Biology subjects

Toro, N.

Publications and source records attributed to Toro, N..

8 recordsLinked to original sources

bioRxiv2026

Murine modeling of IDH-mutant 1p/19q-codeleted oligodendroglioma reveals genotype specific phenotypes

Oligodendroglioma is a primary central nervous system tumor classified by the presence of isocitrate dehydrogenase (IDH) mutations and codeletion of 1p/19q. Here we describe the generation of an IDH-mutant 1p/19q-codeleted oligodendroglioma mouse model using in utero electroporation. We identified IDH1R132H, PIK3CAE545K, CicKO, Fubp1KO and Cdkn2aKO as the optimal combination (termed OligoCdkn2a) to drive fully penetrant tumors that histologically resemble human grade II/III IDH-mutant, 1p/19q-codeleted oligodendroglioma. Replacing Cdkn2a with Trp53 loss in this mouse model shifted tumor histology towards high grade astrocytoma. OligoCdkn2a tumors displayed metabolic and transcriptional changes associated with IDH and CIC mutations, and single cell sequencing identified a bias towards oligodendrocyte differentiation compared to an IDH wild-type glioblastoma mouse model. OligoCdkn2a tumors represent the first mouse model system to recapitulate the genetic, histological and transcriptional features of human IDH-mutant 1p/19q-codeleted oligodendrogliomas, offering a platform to further dissect tumor biology and test new therapeutic strategies.

cancer biology↗

bioRxiv2026

Landscape of retron diversity across the SPIRE prokaryotic metagenome resource reveals candidate novel type XI-like lineages

Retrons are prokaryotic genetic elements encoding a specialized reverse transcriptase (RT) that synthesizes multicopy single-stranded DNA (msDNA) and are increasingly recognized as components of bacterial anti-phage defense systems. However, their diversity and ecological distribution across large-scale genomic resources remain poorly characterized. Here, we surveyed retron RTs across the SPIRE representative metagenome collection, a non-redundant, species-level dataset spanning diverse microbial habitats. Using type-specific hidden Markov models cross-calibrated against all known retron groups, we identified retrons representing all canonical types together with additional divergent lineages. Retron distribution was highly structured across both taxonomy and ecology, with some lineages restricted to specific bacterial phyla and others broadly distributed across habitats. Host-associated environments accounted for the largest fraction of retron candidates, although several retron types showed clear specialization for aquatic or anthropogenic niches. Systematic novelty assessment identified two candidate type XI-like lineages, TXI_C2like and TXI_noncan_h, characterized by protease-independent architectures and lineage-specific accessory modules. De novo computational analyses further identified candidate msr/msd-like non-coding RNA elements upstream of the RT genes in both lineages, indicating that these highly divergent systems retain the defining RT-ncRNA architecture of canonical retrons. Together, these findings expand the known diversity of retron systems and reveal a strong interplay between evolutionary history and ecological specialization.

microbiology↗

bioRxiv2026

Host exonuclease SbcB and a phage-encoded SSB-like protein control activation of the DRT10 reverse transcriptase defense system

Defense-associated reverse transcriptases (DRTs) employ diverse mechanisms of cDNA synthesis to protect bacteria against phage infection, yet their full diversity and regulatory logic remain poorly understood. Here we provide a mechanistic characterization of UG17 (DRT10), a class-2 system within the UG/Abi reverse transcriptase lineage, classifying it into three phylogenetically and architecturally distinct subtypes with subtype-specific ncRNAs and experimentally validating its role in phage defense. DRT10 operates as a tripartite module, comprising a structured ncRNA, a SLATT effector, and an RT that catalyzes processive synthesis of DNA containing 7 nt tandem repeats. The tandem-repeat cDNA intermediate accumulates as both first- and second-strand species. SbcB suppresses DRT10-mediated toxicity and appears to selectively degrade the second strand under basal conditions, while phage infection correlates with enhanced first-strand accumulation. A phage-encoded protein with predicted SSB-like architecture and a conserved C-terminal tip motif is required for efficient DRT10 activation during infection. Together, these findings establish DRT10 as a surveillance system whose activation threshold is jointly controlled by constitutive cDNA synthesis, host exonuclease activity, and a phage-encoded SSB-like trigger that perturbs host ssDNA metabolism. We propose a model in which accumulation of DRT10-derived cDNA triggers activation of the SLATT transmembrane effector to initiate immune defense.

microbiology↗

bioRxiv2026

Post-translational toxin-antitoxin control and RecBCD surveillance underlie phage defense in a constitutively armed Type VI retron

Type VI retrons are bacterial defense systems that couple reverse transcription to phage immunity through dedicated toxin-antitoxin modules, yet the mechanisms linking ssDNA synthesis to toxin activation remain unclear. Here we characterize Retron-Sen3, a Type VI retron from Salmonella enterica encoding a small protein (SP) toxin, an HTH antitoxin, and a reverse transcriptase (RT). Unlike previously examined Type VI retrons, Retron-Sen3 constitutively produces RT-dependent ssDNA species in the absence of phage infection, and these levels remain unchanged during infection, establishing that defense activation is uncoupled from ssDNA synthesis. Comparative analyses revealed a conserved ncRNA architecture across the cl2075 lineage, including a previously undescribed stem-loop essential for defense, and an extended transcript encompassing the SP coding region within a structurally conserved RNA framework. SP is constitutively produced and intrinsically toxic, whereas HTH neutralizes SP toxicity, is required for basal viability, and physically associates with RT in vivo independently of catalytic activity; notably, the HTH-SP toxin-antitoxin module operates independently of RT and ncRNA. Phage escape mutants and genetic analyses establish that inhibition of the host RecBCD complex triggers defense activation, identifying RecBCD surveillance as the signal that couples phage infection to toxin activation. Together, these findings reveal a post-translational regulatory mechanism distinct from the msDNA-dependent translational control described for Retron-Vpa2, establishing mechanistic diversity within this retron family.

