Biology subjects

Schroeder, C. M.

Publications and source records attributed to Schroeder, C. M..

17 recordsLinked to original sources

bioRxiv2026

Actin-related ACTL8 localizes to the nucleus and modulates locus-specific transcription through chromatin regulation

Actin-related proteins (Arps) are evolutionarily ancient and broadly expressed, yet some Arps evolved in mammals and acquired germline-specific expression. Here, we investigate the germline-specific Arp "Actin-like 8" (ACTL8), which is also misexpressed in multiple cancers with unexplored molecular roles. We show that ACTL8 surprisingly localizes to the nucleus of spermatogonia in human testes and breast and lung cancer cells. In breast cancer cells, ACTL8 misexpression alters transcriptional programs primarily in cell migration pathways, and ACTL8 depletion increases migration rate. Mechanistically, we find that ACTL8 interacts with KDM5B, an H3K4 demethylase and transcriptional repressor, and demonstrate that this interaction contributes to changes in migration. Consistent with this, ACTL8 loss increases H3K4me3 at genes associated with migration, indicating transcriptional activation. These findings establish ACTL8 as a novel nuclear Arp that plays a role in KDM5B-mediated transcriptional repression, providing insight into its function in chromatin regulation in cancer and potentially spermatogenesis.

cell biology↗

bioRxiv2026

Ionizable Lipids Promote Curvature Remodeling and Altered Fluctuation Dynamics in Endosomal Membranes

Inefficient endosomal escape is a crucial barrier to intracellular delivery of nucleic acid therapeutics using lipid nanoparticles (LNPs). The use of ionizable lipids (ILs) has significantly improved cargo delivery efficiency, yet the physical basis of their interaction with endosomal membranes and their role in endosomal escape remain unclear. It has been suggested that, as ILs become cationic during endosomal acidification, electrostatic affinity promotes fusion of the LNPs with the endosome. In this paper, we propose an additional mechanism in which ILs are redistributed from LNPs to host membranes, modulating the elastic properties and curvature of the membrane, lowering the energetic threshold for endosome disruption. To test this, we quantified the spontaneous curvature of clinically relevant ILs and ATP-binding lipids and measured the membrane mechanics of giant unilamellar vesicles (GUVs) with an endosome-relevant composition at endosome-relevant pH. Small-angle X-ray scattering (SAXS) measurements reveal that the incorporation of ILs and ATP lipids into endosome-mimetic membranes shifts the spontaneous curvature towards more negative values. Micropipette aspiration experiments indicated a decrease in the apparent area compressibility modulus of membranes doped with ILs and ATP lipids. In addition, membranes showed enhanced fluctuation amplitudes and altered relaxation behavior, consistent with membrane perturbations associated with lipid insertion and pH- or ATP-driven destabilization. Under conditions promoting the partitioning of ILs or ATP-binding lipids, we further observed reduced bending rigidity and increased heterogeneity in membrane tension. Together, these results support a model in which ILs (as well as newly developed ATP-binding lipids) partition into endosomal membranes, softening the membrane and generating local curvature frustration that facilitates endosomal disruption during the natural acidification process. By quantitatively linking lipid composition with changes in membrane elasticity and fluctuation dynamics, this work provides a biophysical framework for understanding how lipid redistribution may contribute to endosomal escape and improve delivery efficiency.

biophysics↗

bioRxiv2026

Role of stereochemistry on electron transport in peptides

Stereochemistry underlies structure-function relationships across biology and materials science, ranging from proteins to electronic and spintronic materials. In this work, we investigate the electron transport properties of different oligopeptide stereoisomers using experiments and computational modeling. Single-molecule electronic experiments show that stereochemical modifications in tyrosine-based peptides lead to significant variations in molecular conductance along the peptide backbone due to enhanced stacking interactions and electronic coupling of aromatic side chains. In addition, stereochemical variations in alanine-based peptides give rise to changes in conductivity due to secondary structure interactions arising from {beta}-turn conformations. All-atom molecular dynamics (MD) simulations and quantum mechanical calculations are used to understand the molecular origins of the effect of stereochemistry on the structural and electronic properties of peptides. Overall, this work shows that stereochemical modification of non-terminal amino acids effectively controls electron transport due to aromatic side chain interactions or secondary structure effects. These insights open new avenues for the molecular design of peptide-based electronic materials with enhanced function.

