Biology subjects

Houston, L.

Publications and source records attributed to Houston, L..

6 recordsLinked to original sources

bioRxiv2026

Highly diverged non-vertebrate Ki-67 proteins with conserved biophysical and functional properties

The Ki-67 protein is a widely used marker of mammalian cell proliferation that plays critical roles in heterochromatin organisation and mitotic perichromosomal layer formation. Thus, its apparent restriction to vertebrates is puzzling. However, sequences with limited homology to subdomains of Ki-67 are present in genomes from some non-vertebrate species. Here, using structural modelling, biophysical and functional analysis, we identify Ki-67-like proteins across diverse non-vertebrate eukaryotes, including tunicates, sponges, molluscs, insects and fungi. Despite extremely low sequence homology, the disordered domains of Ki-67 homologues have generally conserved biophysical and molecular properties. This is further reflected by comparison of cellular localisation, dynamics and effects on chromatin organisation of human, Ciona and Drosophila Ki-67 homologues. These results reinforce the emerging paradigm that functions may be encoded by general biophysical features in highly diverged intrinsically disordered domains. Our approach provides a blueprint for comparative biology of disordered proteins and a foundation for future studies exploring functions of Ki-67 homologues across eukaryotes.

Cell Biology↗

bioRxiv2026

Morphological parameters can capture emergent properties of dynamic disordered cytoskeletal networks

The actin cytoskeleton is an inherently disordered active system. the actomyosin cortex and reconstituted actomyosin systems are globally disordered, yet undergo transitions between distinct disordered states as parameters like motor and crosslinker concentration and filament length and rigidity change. In cells these changes are related to genetic mutations or differences in cell state and dictate fundamental biological processes. However, we dont have well established methods to detect and classify differences in disordered polymer networks. Image-based morphology techniques provide a non-invasive, high-throughput method of extracting information about a system. In this work we simulate biopolymer networks under varying conditions and develop and use morphological descriptors to construct trajectories in morphospace. Using statistical analysis we find that morphological descriptors are able to distinguish between different trajectories of the system, including differences not apparent to the eye. However, no single descriptor alone is able to capture all the differences in the simulated trajectories. Nematic order parameters typically perform the worst for our simulations while curvature and texture descriptors can collectively distinguish between dynamic trajectories. This work helps develop quantification of cytoskeleton dynamics for classification and data-driven modeling.

biophysics↗

bioRxiv2026

HDAC5-encoded Microprotein NISM Mediates Nucleolar Formation and Ribosomal RNA Synthesis

Ribosome biogenesis is the process by which ribosomal RNA (rRNA) and ribosomal proteins are synthesized, processed, and assembled into functional ribosomes. This process begins in the nucleolus, a multiphase liquid condensate. Here, we discover an arginine-rich disordered nucleolar microprotein encoded within the HDAC5 5'-UTR that we termed Nucleolar Integrity and Stress Microprotein (NISM). NISM overexpression leads to impaired rDNA transcription, triggering nucleolar stress, p53 activation, and suppressed proliferation. NISM knockout causes disruption of nucleolar structure and also induces p53 activation. Mechanistically, NISM interacts with the DExH-box RNA helicase DHX9 and regulates its activities related to pre-rRNA synthesis. Computational analyses and polymer physics-based mathematical modeling revealed that NISM coordinates nucleolar formation and pre-rRNA synthesis by enhancing the liquid-liquid phase separation of DHX9. This study establishes NISM as a regulator of nucleolar biology and deepens our understanding of how disordered microproteins can facilitate the formation of membraneless organelles.

molecular biology↗

bioRxiv2026

The Tor pathway, ribosome concentration, and wobble decoding mediate inhibitory effects of the Leu-Pro CUC-CCG codon pair in Saccharomyces cerevisiae.

