Biology subjects

Chandhok, S.

Publications and source records attributed to Chandhok, S..

4 recordsLinked to original sources

bioRxiv2026

Chaperoning through time - defining DNAJA2 co-chaperone client selectivity via pulse-SILAC and BioID.

Molecular chaperones are a major driving force ensuring efficient protein folding and regulating proteostasis in the cell. However, it remains unclear how their clients are selected in most cases, especially after the release of nascent protein chains from ribosomes. Here, we present a novel approach that combines pulse metabolic labelling with SILAC and BioID mass spectrometry to temporally resolve protein-protein interactions of a co-chaperone. Using the Hsp70 co-chaperone DNAJA2 as a benchmark, we reveal that two distinct pools of proteins are enriched. In particular, DNAJA2 displays a preferential association with highly structured recently synthesized proteins enriched in {beta}-strands. In contrast, pre-existing proteins captured in our assay exhibit higher intrinsic disorder. In both cases, these proteins tend to be longer and contain a lower net charge compared to the proteome. Notably, these preferential associations are retained upon heat-shock, while interactions with the "older" pool of proteins become more prevalent under these conditions. Through this methodology, we gain novel insights on how co-chaperone-client interactions may occur over the lifespan of a protein to preserve proteostasis.

biochemistry↗

bioRxiv2026

BAG6 and RNF126 promote the degradation of cytosolic misfolded proteins that contain buried degron motifs

Missense mutations account for the majority of catalogued human disease-associated variants, and many are predicted to destabilize proteins and promote their degradation. To characterize the pathways responsible for recognizing and clearing such variants, we employed a two-pronged approach to identify both quality control components mediating turnover of misfolded proteins and the sequence elements within their substrates that drive this process. Using a panel of unstable cytosolic missense variants in proximity-labeling and RNAi-based experiments, we identified the BAG6-RNF126 pathway as contributing to the clearance of a subset of these substrates. Applying a tile-based approach to a model cytosolic protein, we uncovered strong potential degrons, including a C-terminal degron degraded in part in a BAG6- and RNF126-dependent manner. Modeling supports that this degron can be accommodated by BAG6. Together, our findings add to the growing body of evidence implicating the BAG6-RNF126 pathway as a key mediator of cytosolic protein quality control.

molecular biology↗

bioRxiv2025

Recombinant Laccase Production Causes Alterations of the S. cerevisiae Proteome that are Dependent on the Strain Origins

Saccharomyces cerevisiae yeast is a widely used recombinant protein production host. Recombinant protein expression requires adaptation of the host cell proteome to accommodate recombinant expression. However, this adaptation has not been well characterized. A better understanding of the adaptation to recombinant protein expression may inform us of pathways important to the process of expression. The proteome of a laboratory yeast was measured each of the 4 days of recombinant laccase expression to determine the adaptations of the proteome. Whereas a sizeable portion of the proteome had altered levels in response to nutrient depletion in batch growth, a smaller portion of the changes was specific to the laccase expression. By comparing yeast strains of different origins and laccase production capacities, we found that each strain tends to display a distinct response to heterologous expression, regardless of the origin of the laccase. For example, the chaperones Hsp26 and Kar2 were specifically elevated in a whey-derived strain upon laccase expression. Nonetheless, the higher capacity to produce active recombinant laccase in some strains appears to be more strongly associated with small groups of proteins that are constitutively expressed at different levels. These results indicate that strains of different origins each provide a unique cellular milieu that, in some cases, is more favorable for the expression of a given recombinant protein. This study provides potential new targets for strain engineering to improve the yield of select recombinant proteins and provides the first insights into the dynamics of the yeast proteome during recombinant laccase expression. Key PointsO_LIProteomes of S. cerevisiae strains during recombinant laccase expression determined C_LIO_LIChanges to ribosomal & metabolic protein levels occur during recombinant expression C_LIO_LIUnique cellular milieu, rather than proteome shifts, is linked to higher yields C_LI

molecular biology↗

bioRxiv2024

PI3K/AKT Signaling Mediates Stress-Inducible Amyloid Aggregation Through c-myc

In response to environmental stress, eukaryotic cells reversibly form functional amyloid aggregates, called amyloid bodies (A-bodies). While these solid-like biomolecular condensates share many biophysical characteristics with pathological amyloids, A-body are non-toxic, and induce a protective state of cellular dormancy. As a recently identified structure, the modulators of A-body biogenesis remain uncharacterized, with the seeding noncoding RNA being the only known regulatory factor. Here, we use an image-based high-throughput screen to identify candidate pathways regulating A-body biogenesis. Our data demonstrates that the PI3K signaling axis meditates A-body formation during heat shock, by activating AKT and repressing GSK3-mediated degradation of c-myc. This enhances c-myc binding to regulatory elements of the seeding noncoding RNA, upregulating the transcripts that nucleate A-body formation. Identifying a link between PI3K signaling, c-myc, and physiological amyloid aggregates, extends the range of activity for these well-established regulators, while providing insight into cellular components whose dysregulation could underly amyloidogenic disorders.

cell biology↗