Biology subjects

Parker, J.

Publications and source records attributed to Parker, J..

At least 37 records · Page 2Linked to original sources

bioRxiv2023

Alternative ergosterol biosynthetic pathways confer antifungal drug resistance in the human pathogens within the Mucor species complex

Mucormycoses are emerging fungal infections caused by a variety of heterogeneous species within the Mucorales order. Among the Mucor species complex, Mucor circinelloides is the most frequently isolated pathogen in mucormycosis patients and despite its clinical significance, there is an absence of established genome manipulation techniques to conduct molecular patho-genesis studies. In this study, we generated a spontaneous uracil auxotrophic strain and developed a genetic transformation procedure to analyze molecular mechanisms conferring antifungal drug resistance. With this new model, phenotypic analyses of gene deletion mutants were conducted to define Erg3 and Erg6a as key biosynthetic enzymes in the M. circinelloides ergosterol pathway. Erg3 is a C-5 sterol desaturase involved in growth, sporulation, virulence, and azole susceptibility. In other fungal pathogens, erg3 mutations confer azole resistance because Erg3 catalyzes the production of a toxic diol upon azole exposure. Surprisingly, M. circinelloides produces only trace amounts of this toxic diol and yet, it is still susceptible to posaconazole and isavuconazole due to alterations in membrane sterol composition. These alterations are severely aggravated by erg3{Delta} mutations, resulting in ergosterol depletion and consequently, hy-persusceptibility to azoles. We also identified Erg6a as the main C-24 sterol methyltransferase, whose activity may be partially rescued by the paralogs Erg6b and Erg6c. Loss of Erg6a function diverts ergosterol synthesis to the production of cholesta-type sterols, resulting in resistance to amphotericin B. Our findings suggest that mutations or epimutations causing loss of Erg6 function may arise during human infections, resulting in antifungal drug resistance to first-line treatments against mucormycoses. ImportanceThe Mucor species complex comprises a variety of opportunistic pathogens known to cause mucormycosis, a potentially lethal fungal infection with limited therapeutic options. The only effective first-line treatments against mucormycosis consist of liposomal formulations of amphotericin B and the triazoles posaconazole and isavuconazole, all of which target components within the ergosterol biosynthetic pathway. This study uncovered M. circinelloides Erg3 and Erg6a as key enzymes to produce ergosterol, a vital constituent of fungal membranes. Absence of any of those enzymes leads to decreased ergosterol and consequently, resistance to ergosterol-binding polyenes such as amphotericin B. Particularly, losing Erg6a function pose a higher threat as the ergosterol pathway is channeled into alternative sterols similar to cholesterol, which maintain membrane permeability. As a result, erg6a mutants survive within the host and disseminate the infection, indicating that Erg6a deficiency may arise during human infections and confer resistance to the most effective treatment against mucormycoses.

microbiology↗

bioRxiv2023

Sexual antagonism and sex determination in three syngnathid species alongside male pregnancy gradient and varying sex roles.

The allocation of energy towards gamete production, parental care, mate choice, sex roles, and sexual dimorphism generates divergence in selection pressures between the sexes, leading to opposing fitness strategies and sexual antagonism (SA). Due to the shared genetic makeup, a single genomic locus can contain a gene or allele with differing fitness impacts on each sex. This intralocus sexual conflict can be resolved via intersex bias in gene expression and/or formation of sex-linked genomic regions, that may also regulate sex determination. Sex determination (SD) encompasses environmental SD (ESD), monogenic SD, and polygenic SD. Occasionally, shifts from one SD locus to another can occur. While the precise mechanisms driving these shifts are unknown, SA is believed to be a major contributor. To investigate the link between SA and SD, we selected three syngnathid species along the gradient of male pregnancy that evolved with different sex roles and intensities of sexual dimorphism. By looking at intersex genetic divergence (Fst) and sex-biased expression patterns, we uncovered that sex role and mate competition, rather than male pregnancy, primarily drive SA. Furthermore, we identified processes related to non-coding RNAs and biased allele expression as mediators of SA. Most notably, we discovered intraspecies sex chromosome polymorphism in Hippocampus erectus. Overall, we report important details on the interplay between SA and SD, and suggest that understanding SA and its resolution mechanisms is crucial for unraveling the evolution of SD in diverse species.

evolutionary biology↗

bioRxiv2023

The sterol C-24 methyltransferase encoding gene, erg6, is essential for viability of Aspergillus species.

