Biology subjects

Kruse, E.

Publications and source records attributed to Kruse, E..

8 recordsLinked to original sources

bioRxiv2025

Impact of modification of envelope proteins on the mechanical properties of HIV virus-like particles

The mechanical interactions between virus-like particles and host cells may offer targets for new viral treatments and vaccines with modes of action that are independent of the immune system. The physical properties of structures involved govern the particle-cell interactions. While the mechanical properties of virions and mammalian cells have been widely studied, data on virus-like particles are limited. This study aimed to determine the mechanical and morphological properties of HIV-1 virus-like particles with different envelopes. Three HIV-like particles, i.e. GagM + gp150, GagM + gp140HA2tr, and GagM + gp120HA2, were produced by combining the same Gag protein shell with different trimeric glycoprotein envelopes. The particles spring constant, breaking force, and dimensions were determined using atomic force microscopy, and the elastic modulus was quantified using finite element analysis. Spring constant, elastic modulus, and breaking force were higher for GagM + gp140HA2tr and GagM + gp120HA2 than for GagM + gp150. The particle height was smaller for GagM + gp120HA2 than for GagM + gp150 and GagM + gp140HA2tr. Possible mechanisms underlying the increase of the particles stiffness and mechanical strength are the inclusion of the influenza virus HA transmembrane domain in the HIV Env protein, and the lower expression and packing density of Env in GagM + gp140HA2tr and GagM + gp120HA2 compared to GagM + gp150 found previously. Upon confirmation, the proposed mechanisms offer potential to tailor the mechanics of HIV virus-like particles and guide mechanical interactions between VLPs and host cells towards improving vaccines.

biophysics↗

bioRxiv2023

Divergent recovery trajectories in reef-building corals following a decade of successive marine heatwaves

Increasingly frequent marine heatwaves are devastating coral reefs. Corals that survive these extreme heat stress events must rapidly recover if they are to withstand subsequent events, and long-term survival in the face of rising ocean temperatures may hinge on recovery capacity and acclimatory gains in heat tolerance over an individuals lifespan. To better understand coral recovery trajectories in the face of successive marine heatwaves, we monitored the responses of bleaching-susceptible and bleaching-resistant individuals of two dominant coral species in Hawaii, Montipora capitata and Porites compressa, over a decade that included three marine heatwaves. Bleaching-susceptible colonies of P. compressa exhibited beneficial acclimatization to heat stress (i.e., less bleaching) following repeat heatwaves, becoming indistinguishable from bleaching-resistant conspecifics during and after the third heatwave. In contrast, bleaching-susceptible M. capitata repeatedly bleached during all successive heatwaves and exhibited seasonal bleaching for up to three years following the third heatwave. Encouragingly, bleaching-resistant individuals of both species remained pigmented across the entire time series; however, pigmentation did not necessarily indicate physiological resilience. Specifically, M. capitata displayed incremental yet only partial recovery of symbiont density and tissue biomass across both bleaching phenotypes up to 35 months following the third heatwave. Conversely, P. compressa appeared to recover across most physiological metrics within two years, reverting to predictable seasonal variability. Ultimately, these results indicate that even some visually robust, bleaching-resistant corals can carry the cost of recurring heatwaves over multiple years, leading to divergent recovery trajectories that may erode coral reef resilience in the Anthropocene. Significance StatementCoral reefs are in jeopardy as climate change has led to increasingly frequent marine heatwaves. Some corals can survive these extreme heat stress events, thus acquiring environmental memory that may prime them for increased resistance and resilience in subsequent heatwaves via beneficial acclimatization. Yet, as the time between heatwaves decreases, the accumulation of stress experienced by some individuals may preclude opportunities for beneficial acclimatization. This nearly decade-long study revealed divergent recovery trajectories within and between species in response to successive marine heatwaves, ranging from costly to beneficial. As the climate continues to change, surviving corals must not only gain heat tolerance, but also rapidly recover to maintain the critically important ecosystem services that humanity relies on.

