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bioRxiv2023

Highly amine-reactive graphene-oxide EM grids for biochemical surface modification in aqueous buffer

Graphene oxide (GO), an oxidized derivative of graphene, has found application in cryo-electron microscopy (cryo-EM) as a hydrophilic and transparent solid support on which to adsorb biological macromolecules, providing an alternative to traditional aqueous films. Current applications generally adsorb the macromolecule directly onto unmodified GO or modify the GO surface with polyethylene glycol-amine reagents. This nucleophilic amine reaction must be performed in an aprotic organic solvent and therefore precludes the use of biological samples such as nucleic acids and peptides. The utility of GO could be expanded by the ability to covalently modify its surface with biochemical affinity reagents such as small- molecule metabolites, peptides, or nucleic acids, in aqueous buffer at neutral pH. Presented here is a chemical procedure that converts all oxygen functionalities of GO to highly amine- reactive glycidyl epoxide groups, achieved without the need of specialized laboratory equipment. We show that single sheets of glycidyl epoxide-modified GO react on the EM grid with primary amines at micromolar concentrations in minutes at room temperature in aqueous buffer. Given the ease of derivatizing biochemical reagents with amines, the chemistry described here will enable imaging of macromolecules immobilized on GO through specific biochemical and biologically relevant binding interactions.

molecular biology↗

bioRxiv2024

Parallel pheromone, metabolite, and lipid analyses reveal patterns associated with early life transitions and ovary activation in honey bee (Apis mellifera) queens

Eusocial insects exist in a state of reproductive conflict in which workers forgo reproduction in favor of helping relatives, typically queens, rear offspring. The honest signal hypothesis posits that queens emit pheromonal signals that convey information about their fecundity, which workers use to make decisions around investing in direct vs. indirect fitness and queen acceptance. We evaluated this idea using liquid chromatography-tandem mass spectrometry to measure honey bee queen retinue pheromone (QRP) components in relation to queen age, laying status, and likelihood of acceptance using a protocol that enables QRP to be measured concurrently with metabolomic and lipidomic analyses. We found that older mated queens (>1 month) were more readily accepted by colonies than younger queens (10-12 d), regardless of the queens prior laying status. This is despite non-laying queens having significantly smaller ovaries at the time of introduction. Older queens produced higher levels of the QRP components 9(R)-HDA, LEA, and HVA compared to younger queens, with HVA also positively correlating with ovary mass. However, these data suggest that ovary mass is not an influential fertility metric for worker decision-making; therefore, the relationship between HVA and ovary mass is merely an honest signal of a non-influential metric. Metabolomic and lipidomic analyses showed that samples cluster strongly according to queen age and mating status, but not ovary mass. These data also reveal some of the first hints of the importance of prostanoids in queen maturation, along with many other physiological changes that occur in the first month of a queens life. Significance statementInsect pheromones have historically been evaluated using gas chromatography-mass spectrometry, a technique that is incompatible with parallel lipidomics and metabolomics inquests. Here, we repurposed an established two-phase extraction protocol and optimized a liquid chromatography-tandem mass spectrometry method to acquire pheromone, metabolite, and lipid data concurrently from a single sample. We applied this technique to interrogate the honest signal hypothesis, which relates queen pheromone profiles to reproductive quality, but the approach is broadly applicable to any question in which simultaneous determination of complex pheromone profiles and lipidomics or metabolomics data is asset. Such applications may help uncover new pheromones and reveal relationships between pheromones, hormones, and physiology in diverse biological systems.

molecular biology↗

bioRxiv2024

AI Assisted Native Proteomics: Delineating Ribosomal Protein Conformations Pre- and Post-Assembly

The simultaneous identification of proteins as well as their conformations in a biological system would greatly enhance our understanding of cellular mechanisms and disease. As an emerging technique, native proteomics analyzes proteins in their native states, facilitating the acquisition of protein stoichiometry, post-translational modifications (PTMs), and interactions with ligands. However, revealing protein conformations at the proteome scale remains a significant challenge. In this study, we propose an AI-assisted native proteomics method that integrates a protein structure prediction (PSP) module with top-down proteomics (TDP) and native mass spectrometry (nMS) to acquire both proteome identity and conformations. First, protein sequences and PTMs are obtained using the TDP method, while protein solvent-accessible surface area (SASA) is measured in parallel by nMS. These data are then input into the PSP module to acquire the most probable conformation of the protein under nMS experimental conditions. We validate the feasibility and accuracy of this method through the analysis of both a globular protein and an intrinsically disordered protein. Additionally, we apply this approach to delineate the conformations of ribosomal proteins pre- and post-assembly. Interactions of ribosomal proteins with drug molecules are also explored. By enabling proteome identification and conformation characterization from relatively small amounts of endogenous proteins, this method would bridge the gap between structural biology and conventional proteomics technologies.