Ergosterol is a critical component of fungal plasma membranes. Although many currently available antifungal compounds target the ergosterol biosynthesis pathway for antifungal effect, current knowledge regarding ergosterol synthesis remains incomplete for filamentous fungal pathogens like Aspergillus fumigatus. Here, we show for the first time that the lipid droplet-associated sterol C-24 methyltransferase, Erg6, is essential for A. fumigatus viability. We further show that this essentiality extends to additional Aspergillus species, including A. lentulus, A. terreus, and A. nidulans. Neither the overexpression of a putative erg6 paralog, smt1, nor the exogenous addition of ergosterol could rescue erg6 deficiency. Importantly, Erg6 downregulation results in a dramatic decrease in ergosterol and accumulation in lanosterol and is further characterized by diminished sterol-rich plasma membrane domains (SRDs) at hyphal tips. Unexpectedly, erg6 repressed strains demonstrate wild-type susceptibility against the ergosterol-active triazole and polyene antifungals. Finally, repressing erg6 expression reduced fungal burden accumulation in a murine model of invasive aspergillosis. Taken together, our studies suggest that Erg6, which shows little homology to mammalian proteins, is potentially an attractive antifungal drug target for therapy of Aspergillus infections. IMPORTANCEA. fumigatus is the most common pathogen that causes invasive aspergillosis, a life-threatening fungal infection with more than 300,000 cases reported annually. Available antifungals to treat Aspergillus-related infection are limited to three drug classes targeting the plasma membrane (ergosterol) or the cell wall, each of which suffer from either host toxicity or rising resistance levels. As ergosta-type sterols are absent in mammalian cells but are essential for fungal viability, the ergosterol biosynthesis pathway remains an enticing target for the development of new antifungals. Although ergosterol biosynthesis has been well studied in model yeast, only a few genes have been genetically characterized in A. fumigatus. Here, we characterize Erg6, one of the fungus-specific sterol biosynthesis genes, as an essential gene in Aspergillus species. We further provide in vivo evidence of the importance of Erg6 for establishment of invasive aspergillosis. Given the importance of Erg6 in other fungal systems for growth, stress resistance, and virulence, our study suggests that development of Erg6 inhibitors may be a promising strategy for developing novel broad-spectrum antifungals.

microbiology↗

bioRxiv2023

A bone marrow ECM mimicking, animal-component free hydrogel identifies TNTs as key mediators of druggable cell-cell and cell-ECM crosstalk in an animal replacement organoid model.

Treatment resistance, conferred onto cancer cells largely by the oncogenic niche, remains a clinically unmet need in leukaemia. Tractable and clinically translatable models that mimic cancer-niche crosstalk remain limited, consequently means of clinically drugging microenvironment-driven cancer treatment resistance remain underexplored. Here we develop a prototype bone marrow (BM) like extracellular matrix (ECM), Vitronectin-Alginate-Laminin (VAL), which comprises animal-free components, displays viscoelastic properties like the human BM, and engrafts a range of patient-derived-xenograft acute lymphoblastic leukaemia (PDX-ALL) samples. We discover that following treatment with oxidative stress-inducing apoptotic therapies, such as dexamethasone, ABT-199 and dexamethasone-ABT-199 combination, PDX-ALL cells reach out to MSC via the formation of tunnelling nanotubes (TNT). Nevertheless, we reveal that ALL-VAL-MSC-TNTs are clinically druggable, as they are absent following treatment with CDH2 antagonist ADH-1, a compound well-tolerated in solid cancer Phase I trials. We ultimately expose a triple drug combination of dexamethasone-ABT-199 and ADH-1, with most synergy area (MSA) scores of >30, that shows high efficacy and disrupts functional cancer-niche-TNTs in 4 different high risk PDX-ALL samples. In summary, here we develop prototype cancer-ECM-niche organoids and using leukaemia as a disease paradigm, we provide proof-of-concept insights enabling the beginning of research into drugging functional cancer cell crosstalk with its surrounding cellular and ECM niche.

