Biology subjects

Peralta, C.

Publications and source records attributed to Peralta, C..

14 recordsLinked to original sources

bioRxiv2026

Genomic and proteomic insights into the virulence of a native Heterorhabditis indica-Photorhabdus akhurstii complex active against Spodoptera spp.

A native entomopathogenic nematode isolate, Heterorhabditis indica Che4.1, was recovered from soils in Valencia (Spain), and its symbiotic bacterium, Photorhabdus akhurstii Che4.1, was isolated and characterized. Nematode identification was confirmed by ITS and 28S rDNA sequencing, while genome-based analyses supported the taxonomic assignment of the bacterial symbiont. The nematode-bacterium complex exhibited insecticidal activity against Spodoptera exigua and Spodoptera littoralis. H. indica Che4.1 showed an LC of 53.7 infective juveniles (IJs)/mL against S. exigua, comparable to that of the commercial reference Larvanem (54.3 IJs/mL). Against S. littoralis, Che4.1 exhibited an approximately twofold lower LC than Larvanem (77.3 versus 155.9 IJs/mL), with non-overlapping 95% confidence intervals. The complete genome of P. akhurstii Che4.1 consists of a single circular chromosome of 5.66 Mb encoding a diverse repertoire of putative virulence factors, including toxin complex (Tc) components, YenTc-like proteins, Mcf toxins, App-family proteins, Pra/Prb proteins, and chitinases, together with several predicted secondary metabolite biosynthetic gene clusters. LC-MS/MS analyses of bacterial culture supernatants and infected insect cadavers detected multiple predicted virulence-associated proteins, including Tc-related, YenTc-like, App-family, and Pra/Prb proteins. In addition, bacterial cell-free supernatants caused 68.8-81.3% mortality in S. exigua neonates under laboratory conditions. Together, these findings reveal a diverse repertoire of potential virulence determinants in P. akhurstii Che4.1 and demonstrate the insecticidal potential of its native nematodebacterium complex. The performance of H. indica Che4.1 relative to a commercial reference supports further evaluation of this isolate for biological control of Spodoptera spp., particularly under greenhouse and field conditions.

microbiology↗

bioRxiv2026

KMT2E recruitment by H3 serotonylation regulates neurodevelopmental chromatin dynamics

Histone H3 Gln 5 serotonylation (H3Q5ser) is a recently identified epigenetic modification in brain that modulates reader interactions with adjacent H3 Lys 4 trimethylation (H3K4me3) to promote transcriptional permissiveness. However, whether H3K4me3Q5ser and its associated binding proteins regulate neurodevelopmental gene expression programs remains unknown. Here, we identified the catalytically inactive Lysine methyltransferase 2E (KMT2E) as a reader of combinatorial H3K4me3Q5ser. KMT2E preferentially binds H3K4me3Q5ser over H3K4me3 alone, and enriches at broad chromatin domains marking actively transcribed neurodevelopmental loci. Notably, heterozygous variants in KMT2E have been implicated in ODLURO syndrome, a recently characterized neurodevelopmental disorder (NDD). To identify the molecular mechanisms underlying ODLURO syndrome, we generated a Kmt2e transgenic mouse model that reproduces behavioral, physiological, and cellular endophenotypes associated with this and other NDDs. Furthermore, we observed that KMT2E mediates these effects by recruiting the NCoR/HDAC3 repressor complex to H3K4me3Q5ser-marked loci to restrict spreading of co-localized H3 Lys 9 acetylation (H3K9ac). Inhibition of aberrant H3K9ac spreading was sufficient to rescue transcriptional dysregulation in Kmt2e haploinsufficient neurons. These findings thus establish KMT2E as a critical reader of H3 serotonylation during neurodevelopment and provide mechanistic insights into the pathogenesis of ODLURO syndrome.

neuroscience↗

bioRxiv2026

Comparative genomics reveals extensive genomic conservation and limited microdiversification among Xenorhabdus bovienii isolates recovered from a single Steinernema feltiae isolation event.

