Biology subjects

Flores, V.

Publications and source records attributed to Flores, V..

13 recordsLinked to original sources

bioRxiv2026

A shared molecular target hides distinct genetic routes to diamide resistance in Helicoverpa armigera (Lepidoptera: Noctuidae)

Diamide insecticides target insect ryanodine receptors (RyRs) and are widely used against lepidopteran pests, yet it remains unclear whether compounds sharing this molecular target evolve resistance through the same genetic routes. Here, we integrated RyR sequencing, structural modelling and population genomics to investigate resistance to chlorantraniliprole and flubendiamide in the global agricultural pest Helicoverpa armigera. We identified G4946E together with F4947I, a previously undescribed resistance-associated RyR substitution, in a chlorantraniliprole-resistant strain. Structural modelling indicated that F4947I may modify G4946E's effects on the diamide-binding pocket, while field and population-genomic evidence independently implicated the RyR-containing chromosome 28 region in chlorantraniliprole resistance. By contrast, high-level flubendiamide resistance occurred without amino acid substitutions in the RyR region examined, and field survival was predominantly associated with chromosome 2, independently recapitulating a previously identified resistance locus. Together, our findings reveal that resistance to insecticides sharing the same molecular target can evolve through distinct but potentially overlapping genetic routes, highlighting the limitations of predicting cross-resistance from target-site variation alone and the need for broader genomic approaches to resistance surveillance.

molecular biology↗

bioRxiv2026

TgmRHel drives unified RNA processing of coxI mRNA generated from a complex mitochondrial genomic context

The mitochondrial genome of Toxoplasma gondii is highly fragmented and recombination-prone, creating a structurally dynamic genetic landscape. How such a genome is used efficiently to produce functional mRNAs remains unclear: it is unknown whether transcription draws from many alternative genomic configurations or a restricted subset, and how any resulting precursor RNAs are processed into mature transcripts. More broadly, mitochondrial RNA processing mechanisms in this system are poorly understood. Here, we show that recombination of the T. gondii mitochondrial genome generates a diverse population of structurally distinct precursor RNAs for the essential cytochrome c oxidase subunit I (coxI) protein. Rather than being derived from a single defined primary transcript, these heterogeneous precursors are unified into a single mature mRNA through a post-transcriptional mechanism dependent on the DEAD-box RNA helicase TgmRHel. TgmRHel is required for 5'-end processing of coxI mRNA and for the accumulation of mitochondrial rRNAs, both of which are essential for Complex IV biogenesis, oxidative phosphorylation, and parasite survival. Loss of TgmRHel leads to the accumulation of diverse coxI precursor RNAs and a failure to generate the mature transcript. Our findings reveal an unexpected genome-transcriptome interface in which extensive genomic variability is not suppressed at the DNA level but instead resolved through RNA helicase-mediated processing. This work establishes a new conceptual framework for how gene expression fidelity can be maintained in the context of highly dynamic, recombining genomes.

molecular biology↗

bioRxiv2026

A combinatorial genetics approach reveals limits to redundancy within Plasmodium falciparum invasion ligand families

To maintain infection in the human bloodstream, Plasmodium falciparum parasites undergo repeated cycles of invasion of and multiplication inside red blood cells (RBCs). Two protein families, the Erythrocyte binding-like (EBA) and Reticulocyte binding-like (Rh) proteins, are known to play a key role in invasion, mediating early stages of attachment of the P. falciparum merozoite to the host RBC. There is a degree of redundancy within these families, such that disrupting the function of individual EBA/Rh proteins in vitro is not sufficient to prevent invasion. By employing a novel approach to disrupt multiple EBA and Rh genes in combination, we systematically assessed functional interdependency across these families for the first time. This analysis, and further characterisation of mutant parasites, revealed that disruption of some pairs of EBA/Rh ligands significantly impacted P. falciparum invasion, whereas others did not. Disruption of PfEBA175 in combination with either PfRh2b or PfRh4 significantly reduced parasite multiplication in vitro, indicating that the remaining EBA/Rh proteins could not fully compensate for the absence of these three key invasion ligands. PfEBA175, PfRh2b and PfRh4 may therefore represent a critical nexus of the parasite invasion machinery, and combinatorial approaches that target these specific ligands could be a beneficial therapeutic approach.

