Biology subjects

Martinez, J.

Publications and source records attributed to Martinez, J..

At least 37 records · Page 2Linked to original sources

bioRxiv2025

Transcriptional and functional profiles of muscarinic receptor-expressing neurons in primate lateral prefrontal and anterior cingulate cortices

Acetylcholine modulates anterior cingulate (ACC) and lateral prefrontal (LPFC) cortices for cognitive-motivational integration, via specific m1-m4 muscarinic receptors (mAChR) encoded by CHRM1-4 genes. Single-nucleus RNA sequencing and mRNA-protein histology in macaques revealed CHRM3 to be the most enriched mAChR gene in neurons, while m1 predominates at the protein level, likely due to nuclear retention of CHRM3 and cytoplasmic trafficking of CHRM1. CHRM3 and CHRM1 showed strong co-expression and functional overlap, and were transcriptomically-distinct from CHRM2, which was uniquely enriched in deep layer excitatory and PVALB+ inhibitory neurons. Although CHRM+ cell distributions were similar between areas, CHRM1-3+ excitatory neurons in ACC exhibited upregulation of synaptic plasticity genes relative to LPFC. Functional in vitro experiments confirm a more robust cholinergic-mediated decrease in excitatory:inhibitory synaptic ratio in ACC than in LPFC neurons, accompanied by compensatory changes in spine morphology. These findings highlight region-specific acetylcholine signaling essential for flexible processing, learning and memory.

neuroscience↗

bioRxiv2025

Recombination, truncation and horizontal transfer shape the diversity of cytoplasmic incompatibility patterns

Wolbachia are endosymbiotic bacteria inducing various reproductive manipulations of which cytoplasmic incompatibility (CI) is the most common. CI leads to reduced embryo viability in crosses between males carrying Wolbachia and uninfected females or those carrying an incompatible symbiont strain. In the mosquito Culex pipiens, the Wolbachia wPip causes highly complex crossing patterns. This complexity is linked to the amplification and diversification of the CI causal genes, cidA and cidB, with polymorphism located in the CidA-CidB interaction regions. We previously showed correlations between the identity of gene variants and CI patterns. However, these correlations were limited to specific crosses, and it is still unknown whether cid gene polymorphism in males and females Wolbachia can explain and predict the wide range of crossing types observed in C. pipiens. Taking advantage of a new method enabling full-gene acquisition, we sequenced complete cid repertoires from 45 wPip strains collected worldwide. We demonstrated that the extensive diversity of cid genes arises from recombination and horizontal transfers. We uncovered further cidB polymorphism outside the interface regions and strongly correlated with CI patterns. Most importantly, we showed that in every wPip genome, all but one cidB variant are truncated. Truncated cidBs located in palindromes are partially or completely deprived of their deubiquitinase domain, crucial for CI. The identity of the sole full-length cidB variant seems to dictate CI patterns, irrespective of the truncated cidBs present. Truncated CidBs exhibit reduced toxicity and stability in Drosophila cells, which potentially hinders their loading into sperm, essential for CI induction.

evolutionary biology↗

bioRxiv2024

Metabolic and Cellular Differences Between Sedentary and Active Individuals at Rest and During Exercise