cancer biology↗

bioRxiv2023

Flexible Analysis of Spatial Transcriptomics Data (FAST): A Deconvolution Approach

MotivationSpatial transcriptomics is a state-of-art technique that allows researchers to study gene expression patterns in tissues over the spatial domain. As a result of technical limitations, the majority of spatial transcriptomics techniques provide bulk data for each sequencing spot. Consequently, in order to obtain high-resolution spatial transcriptomics data, performing deconvolution becomes essential. Deconvolution enables the determination of the proportions of different cell types along with the corresponding gene expression levels for each cell type within each spot. Most existing deconvolution methods rely on reference data (e.g., single-cell data), which may not be available in real applications. Current reference-free methods encounter limitations due to their dependence on distribution assumptions, reliance on marker genes, or the absence of leveraging histology and spatial information. Consequently, there is a critical demand for the development of highly adaptable, robust, and user-friendly reference-free deconvolution methods capable of unifying or leveraging case-specific information in the analysis of spatial transcriptomics data. ResultsWe propose a novel reference-free method based on regularized non-negative matrix factorization (NMF), named Flexible Analysis of Spatial Transcriptomics (FAST), that can effectively incorporate gene expression data, spatial coordinates, and histology information into a unified deconvolution framework. Compared to existing methods, FAST imposes fewer distribution assumptions, utilizes the spatial structure information of tissues, and encourages interpretable factorization results. These features enable greater flexibility and accuracy, making FAST an effective tool for deciphering the complex cell-type composition of tissues and advancing our understanding of various biological processes and diseases. Extensive simulation studies have shown that FAST outperforms other existing reference-free methods. In real data applications, FAST is able to uncover the underlying tissue structures and identify the corresponding marker genes.

bioinformatics↗

bioRxiv2023

The genomic and cellular basis of biosynthetic innovation in rove beetles

How evolution at the cellular level potentiates change at the macroevolutionary level is a major question in evolutionary biology. With >66,000 described species, rove beetles (Staphylinidae) comprise the largest metazoan family. Their exceptional radiation has been coupled to pervasive biosynthetic innovation whereby numerous lineages bear defensive glands with diverse chemistries. Here, we combine comparative genomic and single-cell transcriptomic data from across the largest rove beetle clade, Aleocharinae. We retrace the functional evolution of two novel secretory cell types that together comprise the tergal gland--a putative catalyst behind Aleocharinaes megadiversity. We identify key genomic contingencies that were critical to the assembly of each cell type and their organ-level partnership in manufacturing the beetles defensive secretion. This process hinged on evolving a mechanism for regulated production of noxious benzoquinones that appears convergent with plant toxin release systems, and synthesis of an effective benzoquinone solvent that weaponized the total secretion. We show that this cooperative biosynthetic system arose at the Jurassic-Cretaceous boundary, and that following its establishment, both cell types underwent [~]150 million years of stasis, their chemistry and core molecular architecture maintained almost clade-wide as Aleocharinae radiated globally into tens of thousands of lineages. Despite this deep conservation, we show that the two cell types have acted as substrates for the emergence of adaptive, biochemical novelties--most dramatically in symbiotic lineages that have infiltrated social insect colonies and produce host behavior-manipulating secretions. Our findings uncover genomic and cell type evolutionary processes underlying the origin, functional conservation and evolvability of a chemical innovation in beetles.

evolutionary biology↗

bioRxiv2023

Piezo inhibition prevents and rescues scarring by targeting the adipocyte to fibroblast transition

