Biology subjects

Clark, C.

Publications and source records attributed to Clark, C..

At least 19 recordsLinked to original sources

bioRxiv2026

TOPBP1-Dependent DNA Damage Processing Promotes Centromere Loss in an Inviable Xenopus Hybrid

Hybrid incompatibility is associated with chromosome instability, DNA damage, and embryonic lethality, yet how cells respond to genome instability in hybrids is unclear. In inviable hybrids generated by fertilizing Xenopus tropicalis eggs with Xenopus laevis sperm, CENP-A is lost from paternal chromosomes, leading to elimination of two chromosome arms. Using hybrid Xenopus egg extract reactions, we show that CENP-A is removed from X. laevis chromosomes exposed to X. tropicalis cytoplasm through an RNA polymerase II-dependent process associated with DNA damage. Topoisomerase II Binding Protein 1 (TOPBP1) localized to damaged acentric chromosomes during metaphase, and its depletion impaired chromosome alignment, increased DNA damage, and blocked CENP-A removal. Inhibition of DNA polymerase theta increased DNA damage while promoting CENP-A retention, indicating that DNA damage processing rather than damage itself promotes CENP-A loss. Together, our findings reveal separable roles for TOPBP1 in chromosome organization and centromere destabilization, showing how a protective genome surveillance pathway can instead drive chromosome instability in an inviable hybrid.

cell biology↗

bioRxiv2026

An intersectional expression platform for gene complementation using RNA-fragment end joining (REJ)

Gene complementation is a powerful tool for genetic selection and protein functional studies but typically requires extensive screening for complementary components. Here we engineered a platform for gene complementation based on RNA end-joining (REJ) that precisely and efficiently splices separate RNA units into functional coding mRNAs. REJ is mediated by short structured modular RNA segments of ~250bp that: (a) promote RNA::RNA interaction, (b) coopt the intrinsic cell splicing machinery to facilitate RNA trans-splicing, (c) minimizes translation of protein fragments from un-spliced RNA segments, and (d) encodes scar-free protein. We demonstrate that REJ is a broadly applicable system that can reliably split nearly any gene into complementary segments regardless of protein structure. To enable the use of this system we provide a toolbox of reporters and a web-based design tool to facilitate vector design. Demonstrated REJ applications include genetic complementation, intersectional labeling of cell types, and efficient expression of large proteins.

molecular biology↗

bioRxiv2026

Spindle scaling promotes adaptation to polyploidy

How the cell division machinery adapts to increases in genome copy number (ploidy) remains an open question with implications for evolution and cancer. Using Xenopus egg extracts and species spanning 2N to 12N ploidy, we found that stepwise increases in ploidy drove spindle multipolarity, accompanied by larger spindles, increased microtubule density, and differential scaling of spindle assembly factor localization. In contrast, extracts from the dodecaploid species Xenopus longipes supported robust bipolar spindle assembly at all ploidies. Engineering X. laevis extracts to mimic X. longipes by modulating microtubule regulators frequently overexpressed in cancer, or confining spindles inside small droplets, decreased spindle length and significantly rescued bipolarity. Thus, tuning spindle microtubule dynamics and architecture enables adaptation to increased chromosome number across acute and evolutionary timescales.

cell biology↗

bioRxiv2026

Thiamine availability and acquisition differ between natural and controlled environments

Thiamine Deficiency Complex (TDC) is a reproductive disorder that affects recruitment of diverse salmonine populations globally. Typical symptoms include behavioral and neurological abnormalities and high offspring mortality. TDC is common in hatcheries that rear salmonines obtained from wild populations, and symptoms are mitigated by thiamine treatment. However, no studies have quantified thiamine concentrations in wild embryos. Here, we evaluated whether fertilized eggs and/or embryos may acquire thiamine from natural sources (e.g., biotic breakdown products and diet) during development. Lake trout (Salvelinus namaycush) gametes were obtained from feral adults in Lake Champlain and fertilized eggs were grouped by family with paired rearing under natural (Lake Champlain) and artificial (controlled laboratory) conditions. Average thiamine concentrations were similar between lake-reared and laboratory-reared fish prior to hatch; however, lake-reared fish experienced significant increases in thiamine concentrations at and after hatching compared to previous stages and compared to laboratory-reared fish; laboratory-reared fish experienced no increases in thiamine concentrations. Water samples revealed an abundance of thiamine precursors and byproducts in the natural environment, which may serve as sources of thiamine for developing embryos. These results demonstrate that salmonine embryos can acquire thiamine from natural sources during development, which may mitigate effects of TDC.

