Biology subjects

Erben, E.

Publications and source records attributed to Erben, E..

4 recordsLinked to original sources

bioRxiv2025

Genome-wide overexpression screen reveals a novel transcription termination factor in Trypanosoma brucei

Trypanosoma brucei is a protozoan parasite that causes African trypanosomiasis. Understanding essential cellular processes in T. brucei can provide insights into parasite-specific vulnerabilities. We therefore screened for genes whose overexpression impaired parasite growth. Three top-ranking candidates were confirmed to inhibit T. brucei growth upon overexpression. Among them, TbFOP, a previously uncharacterized protein, exhibited distinct phenotypes beyond growth inhibition. TbFOP overexpression caused severe cell-cycle defects, substantially increasing the proportion of sub-G1 cells lacking nuclear DNA. Transcriptome analysis revealed widespread transcriptional dysregulation following TbFOP overexpression. Specifically, antisense transcript levels substantially increased near transcription termination sites (TTSs) across the genome. TbFOP overexpression also increased the expression of normally silent variant surface glycoprotein (VSG) genes across multiple genomic contexts. These phenotypes resemble those observed in trypanosome mutants lacking TTS-associated chromatin marks, including two histone variants and base J, a kinetoplastid-specific DNA modification. The preferential effects at TTSs and VSG loci raise the possibility that TbFOP overexpression interferes with chromatin-associated transcriptional regulation at specific genomic regions. These findings demonstrate that TbFOP overexpression profoundly affects transcription, cell-cycle progression, and parasite growth.

molecular biology↗

bioRxiv2025

Active and Probe-Free Intracellular Rheology via Phase-Sensitive Thermoviscous Flows

Determination of the rheological properties of cells is known to require active measurements, which largely depend on the internalisation of mechanical probes. Here we circumvent this problem via the introduction of Rheo-FLUCS: an active, yet probe-free approach that leverages light-induced flows to access the mechanics of complex systems. While Rheo-FLUCS is facilitated by thermoviscous expansion phenomena rather than external forces, we here show equivalence in its ability to measure canonical viscoelastic properties. Specifically, we demonstrate a phase-lag equivalence with probe-dependent active microrheology in a wide range of physically different, yet chemically identical materials. We exemplify the utility of Rheo-FLUCS in three distinctly different biological systems: compound-treated mouse fibroblasts (NIH-3T3), genetically modified human osteoblasts (U2OS) to elucidate the role of myosins in cytoplasmic mechanics, and early ascidian oocytes of Phallusia mammillata at fertilisation stage. This probe-free methodology represents a transformative advance in cellular rheology, enabling non-invasive and precise mechanical measurements across diverse biological systems without perturbing their natural state through probe internalisation.

biophysics↗

bioRxiv2021

Non-invasive Chromatin Deformation and Measurement of Differential Mechanical Properties in the Nucleus

The nucleus is highly organized to facilitate coordinated gene transcription. Measuring the rheological properties of the nucleus and its sub-compartments will be crucial to understand the principles underlying nuclear organization. Here, we show that strongly localized temperature gradients (approaching 1{degrees}C /m) can lead to substantial intra-nuclear chromatin displacements (>1 m), while nuclear area and lamina shape remain unaffected. Using particle image velocimetry (PIV), intra-nuclear displacement fields can be calculated and converted into spatio-temporally resolved maps of various strain components. Using this approach, we show that chromatin displacements are highly reversible, indicating that elastic contributions are dominant in maintaining nuclear organization on the time scale of seconds. In genetically inverted nuclei, centrally compacted heterochromatin displays high resistance to deformation, giving a rigid, solid-like appearance. Correlating spatially resolved strain maps with fluorescent reporters in conventional interphase nuclei reveals that various nuclear compartments possess distinct mechanical identities. Surprisingly, both densely and loosely packed chromatin showed high resistance to deformation, compared to medium dense chromatin. Equally, nucleoli display particularly high rigidity and strong local anchoring to heterochromatin. Our results establish how localized temperature gradients can be used to drive nuclear compartments out of mechanical equilibrium to obtain spatial maps of their material responses. Main FindingsO_LINovel non-invasive active micro-rheology method to probe spatial intranuclear material responses, unhindered by the nuclear lamina, using strongly localized temperature gradients C_LIO_LIChromatin shows both elastic and viscous properties at the mesoscale with a retardation time of {tau} [~] 1s C_LIO_LICompacted heterochromatin in a model of nuclear inversion shows high resistance to deformation, suggesting dominantly solid-like behavior C_LIO_LIThe nucleus displays spatially distinct material properties for different compartments C_LIO_LIThe nucleolus shows high resistance to deformation on the time scale of seconds C_LIO_LIImmobile nucleoli appear solidly anchored to and retain the deformation of surrounding chromatin C_LI

cell biology↗

bioRxiv2020

A novel essential RNA-binding protein complex in Trypanosoma brucei

ZC3H5 is an essential cytoplasmic trypanosome protein with a single Cx7Cx5Cx3H zinc finger domain. We here show that ZC3H5 forms a complex with three other proteins, encoded by genes Tb927.11.4900, Tb927.8.1500 and Tb927.7.3040. ZC3H5 interacts directly with Tb927.11.4900, which in turn interacts with Tb927.7.3040. Tb927.11.4900 has a circularly permuted GTPase domain, which is required for the Tb927.7.3040 interaction. RNA immunoprecipitation revealed that ZC3H5 is preferentially associated with poorly translated, low-stability mRNAs, the 5-untranslated regions and coding regions of which are enriched in the motif (U/A)UAG(U/A). Tethering of ZC3H5, or other complex components, to a reporter repressed its expression. However, depletion of ZC3H5 in vivo did not increase the abundance of ZC3H5-bound mRNAs: instead, counter-intuitively, there were very minor decreases in a few targets, and marked increases in the abundances of very stable mRNAs encoding ribosomal proteins. Depletion also resulted in an increase in monosomes at the expense of large polysomes, and appearance of "halfmer" disomes containing two 80S subunits and one 40S subunit. We speculate that the ZC3H5 complex might be implicated in quality control during the translation of sub-optimal open reading frames; complex assembly might be regulated by GTP hydrolysis and GTP-GDP exchange.

molecular biology↗