While past studies have suggested that plasticity exists between dermal fibroblasts and adipocytes, it remains unknown whether fat actively contributes to fibrosis in scarring. We show that adipocytes convert to scar-forming fibroblasts in response to Piezo-mediated mechanosensing to drive wound fibrosis. We establish that mechanics alone are sufficient to drive adipocyte-to- fibroblast conversion. By leveraging clonal-lineage-tracing in combination with scRNA-seq, Visium, and CODEX, we define a "mechanically naive" fibroblast-subpopulation that represents a transcriptionally intermediate state between adipocytes and scar-fibroblasts. Finally, we show that Piezo1 or Piezo2-inhibition yields regenerative healing by preventing adipocytes activation to fibroblasts, in both mouse-wounds and a novel human-xenograft-wound model. Importantly, Piezo1-inhibition induced wound regeneration even in pre-existing established scars, a finding that suggests a role for adipocyte-to-fibroblast transition in wound remodeling, the least-understood phase of wound healing. Adipocyte-to-fibroblast transition may thus represent a therapeutic target for minimizing fibrosis via Piezo-inhibition in organs where fat contributes to fibrosis.

cell biology↗

bioRxiv2023

ProT-VAE: Protein Transformer Variational AutoEncoder for Functional Protein Design

The data-driven design of protein sequences with desired function is challenged by the absence of good theoretical models for the sequence-function mapping and the vast size of protein sequence space. Deep generative models have demonstrated success in learning the sequence to function relationship over natural training data and sampling from this distribution to design synthetic sequences with engineered functionality. We introduce a deep generative model termed the Protein Transformer Variational AutoEncoder (ProT-VAE) that furnishes an accurate, generative, fast, and transferable model of the sequence-function relationship for data-driven protein engineering by blending the merits of variational autoencoders to learn interpretable, low-dimensional latent embeddings and fully generative decoding for conditional sequence design with the expressive, alignment-free featurization offered by transformers. The model sandwiches a lightweight, task-specific variational autoencoder between generic, pre-trained transformer encoder and decoder stacks to admit alignment-free training in an unsupervised or semi-supervised fashion, and interpretable low-dimensional latent spaces that facilitate understanding, optimization, and generative design of functional synthetic sequences. We implement the model using NVIDIAs BioNeMo framework and validate its performance in retrospective functional prediction and prospective design of novel protein sequences subjected to experimental synthesis and testing. The ProT-VAE latent space exposes ancestral and functional relationships that enable conditional generation of novel sequences with high functionality and substantial sequence diversity. We anticipate that the model can offer an extensible and generic platform for machine learning-guided directed evolution campaigns for the data-driven design of novel synthetic proteins with "super-natural" function.

synthetic biology↗

bioRxiv2022

Loss of FBXO11 function establishes a stem cell program in acute myeloid leukemia through dysregulation of the mitochondrial protease LONP1

Acute myeloid leukemia (AML) is an aggressive cancer with very poor outcomes. To identify additional drivers of leukemogenesis, we analyzed sequence data from 1,727 unique individual AML patients, which revealed mutations in ubiquitin ligase family genes in 11.2% of adult AML samples with mutual exclusivity. The Skp1/Cul1/Fbox (SCF) E3 ubiquitin ligase complex gene FBXO11 was the most significantly downregulated gene of the SCF complex in AML. FBXO11 catalyzes K63-linked ubiquitination of a novel target, LONP1, which promotes entry into mitochondria, thereby enhancing mitochondrial respiration. Reduced mitochondrial respiration secondary to FBXO11 depletion imparts myeloid-biased stem cell properties in primary CD34+ hematopoietic stem progenitor cells (HSPC). In a human xenograft model, depletion of FBXO11 cooperated with AML1-ETO and mutant KRASG12D to generate serially transplantable AML enriched for primitive cells. Our findings suggest that reduced FBXO11 primes HSPC for myeloid-biased self-renewal through attenuation of LONP1-mediated regulation of mitochondrial respiration.

