Center for RNA Biology

A zoonotic Babesia species previously referred to as Babesia sp. MO1 is formally described and named here as Babesia hegotelforum sp. nov. This taxon is distinct from Babesia divergens based on genome-wide sequence divergence, phylogenetic placement, host associations, and clinical presentation. The parasite infects erythrocytes of humans, and eastern cottontail rabbits (Sylvilagus floridanus), and is transmitted by Ixodes dentatus. The holotype consists of a Giemsa-stained thin blood smear and cryopreserved infected erythrocytes from the cloned isolate BML-Bh-B12 at ≤10 passages in continuous in vitro culture. Paratype material includes five additional clones (BML-Bh-H1, BML-Bh-F12, BML-Bh-H6, BML-Bh-A3, and BML-Bh-F1) derived from BEI Resources strain NR-50441, along with the original mixed isolate NR-50441. This species description meets the requirements of the International Code of Zoological Nomenclature and establishes Babesia hegotelforum sp. nov. as a distinct species of clinical and epidemiological significance in North America.

Phyling is a fast, scalable, and user-friendly tool supporting phylogenomic reconstruction of species phylogenies directly from protein-encoded genomic data. It identifies orthologous genes by searching protein sequences against a curated set of hidden Markov model profiles, consisting of single-copy orthologs derived from the BUSCO database. To optimize the speed of the final inference, Phyling includes a module to filter aligned orthologs based on their phylogenetic informativeness. Finally, Phyling provides a companion wrapper for automated species tree construction using either consensus or concatenation strategies. Phyling efficiently resolves large phylogenies by optimizing memory usage and data processing. Its checkpoint system enables users to incrementally add or remove samples without repeating the entire search process. For analyses involving closely related taxa, Phyling supports the use of nucleotide coding sequences, which may capture phylogenetic signals missed by protein sequences. The benchmark results show that Phyling substantially runs faster than OrthoFinder, a reciprocal best hit based method, while achieving equal or better accuracy.

Neural crest (NC) cells are multipotent cells unique to vertebrates that arise early in development, at the edge of the neural plate, and subsequently undergo an epithelial to mesenchymal transition, migrate throughout the body, and differentiate into many different derivatives, contributing to the formation of many organs and systems. NC induction research from multiple modeling organisms has identified critical roles for a few signaling pathways, including Wnt, BMP, FGF, Notch/ Delta, Indian Hedgehog, and Endothelin signaling (Prasad et al., 2019). Given the limitations of human embryo studies, pluripotent stem cell models of human NC formation have provided a resourceful alternative (Lee et al., 2007). Intriguingly, while TGFβ inhibition had not been identified as a signaling requirement for NC formation in any in vivo model organism, several pluripotent stem cell (PSC) models of human NC induction rely on TGFβ inhibition (Chambers et al., 2009). To address this issue, we evaluate the role of TGFβ in NC formation using our human (hNC) model that depends on WNT signaling and does not require TGFβ inhibition (Leung et al., 2016, Gomez et al., 2019). We report that under our model, TGFβ signaling is required, and that moderate levels of TGFβ and pSMAD2 levels are necessary for optimal NC formation (with negative effects seen upon strong activation or inhibition). Moreover, we demonstrate that PSC cultured in mTeSR1 immediately prior to hNC induction instead required TGFβ modulation in addition to WNT signaling activation to render hNC. Using the chick embryo as an in vivo vertebrate model, we further provide evidence of expression and requirement of relevant TGFβ signaling components during NC formation. This study identifies an important role for TGFβ signaling in early NC development, opening the door for novel players as effectors mediating the multiple signals integrated during early neural crest development.

Computational tools for studying the structure of protein complexes are essential for providing mechanistic insights into protein-protein interactions and therapeutic drug design. Here, we present SPICE (Structural Protein Interaction Complex Evaluator), a web-based platform that allows structural biologists to perform rapid, modular analyses of protein complexes directly from Protein Data Bank (PDB) structures. SPICE allows users to define and execute analysis workflows via an intuitive web interface, reducing analysis times from minutes to seconds. The platform offers a broad range of analytical capabilities, including (i) detection of hydrogen bonds, salt bridges, and disulfide bonds; (ii) protein-protein interface mapping; and (iii) computation of solvent accessibility, van der Waals energetics, and other key geometric descriptors. SPICE further provides interactive 3D visualization and supports comparative analyses across multiple complexes, enabling the study of mutational effects and binding variants. The tool is freely available at https://spice.cs.ucr.edu (no registration required).

Black fungi are among the most stress-resistant organisms known, yet the genetic and ecological foundations of their extraordinary resilience remain poorly understood. This study explores the adaptation strategies of the melanised fungus Elasticomyces elasticus by integrating genomic and ecological data. To uncover the mechanisms of adaptation, we combined whole-genome sequencing, functional annotation, environmental metadata, and large-scale soil metabarcoding analyses. Phylogenomic approaches were employed to delineate evolutionary lineages and assess ploidy levels. The results revealed that the global distribution of Elasticomyces phylotypes is primarily influenced by temperature, UV radiation, and soil organic carbon, suggesting that different phylotypes have evolved heterogeneous strategies for stress resistance. Comparative genomic analyses identified a set of 'sentinel pathways,' notably glutathione metabolism and nucleotide biosynthesis, which were enriched in strains inhabiting the most extreme environments and showed significant correlations with abiotic stressors such as aridity and UV exposure. Furthermore, phylogenomic reconstructions uncovered two independent diploid lineages associated with the harshest environments, pointing to diploidisation as a potential adaptive mechanism to cope with multiple stressors. Overall, the integration of genomic and ecological perspectives provides new insights into how black fungi persist at the edge of habitability. The study highlights specific pathways and genomic traits that underpin resilience to extreme conditions, offering implications that extend beyond terrestrial ecology.

