Biology subjects

Cooperman, B.

Publications and source records attributed to Cooperman, B..

4 recordsLinked to original sources

bioRxiv2026

Active transport of tRNAs facilitates distributed protein synthesis

Large, polarized cells such as cardiomyocytes, skeletal myofibers, and neurons rely on localized protein synthesis to sustain size, remodel and adapt to stress. The subcellular architecture of these cells is also inherently unfavorable for long-range, diffusion-based transport, which may promote their heavy reliance on active transport mechanisms for the localization of RNA and proteins. Transfer RNAs (tRNAs) function as essential regulators of protein synthesis by linking transcription and translation. Since their discovery in the 1950s, tRNA subcellular distribution has been assumed to occur through passive diffusion. Here, we report that there are pools of tRNAs that depend on the microtubule network for distribution in cardiomyocytes, skeletal myofibers and neurons. Employing dual-color live and fixed-cell super-resolution imaging, we demonstrate that active transport of tRNAs involves hitchhiking on the exterior of endolysosomal vesicles (ELV). We establish that leucyl-tRNA synthetase (LeuRS), the tRNA-binding protein that charges leucine to its cognate tRNA and interacts with Rag GTP on the surface of ELVs, is essential for tRNA transport. Disruption of LeuRS-ELV interactions is sufficient to impair long-range, microtubule-dependent tRNA transport, without affecting mRNA or rRNA transport. We also show that preventing tRNA transport is sufficient to impair translation at sites distal from the nucleus as well as globally impair protein synthesis, ultimately reducing cell size. These findings redefine tRNAs as actively trafficked cargo and establish their directed transport as a fundamental layer of translation regulation required for myocyte homeostasis. Highlights1. Pools of tRNAs require an intact microtubule network for distribution in large, complex cells. 2. tRNAs undergo active transport by hitchhiking on endolysosomal vesicles trafficked by microtubule motors. 3. The tRNA synthetase LeuRS functions as a tRNA-specific adaptor linking tRNAs to endolysosomal vesicles, and disrupting this interaction selectively impairs tRNA, but not mRNA or rRNA transport. 4. Loss of tRNA transport reduces distal translation, global protein synthesis, and cell size.

cell biology↗

bioRxiv2024

Roles for the canonical polarity machinery in the de novo establishment of polarity in budding yeast spores

The yeast Saccharomyces cerevisiae buds at sites pre-determined by cortical landmarks deposited during prior budding. During mating between haploid cells in the lab, external pheromone cues override the cortical landmarks to drive polarization and cell fusion. By contrast, in haploid gametes (called spores) produced by meiosis, a pre-determined polarity site drives initial polarized morphogenesis independent of mating partner location. Spore membranes are made de novo so existing cortical landmarks were unknown, as were the mechanisms by which the spore polarity site is made and how it works. We find that the landmark canonically required for distal budding, Bud8, stably marks the spore polarity site along with Bud5, a GEF for the GTPase Rsr1 that canonically links cortical landmarks to the conserved Cdc42 polarity machinery. Cdc42 and other GTPase regulators arrive at the site during its biogenesis, after spore membrane closure but apparently at the site where membrane synthesis began, and then these factors leave, pointing to the presence of discrete phases of maturation. Filamentous actin may be required for initial establishment of the site, but thereafter Bud8 accumulates independent of actin filaments. These results suggest a distinct polarization mechanism that may provide insights into gamete polarization in other organisms. SIGNIFICANCE STATEMENTO_LIDormant budding yeast spores possess a single, stable cortical site that marks the location where polarized growth occurs upon dormancy exit. It was not known how the site forms or which molecules comprise it. C_LIO_LIUsing fluorescently tagged proteins in living cells undergoing sporulation, the authors found proteins canonically involved in polarization of non-spore cells arriving at the polarity site in a choreographed manner and required for site function. C_LIO_LIThese findings point to a distinct polarity mechanism from non-spore cells and raise new questions about polarity protein interactions with membranes that may be applicable to gametogenesis in other organisms. C_LI

cell biology↗

bioRxiv2023

Cytosolic and mitochondrial translation elongation are coordinated through the molecular chaperone TRAP1 for the synthesis and import of mitochondrial proteins

A complex interplay between mRNA translation and cellular respiration has been recently unveiled, but its regulation in humans is poorly characterized in either health or disease. Cancer cells radically reshape both biosynthetic and bioenergetic pathways to sustain their aberrant growth rates. In this regard, we have shown that the molecular chaperone TRAP1 not only regulates the activity of respiratory complexes, behaving alternatively as an oncogene or a tumor suppressor, but also plays a concomitant moonlighting function in mRNA translation regulation. Herein we identify the molecular mechanisms involved, demonstrating that TRAP1: i) binds both mitochondrial and cytosolic ribosomes as well as translation elongation factors, ii) slows down translation elongation rate, and iii) favors localized translation in the proximity of mitochondria. We also provide evidence that TRAP1 is coexpressed in human tissues with the mitochondrial translational machinery, which is responsible for the synthesis of respiratory complex proteins. Altogether, our results show an unprecedented level of complexity in the regulation of cancer cell metabolism, strongly suggesting the existence of a tight feedback loop between protein synthesis and energy metabolism, based on the demonstration that a single molecular chaperone plays a role in both mitochondrial and cytosolic translation, as well as in mitochondrial respiration.

biochemistry↗

bioRxiv2018

Iso-relevance Functions - A Systematic Approach to Ranking Genomic Features by Differential Effect Size

It is common to measure large numbers of features to identify those differing between experimental conditions; for example using RNA-Seq to search for differentially expressed genes. Ranking by p-value allows for statistical control, but has well known issues: unreliability without many replicates; and significance of biologically irrelevant effect sizes. As a result prioritization is typically performed in conjunction with effect size; the canonical one being "fold-change" [Formula]. However fold-change has several issues: division by zero, sensitivity to small values in the denominator, insensitivity to magnitude (1 over 2 equals 100 over 200). To mitigate these problems adding 1 to all values is a widely used heuristic; which we show using real and simulated data is typically highly sub-optimal, while the value 20 is nearly optimal in all cases. From another point of view, adding a fixed "pseudocount" to all values is essentially re-defining effect size from fold-change to something else. To explore this further, we axiomatize the concept of effect size and use this mathematical framework to study the problem in general. We also present the remarkable finding that pseudocounts strike a balance between sorting by fold-change and sorting by difference. Therefore, optimization is equivalent to finding the most harmonious balance between these two extremes. Lastly, the framework is illustrated on a fundamentally different type of problem, that of ranking di-codons by their differential abundance in the ORFeome of different species, where p-values are unavailable and one must solve the problem directly with effect sizes.

bioinformatics↗