Translation elongation and efficiency are modulated by the genetic code. In the yeast Saccharomyces cerevisiae, 17 inhibitory codon pairs, distinguished by requirements for wobble decoding and distinct codon order, result in reduced translation efficiency and slow translation. Nine of these inhibitory pairs are functionally important as they are disproportionately strongly conserved within the orthologous genes in Saccharomyces sensu stricto. For three pairs, including CGA-CGA, inhibition is triggered by ribosome collisions and known quality control responses, but the mechanisms by which other pairs cause inhibition is unknown. Here, we examined of the molecular basis of inhibition by the slowly translated, highly conserved Leu Pro CUC-CCG codon pair yielding four findings. First, inhibition is mediated by tRNALeu(UAG), which decodes CUC by a U[bullet]C wobble interaction and effectively competes with the nonessential W[bullet]C base pairing tRNALeu(GAG). Second, despite nearly universal conservation of U33 in tRNAs, the C33 alteration in tRNALeu(GAG) does not significantly impair its function. Third, inhibition is likely due to ribosome collisions as many suppressors have mutations predicted to reduce ribosome concentration, including mutations in large ribosomal subunit proteins, RNA polymerase I, and ribosome assembly factors. Furthermore, local reduction in ribosome concentration suppresses inhibition. Fourth, we find a link between the metabolic state and CUC-CCG inhibition, as we find six suppressor mutations in SCH9, a downstream effector of TORC1 that mediates ribosome production. As Sch9 is inactive during starvation, causing reduced ribosome concentration, one biological function of inhibitory pairs may be to mediate a change in relative expression during starvation conditions.

molecular biology↗

bioRxiv2021

Frameshifting at collided ribosomes is modulated by elongation factor eEF3 and by Integrated Stress Response regulators Gcn1 and Gcn20

Ribosome stalls can result in ribosome collisions that elicit quality control responses, one function of which is to prevent frameshifting by the stalled ribosome, an activity that entails interaction of the conserved yeast protein Mbf1 with uS3 on colliding ribosomes. However, the full spectrum of factors that mediate frameshifting during ribosome collisions is unknown. To delineate such factors in the yeast Saccharomyces cerevisiae, we used genetic selections for mutants that either suppress or increase frameshifting from a known ribosome stall site, CGA codon repeats. We show that the general translation elongation factor eEF3 promotes frameshifting, while Integrated Stress Response (ISR) pathway components Gcn1 and Gcn20 suppress frameshifting. We found a mutant form of eEF3 that specifically suppressed frameshifting, but not translation inhibition by CGA codons. Thus, we infer that frameshifting at collided ribosomes requires eEF3, which facilitates tRNA-mRNA translocation and E-site tRNA release in yeast and other single cell organisms. By contrast, we found that removal of either Gcn1 or Gcn20, which bind collided ribosomes with Mbf1, increased frameshifting. Thus, we conclude that frameshifting is suppressed by Gcn1 and Gcn20, although these effects are not mediated through activation of the ISR. Furthermore, we examined the relationship of eEF3-mediated frameshifting to other quality control mechanisms, finding that the eEF3-mediated frameshifting competes with No-Go decay, Mbf1 and Gcn1/20. Thus, these results provide evidence of a direct link between translation elongation and frameshifting at collided ribosomes, as well as evidence that frameshifting competes with other quality control pathways that act on collided ribosomes.

molecular biology↗

bioRxiv2020

BrphyB is critical for rapid recovery to darkness in mature Brassica rapa leaves

Crop biomass and yield are tightly linked to how the light signaling network translates information about the environment into allocation of resources, including photosynthates. Once activated, the phytochrome (phy) class of photoreceptors signal and re-deploy carbon resources to alter growth, plant architecture, and reproductive timing. Brassica rapa has been used as a crop model to test for conservation of the phytochrome-carbon network. B. rapa phyB mutants have significantly decreased or absent CO2-stimulated growth responses in seedlings, and adult plants have reduced chlorophyll levels, photosynthetic rate, stomatal index, and seed yield. Here, we examine the transcriptomic response of adult wild-type and BrphyB leaves to darkening and recovery in light. Three days of darkness was sufficient to elicit a response in wild type leaves suggesting a shift from carbon fixation and nutrient acquisition to active redistribution of cellular resources. Upon a return to light, wild-type leaves appeared to transcriptionally return to a pre-darkness state restoring a focus on nutrient acquisition. Overall, BrphyB mutant plants have a similar response with key differences in genes involved in photosynthesis and light response which deviate from the wild type transcriptional dynamics. Genes targeted to the chloroplast are especially affected. Adult BrphyB mutant plants had fewer, larger chloroplasts, further linking phytochromes, chloroplast development, photosynthetic deficiencies and optimal resource allocation.

plant biology↗