biophysics↗

bioRxiv2026

Distinct effects of hypomorphic IFT and dynein-2 skeletal ciliopathy disease alleles on chondrogenic differentiation, ECM composition and wnt signalling in ATDC5 derived cartilage-like organoids

Dysfunction of ciliary intraflagellar transport (IFT) and dynein-2 genes causes severe developmental defects, including skeletal phenotypes characterized by shortened ribs and long bones and polydactyly. Specific gene-phenotype associations suggest individual functions of the different IFT/dynein-2 proteins in development. Since null models disrupt ciliogenesis and hence are not suitable to study individual protein functions, we recreated human hypomorphic disease alleles in IFT-A (IFT43 p.M1V), IFT-B (IFT74 deletion of exon 2), and dynein-2 (WDR60 p.A911V), alongside a WDR60 null model in ATDC5 chondrocyte precursor cells. Hypomorphic mutants did not show alterations in ciliation efficiency or cilia length but displayed distinct defects in IFT88 localization, indicating impaired intraflagellar transport. Despite altered IFT, Hedgehog signalling responses were variably affected across the different genotypes. Transcriptomic analysis revealed concurrent increases in canonical Wnt signalling and expression of genes related to late skeletal development in WDR60 A911V and IFT74 del ex 2 mutants, but not in IFT43 M1V or WDR60 loss-of-function mutants. These changes were accompanied by alterations in ECM composition. In addition, all hypomorphic mutants showed reduced levels of the non-canonical Wnt ligand WNT5A in ECM proteomic analyses. Interestingly, loss of cilia in WDR60 loss-of-function mutants had only modest effects on chondrogenic differentiation and ECM composition. Overall, our data provide new evidence of genotype-dependent altered ECM composition as well as dysregulation of canonical and non-canonical Wnt signalling and accelerated chondrocyte differentiation in skeletal ciliopathies. Furthermore, our findings suggest a modulatory rather than essential role of the primary cilium for ATDC5 cell differentiation.

cell biology↗

bioRxiv2026

Deep phenotyping of ATDC5-derived in vitro cartilage organoids

Cartilage is characterized by a highly specialized extracellular matrix (ECM) secreted by chondrocytes and limited self-regenerative capacity. In vivo investigations of chondrogenesis are limited by difficult and traumatic access, especially in humans. While it is known for decades that disturbances of chondrocyte differentiation and changed cartilage ECM composition cause severe skeletal phenotypes in vertebrates, a detailed molecular understanding of chondrogenesis and cartilage ECM formation is still missing, especially in the context of human genetic skeletal diseases. ATDC5 cells, derived from AT805 mouse teratocarcinoma cells, have been used in the past to model chondrogenic differentiation, however, most studies have investigated few major cellular differentiation markers only so that the composition of the secreted ECM as well as effects on the ATDC5 transcriptome upon differentiation are still unclear. Here, we performed time-resolved transcriptomic and ECM proteomic analyses of differentiating ATDC5 cells. Both datasets confirmed the formation of a cartilage-like matrix with increasing expression of key chondrocyte genes over the course of differentiation. ECM proteomics further revealed a number of ECM components not previously reported in ATDC5 cells or the secreted ECM, encompassing collagens, proteoglycans, glycoproteins and other secreted factors. Overall, our findings provide a more detailed molecular characterization of ATDC5 chondrogenesis and highlight the potential of this model system for ECM-focused studies.