ecology↗

bioRxiv2026

Autophagy Cholesterol Axis Remodeling Supports Malignant Progression and Chemoresistance in Glioma

Glioma progression and resistance to temozolomide (TMZ) remain major clinical challenges. Here, we investigated whether dysregulated autophagy and cholesterol metabolism are coordinately remodeled during glioma progression and TMZ resistance. Tissue microarray analysis of astrocytoma and glioblastoma specimens revealed progressive autophagosome accumulation, reflected by increased LC3{beta} puncta, coupled with impaired autophagic flux compared with adjacent normal brain tissue. These alterations intensified with tumor grade and were associated with upregulation of farnesyl diphosphate synthase (FDPS), linking malignant progression to cholesterol pathway remodeling. TMZ-resistant (R) glioblastoma cells exhibited epithelial-to-mesenchymal transition, mitotic quiescence, and mitochondrial remodeling consistent with a therapy-tolerant phenotype. Bioenergetic profiling demonstrated reduced respiratory reserve, diminished ATP-linked respiration, and elevated proton leak, indicating constrained metabolic flexibility. In parallel, impaired autophagy flux was associated with suppression of de novo cholesterol synthesis and transcriptional downregulation of SREBP-2 and LDL-R. Comprehensive lipidomic profiling revealed marked cholesterol metabolic reprogramming in R cells, characterized by accumulation of specific cholesteryl esters, including CE 22:5, CE 22:6, CE 22:4, and CE 20:4, despite reduced cholesterol biosynthesis. Pharmacologic inhibition of the mevalonate pathway with simvastatin significantly altered cholesteryl ester profiles but failed to restore autophagy flux or sensitize R cells to TMZ-induced apoptosis, even under combined TMZ-simvastatin treatment. Lay AbstractAs gliomas progress from astrocytoma to glioblastoma, autophagy becomes dysregulated and cholesterol metabolism is rewired. This coordinated remodeling supports tumor survival, metabolic plasticity, and resistance to temozolomide therapy. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=133 SRC="FIGDIR/small/697885v2_ufig1.gif" ALT="Figure 1000"> View larger version (79K): org.highwire.dtl.DTLVardef@1183dd2org.highwire.dtl.DTLVardef@82e20dorg.highwire.dtl.DTLVardef@c6c8dforg.highwire.dtl.DTLVardef@adb427_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsAutophagy flux blockade intensifies during progression from astrocytoma to glioblastoma Dysregulated autophagy is coupled to altered cholesterol metabolism in malignant gliomas TMZ-resistant glioblastoma cells undergo epithelial-to-mesenchymal transition and mitotic quiescence Resistant cells exhibit constrained bioenergetic capacity and mitochondrial remodeling Impaired autophagy suppresses de novo cholesterol synthesis and lipid recycling Lipidomics reveals accumulation of long-chain cholesteryl esters in TMZ-resistant cells Statin-based cholesterol inhibition fails to resensitize glioblastoma cells to temozolomide

cancer biology↗

bioRxiv2025

Distinct Electrophysiological Signatures Define Neuronal Subtypes in the Fasciola Cinereum