BackgroundPhysical inactivity is a major contributor to cardiometabolic disease and mortality. Although mitochondrial dysfunction characterizes overt pathology, whether a distinct mitochondrial phenotype is present in apparently healthy sedentary adults remains unclear. MethodsNine sedentary (SED) and ten physically active (AC) healthy males (42 {+/-} 14 yr) were studied. Skeletal muscle bioenergetics were assessed using high-resolution respirometry, fluxomics, metabolomics and protein expression analyses. Whole-body physiology was evaluated using cardiopulmonary exercise testing (CPET) including fat oxidation and blood lactate measurements. ResultsAt rest, SED exhibited marked reductions in mitochondrial capacity, including Complex I (-36%), Complex II (-28%), electron transport system capacity (-34%), and ATP-synthase-coupled respiration (-30%, all p < 0.01). The most pronounced alteration was a 49% reduction in mitochondrial pyruvate carrier (MPC1) expression, which closely correlated with reduced pyruvate oxidation (-37%, p = 0.006) and lower TCA intermediates. SED also showed reduced MCT1 abundance, impaired fatty acid oxidation capacity (-32% to -35%), decreased CPT1 activity (-51%), altered cardiolipin composition and elevated ROS/O flux ratios. During exercise, SED demonstrated lower VO max (-38%), reduced fat oxidation (-35%) and higher blood lactate accumulation (>60%, p < 0.001). Mitochondrial function was strongly associated with exercise performance (r = 0.57-0.78, p < 0.01). ConclusionsHealthy sedentary adults are characterized by reduced mitochondrial function characterized by decreased substrate entry and oxidation, reduced oxidative capacity and diminished metabolic flexibility. CPET-derived fat oxidation and blood lactate responses closely reflect skeletal muscle mitochondrial function, providing non-invasive physiological markers of metabolic health. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=178 SRC="FIGDIR/small/608601v2_fig1.gif" ALT="Figure 1"> View larger version (51K): org.highwire.dtl.DTLVardef@1a3a629org.highwire.dtl.DTLVardef@f1ea48org.highwire.dtl.DTLVardef@4c4a96org.highwire.dtl.DTLVardef@b4f879_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure 1.C_FLOATNO Schematic of skeletal muscle mitochondrion: SED side shows reduced MPC, CPT1, L4CL, and TCA flux with elevated ROS; AC side shows robust OXPHOS, fat oxidation, and lactate clearance. Arrows link to CPET as a non-invasive diagnostic tool for mitochondrial health. C_FIG

biochemistry↗

bioRxiv2024

Porcine Nasal Organoids as a model to study the interactions between the swine nasal microbiota and the host

Interactions between the nasal epithelium, commensal nasal microbiota, and respiratory pathogens play a key role in respiratory infections. Currently there is a lack of experimental models to study such interactions under defined in vitro conditions. Here, we developed a Porcine Nasal Organoid (PNO) system from nasal tissue of pigs as well as from cytological brushes. PNOs exhibited similar structure and cell types than the nasal mucosa, as evaluated by immunostaining. PNOs were inoculated with porcine commensal strains of Moraxella pluranimalium, Rothia nasimurium and the pathobiont Glaesserella parasuis for examining host-commensal-pathogen interactions. All strains adhered to the PNOs, although at different levels. M. pluranimalium and G. parasuis strains stimulated the production of proinflammatory cytokines, whereas R. nasimurium induced the production of IFN{gamma} and diminished the proinflammatory effect of the other strains. Overall, PNOs mimic the in vivo nasal mucosa and can be useful to perform host-microbe interaction studies. In briefInteractions between nasal epithelium, commensal nasal microbiota, and respiratory pathogens play a key role in respiratory infections. We developed porcine nasal organoids to mimic the nasal mucosa and use as a model to study those interactions. Additionally, this development supports the reduction of the number of animals for animal experimentation. HighlightsO_LIFirst generation of Porcine Nasal Organoids (PNOs) from nasal turbinates and swabs C_LIO_LIPNOs recapitulate features of in vivo tissue and maintain self-renewal capacity C_LIO_LIHost-microbe interactions can be studied using the PNO system C_LIO_LIRothia nasimurium inhibits the inflammation induced by other bacteria C_LI

microbiology↗

bioRxiv2024

Resolving multi-image spatial lipidomic responses to inhaled toxicants by machine learning

Regional responses to inhaled toxicants are essential to understand the pathogenesis of lung disease under exposure to air pollution. We evaluated the effect of combined allergen sensitization and ozone exposure on eliciting spatial differences in lipid distribution in the mouse lung that may contribute to ozone-induced exacerbations in asthma. Lung lobes from male and female BALB/c mice were cryosectioned and acquired by high resolution mass spectrometry imaging (MSI). Processed MSI peak annotations were validated by LC-MS/MS data from scraped tissue slides and microdissected lung tissue. Images were normalized and segmented into clusters. Interestingly, segmented clusters overlapped with stained serial tissue sections, enabling statistical analysis across biological replicates for morphologically relevant lung regions. Spatially distinct lipids had higher overall degree of unsaturated fatty acids in distal lung regions compared to proximal regions. Furthermore, the airway and alveolar epithelium exhibited significantly decreased sphingolipid and glycerophospholipid abundance in females, but not in males. We demonstrate the potential role of lipid saturation in healthy lung function and highlight sex differences in regional lung lipid distribution following ozone exposure. Our study provides a framework for future MSI experiments capable of relative quantification across biological replicates and expansion to multiple sample types, including human tissue.