molecular biology↗

bioRxiv2025

LOBSTERS: a modular vector series with a diverse set of Cas nucleases and plasmid selection markers for multiplex genome editing in Saccharomyces cerevisiae

The budding yeast Saccharomyces cerevisiae is a central model organism in genetics and synthetic biology, yet efficient multiplex genome editing remains difficult because many toolkits are restricted by limited plasmid selection markers and reduced efficiency when targeting multiple loci. In our previous work, we introduced a CRISPR-based system incorporating three nucleases with distinct PAM specificities but it was available only with the URA3 marker. Here we present LOBSTERS, an expanded modular vector series that retains the PAM-diverse nucleases (SpCas9, SaCas9, and enAsCas12a) while extending marker options to seven. This design enables the simultaneous use of multiple plasmids in one transformation, supporting scalable and flexible genome editing. Proof-of-concept experiments demonstrated efficient ADE2 and ADE3 deletions with colorimetric readouts, coordinated tagging of essential proteins (Cdc3 and Cse4) without compromising function, and recapitulation of three quantitative trait variants (RME1, TAO3, and MKT1) underlying sporulation efficiency. Together these results establish LOBSTERS as a robust and versatile platform for multiplex genome editing in S. cerevisiae. By enabling coordinated modification of essential proteins, genetic interactions, and quantitative trait variants, LOBSTERS provides a broadly applicable resource for functional cell biology and synthetic biology in yeast. Significance StatementO_LILOBSTERS integrates three PAM-diverse nucleases with seven plasmid selection markers, overcoming the single-marker limitation of previous yeast genome editing toolkits. C_LIO_LIThe system enables efficient simultaneous editing at multiple loci, demonstrated by functional tagging of essential proteins and recapitulation of quantitative trait variants. C_LIO_LIBy broadening the editable space and lowering barriers to complex genotype construction, LOBSTERS provides a widely applicable resource for yeast cell biology and synthetic biology. C_LI

molecular biology↗

bioRxiv2018

Widespread separation of the polypyrimidine tract from 3’ AG by G tracts in association with alternative exons in metazoa and plants

At the end of introns, the polypyrimidine tract (Py) is often close to the 3 AG in a consensus (Y)20NCAGgt in humans. Interestingly, we have found that they could also be separated by purine-rich elements including G tracts in thousands of human genes. These regulatory elements between the Py and 3AG (REPA) mainly regulate alternative 3 splice sites (3SS) and intron retention. Here we show their widespread distribution and special properties across kingdoms. The purine-rich 3SS are found in up to about 60% of the introns among more than 1000 species/lineages by whole genome analysis, and up to 18% of these introns contain the REPA G tracts in about 2.4 millions of 3SS in total. In particular, they are significantly enriched over their 3SS and genome backgrounds in metazoa and plants, and highly associated with alternative splicing of genes in diverse functional clusters. They are also highly enriched (3-6 folds) in the canonical as well as aberrantly used 3 splice sites in cancer patients carrying mutations of the branch point factor SF3B1 or the 3AG binding factor U2AF35. Moreover, the REPA G tract-harbouring 3SS have significantly reduced occurrences of branch point (BP) motifs between the -24 and -4 positions, in particular absent from the -7 - -5 positions in several model organisms examined. The more distant branch points are associated with increased occurrences of alternative splicing in human and zebrafish. The branch points, REPA G tracts and associated 3SS motifs appear to have emerged differentially in a phylum- or species-specific way during evolution. Thus, there is widespread separation of the Py and 3AG by REPA G tracts, likely evolved among different species or branches of life. This special 3SS arrangement contributes to the generation of diverse transcript or protein isoforms in biological functions or diseases through alternative or aberrant splicing.