ecology↗

bioRxiv2023

Single molecule MATAC-seq reveals key determinants of DNA replication origin efficiency

SummaryStochastic origin activation gives rise to significant cell-to-cell variability in the pattern of genome replication. The molecular basis for heterogeneity in efficiency and timing of individual origins is a long-standing question. Here, we developed Methylation Accessibility of TArgeted Chromatin domain Sequencing (MATAC-Seq) to determine single-molecule chromatin accessibility of specific genomic loci after targeted purification in their native chromatin context. Applying MATAC-Seq to selected early-efficient (EE) and late-inefficient (LI) budding yeast replication origins revealed large heterogeneity of chromatin states. Disruption of INO80 or ISW2 chromatin remodeling complexes leads to changes at individual nucleosomal positions that correlate with changes in their replication efficiency. We found a chromatin state with an optimal 100-115bp nucleosome-free region in combination with surrounding well-positioned nucleosomes and open +2 linker region is a strong predictor for efficient origin activation. Thus, MATAC-Seq identifies the large spectrum of alternative chromatin states that co-exist on a given locus previously masked in population-based experiments and provides a mechanistic basis for origin activation heterogeneity during DNA replication of eukaryotic cells. Consequently, our single-molecule assay for chromatin accessibility will be ideal to define single-molecule heterogeneity across many fundamental biological processes such as transcription, replication, or DNA repair in vitro and ex vivo.

biochemistry↗

bioRxiv2023

The CGG triplet repeat binding protein 1 counteracts DNA secondary structure-induced transcription-replication conflicts

Short tracts of trinucleotide repeats with less than 10 repeats are found frequently throughout the genome without any apparent negative impact on DNA replication fork progression or transcription elongation. CGG binding protein 1 (CGGBP1) binds to CGG triplet repeats and has been implicated in multiple cellular processes such as transcription, replication and DNA damage. Here, we show that CGGBP1 binds to human gene promoter sites prone to G-quadruplex and R-loop secondary structure formation. Altering CGGBP1 levels results in the accumulation of R-loops and causes a defect in transcriptional elongation by RNA polymerase II, which subsequently leads to replication fork stalling and transcription-replication conflicts. Together, our work shows that short trinucleotide repeats are a source of genome-destabilizing secondary structures and cells rely on specific DNA-binding factors to maintain proper transcription and replication progression at short trinucleotide repeats.

cell biology↗

bioRxiv2023

Nanopore-based direct RNA sequencing of the Trypanosoma brucei transcriptome identifies novel lncRNAs

Trypanosomatids are single-cell eukaryotic parasites. Unlike higher eukaryotes, they control gene expression posttranscriptionally and not at the level of transcription initiation. This involves all known cellular RNA circuits, from mRNA processing to mRNA decay to translation, in addition to a large panel of RNA-interacting proteins that modulate mRNA abundance. However, other forms of gene regulation, for example, by lncRNAs, cannot be excluded. LncRNAs are poorly studied in trypanosomatids, with only a single lncRNA characterized today. Furthermore, it is not clear whether the complete inventory of trypanosomatid lncRNAs is known because of the inherent cDNA recoding and DNA amplification limitations of short-read RNA sequencing. Here we overcome these limitations by using long-read direct RNA sequencing (DRS) on nanopore arrays. We analyze the native RNA pool of the two main lifecycle stages of the African trypanosome T. brucei with a special emphasis on the inventory of lncRNAs. We identify 207 previously unknown lncRNAs, 109 of which are stage-specifically expressed. We also present insights into the complexity of the T. brucei transcriptome, including alternative transcriptional start and stop sites and potential transcript isoforms to provide a bias-free understanding of the intricate RNA landscape in T. brucei.

molecular biology↗

bioRxiv2021

Marine heatwaves depress metabolic activity and impair cellular acid-base homeostasis in reef-building corals regardless of bleaching susceptibility