pharmacology and toxicology↗

bioRxiv2024

A Mimicry-Based Strategy Between Human and Commensal Antigens for the Development of a New Family of Immune Therapies for Cancer

Peptide vaccines have emerged as a promising strategy for cancer immunotherapy, yet often lack of strong, specific and sustained immune responses against tumor antigens. To achieve a robust immune response, the effective selection of tumour antigens is crucial. While neoantigens trigger potent immune responses, their use suffers from patient specificity and their rarity in low-mutational tumors. Alternatively, the immunogenic potential of tumor-associated antigens (TAAs) is limited by central immune tolerance. Molecular mimicry and T cell cross-reactivity is a proposed mechanism to trigger a robust T cell-mediated antitumor response. Although molecular mimicry between pathogens and tumor antigens has been described, the potential benefits of exploiting this molecular mimicry with commensal bacterial antigens in antitumor immunity have not been thoroughly investigated despite strong evidence that the composition of the human microbiota significantly influences immune competency. Our new approach called OncoMimics, which uses molecular mimicry between commensal bacterial and tumoral antigens to induce cross-reactive cytotoxic T cells against tumor cells. In preclinical studies, vaccination with OncoMimic peptides (OMPs) led to the expansion of CD8+ T cells reacting against homologous tumor-associated antigen peptides and elicits cytotoxic activity against tumor cells. OMPs are efficiently recognized by a prevalent T cell population within the peripheral blood mononuclear cells of healthy individuals. An ongoing clinical trial (NCT04116658) using OncoMimics in patients with glioblastoma demonstrates early, durable, and cross-reactive tumor antigen CD8+ T cell responses with pronounced memory persistence. By overcoming the current vaccine limitations, OncoMimics constitutes a promising strategy for enhancing cancer immunity and improving patient outcomes. Statement of SignificanceThis study introduces OncoMimics, a peptide-based immunotherapy leveraging molecular mimicry to induce robust, cross-reactive T cell responses against tumor antigens, showing promising early results in an ongoing glioblastoma clinical trial (NCT04116658)

immunology↗

bioRxiv2023

Rapid evolution of Wolbachia genomes in mosquito cell culture

Wolbachia bacterial symbionts are widespread across arthropods where they cause reproductive manipulations and/or confer fitness benefits such as protection against viral pathogens. Their self-spreading ability coupled with their antiviral effect has been harnessed in health programmes to curb the transmission of dengue virus. Comparative genomics of Wolbachia strains has been a useful tool to understand the general trends in the evolution of the symbiont genome; however, short-term evolutionary processes occurring within hosts remain poorly explored. Understanding these short-term dynamics is necessary to provide a more complete picture of Wolbachia evolution and will inform ongoing Wolbachia-based disease control interventions. Here we generated six new mosquito cell lines by introducing a range of Wolbachia strains from Drosophila into the symbiont-free Aedes albopictus Aa23 cell line. Following transinfection, we tracked temporal variation in Wolbachia density and identified de novo mutations through re-sequencing of the symbiont genome. Several mutations were associated with major shifts in bacterial density. Moreover, signs of parallel evolution across cell lines, combined with an excess of non-synonymous mutations, indicate that Wolbachia evolution in cell culture is dominated by selective processes rather than genetic drift. Our results also provide new candidate genes likely to be involved in symbiont density regulation. Altogether, our study demonstrates that cell culture is a valuable tool to investigate symbiont short-term evolution, identify the genetic basis of bacterial density variation and for the generation of new higher-density variants for use in control programmes.

evolutionary biology↗

bioRxiv2023

Transgenic expression of cif genes from Wolbachia strain wAlbB recapitulates cytoplasmic incompatibility in Aedes aegypti.