The fasciola cinereum (FC) is a small, conserved hippocampal subregion whose cellular properties remain poorly understood. Anatomically positioned between dorsal CA1 and the third ventricle, the FC receives diverse cortical and subcortical inputs but is often excluded from hippocampal circuit models. Here, we performed ex vivo whole-cell patch-clamp recordings in mouse hippocampal slices to define the intrinsic and synaptic properties of FC neurons. We find that FC neurons are electrophysiologically and morphologically distinct from neighboring CA1 and CA2 pyramidal cells, exhibiting reduced intrinsic excitability, delayed spike initiation, and enhanced afterhyperpolarizations. These properties are strongly shaped by potassium conductances, with Kv2 (KCNB) and Kv7 (KCNQ) channels contributing to the suppression of firing. We find that FC neurons span a continuum of intrinsic excitability which is structured by variability in potassium channel-mediated conductances and is inversely coordinated with excitatory synaptic input, such that less excitable neurons receive stronger synaptic drive. Together, these findings establish a mechanistic framework in which intrinsic membrane properties and synaptic input are co-organized across the FC population, providing new insight into how this understudied hippocampal region may contribute to the regulation of neural excitability. Key PointsO_LIThe fasciola cinereum (FC) is a small and poorly understood hippocampal subregion that has recently been implicated in hippocampal related function and seizure activity. C_LIO_LIHere we show that neurons in the FC are morphologically and functionally distinct from cells in neighboring CA1 and CA2 hippocampal subregions, and find substantial physiological diversity of FC neurons, including differences in firing behavior, membrane properties, and intrinsic excitability. C_LIO_LIPharmacological analyses show that Kv2 and Kv7 potassium channels play a key role in shaping the intrinsic properties of FC neurons. C_LIO_LILess excitable FC neurons receive stronger excitatory synaptic input, revealing an inverse relationship between intrinsic membrane excitability and synaptic drive. C_LIO_LIThese findings identify the FC as a physiologically specialized hippocampal subregion and provide a foundation for understanding its role in hippocampal function and neurological disease. C_LI

neuroscience↗

bioRxiv2025

Uncoupling overeating and fat storage by modulation of different serotonergic receptors

Psychotropic drugs such as antipsychotics improve symptoms of psychiatric disorders. However, they are associated with severe metabolic side effects that remodel energy balance, resulting in weight gain and increased food intake (hyperphagia). Here, we compare how antipsychotics and exogenous serotonin induce hyperphagia by remodeling energy balance. We find that the ability of serotonin and antipsychotics to remodel energy balance strictly depends on the serotonergic receptors SER-7 and SER-5, respectively. While both molecules induce hyperphagia, serotonin does so by increasing energy expenditure and reducing fat stores. In contrast, antipsychotics block the inhibitory effect of fat storage on feeding, thereby inducing hyperphagia and increasing fat stores. Thus, it is possible to manipulate energy balance to induce hyperphagia while either increasing or decreasing fat storage. Inactivation of the germline remodels energy balance similar to antipsychotic treatment, promoting hyperphagia while increasing fat storage. Consistent with overlapping mechanisms, antipsychotics are no longer able to remodel energy balance in both C. elegans and mice lacking an intact germline. Thus, our results uncouple overeating from fat storage and show that overeating can be induced by mechanisms that reduce or increase fat stores.

neuroscience↗

bioRxiv2025

Evolution of the conformational ensemble and allosteric networks of apoptotic caspases in chordates

Caspases, known for their role in apoptosis and inflammation, have recently emerged as potential regulators of cell differentiation and proliferation. The regulation of caspase conformations to affect these specific pathways is not well understood. Understanding the conformational landscapes, intermediate states, and mechanisms for fine-tuning these ensembles is critical for unraveling their diverse regulatory functions. We combined experimental and computational techniques to characterize the evolution of conformational ensemble in caspases. Using ancestral protein reconstruction, molecular dynamics simulations, and network analysis, we identify a network of residues that serve as a scaffold for conformational variation, and the network has been faithfully passed down over 500 million years of apoptotic caspase evolution. In addition, investigations of free energy landscapes provide thermodynamic insights into how initiator and effector caspase subfamilies stabilize monomeric and dimeric conformations while undergoing conformational dynamics. We find, through mutational in-vitro folding analysis, that the small subunit and amino acid networks at the base of the structure are essential for conformational dynamics beyond a ubiquitous intermediate present in the conformational ensemble of all apoptotic chordate caspases. We identify key allosteric hub residues that regulate the equilibrium in the conformational ensembles of all apoptotic caspases in chordates. Lastly, by combining our new data set with previous folding studies we provide a comprehensive model for folding of all apoptotic caspases in chordates.