microbiology↗

bioRxiv2026

Helical Repeat Protein mRSiC is Required for rRNA Fragment Accumulation in T. gondii Mitochondria

Myzozoans, including apicomplexan parasites, possess highly reduced and unusual mitochondrial genomes that encode two to three respiratory chain subunits and extensively fragmented rRNAs forming a divergent mitoribosome. Heptatricopeptide repeat (HPR) proteins are expanded in myzozoans, with some functioning as mitoribosomal constitutes. Additional HPR proteins have been proposed to function in post-transcriptional processes of mitochondrial gene expression, though their specific roles remain unexplored. We present a phylogenetic analysis of HPR proteins that reveals extensive lineage-specific expansions, consistent with diversifications of mitochondrial gene expression systems within myzozoans. We further characterize mRSiC, a coccidian-specific HPR found in Toxoplasma gondii and its closest relatives. Using sRNA sequencing and RNA gel blot analyses, we show that mRSiC is required for the stabilization of two coccidian-specific mitochondrial sRNAs, RNA33 and RNA42. Loss of mRSiC causes rapid depletion of these RNAs, followed by secondary reductions of rRNA fragments, defects in the respiratory chain, and impaired parasite proliferation. Together, these findings highlight the importance of HPRs in apicomplexan mitochondrial gene expression and illustrate how lineage-specific RNA-binding factors support highly derived mitochondrial expression systems.

molecular biology↗

bioRxiv2025

The spatial proteome of the Plasmodium falciparum schizont illuminates the composition and evolutionary trajectories of its organelles

Malaria is caused by apicomplexan parasites of the genus Plasmodium, with all malaria symptoms and pathology caused by parasite stages that develop within, or transit between, host erythrocytes. The ability of Plasmodium cells to parasitise erythrocytes depends on distinctive intracellular compartments associated with invasion, as well as the development of unique cellular niches within the infected host cell. However, our understanding of the biology of the malaria parasite is limited by the fact that a large proportion of the parasites proteome has no known cellular location or function. To address this problem, we have generated comprehensive high-resolution maps of protein subcellular localisation for the invasive stage of the erythrocytic life cycle of Plasmodium falciparum, the major cause of malaria mortality. Using the spatial proteomics technique hyperplexed Localisation of Organelle Proteins by Isotopic Tagging (hyperLOPIT) we generated data for 3000 P. falciparum proteins expressed in late schizont stages. Our hyperLOPIT data resolved 24 distinct cellular niches, and using supervised machine-learning we can classify 1646 proteins into one of these compartments including exported sites within the host cell. Through comparative genomic analyses our data resolve the spatial patterns of cell evolution that have shaped the development of Plasmodium species and ongoing adaptive pressures and responses that challenge our efforts to manage these major disease-causing organisms.

microbiology↗

bioRxiv2025

Receptor-substrate competition for the TonB homologue FusB suggests a model for ferredoxin import in Pectobacterium spp.

TonB-dependent uptake systems of Gram-negative bacterial pathogens constitute prominent virulence factors, allowing nutrient acquisition, primarily siderophore-bound iron, to cross the highly impermeable outer membrane (OM). Remarkably, the ferredoxin uptake system (Fus) of Pectobacteriaceae, a group of soft rot-inducing plant pathogens, imports an entire folded host protein into the periplasm and extracts its bound iron for growth. The inner membrane protein FusB, a TonB homologue, plays two roles in facilitating ferredoxin import. First, like other TonBs, it remodels the globular plug domain obstructing the lumen of the OM receptor FusA to allow ferredoxin passage. Unusually for a TonB protein, FusB then interacts directly with the FusA-bound ferredoxin substrate to facilitate its transport into the periplasm. In this work, we describe structures of FusB-ferredoxin and homodimeric FusB complexes and determine the key features of the binding interfaces formed by FusB with FusA and ferredoxin. We postulate that under resting conditions FusB exists a homodimer, stabilised by an intermolecular R241-D322 salt bridge. The homodimer dissociates when the "FusB-box" of FusA outcompetes one protomer, and FusA D53 displaces FusB D322. Upon ferredoxin binding, FusB undergoes a structural rearrangement, expanding its {beta}-sheet from three to four strands. In agreement with the proposed sequence of events, ferredoxin binding displaces the receptor (FusA) from FusB with Arg241 forming an intramolecular salt bridge with Asp322 to stabilise the newly formed {beta}-hairpin of FusB. We propose a mechanistic model for ferredoxin import in which FusB Arg241 acts as a molecular switch, and two distinct regions function as interaction hotspots.