The endosymbiotic bacteria Wolbachia can invade insect populations by modifying host reproduction through cytoplasmic incompatibility (CI), an effect that results in embryonic lethality when Wolbachia-carrying males mate with Wolbachia-free females. Here we describe a transgenic system for recreating CI in the major arbovirus vector Aedes aegypti using CI factor (cif) genes from wAlbB, a Wolbachia strain currently being deployed to reduce dengue transmission. CI-like sterility was induced when cifA and cifB were co-expressed in testes; this sterility could be rescued by maternal cifA expression, thereby reproducing the pattern of Wolbachia-induced CI. Expression of cifB alone was associated with extensive DNA damage and disrupted spermatogenesis. The strength of rescue by maternal cifA expression was dependent on the comparative levels of cifA/cifB expression in males. These findings are consistent with CifB acting as a toxin and CifA as an antitoxin, with CifA attenuating CifB toxicity in both the male germline and in developing embryos.

microbiology↗

bioRxiv2023

Gene regulatory network inference with popInfer reveals dynamic regulation of hematopoietic stem cell quiescence upon diet restriction and aging

Inference of gene regulatory networks (GRNs) can reveal cell state transitions from single-cell genomics data. However, obstacles to temporal inference from snapshot data are difficult to overcome. Single-nuclei multiomics data offer means to bridge this gap and derive temporal information from snapshot data using joint measurements of gene expression and chromatin accessibility in the same single cells. We developed popInfer to infer networks that characterize lineage-specific dynamic cell state transitions from joint gene expression and chromatin accessibility data. Benchmarking against alternative methods for GRN inference, we showed that popInfer achieves higher accuracy in the GRNs inferred. popInfer was applied to study single-cell multiomics data characterizing hematopoietic stem cells (HSCs) and the transition from HSC to a multipotent progenitor cell state during murine hematopoiesis across age and dietary conditions. From networks predicted by popInfer, we discovered gene interactions controlling entry to/exit from HSC quiescence that are perturbed in response to diet or aging.

systems biology↗

bioRxiv2023

Mechanistic basis for oxidative stress protection of the human tRNA ligase complex by the oxidoreductase PYROXD1

RTCB is the catalytic subunit of the metazoan tRNA ligase complex (tRNA-LC) that plays essential roles in tRNA biogenesis and unfolded protein response. The catalytic center of RTCB contains a conserved cysteine that is susceptible to metal ion-induced oxidative inactivation. The flavin-containing oxidoreductase PYROXD1 preserves the activity of mammalian tRNA-LC in a NAD(P)H-dependent manner, but its protective mechanism remains elusive. Here we report a cryo-EM structure of human RTCB in complex with PYROXD1, revealing that PYROXD1 directly interacts with the catalytic center of RTCB through its C-terminal tail. NAD(P)H binding and FAD reduction allosterically control PYROXD1 activity and RTCB recruitment and PYROXD1, while PYROXD1 reoxidation enables timed release of RTCB. PYROXD1 interaction is mutually exclusive with Archease-mediated RTCB guanylylation, and guanylylated RTCB is intrinsically protected from oxidative inactivation. Together, these findings provide a mechanistic framework for the protective function of PYROXD1 that maintains the activity of tRNA-LC under aerobic conditions.

biochemistry↗

bioRxiv2023

PPAD: A deep learning architecture to predict progression of Alzheimer's disease

Alzheimers disease (AD) is a neurodegenerative disease that affects millions of people worldwide. Mild cognitive impairment (MCI) is an intermediary stage between cognitively normal (CN) state and AD. Not all people who have MCI convert to AD. The diagnosis of AD is made after significant symptoms of dementia such as short-term memory loss are already present. Since AD is currently an irreversible disease, diagnosis at the onset of disease brings a huge burden on patients, their caregivers, and the healthcare sector. Thus, there is a crucial need to develop methods for the early prediction AD for patients who have MCI. Recurrent Neural Networks (RNN) have been successfully used to handle Electronic Health Records (EHR) for predicting conversion from MCI to AD. However, RNN ignores irregular time intervals between successive events which occurs common in EHR data. In this study, we propose two deep learning architectures based on RNN, namely Predicting Progression of Alzheimers Disease (PPAD) and PPAD-Autoencoder (PPAD-AE). PPAD and PPAD-AE are designed for early predicting conversion from MCI to AD at the next visit and multiple visits ahead for patients, respectively. To minimize the effect of the irregular time intervals between visits, we propose using age in each visit as an indicator of time change between successive visits. Our experimental results conducted on Alzheimers Disease Neuroimaging Initiative (ADNI) and National Alzheimers Coordinating Center (NACC) datasets showed that our proposed models outperformed all baseline models for most prediction scenarios in terms of F2 and sensitivity. We also observed that the age feature was one of top features and was able to address irregular time interval problem.

