Biology subjects

Bhaskara, R. M.

Publications and source records attributed to Bhaskara, R. M..

6 recordsLinked to original sources

bioRxiv2026

TBK1 restricts IRGQ-mediated autophagy

The autophagy-lysosome system directs the degradation of a wide variety of cytoplasmic cargo such as damaged organelles, protein aggregates, and invading pathogens. The autophagy receptor IRGQ harbors two distinct LIR domains, with LIR1 exhibiting high selectivity for GABARAPL2. Proteomic, biochemical, and high-throughput microscopy studies revealed that the IRGQ-GABARAPL2 complex functions as a hub for the interaction between hATG8s and the autophagy initiation machinery, promoting their lipidation and overall autophagic flux. The interaction of IRGQ with GABARAPL2 is regulated via TBK1. Upon TBK1 activation, GABARAPL2 is phosphorylated on S10, which disrupts IRGQ-GABARAPL2 complexation and therefore its interaction with the autophagy initiation machinery, resulting in a reduction of the autophagic flux of GABARAPL2 and IRGQ-cargo, without affecting bulk autophagy. These findings broaden IRGQs role in autophagy, identifying it as an interaction hub for autophagy initiation that is negatively regulated by TBK1.

biochemistry↗

bioRxiv2025

Multi-scale classification decodes the complexity of the human E3 ligome

E3 ubiquitin ligases are key regulators of protein homeostasis, targeting specific proteins for degradation via the ubiquitin-proteasome system (UPS). They provide crucial substrate specificity, making them promising candidates for the design of novel therapeutics. This work presents a comprehensive, annotated dataset of high-confidence catalytic human E3 ligases, termed the "E3 ligome". Integrating disparate data from various granularity layers, including protein sequence, domain architecture, 3D structure, function, localization, and expression, we learn an emergent distance metric, capturing authentic relationships within this heterogeneous group. A weakly-supervised hierarchical classification framework identifies conserved features of E3 families and subfamilies, consistent with RING, HECT, and RBR classes. This classification explains functional segregation, identifies multi-subunit and standalone enzymes, and integrates substrate and small molecule interaction networks. Our analysis provides a global view of E3 biology, opening new strategies for drugging E3-substrate networks, including drug re-purposing and designing new E3 handles.

bioinformatics↗

bioRxiv2024

Intrinsically disordered region amplifies membrane remodeling to augment selective ER-phagy

Intrinsically disordered regions (IDRs) play a pivotal role in organellar remodeling. They transduce signals across membranes, scaffold signaling complexes, and mediate vesicular traffic. Their functions are regulated by constraining conformational ensembles through specific intra- and inter-molecular interactions, physical tethering, and post-translational modifications. The ER-phagy receptor FAM134B/RETREG1, known for its Reticulon homology domain (RHD), includes a substantial C-terminal intrinsically disorder region (IDR) housing the LC3 interacting (LIR) motif. Beyond engaging the autophagic machinery, the function of the FAM134B-IDR is unclear. Here, we investigate the characteristics of the FAM134B-IDR by extensive modeling and molecular dynamics (MD) simulations. We present detailed structural models for the IDR, mapping its conformational landscape in solution and membrane-anchored configurations. Our analysis reveals that depending on the membrane anchor, the IDRs collapse onto the membrane and induce positive membrane curvature to varying degrees. The charge patterns underlying this Janus-like behavior are conserved across other ER-phagy receptors. We found that IDRs alone are sufficient to sense curvature. When combined with RHDs, they intensify membrane remodeling and drive efficient protein clustering, leading to faster budding, thereby amplifying RHD remodeling functions. Our simulations provide a new perspective on IDRs of FAM134B, their Janus-like membrane interactions, and the resulting modulatory functions during large-scale ER remodeling.

biophysics↗

bioRxiv2023

Identification of potential selective autophagy receptors from protein-content profiling of autophagosomes