molecular biology↗

bioRxiv2019

Crystal Structure of the Dog Allergen Can f 6

Lipocalins represent the most important protein family of the mammalian respiratory allergens. Four of the seven named dog allergens are lipocalins: Can f 1, Can f 2, Can f 4, and Can f 6. We present the structure of Can f 6 along with data on the biophysical and biological activity of this protein in comparison with other animal lipocalins. The Can f 6 structure displays the classic lipocalin calyx-shaped ligand binding cavity within a central {beta}-barrel similar to other lipocalins. Despite low sequence identity between the different dog lipocalin proteins, there is a high degree of structural similarity. On the other hand, Can f 6 has a similar primary sequence to cat, horse, mouse lipocalins as well as a structure that may underlie their cross reactivity. Interestingly, the entrance to the ligand binding pocket is capped by a His instead of the usually seen Tyr that may help select its natural ligand binding partner. Our highly pure recombinant Can f 6 is able to bind to human IgE (hIgE) demonstrating biological antigenicity.

molecular biology↗

bioRxiv2021

A Methodology for Vertical Translation Between Molecular and Organismal Level in Biological Feedback Loops

Feedback loops are among the primary network motifs in living organisms, ensuring survival via homeostatic control of key metabolites and physical properties. However, from a scientific perspective, their characterization is unsatisfactory since the usual modelling methodology is incompatible with the physiological and biochemical basis of metabolic networks. Therefore, any "vertical translation", i.e. the study of the correspondence between molecular and organismal levels of causality, is difficult and in most cases impossible. As a viable solution, we demonstrate an alternative modelling platform for biological feedback loops that is based on key biochemical principles, including mass action law, enzyme kinetics, binding of mediators to transporters and receptors, and basic pharmacological properties. Subsequently, we show how this framework can be used for translating from molecular to systems-level behaviour. Basic elements of the proposed modelling platform include Michaelis-Menten kinetics defining nonlinear dependence of the output y(t) on an input signal x(t) with the Hill-Langmuir equation y(t) = G * x(t)n / (D + x(t)n), non-competitive inhibition for linking stimulatory and inhibitory inputs with y(t) = G + x1(t) / ((D + x1(t) * (1 + x2(t) / KI)) and processing structures for distribution and elimination. Depending on the structure of the feedback loop, its equifinal (steady-state) behaviour can be solved in form of polynomials, with a quadratic equation for the simplest case with one feedback loop and a Hill exponent of 1, and higher-grade polynomials for additional feedback loops and/or integer Hill exponents > 1. As a companion to the analytical solution, a flexible class library (CyberUnits) facilitates computer simulations for studying the transitional behaviour of the feedback loop. Unlike other modelling strategies in biocybernetics and systems biology, this platform allows for straightforward translation from the statistical properties of single molecules on a "microscopic" level to the behaviour of the whole feedback loop on an organismal "macroscopic" level. An example is the Michaelis constant D, which is equivalent to (k-1 + k2) / k1, where k1, k-1 and k2 denote the rate constants for the association and dissociation of the enzyme-substrate or receptor-hormone complex, respectively. From the perspective of a single molecule the rate constants represent the probability (per unit time) that the corresponding reaction will happen in the subsequent time interval. Therefore 1/k represents the mean lifetime of the complex. Very similar considerations apply to the other described constants of the feedback loop. In summary, this modelling technique renders the translation from a molecular level to a systems perspective possible. In addition to providing new insights into the physiology of biological feedback loops, it may be a valuable tool for multiple disciplines of biomedical research, including drug design, molecular genetics and investigations on the effects of endocrine disruptors.

systems biology↗

bioRxiv2020

Near-Physiological-Temperature Serial Femtosecond X-ray Crystallography Reveals Novel Conformations of SARS-CoV-2 Main Protease Active Site for Improved Drug Repurposing

The COVID19 pandemic has resulted in 25+ million reported infections and nearly 850.000 deaths. Research to identify effective therapies for COVID19 includes: i) designing a vaccine as future protection; ii) structure-based drug design; and iii) identifying existing drugs to repurpose them as effective and immediate treatments. To assist in drug repurposing and design, we determined two apo structures of Severe Acute Respiratory Syndrome CoronaVirus-2 main protease at ambienttemperature by Serial Femtosecond X-ray crystallography. We employed detailed molecular simulations of selected known main protease inhibitors with the structures and compared binding modes and energies. The combined structural biology and molecular modeling studies not only reveal the dynamics of small molecules targeting main protease but will also provide invaluable opportunities for drug repurposing and structure-based drug design studies against SARS-CoV-2. One Sentence SummaryRadiation-damage-free high-resolution SARS-CoV-2 main protease SFX structures obtained at near-physiological-temperature offer invaluable information for immediate drug-repurposing studies for the treatment of COVID19.