bioinformatics↗

bioRxiv2022

Using deep convolutional neural networks to test why human face recognition works the way it does

Human face recognition is highly accurate, and exhibits a number of distinctive and well documented behavioral "signatures" such as the use of a characteristic representational space, the disproportionate performance cost when stimuli are presented upside down, and the drop in accuracy for faces from races the participant is less familiar with. These and other phenomena have long been taken as evidence that face recognition is "special". But why does human face perception exhibit these properties in the first place? Here we use deep convolutional neural networks (CNNs) to test the hypothesis that all of these signatures of human face perception result from optimization for the task of face recognition. Indeed, as predicted by this hypothesis, these phenomena are all found in CNNs trained on face recognition, but not in CNNs trained on object recognition, even when additionally trained to detect faces while matching the amount of face experience. To test whether these signatures are in principle specific to faces, we optimized a CNN on car discrimination and tested it on upright and inverted car images. As for face perception, the car-trained network showed a drop in performance for inverted versus upright cars. Similarly, CNNs trained only on inverted faces produce an inverted inversion effect. These findings show that the behavioral signatures of human face perception reflect and are well explained as the result of optimization for the task of face recognition, and that the nature of the computations underlying this task may not be so "special" after all. Significance StatementFor decades, cognitive scientists have collected and characterized behavioral signatures of face recognition. Here we move beyond the mere curation of behavioral phenomena to asking why the human face system works the way it does. We find that many classic signatures of human face perception emerge spontaneously in CNNs trained on face discrimination, but not in CNNs trained on object classification (or on both object classification and face detection), suggesting that these long-documented properties of the human face perception system reflect optimizations for face recognition per se, not by-products of a generic visual categorization system. This work further illustrates how CNN models can be synergistically linked to classic behavioral findings in vision research, thereby providing psychological insights into human perception.

neuroscience↗

bioRxiv2022

Metabolic Signatures of Performance in Elite World Tour Professional Cyclists

IntroductionMetabolomics studies of recreational and elite athletes have been so far limited to venipuncture-dependent blood sample collection in the setting of controlled training and medical facilities. However, limited to no information is currently available if findings in laboratory settings are translatable to real world scenario in elite competitions. MethodsTo characterize molecular profiles of exertion in elite athletes during cycling, we performed metabolomics analyses on blood isolated from twenty-eight international-level elite World Tour professional male athletes from a Union Cycliste Internationale (UCI) World Team taken before and after a graded exercise test (GXT) to volitional exhaustion and before and after a long aerobic training session. Moreover, established signatures were then used to characterize the metabolic physiology of five of these cyclists that were selected to represent the same UCI World Team during a 7-stage elite World Tour race. ResultsUsing dried blood spot collection to circumvent logistical hurdles associated with field sampling, these studies defined metabolite signatures and fold change ranges of anaerobic or aerobic exertion in elite cyclists, respectively. Blood signatures derived in controlled settings enabled comparison with blood sampled during competition, thus providing insight into fatigue status of the cyclists during the course of the race. Collectively, these studies provide a unique view of alterations in the blood metabolome of elite athletes during competition and at the peak of their performance capabilities. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=146 SRC="FIGDIR/small/507793v4_ufig1.gif" ALT="Figure 1"> View larger version (54K): org.highwire.dtl.DTLVardef@1a6bddeorg.highwire.dtl.DTLVardef@1fb6df5org.highwire.dtl.DTLVardef@1f0034eorg.highwire.dtl.DTLVardef@69053c_HPS_FORMAT_FIGEXP M_FIG C_FIG SummaryNemkov et al. leveraged field sampling and blood metabolomics and lipidomics approaches to follow a professional Team of elite cyclists upon graded exercise test to volitional exhaustion, field aerobic training (180 km) and a during multi-stage World Tour race. They identify markers of cycling performance beyond lactate thresholds (ranging from 3.75 to 6.5 watts per kilogram in this group), including carboxylic acids, fatty acids and acylcarnitines. Key pointsO_LIWe profiled metabolism of 28 international-level elite World Tour professional male athletes from a Union Cycliste Internationale UCI World Team during training and World Tour multi-stage race; C_LIO_LIDried blood spot sampling affords metabolomics analyses to monitor exercise performance; C_LIO_LIDetermination of lactate thresholds during graded exercise test (GXT) to volitional exhaustion shows a range of from 3.75 to 6.5 watts per kilogram in this group; C_LIO_LIBlood profiles of lactate, carboxylic acids, fatty acids and acylcarnitines differed between different exercise modes (GXT and 180 km aerobic training session); C_LIO_LIMetabolic profiles were affected by stage-specific challenges (sprint vs climbing) during a World Tour multi-stage race. C_LI