cancer biology↗

bioRxiv2022

An Integrated Model for Predicting KRAS Dependency

BackgroundThe clinical approvals of KRAS G12C inhibitors has been a revolutionary advance in precision oncology, but response rates are often modest. To improve patient selection, we developed an integrated model to predict KRAS dependency. Methods and FindingsBy integrating molecular profiles of a large panel of cell lines from the DEMETER2 dataset, we built a binary classifier to predict a tumors KRAS dependency. Monte Carlo cross validation via ElasticNet within the training set was used to compare model performance and to tune parameters. The final model was then applied to the validation set. We validated the model with genetic depletion assays and an external dataset of lung cancer cells treated with a G12C inhibitor. We then applied the model to several Cancer Genome Atlas (TCGA) datasets. The final "K20" model contains 20 features, including expression of 19 genes and KRAS mutation status. In the validation cohort, K20 had an AUC of 0.94 and accurately predicted KRAS dependency in both mutant and KRAS wild-type cell lines following genetic depletion. It was also highly predictive across an external dataset of lung cancer lines treated with KRAS G12C inhibition. When applied to TCGA datasets, specific subpopulations such as the invasive subtype in colorectal cancer and copy number high pancreatic adenocarcinoma were predicted to have higher KRAS dependency. ConclusionThe K20 model has simple yet robust predictive capabilities that may provide a useful tool to select patients with KRAS mutant tumors that are most likely to respond to direct KRAS inhibitors.

bioinformatics↗

bioRxiv2022

A human mesenchymal spheroid prototype to replace moderate severity animal procedures in leukaemia drug testing

Patient derived xenograft (PDX) models are regarded as gold standard preclinical models in leukaemia research, especially in testing new drug combinations where typically 45-50 animals are used per assay. 9000 animal experiments are performed annually in leukaemia research with these expensive procedures being described as moderate severity, meaning they cause significant pain, suffering and visible distress to animals state. Furthermore, not all clinical leukaemia samples engraft and when they do data turnaround time can be between 6-12 months. Heavy dependence on animal models is because clinical leukaemia samples do not proliferate in vitro. Alternative cell line models though popular for drug testing are not biomimetic - they are not dependent on the microenvironment for survival, growth and treatment response and being derived from relapse samples they do not capture the molecular complexity observed at disease presentation. Here we have developed an in vitro platform to rapidly establish co-cultures of patient-derived leukaemia cells with 3D bone marrow mesenchyme spheroids, BM-MSC-spheroids. We optimise protocols for developing MSC-spheroid leukaemia co-culture using clinical samples and deliver drug response data within a week. Using three patient samples representing distinct cytogenetics we show that patient-derived-leukaemia cells show enhanced proliferation when co-cultured with MSC-spheroids. In addition, MSC-spheroids provided improved protection against treatment. This makes our spheroids suitable to model treatment resistance - a major hurdle in current day cancer management Given this 3Rs approach is 12 months faster (in delivering clinical data), is a human cell-based biomimetic model and 45-50 animals/drug-response assay cheaper the anticipated target end-users would include academia and pharmaceutical industry. This animal replacement prototype would facilitate clinically translatable research to be performed with greater ethical, social and financial sustainability. Research HighlightsO_ST_ABSScientific BenefitC_ST_ABSA 3D spheroid-based approach for ex vivo co-culture of clinical leukaemia samples for further investigation into cancer biology such as blast-niche interactions, blast proliferation and treatment resistance 3Rs BenefitTo replace moderate severity animal procedures in leukaemia research and drug testing Practical Benefit3Rs approach that yields drug response data quickly and is more ethically, socially and financially sustainable than its in vivo counterparts Current applicationsExploration of leukaemia biology such as blasts proliferation, blast-niche interactions, niche-impacted treatment resistance and obtain drug response data Potential applicationsExtend the approach to include other haematological cancers as well as bone cancers.

cancer biology↗

bioRxiv2022

Human iPSC-Vascular Smooth Muscle Cell Spheroids Demonstrate Size-dependent Alterations in Cellular Viability and Secretory Function

