagonism.

microbiology↗

bioRxiv2021

Genome-wide protein-DNA interaction site mapping using a double strand DNA-specific cytosine deaminase

DNA-protein interactions (DPIs) are central to such fundamental cellular processes as transcription and chromosome maintenance and organization. The spatiotemporal dynamics of these interactions dictate their functional consequences; therefore, there is great interest in facile methods for defining the sites of DPI within cells. Here, we present a general method for mapping DPI sites in vivo using the double stranded DNA-specific cytosine deaminase toxin DddA. Our approach, which we term DddA-sequencing (3D-seq), entails generating a translational fusion of DddA to a DNA binding protein of interest, inactivating uracil DNA glycosylase, modulating DddA activity via its natural inhibitor protein, and DNA sequencing for genome-wide DPI detection. We successfully applied this method to three Pseudomonas aeruginosa transcription factors that represent divergent protein families and bind variable numbers of chromosomal locations. 3D-seq offers several advantages over existing technologies including ease of implementation and the possibility to measure DPIs at single-cell resolution.

genetics↗

bioRxiv2020

An interbacterial DNA deaminase toxin directly mutagenizes surviving target populations

When bacterial cells come in contact, antagonism mediated by the delivery of toxins frequently ensues. The potential for such encounters to have long-term beneficial consequences in recipient cells has not been investigated. Here we examined the effects of intoxication by DddA, a cytosine deaminase delivered via the type VI secretion system (T6SS) of Burkholderia cenocepacia. Despite its killing potential, we observed that several bacterial species resist DddA and instead accumulate mutations installed by the toxin, indicating that even in the absence of killing, interbacterial toxins can have profound consequences on target populations. Investigation of additional toxins from the deaminase superfamily revealed that mutagenic activity is a common feature of these proteins, including a representative we show targets single-stranded DNA and displays a markedly divergent structure. Our findings suggest that a surprising consequence of antagonistic interactions between bacteria could be the promotion of adaptation via the action of directly mutagenic toxins.

microbiology↗