biochemistry↗

bioRxiv2022

Genome sequencing and comparative analysis of Wolbachia strain wAlbA reveals Wolbachia-associated plasmids are common

Wolbachia are widespread maternally-transmitted bacteria of arthropods that often spread by manipulating their hosts reproduction through cytoplasmic incompatibility (CI). Their invasive potential is currently being harnessed in field trials aiming to control mosquito-borne diseases. Wolbachia genomes commonly harbour prophage regions encoding the cif genes which confer their ability to induce CI. Recently, a plasmid-like element was discovered in wPip, a Wolbachia strain infecting Culex mosquitoes; however, it is unclear how common such extra-chromosomal elements are in Wolbachia. Here we sequenced the complete genome of wAlbA, a strain of the symbiont found in Aedes albopictus. We show that wAlbA is associated with two new plasmids and identified additional Wolbachia plasmids and related chromosomal islands in over 20% of publicly available Wolbachia genome datasets. These plasmids encode a variety of accessory genes, including several phage-like DNA packaging genes as well as genes potentially contributing to host-symbiont interactions. In particular, we recovered divergent homologues of the cif genes in both Wolbachia- and Rickettsia-associated plasmids. Our results indicate that plasmids are common in Wolbachia and raise fundamental questions around their role in symbiosis. In addition, our comparative analysis provides useful information for the future development of genetic tools to manipulate and study Wolbachia symbionts.

genomics↗

bioRxiv2022

MicroRNA-27a is essential for bone remodeling by modulating p62-mediated osteoclast signaling

The ability to simultaneously modulate a set of genes for lineage-specific development has made microRNA an ideal master regulator for organogenesis. However, most microRNA deletions do not exhibit obvious phenotypic defects possibly due to functional redundancy. MicroRNAs are known to regulate skeletal lineages as the loss of their maturation enzyme Dicer impairs bone remodeling processes. Therefore, it is important to identify specific microRNA essential for bone homeostasis. We report the loss of miR-27a causing severe osteoporosis in mice. MiR-27a affects osteoclast-mediated bone resorption but not osteoblast-mediated bone formation during skeletal remodeling. Gene profiling and bioinformatics further identify the specific targets of miR-27a in osteoclast cells. MiR-27a exerts its effects on osteoclast differentiation through modulation of Squstm1/p62 whose mutations have been linked to Pagets disease of bone. Our findings reveal a new miR-27a-p62 axis necessary and sufficient to mediate osteoclast differentiation and highlight a therapeutic implication for osteoporosis.

developmental biology↗

bioRxiv2022

Structural and functional insight into the plant unique multimodular triphosphosphate tunnel metalloenzymes of Arabidopsis thaliana