Human induced pluripotent stem cells and their differentiated vascular cells have been revolutionizing the field of regenerative wound healing. These cells are shown to be rejuvenated with immense potentials in secreting paracrine factors. Recently, hiPSC-derived vascular smooth muscle cells (hiPSC-VSMC) have shown regenerative wound healing ability via their paracrine secretion. The quest to modulate the secretory function of these hiPSC-VSMC is an ongoing effort and involves the use of both biochemical and biophysical stimuli. This study explores the development and optimization of a reproducible, inexpensive protocol to form hiPSC-VSMC derived spheroids to investigate the implications of spheroid size on viability and paracrine secretion. Our data shows the successful formation of different sizes of spheroids using various amount of hiPSC-VSMC. The hiPSC-VSMC spheroids formed with 10000 cells strike an ideal balance between overall cell health and maximal paracrine secretion. The conditioned medium from these spheroids was found to be bioactive in enhancing human dermal fibroblast cell proliferation and migration. This research will inform future studies on the optimal spheroid size for regenerative wound healing applications.

bioengineering↗

bioRxiv2022

Abnormal molecular signatures of inflammation, energy metabolism and vesicle biology in human Huntington disease peripheral tissues

BackgroundA major challenge in neurodegenerative diseases concerns identifying biological disease signatures that track with disease progression or respond to an intervention. Several clinical trials in Huntington disease (HD), an inherited, progressive neurodegenerative disease, are currently ongoing. Therefore, we examined whether peripheral tissues can serve as a source of readily accessible biological signatures at the RNA and protein level in HD patients. ResultsWe generated large, high-quality human datasets from skeletal muscle, skin and adipose tissue to probe molecular changes in human premanifest and early manifest HD patients - those most likely involved in clinical trials. In-depth single nucleotide polymorphism data across the HTT gene will facilitate the use of the generated primary- and iPSC cell lines in allele-specific targeting approaches. The analysis of the transcriptomics and proteomics data shows robust, stage-dependent dysregulation. Gene ontology analysis confirmed the involvement of inflammation and energy metabolism in peripheral HD pathogenesis. Furthermore, we observed changes in the homeostasis of extracellular vesicles, where we found consistent changes of genes and proteins involved in this process. ConclusionsOur omics data document the involvement of inflammation, energy metabolism and extracellular vesicle homeostasis. This demonstrates the potential to identify biological signatures from peripheral tissues in HD suitable as biomarkers in clinical trials. Together with the primary cell lines established from peripheral tissues and a large panel of iPSC lines that can serve as human models of HD, the generated data are a valuable and unique resource to advance the current understanding of molecular mechanisms driving HD pathogenesis.

neuroscience↗

bioRxiv2021

Loss-of-function ROX1 mutations suppress the fluconazole susceptibility of upc2AΔ mutation in Candida glabrata, implicating additional positive regulators of ergosterol biosynthesis

Two of the major classes of antifungal drugs in clinical use target ergosterol biosynthesis. Despite its importance, our understanding of the transcriptional regulation of ergosterol biosynthesis genes in pathogenic fungi is essentially limited to the role of hypoxia and sterol-stress induced transcription factors such as Upc2 and Upc2A as well as homologs of Sterol Response Element Binding (SREB) factors. To identify additional regulators of ergosterol biosynthesis in Candida glabrata, an important human fungal pathogen with reduced susceptibility to ergosterol biosynthesis inhibitors relative to other Candida spp., we used a serial passaging strategy to isolate suppressors of the fluconazole hypersusceptibility of a upc2A{Delta} deletion mutant. This led to the identification of loss of function mutants in two genes: ROX1, the homolog of a hypoxia gene transcriptional suppressor in Saccharomyces cerevisiae, and CST6, a transcription factor that is involved in the regulation of carbon dioxide response in C. glabrata. Here, we describe a detailed analysis of the genetic interaction of ROX1 and UPC2A. In the presence of fluconazole, loss of Rox1 function restores ERG11 expression to the upc2A{Delta} mutant and inhibits the expression of ERG3 and ERG6, leading to increased levels or ergosterol and decreased levels of the toxic sterol, 14 methyl-ergosta-8,24(28)-dien-3{beta}, 6-diol, relative to upc2A{Delta}. Our observations establish that Rox1 is a negative regulator of ERG gene biosynthesis and indicate that a least one additional positive transcriptional regulator of ERG gene biosynthesis must be present in C. glabrata. ImportanceCandida glabrata is one of the most important human fungal pathogens and has reduced susceptibility to azole class inhibitors of ergosterol biosynthesis. Although ergosterol is the target of two of the three classes of antifungal drugs, relatively little is known about the regulation of this critical cellular pathway. Sterols are both essential components of the eukaryotic plasma membrane and potential toxins; therefore, sterol homeostasis is critical for cell function. Here, we identified two new negative regulators of C. glabrata of ergosterol (ERG) biosynthesis gene expression. Our results also indicate that in addition to Upc2A, the only known activator of ERG genes, additional positive regulators of this pathway must exist.s