cell biology↗

bioRxiv2025

A microexon in Arp2 alters tissue-specific Arp2/3-generated actin structures

Arp2, a subunit within the actin nucleator Arp2/3, encodes two splice variants that differ by five residues in the D-loop, a critical element for catalyzing actin polymerization. It is unknown if this alternative exon, or "microexon," impacts Arp2/3 function. Here, we find that the microexon has been evolutionarily retained for over 600 million years yet varies in sequence. We investigate the unique microexon in Drosophila Arp2 and show that the longer "Arp2L" variant is expressed, though less than the short variant, "Arp2s." We purify recombinant Drosophila Arp2/3 containing Arp2s or Arp2L, and although we do not detect differences in actin polymerization bulk assays, the microexon attenuates inhibition by Arp2/3 inhibitors in vitro, suggesting intrinsic differences. We generate flies expressing only Arp2s or Arp2L, and while both splice variants rescue Arp2-knockout lethality, they functionally diverge in late sperm development due to the microexon sequence, not the length. Overall, our findings demonstrate that the Arp2 microexon alters Arp2/3 function in certain contexts.

cell biology↗

bioRxiv2025

Ligand-dependent G protein dynamics underlying opioid signaling efficacy

Activation of heterotrimeric G proteins by G protein-coupled receptors (GPCRs) requires large-scale opening of the G -helical domain (AHD) to expose the nucleotide-binding site and facilitate GDP-GTP exchange. While orthosteric ligands are known to modulate GPCR conformation and signaling efficacy, how these effects propagate to the G protein itself remains unclear. Using single-molecule fluorescence resonance energy transfer (smFRET) imaging, we monitored AHD motions in Gi proteins coupled to the -opioid receptor (OR) across a spectrum of ligand- and nucleotide-bound states. We find that receptor ligands differentially modulate these dynamics from over 70 [A] away, with higher-efficacy agonists more effectively promoting transitions to an open, low-nucleotide-affinity conformation. These data also capture transient OR-Gi intermediates during nucleotide binding and suggest that -opioid ligand efficacy arises in part from allosteric control over G protein conformational equilibria that kinetically gate activation.

biophysics↗

bioRxiv2024

Secondary structure determines electron transport in peptides

Proteins play a key role in biological electron transport, but the structure-function relationships governing the electronic properties of peptides are not fully understood. Despite recent progress, understanding the link between peptide conformational flexibility, hierarchical structures, and electron transport pathways has been challenging. Here, we use single-molecule experiments, molecular dynamics (MD) simulations, non-equilibrium Greens function-density functional theory (NEGF-DFT) calculations, and unsupervised machine learning to understand the role of primary amino acid sequence and secondary structure on charge transport in peptides. Our results reveal a two-state molecular conductance behavior for peptides across several different amino acid sequences. MD simulations and Gaussian mixture modeling are used to show that this two-state molecular conductance behavior arises due to the conformational flexibility of peptide backbones, with a high-conductance state arising due to a more defined secondary structure (beta turn) and a low-conductance state occurring for extended peptide structures. Conformer selection for the peptide structures is rationalized using principal component analysis (PCA) of intramolecular hydrogen bonding distances along peptide backbones. Molecular conformations from MD simulations are used to model charge transport in NEGF-DFT calculations, and the results are in reasonably good agreement with experiments. Projected density of states (PDOS) calculations and molecular orbital visualizations are further used to understand the role of amino acid side chains on transport. Overall, our results show that secondary structure plays a key role in electron transport in peptides, which provides new avenues for understanding the electronic properties of longer peptides or proteins. Significance StatementElectron transport in proteins serves as a biological power line that fuels cellular activities such as respiration and photosynthesis. Within cells, proteins act as conduits, shuttling electrons through a series of reactions and pathways to generate proton gradients and to fuel ATP synthesis. Despite recent progress, the mechanisms underlying the flow of energy in protein complexes are not fully understood. Here, we study electron transport in peptides at the single-molecule level by combining experiments and molecular modeling. Our results reveal two distinct molecular sub-populations underlying electron transport that arise due to the flexibility of peptide backbones and the ability to fold into compact structures. This work provides a basis for understanding energy flow in larger proteins or biomolecular assemblies.