Ocean warming is causing global coral bleaching events to increase in frequency, resulting in widespread coral mortality and disrupting the function of coral reef ecosystems. However, even during mass bleaching events, many corals resist bleaching despite exposure to abnormally high temperatures. While the physiological effects of bleaching have been well documented, the consequences of heat stress for bleaching resistant individuals are not well understood. In addition, much remains to be learned about how heat stress affects cellular level processes that may be overlooked at the organismal level, yet are crucial for coral performance in the short term and ecological success over the long term. Here we compared the physiological and cellular responses of bleaching resistant and bleaching susceptible corals throughout the 2019 marine heatwave in Hawai i, a repeat bleaching event that occurred four years after the previous regional event. Relative bleaching susceptibility within species was consistent between the two bleaching events, yet corals of both resistant and susceptible phenotypes exhibited pronounced metabolic depression during the heatwave. At the cellular level, bleaching susceptible corals had lower intracellular pH than bleaching resistant corals at the peak of bleaching for both symbiont-hosting and symbiont-free cells, indicating greater disruption of acid-base homeostasis in bleaching susceptible individuals. Notably, cells from both phenotypes were unable to compensate for experimentally induced cellular acidosis, indicating that acid-base regulation was significantly impaired at the cellular level even in bleaching resistant corals and in cells containing symbionts. Thermal disturbances may thus have substantial ecological consequences, as even small reallocations in energy budgets to maintain homeostasis during stress can negatively affect fitness. These results suggest concern is warranted for corals coping with ocean acidification alongside ocean warming, as the feedback between temperature stress and acid-base regulation may further exacerbate the physiological effects of climate change.

ecology↗

bioRxiv2019

Mathematical Model of Mechanical Virion-Cell Interaction During Early Engulfment in HIV

Viral endocytosis involves elastic cell deformation, driven by chemical adhesion energy, and depends on physical interactions between virion and cell membrane. These interactions are not easy to quantify experimentally. Hence, this study aimed to develop a mathematical model of the interactions of HIV particles with host cells and explore the effects of mechanical and morphological parameters during full virion engulfment. The invagination force and engulfment energy were described as viscoelastic and linear-elastic functions of radius and elastic modulus of virion and cell, ligand-receptor energy density and engulfment depth. The influence of changes in the virion-cell contact geometry representing different immune cells and ultrastructural membrane features and the decrease in virion radius and shedding of gp120 proteins during maturation on invagination force and engulfment energy was investigated. A low invagination force and high ligand-receptor energy are associated with high virion entry ability. The required invagination force was the same for immune cells of different sizes but lower for a local convex geometry of the cell membrane at the virion length scale. This suggests that localized membrane features of immune cells play a role in viral entry ability. The available engulfment energy decreased during virion maturation, indicating the involvement of additional biological or biochemical changes in viral entry. The developed mathematical model offers potential for the mechanobiological assessment of the invagination of enveloped viruses towards improving the prevention and treatment of viral infections.

biophysics↗

bioRxiv2017

Surface-driven RNA-refolding by the OB-fold proteins of the Trypanosoma brucei editosome

RNA editing in African trypanosomes represents an RNA-processing reaction that generates functional mitochondrial transcripts from sequence-deficient pre-mRNAs. The reaction is catalyzed by a macromolecular protein complex known as the editosome. Editosomes have been demonstrated to execute RNA-chaperone activity to overcome the highly folded nature of pre-edited substrate mRNAs. The molecular basis of this activity is unknown. Here we test five OB-fold proteins of the editosome as potential candidates. We show that the different proteins interact by hetero-oligomerization and we demonstrate that all proteins execute RNA-chaperone activity. Activity differences correlate with the surface areas of the proteins and map predominantly to the intrinsically disordered subdomains of the polypeptides. To provide a structural context for our findings we present a coarse-grained model of the editosome. The model suggests that an inner core of catalytically active editosome components is separated from an outer shell of IDP-domains that act as RNA-remodeling sites.

molecular biology↗