Triphosphate tunnel metalloenzymes (TTMs) are found in all biological kingdoms and have been characterized in microorganisms and animals. Members of the TTM family already characterized have divergent biological functions and act on a range of triphosphorylated substrates (RNA, thiamine triphosphate, inorganic polyphosphate). TTM proteins in plants have received considerably less attention and are unique in that some homologs harbor additional domains including a P-loop kinase and transmembrane domain. Here we report on structural and functional aspects of the multimodular TTM1 and TTM2 of Arabidopsis thaliana. Tissue and cellular microscopy studies show that both AtTTM1 and AtTTM2 are expressed in actively dividing (meristem) tissue and are tail-anchored proteins at the outer mitochondrial membrane - mediated by the single transmembrane domain at the C-terminus, supporting earlier studies. Crystal structures of AtTTM1 in the presence and absence of a non-hydrolyzable ATP analog reveal a catalytically incompetent TTM tunnel domain tightly interacting with the P-loop kinase domain that is locked in an inactive conformation. Structural comparison reveals that a helical hairpin may facilitate movement of the TTM domain thereby activating the kinase. Genetic studies show that AtTTM2 is important for the developmental transition from the vegetative to the reproductive phase in Arabidopsis, whereas its closest paralog AtTTM1 is not. Rational design of mutations based on the 3D structure demonstrates that both the P-loop kinase and TTM tunnel modules of AtTTM2 are required for the developmental switch.

plant biology↗

bioRxiv2022

Genomic and phenotypic comparisons reveal distinct variants of Wolbachia strain wAlbB

The intracellular bacterium Wolbachia inhibits virus replication and is being harnessed around the world to fight mosquito-borne diseases through releases of mosquitoes carrying the symbiont. Wolbachia strains vary in their ability to invade mosquito populations and suppress viruses in part due to differences in their density within the insect and associated fitness costs. Using whole-genome sequencing, we demonstrate the existence of two variants in wAlbB, a Wolbachia strain being released in natural populations of Aedes aegypti mosquitoes. The two variants display striking differences in genome architecture and gene content. Differences in the presence/absence of 49 genes between variants include genes located in prophage regions and others potentially involved in controlling the symbionts density. Importantly, we show that these genetic differences correlate with variation in wAlbB density and its tolerance to heat stress, suggesting that different wAlbB variants may be better suited for field deployment depending on local environmental conditions. Finally, we found that the wAlbB genome remained stable following its introduction in a Malaysian mosquito population. Our results highlight the need for further genomic and phenotypic characterization of Wolbachia strains in order to inform ongoing Wolbachia-based programmes and improve the selection of optimal strains in future field interventions. ImportanceDengue is a viral disease transmitted by Aedes mosquitoes that threatens around half of the world population. Recent advances in dengue control involve the introduction of Wolbachia bacterial symbionts with antiviral properties into mosquito populations which can lead to dramatic decreases in the incidence of the disease. In light of these promising results, there is a crucial need to better understand the factors affecting the success of such strategies, in particular the choice of Wolbachia strain for field releases and the potential for evolutionary changes. Here we characterized two variants of a Wolbachia strain used for dengue control that differ at the genomic level and in their ability to replicate within the mosquito. We also found no evidence for the evolution of the symbiont within the two years following its deployment in Malaysia. Our results have implications for current and future Wolbachia-based health interventions.

genomics↗

bioRxiv2021

Compositional analysis of Sindbis virus ribonucleoproteins reveals an extensive co-opting of key nuclear RNA-binding proteins

RNA is a central molecule for RNA viruses, acting as mRNA and genome. However, the interactions that viral (v)RNA establishes with the host cell is only starting to be elucidated. Here, we determine with unprecedented depth the composition of the ribonucleoproteins (RNPs) of the prototypical arthropod-borne Sindbis virus (SINV) using viral RNA interactome capture. We show that SINV RNAs engage with hundreds of cellular proteins and pathways, including a group of nuclear RNA-binding proteins (RBPs) with unknown roles in infection. Combining subcellular fractionation and proteomics with several orthogonal approaches, we demonstrate that these nuclear RBPs are selectively redistributed to the cytoplasm after infection, where they associate with the viral replication organelles. These nuclear RBPs potently supress viral gene expression, with activities spanning viral species and families. Our study provides a comprehensive and systematic analysis of SINV RNP composition, revealing a network of nuclear RBPs with moonlighting antiviral function. Research highlightsO_LISINV RNAs interact with over four hundred cellular RBPs C_LIO_LISINV induces selective cytoplasmic translocation of a subset of nuclear RBPs C_LIO_LIThese nuclear RBPs display potent antiviral effects C_LIO_LIThe SF3B complex binds to SINV RNA and supresses infection in a splicing-independent manner C_LI

microbiology↗