biophysics↗

bioRxiv2024

Plastid translocon recycling in dinoflagellates demonstrates the portability of complex plastids between hosts

The plastids of photosynthetic organisms on land are predominantly primary plastids derived from an ancient endosymbiosis of a cyanobacterium. Conversely, marine photosynthetic diversity is dominated by plastids gained by subsequent endosymbioses of photosynthetic eukaryotes, so-called complex plastids. The plastids of major eukaryotic lineages including cryptophytes, haptophytes, stramenopiles, dinoflagellates and apicomplexans, were originally all posited to derive from a single secondary endosymbiosis of a red alga--the chromalveloate hypothesis 1. Subsequent phylogenetic resolution of eukaryotes indicated that separate events of plastid acquisition must have occurred to account for this distribution of plastids 2,3. The number of such events, however, and the donor organisms for the new plastid endosymbioses are still not resolved. A perceived bottleneck of endosymbiotic plastid gain is the development of protein targeting from the hosts into new plastids, and this supposition has often driven hypotheses towards minimising the number of plastid-gain events to explain plastid distribution in eukaryotes. But how plastid protein-targeting is established for new endosymbionts is often unclear, which makes it difficult to assess the likelihood of plastid transfers between lineages. Here we show that Kareniaceae dinoflagellates, that possess complex plastids known to be derived from haptophytes, acquired all the necessary protein import machinery from these haptophytes. Furthermore, cryo-electron tomography revealed that no additional membranes were added to the Kareniaceae complex plastid during serial endosymbiosis, suggesting that the haptophyte-derived import processes were sufficient. Our analyses suggests that complex red plastids are preadapted for horizontal transmission, potentially explaining their widespread distribution in aquatic algal diversity.

evolutionary biology↗

bioRxiv2024

Dietary isoleucine content defines the metabolic and molecular response to a Western diet

The amino acid composition of the diet has recently emerged as a critical regulator of metabolic health. Consumption of the branched-chain amino acid isoleucine is positively correlated with body mass index in humans, and reducing dietary levels of isoleucine rapidly improves the metabolic health of diet-induced obese male C57BL/6J mice. However, it is unknown how sex, strain, and dietary isoleucine intake may interact to impact the response to a Western Diet (WD). Here, we find that although the magnitude of the effect varies by sex and strain, reducing dietary levels of isoleucine protects C57BL/6J and DBA/2J mice of both sexes from the deleterious metabolic effects of a WD, while increasing dietary levels of isoleucine impairs aspects of metabolic health. Despite broadly positive responses across all sexes and strains to reduced isoleucine, the molecular response of each sex and strain is highly distinctive. Using a multi-omics approach, we identify a core sex- and strain-independent molecular response to dietary isoleucine, and identify mega-clusters of differentially expressed hepatic genes, metabolites, and lipids associated with each phenotype. Intriguingly, the metabolic effects of reduced isoleucine in mice are not associated with FGF21 - and we find that in humans plasma FGF21 levels are likewise not associated with dietary levels of isoleucine. Finally, we find that foods contain a range of isoleucine levels, and that consumption of dietary isoleucine is lower in humans with healthy eating habits. Our results demonstrate that the dietary level of isoleucine is critical in the metabolic and molecular response to a WD, and suggest that lowering dietary levels of isoleucine may be an innovative and translatable strategy to protect from the negative metabolic consequences of a WD.

physiology↗

bioRxiv2022

Dietary restriction of isoleucine increases healthspan and lifespan of genetically heterogeneous mice