biochemistry↗

bioRxiv2025

MeQTL Mapping in African American Hepatocytes Reveals Shared Genetic Regulators of DNA Methylation and Gene Expression

Methylation quantitative trait loci (meQTL) mapping can provide insight into the genetic architecture underlying the epigenome by identifying single-nucleotide polymorphisms (SNPs) associated with differential methylation at methylation sites (CpGs) across the genome. Given that the epigenetic architecture underlying differences in gene expression can vary across racial populations, performing epigenomic studies in African Americans is crucial for understanding the interplay between genetic variation, DNA methylation, and gene expression in this understudied group. By performing cis-meQTL mapping in African American hepatocytes, we identified 410,186 cis-meQTLs associated with methylation at 24,425 CpGs in the liver. Through colocalization analysis, we found that 18,206 of these meQTLs are also colocalized with known liver eQTLs. Additionally, we found that using African American eQTL data results in an increased ability to detect additional colocalized variants that exhibit strong differences in allele frequency between people of European and African ancestry. Furthermore, the presence of smaller linkage disequilibrium blocks in African Americans allows us to identify narrower genomic regions of potentially causal variants compared to when data from Europeans is used. Importantly, these colocalized SNPs are significantly enriched for genetic associations with lipid and inflammatory traits in the GWAS catalog, suggesting that DNA methylation may contribute to the etiologies of these diseases. Furthermore, while it is generally presumed that the genetic regulation of DNA methylation is shared between blood and liver, we found that only 5.4% of African American liver meQTLs colocalize with blood meQTLs. Overall, our results reveal that studying African American populations results in the identification of additional genetic and epigenetic factors that may regulate gene expression in the liver, thereby expanding our understanding of gene regulation in African Americans.

genomics↗

bioRxiv2024

Bwa, an ortholog of alkaline ceramidase-ACER2, promotes intestinal stem cell proliferation through pro-inflammatory cytokine signaling in Drosophila melanogaster

Sphingolipids, including ceramides, are an important component of high-fat diets. These molecules can regulate fatty acid oxidation and intestinal stem cell proliferation, predisposing the gut to tumorigenesis. However, the molecular mechanisms involved in ceramide metabolism-mediated intestinal stem cell (ISC) proliferation and tumorigenesis are poorly understood. To understand how changes in sphingolipid metabolite flux affect intestinal stem cells, we manipulated the activities of each of the enzymes of the ceramide synthetic pathway using cell type-specific over-expression or depletion of the corresponding mRNAs in each intestinal cell type of the Drosophila midgut. We documented cell-autonomous and non-cell-autonomous effects, including alterations in cell size, number, differentiation, and proliferation. In our screen, the altered expression of several ceramide metabolism enzymes led to changes in ISC proliferation, cell sizes, and overall cellularity. Among other genes, over-expression of ceramidase homolog, Brain washing (bwa) in gut enteroblasts (EB) increased EB cell size and caused a non-cell-autonomous, 7-8-fold increase in ISC proliferation. Our analysis confirmed previous reports that bwa does not have ceramidase activity, and lipidomic studies indicated that bwa increases the saturation status of sphingolipids, free fatty acids, and other lipids. The pro-proliferative effects of bwa could be counter-acted by depleting a serine palmitoyltransferase, Lace, or a sphingosine acyltransferase, Schlank, which are needed for ceramide synthesis, or by co-expressing a ceramide desaturase enzyme, ifc, indicating that increased saturated ceramides were causal for ISC proliferation and the disruption of gut homeostasis. Accumulating saturated sphingolipids and fatty acids induced inflammatory signaling in the gut, and activated ISC proliferation through the pro-inflammatory cytokines, Upd3 and Upd2. We propose that saturated sphingolipids promote ISC proliferation through pro-inflammatory pathways.