Nucleotide salvage is crucial for maintaining DNA replication when de novo nucleotide synthesis is limited, but this metabolic flexibility poses potential threats to genome stability. Salvage kinases phosphorylate nucleosides broadly, allowing for oxidized and alkylated 2-deoxynucleosides as well as posttranscriptionally modified ribonucleosides to enter the 2-deoxynucleoside triphosphate (dNTP) pool. The ensuing contamination of the dNTP pool and the subsequent incorporation of modified nucleotides into genomic DNA promote mutagenesis, induce replication stress, elicit double-strand breaks, and disrupt epigenetic signaling. Although only a small subset of modified nucleosides have been assessed for salvage and genomic incorporation, the scope of salvageable substrates is probably much wider, with significant implications in mutational burden, chromatin instability, and epigenetic regulation. This overlooked aspect of genome instability is especially relevant in biological contexts of high salvage activity or elevated nucleoside damage, including chronic inflammation, cancer, aging, and dietary/microbiome exposures. Emerging evidence links salvage metabolism to tumor progression, where incorporation of salvage-derived nucleotides may contribute to unexplainable mutational signatures detected in cancers, such as gastrointestinal cancer. Recognizing salvage as a hidden source of mutagenesis reshapes our understanding of genome instability and provides potential opportunities for disease prevention, diagnosis, and therapeutic intervention.

The small interfering RNA (siRNA) pathway directs broad-spectrum antiviral defense through RNA silencing so that virulent infection requires efficient suppression of the defense mechanism. Here, we show that strigolactone (SL) hormone signaling promotes antiviral silencing in rice plants by transcriptional activation of RNA-dependent RNA polymerase 1 (RDR1) and RDR6. We demonstrate that protein P3 of the rice grassy stunt virus (RGSV) blocks SL signaling by directly sequestering the receptor DWARF14 from DWARF3. Structural and functional analyses of the P3-DWARF14 complex reveal that the aspartic acid at position 102 (D102) of DWARF14 is essential for the P3 interaction but not for SL perception. Notably, a single D102N substitution of DWARF14, introduced into two rice cultivars by cytosine base editing (CBE) confers resistance against RGSV by blocking viral suppression of SL signaling-dependent antiviral silencing. Our findings establish a transgene-free strategy for engineering disease resistance by precise genome editing of the SL receptor to escape pathogen suppression of the endogenous defense pathway.

Gene expression patterns are determined to a large extent by transcription factor (TF) binding to noncoding regulatory regions in the genome. However, gene expression cannot yet be systematically predicted from genome sequences, in part because nonfunctional matches to the sequence patterns (motifs) recognized by TFs occur frequently throughout the genome. Large-scale functional genomics data for many TFs has enabled characterization of regulatory networks in experimentally accessible cells such as budding yeast. Beyond yeast, fungi are important industrial organisms and pathogens, but large-scale functional data is only sporadically available. Uncharacterized regulatory networks control key pathways and gene expression programs associated with fungal phenotypes. Here, we explore a sequence-only approach to inferring regulatory networks by leveraging the 100s of genomes now available for many clades of fungi. We use gene orthology as the learning signal to infer interpretable, TF motif-based representations of noncoding regulatory regions. Using these representations to identify conserved signals for motifs, comparative genomics can be scaled to evolutionary comparisons where sequence similarity cannot be detected. We show that similarity of these conserved motif signals predicts gene expression and regulation better than using experimental data, and that we can infer known and novel regulatory connections in diverse fungi. Our new predictions include a pathway for recombination in Candida albicans and pathways for mating and an RNAi immune response in Neurospora. Taken together, our results indicate that specific hypotheses about transcriptional regulation in fungi can be obtained for many genes from genome sequence analysis alone.

BackgroundEastern hellbenders (Cryptobranchus alleganiensis alleganiensis) have undergone substantial population declines throughout their range, leading them to become the focus of increased conservation efforts, including care in zoo and university settings. However, effective implementation of such conservation strategies often relies on a comprehensive understanding of host health, which can be directly influenced by the gut microbiome, yet characterization of gut microbiota often remains overlooked in ex situ conservation facilities. Additionally, effects on the gut microbiome associated with releasing zoo-reared animals into the wild are poorly understood. Therefore, these circumstances make hellbenders an ideal species to examine the relationship between zoo management strategies and gut microbial dynamics.Methods16S rRNA sequencing was used to investigate dissimilarities between the gut microbiome of hellbenders in zoo and wild settings and to evaluate the impact of implementing a wild diet in zoo-reared hellbenders. Additionally, the bacterial composition of zoo-released individuals and wild resident hellbenders was compared to examine the response of the gut microbiome upon release into natural habitat. Selected samples were also chosen for ITS1 rDNA sequencing as a preliminary investigation of the hellbender gut mycobiome.ResultsHuman rearing strongly affected the gut microbiome, leading to reduced bacterial richness as well as differing community structure than wild hellbenders. However, implementation of a wild diet in a zoo setting modulated the microbiome and appeared to be mainly driven by bacterial turnover. Additionally, both bacterial and fungal gut assemblages demonstrated the capacity for restructuring upon release into native habitat to become more reflective of a wild-type microbiome.ConclusionsWe completed the first study elucidating the gut microbial composition patterns of hellbenders, across both zoo and wild settings. These results provide an understanding of the potential impacts of conservation populations in zoos on gut microbial communities and also inform headstart programs of the transition of the gut microbiome post-reintroduction to the wild.