Low protein (LP) diets promote health and longevity in diverse species. Although the precise components of an LP diet that mediate its beneficial effects have not been defined, reducing dietary levels of the three branched-chain amino acids (BCAAs) leucine, isoleucine and valine promotes metabolic health in both sexes, and increases lifespan while reducing frailty in male, but not female, C57BL/6J mice. Each BCAA has unique metabolic effects, and we recently showed that restriction of isoleucine is both sufficient to promote metabolic health and required for the metabolic benefits of an LP diet in male C57BL/6J mice. Here, we tested the hypothesis that specifically restricting isoleucine could promote healthy aging in genetically heterogenous UM-HET3 mice. We find that a reduced isoleucine diet improves the metabolic health of both young and old HET3 mice, promoting leanness and glycemic control. Restriction of isoleucine starting in adult, 6 month old HET3 mice reprograms hepatic metabolism in a way distinct from an LP diet. Finally, we find that a reduced isoleucine diet reduces frailty and extends the lifespan of both male and female HET3 mice, but to a much greater degree in males. Our results demonstrate that restricting dietary isoleucine can increase health span and longevity in a genetically diverse population of mice, and suggests that reducing dietary levels of isoleucine may have great potential as a geroprotective intervention.

physiology↗

bioRxiv2022

Regulation of metabolic health by dietary histidine in mice

Low protein (LP) diets are associated with a decreased risk of diabetes in humans, and a low protein diet promotes leanness and glycemic control in both rodents and humans. While the effects of a LP diet on glycemic control are mediated by reduced dietary levels of the branched- chain amino acids (BCAAs), we have observed that reducing dietary levels of the other six essential amino acids leads to changes in body composition. Here, we find that dietary histidine plays a key role in the response to a LP diet in male C57BL/6J mice. Specifically reducing dietary levels of histidine by 67% reduces weight gain of young, lean male mice, reducing both adipose and lean mass gain, without altering glucose metabolism. Specifically reducing dietary histidine rapidly reverses diet-induced obesity and hepatic steatosis in diet-induced obese male mice, increasing insulin sensitivity; this normalization of metabolic health was associated not with caloric restriction or increased activity, but with increased energy expenditure. We find that the effects of histidine restriction surprisingly does not require the energy balance hormone Fgf21. Histidine restriction started in mid-life promoted leanness and glucose tolerance in aged males but not females, but did not affect frailty or lifespan in either sex. Finally, we demonstrate that variation in dietary histidine levels helps to explain body mass index differences in humans. Overall, our findings demonstrate that dietary histidine is a key regulator of weight and body composition in male mice and in humans, and suggest that reducing dietary levels of histidine may be a highly translatable option for the treatment of obesity. Key PointsO_LIProtein restriction (PR) promotes metabolic health in rodents and humans and extends rodent lifespan. C_LIO_LIRestriction of specific individual essential amino acids can recapitulate the benefits of PR. C_LIO_LIReduced histidine promotes leanness and increased energy expenditure in mice. C_LIO_LIReduced histidine does not extend the lifespan of mice when begun in mid-life. C_LIO_LIDietary levels of histidine are positively associated with BMI in humans. C_LI

physiology↗

bioRxiv2022

Mitochondrial genomes in Perkinsus decode conserved frameshifts in all genes

Mitochondrial genomes of apicomplexans, dino-flagellates and chrompodellids, that collectively make up the Myzozoa, are uncommonly reduced in coding capacity and display divergent gene configuration and expression mechanisms. They encode only three proteins -- COB, COX1, COX3 -- contain rRNAs fragmented to [~]100-200 base pair elements, and employ extensive recombination, RNA trans-splicing, and RNA-editing for genome maintenance and expression. The early-diverging Perkinsozoa is the final major myzozoan lineage whose mitochondrial genomes remain poorly characterized. Previous reports of Perkinsus cox1 and cob partial gene sequences have indicated independent acquisition of non-canonical features, namely the occurrence of multiple frameshifts in both genes. To determine ancestral myzozoan mitochondrial genome features, as well as any novel ones in Perkinsozoa, we sequenced and assembled four Perkinsus species mitochondrial genomes. These data show a simple ancestral genome with the common reduced coding capacity, but one already prone to rearrangement. Moreover, we identified 75 frameshifts across the four species that are present in all genes, that are highly conserved in gene location, and that occur as four distinct types. A decoding mechanism apparently employs unused codons at the frameshift sites that advance translation either +1 or +2 frames to the next used codon. The locations of the frameshifts are seemingly positioned to regulate protein folding of the nascent protein as it emerges from the ribosome. COX3 is distinct in containing only one frameshift and showing strong selection against residues that are otherwise frequently encoded at the frameshift positions in COX3 and COB. All genes also lack cysteine codons implying a further constraint on these genomes with reduction to only 19 different amino acids. Furthermore, mitochondrion-encoded rRNA fragment complements are incomplete in Perkinsus spp. but some are found in the nuclear DNA, suggesting these may be imported into the organelle as for tRNAs. Perkinsus demonstrates additional remarkable trajectories of organelle genome evolution including pervasive integration of frameshift translation into genome expression.