cell biology↗

bioRxiv2024

BCL2L13 Influences Autophagy and Ceramide Metabolism without Affecting Temozolomide Resistance in Glioblastoma

Temozolomide (TMZ) resistance in glioblastoma (GBM) arises through metabolic rewiring that links mitochondrial function, autophagy balance, and sphingolipid metabolism. TMZ resistant (R) U251 cells exhibited suppressed apoptosis and complete blockade of autophagy flux, evidenced by LC3II and p62 accumulation and insensitivity to Bafilomycin A1. BCL2L13, strongly upregulated in R cells, emerged as a dual regulator of mitophagy and ceramide metabolism. BCL2L13 knockdown (KD) produced opposite effects in TMZ sensitive (NR) and resistant cells: in NR cells, KD elevated LC3II, reduced respiratory reserve, and triggered compensatory lipid synthesis; in R cells, KD decreased LC3II without restoring flux or TMZ sensitivity. Lipidomic profiling revealed that BCL2L13 loss reactivated CerS6 in NR cells, increasing C16:0 and mid-chain ceramides, while relieving CerS2 inhibition in R cells, elevating very long chain (C22 to C24) and glycosylated ceramides. These distinct sphingolipid signatures were confirmed by PLS-DA and KEGG enrichment, which highlighted steroid hormone, arachidonic, and linoleic acid metabolism in NR KD cells versus neuroactive ligand-receptor and signaling pathways in R KD cells. Together, these findings position BCL2L13 as a molecular integrator of mitochondrial respiration, autophagy flux, and CerS-dependent lipid remodeling, unveiling a context-specific metabolic mechanism that supports GBM cell survival under chemotherapeutic stress.

cancer biology↗

bioRxiv2024

Assessing Autophagy Flux in Glioblastoma Temozolomide Resistant Cells

Autophagy is a critical cellular process involved in the degradation and recycling of cytoplasmic components, playing a dual role in cancer by either promoting cell survival or facilitating cell death. In glioblastoma (GB), autophagy has been implicated in resistance to the chemotherapeutic agent Temozolomide (TMZ). This study presents a novel method to accurately measure autophagy flux in TMZ-resistant glioblastoma cells, combining advanced imaging techniques with biochemical assays. By quantifying key autophagy markers such as LC3-II and SQSTM1, our approach provides detailed insights into the dynamic processes of autophagosome formation and clearance under therapeutic stress. This method not only advances our understanding of autophagy in GB chemoresistance but also has significant implications for the development of autophagy-targeted therapies. The ability to monitor and manipulate autophagy flux in real-time offers a promising avenue for monitoring and understnading TMZ resistance and improving patient outcomes in glioblastoma treatment.

molecular biology↗

bioRxiv2024

Vancomycin impairs macrophage fungal killing by disrupting mitochondrial morphology and function

Vancomycin is a widely prescribed antibiotic used in the treatment of Gram-positive bacterial infections. We recently showed that this antibiotic disrupted protective anti-fungal immune responses via microbiome dysbiosis, enhancing susceptibility to invasive candidiasis. Antibiotics are an independent risk factor for developing this life-threatening fungal infection, but whether microbiota-independent mechanisms also drive this association is not clear. Here, we show that vancomycin directly impairs macrophage responses to Candida albicans, the main causative agent of invasive candidiasis. Vancomycin-treated macrophages were less able to kill C. albicans despite normal phagocytosis rates and were hyper-inflammatory and more likely to die during infection. We found that vancomycin bound to macrophage mitochondria, leading to depolarisation, reduced respiratory capacity and a hyper-fragmented morphology associated with increased ROS production. Taken together, this work demonstrates direct effects of vancomycin on mammalian immune cells, helping us to understand pro-inflammatory effects of this drug and how it promotes susceptibility to life-threatening fungal infection.