biophysics↗

bioRxiv2021

Viral E Protein Neutralizes BET Protein-Mediated Post-Entry Antagonism of SARS-CoV-2

Inhibitors of Bromodomain and Extra-terminal domain (BET) proteins are possible anti-SARS-CoV-2 prophylactics as they downregulate angiotensin-converting enzyme 2 (ACE2). Here, we show that BET proteins should not be inactivated therapeutically as they are critical antiviral factors at the post-entry level. Knockouts of BRD3 or BRD4 in cells overexpressing ACE2 exacerbate SARS-CoV-2 infection; the same is observed when cells with endogenous ACE2 expression are treated with BET inhibitors during infection, and not before. Viral replication and mortality are also enhanced in BET inhibitor-treated mice overexpressing ACE2. BET inactivation suppresses interferon production induced by SARS-CoV-2, a process phenocopied by the envelope (E) protein previously identified as a possible "histone mimetic." E protein, in an acetylated form, directly binds the second bromodomain of BRD4. Our data support a model where SARS-CoV-2 E protein evolved to antagonize interferon responses via BET protein inhibition; this neutralization should not be further enhanced with BET inhibitor treatment.

molecular biology↗

bioRxiv2021

In Vivo Subcellular Mass Spectrometry Enables Proteo-Metabolomic Single-cell Systems Biology in a Chordate Embryo Developing to a Normally Behaving Tadpole (X. laevis)

We present the first example of in vivo high-resolution mass spectrometry (HRMS) for subcellular molecular systems biology of proteins and metabolites. With light microscopy, we identified the left-dorsal and left-ventral animal cells in cleavage-stage non-sentient Xenopus laevis embryos. Using precision-translated fabricated microcapillaries, the subcellular content of each cell was double-probed, each time collecting <5% of cell volume (~10 nL) swiftly (<5 s/event). The proteins and metabolites were analyzed by custom-built ultrasensitive capillary electrophoresis electrospray ionization employing Orbitrap and time-of-flight HRMS. Label-free detection of ~150 metabolites (57 identified) and 738 proteins found proteo-metabolomic networks with differential quantitative activities between the cell types. Spatially and temporally scalable sampling the technology preserved the integrity of the analyzed cells, the neighboring cells, and the embryo. 95% of the analyzed embryos developed into sentient tadpoles that were indistinguishable from their wild-type siblings based on anatomy and visual function in a background color preference assay.

developmental biology↗

bioRxiv2021

iMUT-seq: high-resolution mapping of DSB mutational landscapes reveals new insights into the mutagenic mechanisms of DSB repair

DNA double-strand breaks (DSBs) are the most mutagenic form of DNA damage, and play a significant role in cancer biology, neurodegeneration and aging. However, studying DSB-induced mutagenesis is currently limited by the tools available for mapping these mutations. Here, we describe iMUT-seq, a technique that profiles DSB-induced mutations at high-sensitivity and single-nucleotide resolution around endogenous DSBs spread across the genome. By depleting 20 different DSB-repair factors we defined their mutational signatures in detail, revealing remarkable insights into the mechanisms of DSB-induced mutagenesis. We find that homologous-recombination (HR) is mutagenic in nature, displaying high levels of base substitutions and mononucleotide deletions due to DNA-polymerase errors, but simultaneously reduced translocation events, suggesting the primary role of HR is the specific suppression of genomic rearrangements. The results presented here offer new fundamental insights into DSB-induced mutagenesis and have significant implications for our understanding of cancer biology and the development of DDR-targeting chemotherapeutics.