biophysics↗

bioRxiv2023

Evolutionary diversification reveals distinct somatic versus germline cytoskeletal functions of the Arp2 branched actin nucleator protein

Branched actin networks are critical in many cellular processes, including cell motility and division. Arp2, a protein within the 7-membered Arp2/3 complex, is responsible for generating branched actin. Given its essential roles, Arp2 evolves under stringent sequence conservation throughout eukaryotic evolution. We unexpectedly discovered recurrent evolutionary diversification of Arp2 in Drosophila, yielding independently arising paralogs Arp2D in obscura species and Arp2D2 in montium species. Both paralogs are unusually testis-enriched in expression relative to Arp2. We investigated whether their sequence divergence from canonical Arp2 led to functional specialization by replacing Arp2 in D. melanogaster with either Arp2D or Arp2D2. Despite their divergence, we surprisingly found both complement Arp2s essential function in the soma, suggesting they have preserved the ability to polymerize branched actin even in a non-native species. However, we found that Arp2D-expressing males are subfertile and display many defects throughout sperm development. We pinpointed two highly diverged structural regions in Arp2D that contribute to these defects: subdomain 2 and the C-terminus. We expected that germline function would be rescued by replacing Arp2Ds long and charged C-terminus with Arp2s short C-terminus, yet surprisingly, the essential somatic function of Arp2D was lost. Therefore, while Arp2Ds structural divergence is incompatible with D. melanogaster sperm development, its unique C-terminus has evolved a critical role in actin polymerization. Our findings suggest canonical Arp2s function differs between somatic versus germline contexts, and Arp2 paralogs have recurrently evolved and specialized for actin branching in the testis.

evolutionary biology↗

bioRxiv2022

Understanding Supramolecular Assembly of Supercharged Proteins

Ordered supramolecular assemblies of supercharged synthetic proteins have recently been created using electrostatic interactions between oppositely charged proteins. Despite recent progress, the fundamental mechanisms governing the assembly process between oppositely supercharged proteins are not fully understood. In this work, we use a combination of experiments and computational modeling to systematically study the supramolecular assembly process for a series of oppositely supercharged green fluorescent protein (GFP) variants. Our results show that the assembled structures of oppositely supercharged proteins critically depend on surface charge distributions. In addition, net charge is a sufficient molecular descriptor to predict the interaction fate of oppositely charged proteins under a given set of solution conditions (e.g., ionic strength). Interestingly, our results show that a large excess of charge is necessary to nucleate assembly and that charged residues that are not directly involved in interprotein interactions contribute to a substantial fraction ([~]30%) of the interaction energy between oppositely charged proteins via long-range electrostatic interactions. Dynamic subunit exchange experiments enabled by Forster resonance energy transfer (FRET) further show that relatively small, 16-subunit assemblies of oppositely charged proteins have kinetic lifetimes on the order of [~]10-40 minutes, which is governed by protein composition and solution conditions. Overall, our work shows that a balance between kinetic stability and electrostatic charge ultimately determine the fate of supramolecular assemblies of supercharged proteins. Broadly, our results inform how protein supercharging can be used to generate different ordered supramolecular assemblies from a single parent protein building block.

bioengineering↗

bioRxiv2021

Expanding the Molecular Alphabet of DNA-Based Data Storage Systems with Neural Network Nanopore Readout Processing

DNA is a promising next-generation data storage medium, but the recording latency and synthesis cost of oligos using the four natural nucleotides remain high. Here, we describe an improved DNA-based storage system that uses an extended 11-letter molecular alphabet combining natural and chemically modified nucleotides. Our extended-alphabet molecular storage paradigm offers a nearly two-fold increase in storage density and potentially the same order of reduction in the recording time. Experimental results involving a library of 77 custom-designed hybrid sequences reveal that one can readily detect and discriminate different combinations and orders of monomers via MspA nanopores. Furthermore, a neural network architecture designed to classify raw current signals generated by Oxford Nanopore Technologies sequencing ensures an average accuracy exceeding 60%, which is 39 times higher than that of random guessing. Molecular dynamics simulations reveal that the majority of modified nucleotides do not induce dramatic disruption of the DNA double helix, making the extended alphabet system potentially compatible with PCR-based random access data retrieval. The methodologies proposed provide a forward path for new implementations of molecular recorders.