microbiology↗

bioRxiv2025

A UG5 reverse transcriptase-nitrilase antiviral module confers phage immunity in the plant symbiont Sinorhizobium meliloti

Bacteriophages exert strong selective pressure on soil- and rhizosphere-associated bacteria, including plant-associated symbionts. Reverse transcriptase-associated defense systems of the UG family are widespread across bacterial lineages, yet their ecological roles remain largely undefined. Within this family, UG5 systems are distinguished by reverse transcriptases fused to or associated with a nitrilase domain. Here, we combine phylogenetic, metagenomic, and functional analyses to investigate the evolutionary context and antiviral activity of UG5-associated systems. Phylogenetic analysis of 728 nitrilase domains places UG5-associated nitrilases within a well-supported UG-related radiation encompassing the UG1, UG5, and UG6 families, with UG1 nested within a broader UG5 lineage. Metagenomic analysis further revealed UG5-associated reverse transcriptases in soil- and rhizosphere-derived metagenomes. Based on this observation, we characterized a UG5-large RT-associated system, here designated DRT11, encoded on the pSymA megaplasmid of Sinorhizobium meliloti RMO17, a nitrogen-fixing symbiont of Medicago sativa. Despite lacking the transmembrane protein typical of canonical UG5-large architectures, DRT11 confers protection against naturally occurring M. sativa rhizosphere phages with Podoviridae-like morphology. Phage infection assays reveal protection at low multiplicities of infection, consistent with an abortive-infection-like mechanism. Moreover, mutational analyses demonstrate that antiviral activity requires only the RT and its fused C-terminal nitrilase domain, establishing DRT11 as a minimal UG5-associated antiviral system.

microbiology↗

bioRxiv2024

Spacer acquisition in type VI CRISPR-Cas systems associated with reverse transcriptase-Cas1 fusion proteins

In prokaryotes, CRISPR-Cas systems store memories of past infections in the form of spacers integrated into CRISPR arrays. When associated with type III CRISPR-Cas systems, Reverse transcriptase-Cas1 fusion proteins (RT-Cas1) enable these defense systems to acquire spacers from RNA sources. However, despite the specific targeting of RNA by the Cas13-containing type VI CRISPR-Cas systems, there is no evidence of RNA-origin spacer acquisition. Using computational analyses, we recently reported the association of RT-Cas1 fusion proteins with type VI-A systems. In this study, we found that RT-Cas1 fusion proteins were also associated with complete type VI-B systems in bacteria from gut metagenomes, constituting a variant system that harbors a linked CorA-encoding locus in addition to the CRISPR array and adaptation RT-Cas1/Cas2 module. By combining in vitro and in vivo experiments, we demonstrated that type VI RT-CRISPR systems are functional for spacer acquisition and CRISPR array processing, and that the associated RT enables spacer acquisition from RNA molecules, thus demonstrating that the system is capable of functioning independently of other in-trans systems. These findings highlight the importance of RTs in RNA-targeting CRISPR-Cas systems, suggesting a potential defense mechanism against RNA-based invaders in specific environments.

microbiology↗

bioRxiv2024

Similar mechanisms of retron-mediated anti-phage defense for different families of tailed phages

Bacterial retrons are tripartite systems consisting of a cognate non-coding RNA, reverse transcriptase, and additional (effector) protein with diverse predicted enzymatic functions. In this study, we investigated the role and mechanism of Retron-Eco11, a novel type III-A3 retron system associated with a phosphoribosyltransferase-like effector protein, in phage defense. Here, we show that the Retron-Eco11 tripartite system protects against phage infection and that UvsW and D10, two functional homolog helicases found in T4 and T5 phages, respectively, serve as specific triggers for the Retron-Eco11 defense system. Our findings confirmed that msDNA and both protein components of the intron complex are indispensable for its protective function. Once the retron system detects the activity of these helicase proteins, it activates the toxicity of the effector protein bound to the retron complex, leading to an abortive infection. These findings underscore the application of a comparable anti-phage defense strategy using Retron-Eco11 across diverse phage families. This should aid in deciphering the processes through which the Retron complex detects and identifies the invading phages.

microbiology↗

bioRxiv2021

UG/Abi: a highly diverse family of prokaryotic reverse transcriptases associated with defense functions

Reverse transcriptases (RTs) are enzymes capable of synthesizing DNA using RNA as a template. Within the last few years, a burst of research has led to the discovery of novel prokaryotic RTs with diverse antiviral properties, such as DRTs (Defense-associated RTs), which belong to the so-called group of unknown RTs (UG) and are closely related to the Abortive Infection system (Abi) RTs. In this work, we performed a systematic analysis of UG and Abi RTs, increasing the number of UG/Abi members up to 42 highly diverse groups, most of which are predicted to be functionally associated with other gene(s) or domain(s). Based on this information, we classified these systems into three major classes. In addition, we reveal that most of these groups are associated with defense functions and/or mobile genetic elements, and demonstrate the antiphage role of four novel groups. Besides, we highlight the presence of one of these systems in novel families of human gut viruses infecting members of the Bacteroidetes and Firmicutes phyla. This work lays the foundation for a comprehensive and unified understanding of these highly diverse RTs with enormous biotechnological potential.

evolutionary biology↗