molecular biology↗

bioRxiv2021

RTX-KG2: a system for building a semantically standardized knowledge graph for translational biomedicine

BackgroundBiomedical translational science is increasingly using computational reasoning on repositories of structured knowledge (such as UMLS, SemMedDB, ChEMBL, Reactome, DrugBank, and SMPDB in order to facilitate discovery of new therapeutic targets and modalities. The NCATS Biomedical Data Translator project is working to federate autonomous reasoning agents and knowledge providers within a distributed system for answering translational questions. Within that project and the broader field, there is a need for a framework that can efficiently and reproducibly build an integrated, standards-compliant, and comprehensive biomedical knowledge graph that can be downloaded in standard serialized form or queried via a public application programming interface (API). ResultsTo create a knowledge provider system within the Translator project, we have developed RTX-KG2, an open-source software system for building--and hosting a web API for querying--a biomedical knowledge graph that uses an Extract-Transform-Load (ETL) approach to integrate 70 knowledge sources (including the aforementioned core six sources) into a knowledge graph with provenance information including (where available) citations. The semantic layer and schema for RTX-KG2 follow the standard Biolink model to maximize interoperability. RTX-KG2 is currently being used by multiple Translator reasoning agents, both in its downloadable form and via its SmartAPI-registered interface. Serializations of RTX-KG2 are available for download in both the pre-canonicalized form and in canonicalized form (in which synonyms are merged). The current canonicalized version (KG2.7.3) of RTX-KG2 contains 6.4M nodes and 39.3M edges with a hierarchy of 77 relationship types from Biolink. ConclusionRTX-KG2 is the first knowledge graph that integrates UMLS, SemMedDB, ChEMBL, DrugBank, Reactome, SMPDB, and 64 additional knowledge sources within a knowledge graph that conforms to the Biolink standard for its semantic layer and schema. RTX-KG2 is publicly available for querying via its API at arax.rtx.ai/api/rtxkg2/v1.2/openapi.json. The code to build RTX-KG2 is publicly available at github:RTXteam/RTX-KG2.

bioinformatics↗

bioRxiv2018

The Impact of fodder on Bombyx Mori

Silk production by the Chilean silkworm, although an important source of revenue, has not been extensively studied. In the current study, we research 564 Mountain Silkworm (Bombyx mori), analyzing their silk harvests, silk production incubation periods and demographic profiles. The mountain silkworms were randomly divided into two clusters (cluster#1, cluster#2), each of which had 56 mountain silkworms. Crumpled maize were replaced by steam-flaked maize 30%, 50%, 100%, then researched the effects of nourishing steam-flaked maize on production performance of silk production by silkworm. The outcomes showed that the cluster#2 had better median silk harvest than cluster#1, the mean of these increment silk harvests was 3.48pounds (P-value <0.05); the protein proportion and the sugar in silk of cluster#2 went up than cluster#1; for the urine nitrogen and somatic cell count of cluster#2 were lower than cluster#1 by 0.9% (P-value >0.05), 30,800 cells/ml (P-value<0.05), respectively. The current research confirmed that utilizing the JHO nutrition heightened silk harvest, improved silk production characteristics, and enhanced the performance of mountain silkworms; furthermore, it heightened resistance to the sickness due to strengthened resistance.

zoology↗