microbiology↗

bioRxiv2021

Large-scale comparative genomics unravels great genomic diversity across the Rickettsia and Ca. Megaira genera and identifies Torix group as an evolutionarily distinct clade.

Rickettsia are intracellular bacteria originally described as arthropod borne pathogens that are emerging as a diverse group of often biologically important, non-pathogenic symbionts of invertebrates and microeukaryotes. However, sparse genomic resources for symbiotic strains and for the sister genus (Candidatus Megaira) inhibit our understanding of Rickettsia evolution and biology. Here, we present the first closed genomes of Ca. Megaira from an alga (Mesostigma viride), and Torix Rickettsia from midge (Culicoides impunctatus) and bed bug (Cimex lectularius) hosts. Additionally, we sequenced and constructed draft genomes for Ca. Megaira from another alga (Carteria cerasiformis), Transitional group Rickettsia from tsetse fly (Glossina morsitans submorsitans), and Torix Rickettsia from a spider mite (Bryobia graminum). We further extract 22 draft genomes from arthropod genome sequencing projects, including 1 Adalia, 4 Transitional, 1 Spotted Fever, 7 Torix, 7 Belli and the first Rhyzobius and Meloidae Rickettsia group genomes. We used new and existing Rickettsia genomes to estimate the phylogeny and metabolic potential across groups and reveal transitions in genomic properties. These data reveal Torix as unique amongst currently described Rickettsia, with highly distinct and diverse accessory genomes. We confirm the presence of a third subclade of Torix, previously only known from gene marker sequences. Further, Torix share an intact pentose phosphate pathway with Ca. Megaira, not observed in other Rickettsia. Considering the distinctness and diversity of Torix, we propose that the group be named Candidatus Tisiphia. The wide host range of Ca. Tisiphia symbionts necessitates onward research to understand the biological and physiological bases of Ca. Tisiphia-host interactions. Importance statementMembers of the genus Rickettsia were originally identified as causative agents of mammalian vector-borne disease. In the last 25 years we have recognised that many Rickettsia are arthropod symbionts, and sit alongside a sister taxon, Ca. Megaira, which are symbiotic associates of microeukaryotes. The lack of genomic information for symbiotic strains affects our ability to determine the evolutionary relationships between strains and understand the biological underpinnings of the different symbioses. We clarify these relationships by assembling 26 genomes of Rickettsia from understudied groups, and the first two Ca. Megaira, from various insects and microeukaryotes. Of note, the accessory genome diversity and broad host range of Torix Rickettsia parallels all other Rickettsia combined. This diversity, alongside the breadth of host species, make the Torix clade an important hidden player in invertebrate biology and physiology. We argue this clade should be given its own genus status, for which we propose Ca. Tisiphia.