Xenorhabdus bovienii is a symbiotic bacterium associated with entomopathogenic nematodes of the genus Steinernema. Comparative genomic analyses of closely related isolates provide an opportunity to investigate fine-scale diversification, genome plasticity, and the evolutionary processes shaping symbiotic bacterial populations. Here, we analyzed four X. bovienii isolates (XenUTI4.1-XenUTI4.4) recovered from a single Steinernema feltiae isolation event using comparative genomics approaches integrating average nucleotide identity (ANI), single-nucleotide polymorphism (SNP) analyses, pangenome reconstruction, biosynthetic gene cluster (BGC) prediction, and mobile element-associated annotation screening. Whole-genome comparisons revealed extremely high genomic similarity among isolates, with ANI values exceeding 99.84%. Read-based SNP analyses identified only 23-36 annotated variants relative to the XenUTI4.1 reference genome, indicating limited sequence divergence despite detectable microvariation. Functional annotation of these variants showed that most corresponded to missense or synonymous substitutions affecting a small number of coding sequences. Pangenome analysis identified 4,712 orthologous gene clusters, including a highly conserved core genome of 4,256 clusters (90.3%) shared by all isolates and a relatively small accessory genome comprising 456 clusters. antiSMASH analyses revealed broadly conserved secondary metabolite biosynthetic potential across the four genomes, whereas screening of genome annotations identified abundant phage-related, transposase-associated, and recombination-associated genes consistent with ongoing genome plasticity. Collectively, these results demonstrate that the analyzed X. bovienii isolates represent a highly conserved population exhibiting limited but detectable genomic microdiversification. The coexistence of a large core genome, a modest accessory gene complement, and numerous mobile element-associated functions suggests that localized sequence variation and mobile genetic elements contribute to genomic diversification within S. feltiae-associated X. bovienii populations.

genetics↗

bioRxiv2026

Secretome analysis of Bacillus toyonensis Bto_UNVM-42 reveals extracellular pesticidal protein homologs and enzymes consistent with its nematicidal activity.

Previous studies demonstrated that cell-free supernatants of Bacillus toyonensis biovar Thuringiensis Bto_UNVM-42 exhibit nematicidal activity against Panagrellus redivivus, although the molecular basis of this phenotype remains unclear. While pesticidal proteins in Bacillus thuringiensis and related species are classically considered intracellular and associated with parasporal crystals, their occurrence in extracellular fractions remains poorly explored. Here, we characterized the extracellular protein repertoire of biologically active supernatants and evaluated their effects on Caenorhabditis elegans N2. LC-MS/MS analysis of LB-derived cell-free supernatants revealed the presence of pesticidal protein homologs related to Cry32-, Cyt1, and Mpp3-like protein families, together with degradative enzymes including collagenases, chitinases, proteases, phospholipases, and cytolysins. Signal peptide prediction suggested classical secretion pathways for several proteins, whereas others may reach extracellular fractions through alternative localization mechanisms. Comparative DIA-based proteomic analyses of LB and CCY supernatants revealed marked medium-dependent differences in the extracellular protein repertoire, including differential enrichment of Bt-like pesticidal homologs and degradative enzymes associated with distinct physiological states. Exposure assays showed that concentrated cell-free supernatants from both conditions caused severe loss of mobility and morphological alterations consistent with tissue disruption in C. elegans. Together, these findings provide proteomic evidence for the extracellular occurrence of pesticidal and degradative protein homologs in Bto_UNVM-42 and identify candidate extracellular factors potentially associated with the nematicidal activity of this strain. More broadly, the results support the view that soluble extracellular components may contribute to the biological activity of Bt-related bacteria beyond the classical spore-crystal paradigm.

microbiology↗

bioRxiv2026

A 16S rRNA gene-based analysis of microbial communities in compost-bedded pack barns from dairy farms in Argentina.

Microbial communities play a central role in compost-bedded pack (CBP) systems by driving organic matter decomposition and nutrient cycling. The objective of this study was to characterize and compare the bacterial community structure of CBP from two dairy farms in Cordoba, Argentina, using 16S rRNA gene sequencing. Two CBP systems were evaluated: Martin Bono (MB; 30 months in operation) and Angela Teresa (AT; 20 months). The MB system was established on natural soil without bedding addition and included concrete feed alleys, whereas AT was initiated with peanut shell bedding and lacked concrete alleys. In both systems, compost was tilled twice daily. Two samples per farm were collected at a depth of 30 cm during winter 2019. Raw Illumina reads were processed using the DADA2 pipeline, including quality filtering, error modeling, denoising, and chimera removal. A total of four samples yielded 2,503 amplicon sequence variants (ASVs), with approximately 76% of reads retained after filtering and chimera removal, indicating high-quality sequencing data. Taxonomic analysis revealed that bacterial communities in both systems were dominated by phyla typically associated with compost environments, including Actinobacteriota, Proteobacteria, and Firmicutes. Differences in relative abundance between systems suggested shifts in community composition associated with management conditions.

microbiology↗

bioRxiv2026

Draft Genome Sequence of Bacillus pergaminensis sp. nov. strain Bva_UNVM-123: A Promising Candidate for Bioremediation.