synthetic biology↗

bioRxiv2021

Rewritable Two-Dimensional DNA-Based Data Storage with Machine Learning Reconstruction

DNA-based data storage platforms traditionally encode information only in the nucleotide sequence of the molecule. Here we report on a two-dimensional molecular data storage system that records information in both the sequence and the backbone structure of DNA and performs nontrivial joint data encoding, decoding and processing. Our 2DDNA method efficiently stores high-density images in synthetic DNA and embeds pertinent metadata as nicks in the DNA backbone. To avoid costly worst-case redundancy for correcting sequencing/rewriting errors and to mitigate issues associated with mismatched decoding parameters, we develop machine learning techniques for automatic discoloration detection and image inpainting. The 2DDNA platform is experimentally tested by reconstructing a library of images with undetectable or small visual degradation after readout processing, and by erasing and rewriting copyright metadata encoded in nicks. Our results demonstrate that DNA can serve both as a write-once and rewritable memory for heterogenous data and that data can be erased in a permanent, privacy-preserving manner. Moreover, the storage system can be made robust to degrading channel qualities while avoiding global error-correction redundancy.

synthetic biology↗

bioRxiv2020

Initial ciliary assembly in Chlamydomonas requires Arp2/3-dependent recruitment from a ciliary protein reservoir in the plasma membrane

Ciliary assembly, trafficking, and regulation are dependent on microtubules, but the mechanisms of ciliary assembly also require the actin cytoskeleton. Here, we dissect subcellular roles of actin in ciliogenesis by focusing on actin networks nucleated by the Arp2/3 complex in the powerful ciliary model, Chlamydomonas. We find the Arp2/3 complex is required for the initial stages of ciliary assembly when protein and membrane are in high demand but cannot yet be supplied from the Golgi complex. We provide evidence for Arp2/3 complex-dependent endocytosis of ciliary proteins, an increase in endocytic activity upon induction of ciliary growth, and relocalization of plasma membrane proteins to newly formed cilia. Our data support a new model of ciliary protein and membrane trafficking during early ciliogenesis whereby proteins previously targeted to the plasma membrane are reclaimed by Arp2/3 complex-dependent endocytosis for initial ciliary assembly. SUMMARYUsing the ciliary model system Chlamydomonas, we find Arp2/3 complex-mediated endocytosis is needed to reclaim cell body plasma membrane for early ciliary assembly.

cell biology↗

bioRxiv2020

A rapidly evolving actin mediates fertility and developmental tradeoffs in Drosophila

Most actin-related proteins (Arps) are highly conserved in eukaryotes, where they carry out well-defined cellular functions. Drosophila and mammals also encode divergent non-canonical Arps in their male-germline whose roles remain unknown. Here, we show that Arp53D, a rapidly-evolving Drosophila Arp, localizes to fusomes and actin cones, two male germline-specific actin structures critical for sperm maturation, via its non-canonical N-terminal tail. Although we expected that Arp53D loss would reduce male fertility, we instead find that Arp53D-KO males are more fertile, both in isolation and in competition with wildtype males. Upon investigating why evolution would retain a gene that negatively impacts male fertility, we unexpectedly found that Arp53D-KO females are less fertile. Moreover, KO embryos exhibit reduced viability, which worsens under heat stress. We conclude that testis-specific Arp53D is detrimental to male fertility, but is required for female fertility and early development, leading to its long-term retention and recurrent adaptation in Drosophila.

cell biology↗

bioRxiv2019

Assembly of novel, nuclear dimers of the PI3-Kinase regulatory subunits underpins the pro-proliferative activity of the Cdc42-activated tyrosine kinase, ACK