molecular biology↗

bioRxiv2023

Loss of zebrafish dcst2 expression is not associated with muscle abnormalities

In this study we examined if the gene encoding Dendritic Cell-specific Six Transmembrane domain containing protein 2 (dcst2) plays a role in vertebrate muscle biology. Using the CRISPR/Cas9 mutagenic system we generated a 2 nucleotide deletion in exon 3 of the zebrafish ortholog dcst2 which resulted in a premature stop codon. Homozygous carriers of the mutation displayed reduced transcriptional expression of dcst2 suggesting that our mutation was indeed disrupting gene function. Mutant dcst2 zebrafish developed normally to adulthood and displayed no differences in motor function using a free-swim and swim tunnel assays. Furthermore, histological examination of muscle cells revealed no differences in slow-twitch or fast-twitch muscle cell cross-sectional area in our mutants. We did observe that dcst2-/- zebrafish were slightly heavier in weight and males were infertile. The data collected here, suggest that dcst2 does not play a role in zebrafish muscle cell biology.

molecular biology↗

bioRxiv2025

Peripheral tissues of deep-sea mussels exhibit autonomous circadian timing via an atypical mechanism

While biological rhythms are crucial to life, the deep sea has long been considered an arrhythmic exception. However, at hydrothermal vents - devoid of diel cues yet shaped by tides - the mussel Bathymodiolus azoricus shows both tidal and, unexpectedly, circadian rhythms at -1700 m. Whether endogenous clock(s) drive these cycles remained unanswered. Here, we report endogenous circadian rhythms in B. azoricus cell cultures under constant conditions: isolated cells displayed a circadian oscillator despite tidal-dominant rhythms in situ. Reporter assays using genomic regions upstream of the mussels per gene and containing E-box motifs indicate that a functional transcription-translation feedback loop (TTFL) underpins circadian timing even in the deep sea. In contrast to conventional models, however, BazPeriod lacks autonomous repressive activity but modulates BazCry2. As BazPeriod itself oscillates tidally, it may explain how a single endogenous clock yields both tidal and diel rhythms. The work also spotlights the highly time-sensitive biology of vastly unexplored deep-sea biology.

molecular biology↗

bioRxiv2025

Single Domain Antibody Inhibitors Target the Coiled Coil Arms of the Bacillus subtilis SMC complex

Synthetic nanobodies--also called sybodies--have proven valuable for stabilizing conformations of purified proteins, advancing structural and functional studies for example of transmembrane protein complexes. However, their utility in modulating protein function in living cells has remained less well explored. Structural Maintenance of Chromosomes (SMC) complexes facilitate chromosome organization by DNA loop extrusion, a fundamental process in all domains of life. In this study, we target the bacterial SMC complex, Smc-ScpAB, in Bacillus subtilis with synthetic nanobodies, aiming to identify key functional regions of the protein complex in a largely unbiased manner. We first isolate sybodies that specifically bind purified Smc-ScpAB and then express them in B. subtilis to select binders capable of disrupting Smc-ScpAB function, leading to chromosome segregation defects and cell death. Mapping and biochemical characterization show that the fourteen disruptive sybodies belong to one of three library designs, target the Smc subunit near the same coiled coil arm interface and modulate its ATPase activity in two principal ways, highlighting the mid-region of the Smc coiled coil as critical feature of the DNA folding process. These findings underscore the potential of sybodies--and, by extension, designed binders--as versatile tools for probing dynamic protein function in living cells, with potentially broad applications in cell and synthetic biology.

molecular biology↗

bioRxiv2018

The Human RNA-Binding Proteome and Its Dynamics During Arsenite-Induced Translational Arrest

Proteins and RNA functionally and physically intersect in multiple biological processes, however, currently no universal method is available to purify protein-RNA complexes. Here we introduce XRNAX, a method for the generic purification of protein-crosslinked RNA, and demonstrate its versatility to study the composition and dynamics of protein-RNA interactions by various transcriptomic and proteomic approaches. We show that XRNAX captures all RNA biotypes, and use this to characterize the sub-proteomes that interact with coding and non-coding RNAs (ncRNAs), and to identify hundreds of protein-RNA interfaces. Exploiting the quantitative nature of XRNAX, we observe drastic remodeling of the RNA-bound proteome during arsenite-induced stress, distinct from autophagy-induced changes in the total proteome. In addition, we combine XRNAX with CLIP-seq to validate the interaction of ncRNA with Lamin B and EXOSC2. Thus, XRNAX is a resourceful approach to study structural and compositional aspects of protein-RNA interactions to address fundamental questions in RNA-biology.

molecular biology↗

bioRxiv2018

Hidden in plain sight: What remains to be discovered in the eukaryotic proteome?