The Bacillus genus comprises physiologically versatile, endospore-forming bacteria widely distributed in natural environments. In this study, we report the isolation and genomic characterization of strain Bva_UNVM-123, recovered from agricultural soil in Pergamino, Argentina. Whole-genome sequencing using Illumina technology yielded a 5.1 Mbp draft genome assembled in 67 contigs with a GC content of 36%. Comparative genomic analyses using the TYGS server and digital DNA-DNA hybridization (dDDH) values supported its classification as a potentially novel species within the Bacillus sensu lato (s.l.) group. Genome annotation revealed 4,866 protein-coding genes, including multiple determinants conferring resistance to antibiotics (e.g., fosfomycin, tetracycline, beta-lactams) and toxic heavy metals (e.g., arsenic, cadmium, mercury), supporting its potential application in bioremediation. Additionally, PathogenFinder predicted a low probability of human pathogenicity (0.207), reinforcing its safety for environmental use. Functional classification based on Swiss-Prot further supported a metabolically versatile profile and revealed the presence of resistance-related categories associated with environmental adaptation. This study adds to the growing knowledge of environmental Bacillus species and their biotechnological potential.

microbiology↗

bioRxiv2026

A 5-hydroxymethylcytosine DNA glycosylase provides defense against T-even bacteriophages

The most abundant prokaryotic mechanisms of defense against phage predation involve the recognition and destruction of the infecting DNA. One method of counter-defense is the incorporation of modified nucleobases into the phage genome to avoid interaction with enzymes that target the viral DNA. T-even coliphages replace cytosine with 5-hydroxymethylcytosine (5hmC) that in some cases are further decorated with glucosyl groups. To explore the diversity of immunity genes that recognize 5hmC, we infected a library of metagenomic DNA inserts from uncultured, non-sequenced soil bacteria with a mutant T4 phage that harbored only non-glucosylated 5hmC on its genome. Bacteria that resisted infection carried a DNA glycosylase, Brig3, that specifically excises 5hmC nucleobases to generate abasic sites in the phage genome and prevent viral proliferation. The crystal structure of Brig3 bound to its substrate revealed a catalytic mechanism in which the 5hmC nucleobase is flipped out of the DNA into the active site and replaced by an asparagine residue that inserts into the double helix to contact the complementary guanosine. Brig3 is encoded within an operon that also encodes BapA, a hydrolase that removes glucosyl groups from glucosyl-5hmC present in the genome of otherwise Brig3-resistant T-even phages carrying this hypermodified base. Our results uncover a defense strategy in which the combined action of BapA and Brig3 widens the immune response to restrict the infection of T-even phages with genomes that are either partially or completely glucosylated.

microbiology↗

bioRxiv2026

Divergent mitochondrial and metabolic adaptations shape selective vulnerability in ALS

Neurodegenerative diseases like amyotrophic lateral sclerosis (ALS) exhibit striking cell-type selectivity, yet the basis for this vulnerability remains elusive. Here, we uncover that even closely related neurons can harbor distinct mitochondrial properties that shape their response to disease. Using TOM-Tag, a circuit-based AAV-based strategy for cell type-specific mitochondrial immunopurification from projection neurons, we performed integrative proteomic, metabolomic, transcriptomic, and functional analyses of mitochondria from ALS-vulnerable corticospinal projection neurons (CSPNs) and resilient corticothalamic projection neurons (CTPNs) in vivo. We discovered that CSPNs and CTPNs exhibit divergent mitochondrial profiles at baseline, despite sharing cortical layer and developmental origin. CTPNs were primed for antioxidant buffering and fatty acid metabolism, whereas CSPNs were enriched for oxidative phosphorylation components. In ALS, CTPNs employed mitochondrial flexibility and redox defense, whereas CSPNs exhibited respiratory failure and metabolic stress. These findings reveal that intrinsic mitochondrial programs vary even between similar neurons, and that this hidden layer of diversity may critically shape susceptibility to neurodegeneration. By enabling high-resolution access to mitochondria in defined neuronal circuits, TOM-Tag offers a powerful new lens for dissecting disease mechanisms and identifying cell-specific therapeutic targets.