microbiology↗

bioRxiv2021

Structure of an ant-myrmecophile-microbe community

Superorganismal ant colonies play host to a menagerie of symbiotic arthropods, termed myrmecophiles, which exhibit varying degrees of social integration into colony life. Such systems permit examination of how animal community interactions influence microbial assemblages. Here, we present an ecologically and phylogenetically comprehensive characterization of an ant-myrmecophile-microbe community in Southern California. Using 16S rRNA profiling, we find that microbiotas of the velvety tree ant (Liometopum occidentale) and its cohort of myrmecophiles are distinguished by species-specific characteristics but nevertheless bear signatures of their behavioral interactions. We found that the host ant microbiome was diverse at all taxonomic levels; that of a myrmecophilous cricket was moderately diverse, while microbiotas of three myrmecophilous rove beetles (Staphylinidae), which have convergently evolved symbiosis with Liometopum, were dominated by intracellular endosymbionts. Yet, despite these compositional differences, similarities between ant and myrmecophile microbiotas correlated with the nature and intimacy of their behavioral relationships. Physical interactions such as grooming and trophallaxis likely facilitate cross-species extracellular microbial sharing. Further, phylogenetic comparisons of microbiotas from myrmecophile rove beetles and outgroups revealed a lack of co-cladogenesis of beetles and intracellular endosymbionts, and limited evidence for convergence among the myrmecophiles intracellular microbiotas. Comparative genomic analyses of the dominant Rickettsia endosymbiont of the most highly socially integrated myrmecophile imply possible functions unrelated to nutrient-provisioning in the host beetles specialized lifestyle. Our findings indicate that myrmecophile microbiotas evolve largely independently of the constraints of deep evolutionary history, and that the transition to life inside colonies, including social interactions with hosts, plays a significant role in structuring bacterial assemblages of these symbiotic insects.

ecology↗

bioRxiv2021

Optimal dynamic incentive scheduling for Hawk-Dove evolutionary games

The Hawk-Dove mathematical game offers a paradigm of the trade-offs associated with aggressive and passive behaviors. When two (or more) populations of players (animals, insect populations, countries in military conflict, economic competitors, microbial communities, populations of co-evolving tumor cells, or reinforcement learners adopting different strategies) compete, their success or failure can be measured by their frequency in the population (successful behavior is reinforced, unsuccessful behavior is not), and the system is governed by the replicator dynamical system. We develop a time-dependent optimal-adaptive control theory for this nonlinear dynamical system in which the payoffs of the Hawk-Dove payoff matrix are dynamically altered (dynamic incentives) to produce (bang-bang) control schedules that (i) maximize the aggressive population at the end of time T, and (ii) minimize the aggressive population at the end of time T. These two distinct time-dependent strategies produce upper and lower bounds on the outcomes from all strategies since they represent two extremizers of the cost function using the Pontryagin maximum (minimum) principle. We extend the results forward to times nT (n = 1, ..., 5) in an adaptive way that uses the optimal value at the end of time nT to produce the new schedule for time (n + 1)T. Two special schedules and initial conditions are identified that produce absolute maximizers and minimizers over an arbitrary number of cycles for 0 [≤] T [≤] 3. For T > 3, our optimum schedules can drive either population to extinction or fixation. The method described can be used to produce optimal dynamic incentive schedules for many different applications in which the 2 x 2 replicator dynamics is used as a governing model.

evolutionary biology↗

bioRxiv2021

Evolutionary assembly of cooperating cell types in an animal chemical defense system

A long-standing challenge in biology is explaining how the functions of multicellular organs emerge from the underlying evolution of cell types. We deconstructed evolution of an organ novelty: a rove beetle gland that secretes a defensive cocktail. We show that gland function was pieced together via assembly of two cell types that manufacture distinct compounds. One cell type forms a chemical reservoir in the beetles abdomen and produces alkane and ester compounds. We demonstrate that this cell type is a hybrid of cuticle cells and ancient pheromone and adipocyte-like cells, and executes its function via a mosaic of enzymes sourced from each parental cell type. The second cell type synthesizes noxious benzoquinones using a chimeric pathway derived from conserved cellular energy and cuticle formation pathways. We present evidence that evolution of each cell type was shaped by coevolution between the two cell types: the benzoquinones produced by the second cell type dissolve in solvents produced by the first, yielding a potent secretion that confers adaptive value onto the gland as a whole. Our findings illustrate how cooperation between cell types can arise, generating new, organ-level behaviors.

evolutionary biology↗