The first decade of genome sequencing stimulated an explosion in the characterization of unknown proteins. More recently, the pace of functional discovery has slowed, leaving around 20% of the proteins even in well-studied model organisms without informative descriptions of their biological roles. Remarkably, many uncharacterized proteins are conserved from yeasts to human, suggesting that they contribute to fundamental biological processes. To fully understand biological systems in health and disease, we need to account for every part of the system. Unstudied proteins thus represent a collective blind spot that limits the progress of both basic and applied biosciences.\n\nWe use a simple yet powerful metric based on Gene Ontology (GO) biological process terms to define characterized and uncharacterized proteins for human, budding yeast, and fission yeast. We then identify a set of conserved but unstudied proteins in S. pombe, and classify them based on a combination of orthogonal attributes determined by large-scale experimental and comparative methods. Finally, we explore possible reasons why these proteins remain neglected, and propose courses of action to raise their profile and thereby reap the benefits of completing the catalog of proteins biological roles.

molecular biology↗

bioRxiv2026

Sex-specific DNA methylation in adult skeletal muscle

DNA methylation is a key epigenetic mechanism influencing gene regulation and cellular identity. In skeletal muscle, methylation contributes to fiber-type specification, metabolic programming, and satellite cell function, with evidence of sex-specific differences. Here, we investigated whether spatial regionalization of gene expression along the proximal-distal axis of the tibialis anterior (TA) is mirrored by corresponding patterns of DNA methylation. Using MeDseq on TA sections from muscles previously analyzed by spatial transcriptomics, we profiled methylation across transcriptional start sites (TSS), gene bodies, and regulatory elements. Despite robust spatial differences in transcriptomes, methylation patterns were largely uniform along the proximal-distal axis, indicating that DNA methylation does not underlie regional gene expression in adult TA muscle. In contrast, sex emerged as the primary determinant of methylation variation. Male muscles exhibited widespread hypermethylation at TSS, gene-bodies and regulatory regions, corresponding with sex-specific transcriptional programs, including glycolytic fiber enrichment in males and oxidative fiber markers in females. Notably, chromatin- and methylation-associated regulators such as Setd7, Gsk3a, and Bmyc were upregulated in males, suggesting mechanisms linking transcriptional control to epigenetic state. These findings highlight that while spatial gene expression is transcriptionally driven, sex-specific epigenetic programs dominate adult skeletal muscle, underscoring the need to consider sex in multi-omic studies of muscle biology.

molecular biology↗

bioRxiv2026

Detecting misfolded non-covalent lasso entanglements in protein structures, simulation trajectories, and mass spectrometry data

A previously overlooked class of protein entanglements, non-covalent lasso entanglements (NCLEs), has been found to play a role in widespread protein misfolding. However, understanding the influence NCLEs have on biological processes is hindered by the absence of dedicated algorithms and computational tools to detect and characterize these geometries in protein structures, molecular dynamics simulations, and in comparison to experimental data from limited proteolysis (LiP) and cross-linking (XL) mass spectrometry (MS). Here, we present EntDetect, a software tool designed to: (1) identify non-redundant NCLEs in protein structures, (2) detect misfolded states by comparing NCLE changes through pairwise comparisons of structures, (3) extract structural ensembles consistent with experimental signals from LiP-MS and XL-MS, and (4) investigate proteome-wide protein misfolding using high-throughput MS data. We demonstrate the utility of EntDetect on a simulated structural ensemble of phosphoglycerate kinase (PGK), alongside corresponding LiP- and XL-MS experimental data. Additionally, we detail the application of EntDetect to detect misfolding associated with native NCLEs on a proteome-wide MS dataset and select candidate proteins for further investigation. This protocol is intended for biophysicists, structural biologists, and molecular biologists with domain knowledge of protein structure, mass spectrometry proteomics data, and beginner experience with Python who want to interpret their experimental observations and computer simulations results through the presence and potential misfolding of NCLE topologies. EntDetect is open-source and freely available (https://github.com/obrien-lab-psu/EntDetect). NCLEweb is also available which is a webserver that identifies NCLEs within a given user-uploaded structure (https://www.ncleweb.org/).

molecular biology↗