neuroscience↗

bioRxiv2025

Exercise intensity modulates the human plasma secretome and interorgan communication

Exercise is recognized as first-line therapy for many cardiometabolic diseases, including obesity, type 2 diabetes, and hypertension. Despite the abundant health-promoting effects of exercise, in-depth characterization of circulatory factors that mediate these benefits in humans remains incomplete. Moreover, how different modes and intensities of exercise uniquely regulate these processes is unclear. Here, we address these questions by conducting a multi-cohort human exercise intervention, incorporating sprint-interval exercise (SIE) and moderate-intensity exercise (MIE) to analyze intensity-dependent regulation of interorgan crosstalk. We find that exercise intensity distinctly influences the plasma proteome and metabolome in both untrained and trained participants. SIE led to immediate and robust changes to the plasma proteome, whereas MIE resulted in delayed secretory kinetics. By leveraging large, multi-organ gene and protein expression datasets, in combination with in vitro and in vivo tissue sampling, we map the differentially regulated proteins to their predicted tissue of origin and destination. We find that adipocytes are particularly sensitive to exercise intensity, undergoing broad transcriptomic remodeling following in vitro incubation with SIE as compared to MIE plasma. These findings underscore the integrated whole-body response following acute exercise and highlight exercise intensity as a key factor influencing interorgan communication.

physiology↗

bioRxiv2024

Hippocampal γCaMKII dopaminylation promotes synaptic-to-nuclear signaling and memory formation

Protein monoaminylation is a class of posttranslational modification (PTM) that contributes to transcription, physiology and behavior. While recent analyses have focused on histones as critical substrates of monoaminylation, the broader repertoire of monoaminylated proteins in brain remains unclear. Here, we report the development/implementation of a chemical probe for the bioorthogonal labeling, enrichment and proteomics-based detection of dopaminylated proteins in brain. We identified 1,557 dopaminylated proteins - many synaptic - including {gamma}CaMKII, which mediates Ca2+-dependent cellular signaling and hippocampal-dependent memory. We found that {gamma}CaMKII dopaminylation is largely synaptic and mediates synaptic-to-nuclear signaling, neuronal gene expression and intrinsic excitability, and contextual memory. These results indicate a critical role for synaptic dopaminylation in adaptive brain plasticity, and may suggest roles for these phenomena in pathologies associated with altered monoaminergic signaling.

neuroscience↗

bioRxiv2024

The lipid droplet protein DHRS3 is a regulator of melanoma cell state

Lipid droplets are fat storage organelles composed of a protein envelope and lipid rich core. Regulation of this protein envelope underlies differential lipid droplet formation and function. In melanoma, lipid droplet formation has been linked to tumor progression and metastasis, but it is unknown whether lipid droplet proteins play a role. To address this, we performed proteomic analysis of the lipid droplet envelope in melanoma. We found that lipid droplet proteins were differentially enriched in distinct melanoma states; from melanocytic to undifferentiated. DHRS3, which converts all-trans-retinal to all-trans-retinol, is upregulated in the MITFLO/undifferentiated/neural crest-like melanoma cell state and reduced in the MITFHI/melanocytic state. Increased DHRS3 expression is sufficient to drive MITFHI/melanocytic cells to a more undifferentiated/invasive state. These changes are due to retinoic acid mediated regulation of melanocytic genes. Our data demonstrate that melanoma cell state can be regulated by expression of lipid droplet proteins which affect downstream retinoid signaling.