immunology↗

bioRxiv2023

Geographic variation in the songs of two closely related song-learning species, Anna's and Costa's hummingbird (Calypte anna, C. costae)

In species that learn their song, cultural transmission of song components can lead to the accumulation of variants that differ among populations, resulting in the formation of dialects. Three avian clades are thought to have independently evolved song learning - parrots, oscine passerines, and hummingbirds. Dialects have mainly been studied in passerines. We extend the study of dialects to the bee hummingbird clade, focusing on Annas and Costas hummingbirds (Calypte anna and C. costae). Both species are vocal learners. Annas produces complex, three phrase, multi-syllable songs and Costas produces simple, one phrase songs. We recorded 5-24 males per population (5 Costas and 6 Annas populations) across the species ranges in the Western United States and tested for evidence of geographic variation in song. We found minor population differences in frequency measures of Costas song, but song form was invariant across populations. Annas song was contrastingly variable with population differences in both syllable use and multiple spectral and temporal measures. The most strongly differentiated Annas population in our study, Seattle (Washington State), is the product of a recent northward range expansion facilitated by human activities that provide additional food sources for hummingbirds. The loss and modification of syllables in this population is suggestive of a founder effect on song. This study provides insight into song evolution in non-passerine vocal learners and contributes to understanding of how complex signals evolve.

animal behavior and cognition↗

bioRxiv2023

The incidence of movement disorders increases with age and contrasts with subtle and limited neuroimaging abnormalities in argininosuccinic aciduria.

Argininosuccinate lyase is integral to the urea cycle detoxifying neurotoxic ammonia and the nitric oxide biosynthesis cycle. Inherited argininosuccinate lyase deficiency causes argininosuccinic aciduria (ASA), a rare disease with hyperammonaemia and nitric oxide deficiency. Patients present with developmental delay, epilepsy and movement disorders, associated with nitric oxide-mediated downregulation of central catecholamine biosynthesis. A neurodegenerative phenotype has been proposed in ASA. To better characterise this neurodegenerative phenotype in ASA, we conducted a retrospective study in six paediatric and adult metabolic centres in the UK in 2022. We identified 60 patients and specifically looked for movement disorders-related symptoms: movement disorders such as ataxia, tremor and dystonia, hypotonia and abnormal behaviour. We analysed neuroimaging with diffusion tensor imaging (DTI) magnetic resonance imaging (MRI) in an ASA patient with movement disorders. We assessed conventional and DTI MRI alongside single photon emission computer tomography (SPECT) with dopamine analogue radionuclide 123I-ioflupane, in Asl-deficient mice treated by hASL mRNA with normalised ureagenesis. Movement disorders in ASA appears in the 2nd and 3rd decades of life, becoming more prevalent with ageing and independent from the age of onset of hyperammonaemia. Neuroimaging can show abnormal DTI features affecting both grey and white matter, preferentially basal ganglia. ASA mouse model with normalised ureagenesis did not recapitulate these DTI findings and showed normal 123I-ioflupane SPECT and cerebral dopamine metabolomics. Altogether these findings support the pathophysiology of a late-onset movement disorders with functional central catecholamine dysregulation but without or limited neurodegeneration of dopaminergic neurons, making these symptoms amenable to targeted therapy. SynopsisMovement disorders-related symptoms in ASA appear in the 2nd and 3rd decades of life, becoming more prevalent with age and shows abnormal neuroimaging features of basal ganglia in ASA patients, not recapitulated in ASA mice.

genetics↗

bioRxiv2023

Autometa 2: A versatile tool for recovering genomes from highly-complex metagenomic communities