The tyrosine kinase ACK is an oncogene associated with poor prognosis in human cancers. ACK promotes proliferation, in part, by contributing to the activation of Akt, the major PI3-Kinase effector. We show that ACK also regulates PI3-Kinase directly, via interactions with the PI3-Kinase regulatory subunits. ACK interacts with all five regulatory subunit isoforms and directly phosphorylates p85, p85{beta}, p55 and p50 on Tyr607 (or equivalent). Phosphorylation of p85{beta} at this residue promotes cell proliferation but, counterintuitively, ACK does not stimulate PI3-Kinase catalytic activity. We show that ACK stabilizes p85 levels by promoting an interaction between the p85 nSH2 domain and pTyr607, protecting p85 from ubiquitination. We demonstrate that ACK interacts with p85 exclusively in nuclear-enriched cell fractions where the increased levels of the regulatory subunits, together with the nSH2-pTyr607 interaction, promote formation of dimeric p85. We postulate that these novel dimers undertake nuclear functions that contribute to Cdc42-ACK driven oncogenesis. We propose that ACK shapes PI3-Kinase signalling by dampening the PIP3 response, whilst continuing to drive cell proliferation through Akt activation and hereto unexplored but crucial functions of nuclear dimeric p85. These new regulatory subunit dimers represent a previously undescribed mode of regulation for PI3-Kinase and potentially reveal additional avenues for therapeutic intervention.

molecular biology↗

bioRxiv2019

Eomes and Brachyury control pluripotency exit and germ layer segregation by changes of chromatin state

The first lineage specification of pluripotent mouse epiblast segregates neuroectoderm (NE) from mesoderm and endoderm (ME) by currently poorly understood mechanisms. Here we demonstrate that the induction of any ME-gene programs critically relies on the T-box (Tbx) transcription factors Eomes and Brachyury that concomitantly repress pluripotency and NE gene programs. Tbx-deficient cells retain pluripotency and differentiate to NE lineages despite the presence of ME-inducing signals TGF{beta}/Nodal and WNT. Pluripotency and NE gene networks are additionally repressed by Tbx-induced ME factors, demonstrating a remarkable redundancy in program regulation to safeguard mutually exclusive lineage specification. Chromatin analyses revealed that accessibility of ME-gene enhancers depends on Tbx-binding, while NE-gene enhancers are accessible and activation-primed already at pluripotency state. This asymmetry of chromatin landscape thus explains the default differentiation of pluripotent cells to NE in the absence of ME-induction mediated through the activating and repressive functions of early Tbx factors Eomes and Brachyury.

developmental biology↗

bioRxiv2019

A burst of genetic innovation in actin-related proteins (Arps) for testis-specific function in a Drosophila lineage

Many cytoskeletal proteins form the core of fundamental biological processes and are evolutionarily ancient. For example, the superfamily of actin-related proteins (Arps) specialized early in eukaryotic evolution for diverse cellular roles in the cytoplasm and the nucleus. Despite its strict conservation across eukaryotes, we find that the Arp superfamily has undergone dramatic lineage-specific diversification in Drosophila. Our phylogenomic analyses reveal four independent Arp gene duplications that originated in the common ancestor of the obscura group of Drosophila species and have been mostly preserved in this lineage. All four Arp paralogs have evolved under positive selection and are predominantly expressed in the male germline. We focus our analyses on the divergent Arp2D paralog, which arose via a retroduplication event from Arp2, a component of the 7-membered Arp2/3 complex that polymerizes branched actin networks. Computational modeling analyses suggest that Arp2D should be able to replace Arp2 in the Arp2/3 complex and bind daughter actin monomers, suggesting that Arp2D may augment Arp2s functions in the male germline. We find that Arp2D is expressed during and following meiosis in the male germline, where it localizes to distinct locations such as actin cones-pecialized cytoskeletal structures that separate bundled spermatids into individual mature sperm. We hypothesize that this unprecedented burst of genetic innovation in cytoskeletal proteins may have been driven by the evolution of sperm heteromorphism in the obscura group of Drosophila.

evolutionary biology↗