Selective autophagy receptors (SARs) are central to cellular homeostatic and organellar recycling pathways. Over the last two decades, more than 30 SARs have been discovered and validated using a variety of experimental approaches ranging from cell biology to biochemistry, including high-throughput imaging and screening methods. Yet, the extent of selective autophagy pathways operating under various cellular contexts e.g., under basal and starvation conditions, remains unresolved. Currently, our knowledge of all known SARs and their associated cargo components is fragmentary and limited by experimental data with varying degrees of resolution. Here, we use classical predictive and modeling approaches to integrate high-quality autophagosome content profiling data with disparate datasets. We identify a global set of potential SARs and their associated cargo components active under basal autophagy, starvation-induced, and proteasome-inhibition conditions. We provide a detailed account of cellular components, biochemical pathways, and molecular processes that are degraded via autophagy. Our analysis yields a catalog of new potential SARs that satisfy the characteristics of bonafide, well-characterized SARs. We categorize them by the subcellular compartments they emerge from and classify them based on their likely mode of action. Our structural modeling validates a large subset of predicted interactions with the human ATG8 family of proteins and shows characteristic, conserved LC3-interacting region (LIR)-LIR-docking site (LDS) and Ubiquitin-interacting motif (UIM)-UIM-docking site (UDS) binding modes. Our analysis also revealed the most abundant cargo molecules targeted by these new SARs. Our findings expand the repertoire of SARs and provide unprecedented details into the global autophagic state of HeLa cells. Taken together, our findings provide motivation for the design of new experiments, testing the role of these novel factors in selective autophagy.

cell biology↗

bioRxiv2021

FAM134B-RHD Protein Clustering Drives Spontaneous Budding of Asymmetric Membranes

Living cells constantly remodel the shape of their lipid membranes. In the endo-plasmic reticulum (ER), the reticulon homology domain (RHD) of the reticulophagy regulator 1 (RETR1/FAM134B) forms dense autophagic puncta that are associated with membrane removal by ER-phagy. In molecular dynamics (MD) simulations, we find that FAM134B-RHD spontaneously forms clusters, driven in part by curvature-mediated attraction. At a critical size, the FAM134B-RHD clusters induce the formation of membrane buds. The kinetics of budding depends sensitively on protein concentration and bilayer asymmetry. Our MD simulations shed light on the role of FAM134B-RHD in ER-phagy and show that membrane asymmetry can be used to modulate the kinetics barrier for membrane remodeling. Graphical TOC Entry O_FIG_DISPLAY_L [Figure 1] M_FIG_DISPLAY C_FIG_DISPLAY

biophysics↗

bioRxiv2019

TBK1-mediated phosphorylation of LC3C and GABARAP-L2 controls autophagosome shedding by ATG4 protease

Autophagy is a highly conserved catabolic process through which defective or otherwise harmful cellular components are targeted for degradation via the lysosomal route. Regulatory pathways, involving post-translational modifications such as phosphorylation, play a critical role in controlling this tightly orchestrated process. Here, we demonstrate that TBK1 regulates autophagy by phosphorylating autophagy modifiers LC3C and GABARAP-L2 on surface-exposed serine residues (LC3C S93 and S96; GABARAP-L2 S87 and S88). This phosphorylation event impedes their binding to the processing enzyme ATG4 by destabilizing the complex. Phosphorylated LC3C/GABARAP-L2 cannot be removed from liposomes by ATG4 and are thus protected from ATG4-mediated premature removal from nascent autoph-agosomes. This ensures a steady coat of lipidated LC3C/GABARAP-L2 throughout the early steps in autophagosome formation and aids in maintaining a unidirectional flow of the autophagosome to the lysosome. Taken together, we present a new regulatory mechanism of autophagy, which influences the conjugation and de-conjugation of LC3C and GABARAP-L2 to autophagosomes by TBK1-mediated phosphorylation.

biochemistry↗