In 2019, we developed Autometa, an automated binning pipeline that is able to effectively recover metagenome-assembled genomes from complex environmental and non-model host-associated microbial communities. Autometa has gained widespread use in a variety of environments and has been applied in multiple research projects. However, the genome-binning workflow was at times overly complex and computationally demanding. As a consequence of Autometas diverse application, non-technical and technical researchers alike have noted its burdensome installation and inefficient as well as error-prone processes. Moreover its taxon-binning and genome-binning behaviors have remained obscure. For these reasons we set out to improve its accessibility, efficiency and efficacy to further enable the research community during their exploration of Earths environments. The highly augmented Autometa 2 release, which we present here, has vastly simplified installation, a graphical user interface and a refactored workflow for transparency and reproducibility. Furthermore, we conducted a parameter sweep on standardized community datasets to show that it is possible for Autometa to achieve better performance than any other binning pipeline, as judged by Adjusted Rand Index. Improvements in Autometa 2 enhance its accessibility for non-bioinformatic oriented researchers, scalability for large-scale and highly-complex samples and interpretation of recovered microbial communities. Graphical abstractAutometa: An automated taxon binning and genome binning workflow for single sample resolution of metagenomic communities.

bioinformatics↗

bioRxiv2023

Elevated Expression of srp RiPPs Across Bacterial Phyla in Marine Sponges

We investigated transcriptional activity, at a genome-resolved level, of bacterial communities in two S. officinalis and two I. felix sponges, both of which are considered high microbial abundance (HMA) sponges that harbor similar bacterial communities. Overlap of metatranscriptional data on genome-resolved metagenomic data showed that genome bins classified within the Chloroflexota and Poribacteria phyla were the most abundant and transcriptionally active. However, abundant bins in general were not the most transcriptionally active, instead less abundant bins of the same phyla were most active indicating that numerical dominance does not imply transcriptional dominance. We found that although some primary metabolic functions appeared upregulated, they were not obviously attributable to any particular bacterial species. However, assessment of transcription levels of biosynthetic gene clusters (BGCs) encoding secondary metabolites revealed a high transcription of ribosomally synthesized and post-translationally modified peptides (RiPPs) in genome bins across diverse bacterial phyla, most of which were likely srp RiPPs encoding brominated azol(in)e-containing compounds. However, the ecological role of these compounds remains elusive. IMPORTANCEMarine sponges and bacteria have formed close associations over several million years with many bacteria performing specialized functions within their sponge host. Previous studies have either assessed the genomes of a given sponge or the expression profile for a sponge holobiont as a whole. Here, we present the first genome-resolved transcriptomic study which gives us a snapshot of the transcriptional activity of individual bacteria in the context of four different sponge holobionts. Using this approach we found that the numerically dominant bacteria were not the most transcriptionally active and that relatively high expression of a ubiquitous biosynthetic gene cluster was evident in many different bacterial phyla in all four sponge samples.

ecology↗

bioRxiv2023

Conserved folding landscape of monomeric initiator caspases

The apoptotic caspase subfamily evolved into two subfamilies - monomeric initiators and dimeric effectors. Sequence variations in the conserved caspase-hemoglobinase fold resulted in changes in oligomerization, enzyme specificity, and regulation, making caspases an excellent model for examining the mechanisms of molecular evolution in fine-tuning structure, function, and allosteric regulation. We examined the urea-induced equilibrium folding/unfolding of two initiator caspases, monomeric caspase-8 and cFLIPL, over a broad pH range. Both proteins unfold by a three-state equilibrium mechanism that includes a partially folded intermediate. In addition, both proteins undergo a conserved pH-dependent conformational change that is controlled by an evolutionarily conserved mechanism. We show that the conformational free energy landscape of the caspase monomer is conserved in the monomeric and dimeric subfamilies. Molecular dynamics simulations in the presence or absence of urea, coupled with limited trypsin proteolysis and mass spectrometry, show that the small subunit is unstable in the protomer and unfolds prior to the large subunit. In addition, the unfolding of helix 2 in the large subunit results in disruption of a conserved allosteric site. Because the small subunit forms the interface for dimerization, our results highlight an important driving force for the evolution of the dimeric caspase subfamily through stabilizing the small subunit.

biophysics↗