cancer biology↗

bioRxiv2019

DNA clamp function of the mono-ubiquitinated Fanconi Anemia FANCI-FANCD2 complex

The FANCI-FANCD2 (ID) complex, mutated in the Fanconi Anemia (FA) cancer predisposition syndrome, is required for the repair of replication forks stalled at DNA interstrand crosslinks (ICL) and related lesions1. The FA pathway is activated when two replication forks converge onto an ICL2, triggering the mono-ubiquitination of the ID complex. ID mono-ubiquitination is essential for ICL repair by excision, translesion synthesis and homologous recombination, but its function was hitherto unknown1,3. Here, the 3.48 [A] cryo-EM structure of mono-ubiquitinated ID (IDUb) bound to DNA reveals that it forms a closed ring that encircles the DNA. Compared to the cryo-EM structure of the non-ubiquitinated ID complex bound to ICL DNA, described here as well, mono-ubiquitination triggers a complete re-arrangement of the open, trough-like ID structure through the ubiquitin of one protomer binding to the other protomer in a reciprocal fashion. The structures, in conjunction with biochemical data, indicate the mono-ubiquitinated ID complex looses its preference for ICL and related branched DNA structures, becoming a sliding DNA clamp that can coordinate the subsequent repair reactions. Our findings also reveal how mono-ubiquitination in general can induce an alternate structure with a new function.

molecular biology↗

bioRxiv2019

Structure of the Fanconi Anemia Core-UBE2T complex poised to ubiquitinate bound FANCI-FANCD2

The Fanconi Anemia (FA) pathway is essential for the repair of DNA interstrand crosslinks (ICLs). The pathway is activated when a replication fork stalls because of an ICL or other replication stress. A central event in pathway activation is the mono-ubiquitination of the FANCI-FANCD2 (ID) complex by the FA Core complex, a ubiquitin ligase of nine subunits. Here we describe the cryo-EM structures of the 1.1 MDa FA Core at 3.1 angstroms, except for the FANCA subunit at 3.4, and of the complex containing Core, ID and the UBE2T ubiquitin conjugating enzyme at 4.2 angstroms. The Core has unusual stoichiometry with two copies of FANCB, FAAP100, FANCA, FAAP20, FANCG, FANCL, but only a single copy of FANCC, FANCE and FANCF. This is due to homodimers of FANCA and FANCB having incompatible 2-fold symmetry, resulting in an overall asymmetric assembly of the other subunits. The asymmetry is crucial, as it prevents the binding of a second FANC-C-E-F sub-complex that inhibits UBE2T recruitment by FANCL, and instead creates an ID binding site. The single active FANCL-UBE2T binds next to the FANCD2 ubiquitination site, prying open the FANCI-FANCD2 interface within which the ubiquitination sites are buried. These structures and biochemical data indicate a single active site ubiquitinates FANCD2 and FANCI sequentially, shedding light on a central event in the FA pathway.

molecular biology↗

bioRxiv2019

Structure of the cell-binding component of the Clostridium difficile binary toxin reveals a novel macromolecular assembly

Targeting Clostridium difficile infection (CDI) is challenging because treatment options are limited, and high recurrence rates are common. One reason for this is that hypervirulent CDI often has a binary toxin termed the C. difficile toxin (CDT), in addition to the enterotoxins TsdA and TsdB. CDT has an enzymatic component, termed CDTa, and a pore-forming or delivery subunit termed CDTb. CDTb was characterized here using a combination of single particle cryoEM, X-ray crystallography, NMR, and other biophysical methods. In the absence of CDTa, two novel di-heptamer structures for activated CDTb (aCDTb; 1.0 MDa) were solved at atomic resolution including a symmetric (SymCDTb; 3.14 [A]) and an asymmetric form (AsymCDTb; 2.84 [A]). Roles played by two receptor-binding domains of aCDTb were of particular interest since RBD1 lacks sequence homology to any other known toxin, and the RBD2 domain is completely absent in other well-studied heptameric toxins (i.e. anthrax). For AsymCDTb, a novel Ca2+ binding site was discovered in RBD1 that is important for its stability, and RBD2 was found to be critical for host cell toxicity and the novel di-heptamer fold for both forms of aCDTb. Together, these studies represent a starting point for structure-based drug-discovery strategies to targeting CDT in the most severe strains of CDI. SIGNIFICANCE STATEMENTThere is a high burden from C. difficile infection (CDI) throughout the world, and the Center for Disease Control (CDC) reports more than 500,000 cases annually in the United States, resulting in an estimated 15,000 deaths. In addition to the large clostridial toxins, TcdA/TcdB, a third C. difficile binary toxin (CDT) is associated with the most serious outbreaks of drug resistant CDI in the 21st century. Here, structural biology and biophysical approaches were used to characterize the cell binding component of CDT, termed CDTb, at atomic resolution. Surprisingly, two novel structures were solved from a single sample that help to explain the molecular underpinnings of C. difficile toxicity. These structures will also be important for targeting this human pathogen via structure-based therapeutic design methods.

biophysics↗