Biology subjects

Tarbox, H. E.

Publications and source records attributed to Tarbox, H. E..

5 recordsLinked to original sources

bioRxiv2026

Translation fidelity mechanisms and their changes in aging

Protein errors (amino acid misincorporations) are associated to protein misfolding and misfunction, and lower levels correlate with longer lifespan. Despite their prevalence, proteome-wide tracking of misincorporations in eukaryotes is challenging, with most insights being recent and coming from the mining of extensive proteomics data sets. These experimental challenges have precluded the direct in vivo probing and full understanding of the bases of fidelity in higher eukaryotes, and their influence in complex processes such as aging. Here we measured proteome-wide misincorporation frequencies in two experimentally tractable eukaryotic systems, yeast and mouse, using mass spectrometry. We find translation fidelity is organism and organ specific. The measured error frequencies correlate with codon:anticodon pairing thermodynamics and tRNA pool composition, which can have synergistic or opposing effects on fidelity depending on organism or tissue type. Most identified protein errors carry a negative fitness burden. Aging experiments in our two systems reveal that, with age, error frequencies increase in post-mitotic cells, but not so in mitotic ones. These changes correlate with remodeling of the tRNA pool, which we identify as a crucial regulator of translation fidelity during lifespan.

molecular biology↗

bioRxiv2025

Transient Poly(ADP-Ribose) Triggers FUS Condensation Hysteresis via a Prion-Like Mechanism

Hysteresis--where a system retains memory of a transient stimulus--is common in signaling but can also arise in intracellular organization. DNA repair foci, a type of biomolecular condensate, are initiated by the short-lived noncanonical nucleic acid poly(ADP-ribose) (PAR). PAR recruits proteins with prion-like domains (PrLDs), such as Fused in Sarcoma (FUS), and initiates their condensation, which persists even after PAR degradation. How FUS transitions from PAR-dependent to PAR-independent condensation remains unclear. Here, we show that PAR binding triggers a conformational switch in FUS, enabling sustained condensation. PAR binds to the C-terminal arginine-rich region of FUS, displacing intramolecular contacts, and exposing the N-terminal PrLD. This conformational opening allows PrLD interactions in trans, stabilizing condensates independently of PAR. FUS thus undergoes a regulated, nucleated conformational conversion--reminiscent of classical prions. This mechanism implies a paradigm of nucleic acid-induced conformational memory that may underlie hysteresis in intracellular organization in health and disease. HIGHLIGHTS[bullet] PAR-initiated FUS condensation follows a bi-modular mechanism involving both FUS termini. [bullet]Simulations predict and experiments confirm PAR disrupts FUS intramolecular contacts. [bullet]Upon condensation, FUS adopts a conformation with its N-terminus open for interactions. [bullet]N-terminal interactions maintain FUS condensation when PAR degrades during DNA repair.

molecular biology↗

bioRxiv2024

Cognition-Associated Protein Structural Changes in a Rat Model of Aging are Related to Reduced Refolding Capacity

Cognitive decline during aging represents a major societal burden, causing both personal and economic hardship in an increasingly aging population. There are a few well-known proteins that can misfold and aggregate in an age-dependent manner, such as amyloid {beta} and -synuclein. However, many studies have found that the proteostasis network, which functions to keep proteins properly folded, is impaired with age, suggesting that there may be many more proteins that incur structural alterations with age. Here, we used limited-proteolysis mass spectrometry (LiP-MS), a structural proteomic method, to globally interrogate protein conformational changes in a rat model of cognitive aging. Specifically, we compared soluble hippocampal proteins from aged rats with preserved cognition to those from aged rats with impaired cognition. We identified several hundred proteins as having undergone cognition-associated structural changes (CASCs). We report that CASC proteins are substantially more likely to be nonrefoldable than non-CASC proteins, meaning they typically cannot spontaneously refold to their native conformations after being chemically denatured. The potentially cofounding variable of post-translational modifications is systematically addressed, and we find that oxidation and phosphorylation cannot significantly explain the limited proteolysis signal. These findings suggest that noncovalent, conformational alterations may be general features in cognitive decline, and more broadly, that proteins need not form amyloids for their misfolded states to be relevant to age-related deterioration in cognitive abilities. TEASERUp to 10% of rat hippocampal proteins can undergo structural changes that associate with age-related decline in spatial learning.

biophysics↗

bioRxiv2023

Intrinsically Disordered Regions Promote Protein Refoldability and Facilitate Retrieval from Biomolecular Condensates

Many eukaryotic proteins contain intrinsically disordered regions (IDRs) that intersperse globular folded domains, in contrast with bacterial proteins which are typically highly globular1, 2. Recent years have seen great progress in identifying biological functions associated with these elusive protein sequence: in specific cases, they mediate liquid liquid phase separation3, perform molecular recognition4, or act as sensors to changes in the environment5. Nevertheless, only a small number of IDRs have annotated functions6 despite their presence in 64% of yeast proteins,7 stimulating some to question what general purpose they may serve8, 9. Here, by interrogating the refoldability of two fungal proteomes (Saccharomyces cerevisiae and Neurosporra crassa), we show that IDRs render their host proteins more refoldable from the denatured state, allowing them to cohere more closely to Anfinsens thermodynamic hypothesis10, 11. The data provide an exceptionally clear picture of which biophysical and topological characteristics enable refoldability. Moreover, we find that almost all yeast proteins that partition into stress granules during heat shock are refoldable, a finding that holds for other condensates such as P-bodies and the nucleolus. Finally, we find that the Hsp104 unfoldase12 is the principal actor in mediating disassembly of heat stress granules and that the efficiency with which condensed proteins are returned to the soluble phase is also well explained by refoldability. Hence, these studies establish spontaneous refoldability as an adaptive trait that endows proteins with the capacity to reform their native soluble structures following their extraction from condensates. Altogether, our results provide an intuitive model for the function of IDRs in many multidomain proteins and clarifies their relationship to the phenomenon of biomolecular condensation.

biochemistry↗

bioRxiv2020

Non-Refoldability is Pervasive Across the E. coli Proteome

The foundational paradigm of protein folding is that the primary sequence of a protein contains all the information needed for it to adopt a specific native structure1,2. This remarkable property is explained by Anfinsens thermodynamic hypothesis3,4, which asserts that because native states minimize the Gibbs free energy of a protein molecule under physiological conditions, proteins can reliably navigate to their native structures and remain in those states by ergodically sampling their free energy landscapes5. Most experiments of protein folding - conducted on purified, small, single-domain soluble proteins - follow the proportion of protein molecules that are folded as a function of time, temperature, denaturant concentration, or sequence6-8, and have yielded immense insight into the molecular determinants that underpin stable globular folds9,10. However, our reliance on the thermodynamic hypothesis as a ground truth to interpret these experiments has limited our ability to study the folding of complex proteins or to consider alternative non-thermodynamic scenarios11,12. Here, we introduce an experimental approach to probe protein refolding for whole proteomes. We accomplish this by first unfolding and refolding E. coli lysates, and then interrogating the resulting protein structures using a permissive protease that preferentially cleaves at flexible regions. Using mass spectrometry, we analyze the digestion patterns to globally assess structural differences between native and refolded proteins. These studies reveal that following denaturation, many proteins are incapable of navigating back to their native structures. Our results signal a pervasive role for co-translational folding in shaping protein biogenesis, and suggest that the apparent stability of many native states derive from kinetic persistence rather than thermodynamic stability.

biophysics↗