Recent groundbreaking research unveils the intricate molecular choreography that underpins the activation of mTORC1, a pivotal signaling complex controlling cellular growth and metabolism, on the lysosomal membrane. Although mTORC1’s role in translating nutrient and growth factor cues into anabolic programs is well recognized, the precise structural basis for its activation in the cellular context has remained elusive—until now. Using state-of-the-art cryo-electron microscopy (cryo-EM) combined with biochemical reconstitution on membranes, scientists have decoded an elegant mechanism that reconciles previously puzzling biochemical observations and illuminates new regulatory layers that operate at the nexus of signaling and membrane architecture.
One longstanding enigma clarified by this study concerns why RHEB–GTP, the key growth factor-dependent activator of mTORC1, exhibits surprisingly low affinity for mTORC1 in solution. By incorporating physiological concentrations of lipidated RHEB–GTP and anchoring it to liposomal membranes alongside membrane-bound Ragulator and the RAG GTPase dimer, researchers recreated a near-native environment that sharply potentiated mTORC1 kinase activation. This reflects a profound impact of spatial organization: tethering RHEB to the membrane boosts its local concentration around mTORC1, facilitating interaction and activation in a way unattainable in solution. This finding underscores the critical importance of ‘reduction of dimensionality’—the confinement of diffusible molecules to two-dimensional membrane surfaces—which effectively increases the encounter rate between regulators and their targets.
Yet membrane tethering alone could not explain the full extent of mTORC1 activation. High-resolution cryo-EM revealed that both the mTOR kinase itself and the RAPTOR subunit establish direct physical contacts with the lysosomal membrane, prompting sweeping conformational rearrangements across the mTORC1 complex. These allosteric shifts span multiple domains separated by vast molecular distances exceeding 230 angstroms, from the HEAT repeats through the FAT domain to the kinase lobes. Such large-scale remodeling reorients critical kinase elements, fine-tuning the active site geometry to achieve maximal catalytic efficiency. This multi-domain membrane engagement emerges as a central theme in mTORC1 activation, highlighting the lysosomal membrane not merely as a localization platform but as an active allosteric modulator.
In a particularly intriguing extension, membrane shape dynamics appear to contribute meaningfully to mTORC1 regulation. Lysosomes, known to undergo marked tubulation and swelling during their functional cycles and stress responses, potentially influence kinase activation by altering the curvature and tension of the membrane interface. The study’s biochemical reconstitutions demonstrate that mTORC1 activation correlates with liposome shape, suggesting that the mechanical properties of membranes provide an additional regulatory axis modulating the signaling output. Such findings hint at a sophisticated integration of biophysical and biochemical signals in the spatial control of cell growth pathways.
From an evolutionary perspective, the distinctive membrane anchoring mode of mTOR diverges from other PIKK family kinases, which commonly respond to damage signals via localized rearrangements. However, the structural alignments between activated mTORC1 and relatives like ATM, ATR (MEC1), and DNA-PK reveal conserved rearrangements in the kinase active sites, situating mTOR within a broader family of stress-responsive enzymes while also highlighting its unique spatial regulation on membranes. This alignment of ATP binding sites across PIKKs reinforces the functional significance of the membrane-induced conformational transitions discovered.
Furthermore, an unexpected finding emerged with the identification of a second RAG–Ragulator binding site localized on the MLST8 subunit, a component shared between mTORC1 and mTORC2. Intriguingly, this site is sterically occluded in mTORC2 by SIN1, consistent with mTORC2’s lack of interaction with RAG GTPases. The new binding interface also overlaps with the docking site of the inhibitory protein PRAS40, an insulin-responsive antagonist of mTORC1. Although MLST8 is dispensable for mTORC1’s basal activity, the discovery raises compelling questions about how RAG–Ragulator might modulate inhibition by PRAS40 or influence lysosomal recruitment, suggesting additional layers of nuanced regulation.
The integration of nutrient and growth factor signaling on the lysosome emerges through a finely tuned four-step mechanism delineated by this work. Initially, the RAG–Ragulator complex tethers mTORC1 in proximity to the lysosomal membrane within approximately 10 nanometers, creating a spatial microenvironment conducive to subsequent interactions. Next, RHEB–GTP, itself membrane-anchored at variable distances from the membrane, captures mTORC1 within a target zone of roughly 1.5 to 4 nanometers, initiating the hallmark conformational changes indicative of kinase activation. Membrane docking is then driven initially by the RAPTOR ‘finger’ motif, which contacts the membrane in both intermediate and fully active states. Finally, the direct engagement of mTOR’s membrane-interacting site solidifies the fully active conformation, signifying maximal enzymatic output.
This comprehensive structural model reconciles how a transient and spatially restricted pool of RHEB localized on lysosomes can exert powerful control over mTORC1 activity amidst abundant competing cellular signals. By invoking both biochemical specificity and mechanical membrane interactions, it reveals how nutrient availability and growth factor cues converge physically and functionally on mTORC1. Notably, these findings also open new avenues investigating how membrane shape fluctuations and lipid composition dynamically regulate the growth machinery, with implications for understanding lysosomal physiology and pathologies marked by dysregulated mTOR signaling.
Although the current cryo-EM analyses represent major advances compared to previous membrane-free structures, the authors prudently acknowledge the possibility of further structural nuances emerging once atomistic resolution of mTORC1 on native lysosomal membranes in living cells becomes achievable. Such in situ structural elucidations will likely refine our understanding of the precise kinetics and thermodynamics underlying membrane engagement and enzymatic activation. Moreover, the study highlights the value of future biophysical assays—such as single-molecule Förster resonance energy transfer—to dissect the temporal coordination between conformational dynamics and catalytic rates.
An additional unresolved question pertains to how membrane interactions influence mTORC1’s phosphorylation of noncanonical substrates like TFEB, which depend on RAG–Ragulator but not RHEB. The complex interplay between multiple regulatory axes, including these discrete phosphorylation events, underscores the multifaceted nature of mTORC1 as a signaling hub. Further mechanistic insight into these distinct modalities promises to deepen our understanding of how cellular metabolic homeostasis is finely tuned in physiological and pathological states.
Collectively, this study elegantly elucidates the structural logic of mTORC1 activation on the lysosomal membrane, elevating our molecular understanding of a crucial signaling node that governs cell growth and metabolism. By integrating biochemical reconstitution, high-resolution cryo-EM, and mechanistic modeling, the work captures the spatial and dynamic intricacies that enable mTORC1 to serve as a central integrator of nutritional and growth factor signals. These revelations have profound implications, potentially informing targeted modulation of mTOR signaling in cancer, metabolic diseases, and aging.
As researchers continue to unravel the crosstalk between membrane biophysics and kinase activation, this work exemplifies how synergizing structural biology with cellular biochemistry can decode complex signaling circuits. Emerging methods to probe mTORC1 within endogenous lysosomal membranes in live cells, alongside kinetic analyses, will undoubtedly enrich the current model and may catalyze novel therapeutic strategies aimed at fine-tuning mTOR activity with exquisite spatiotemporal control.
Subject of Research: Structural Basis and Mechanism of mTORC1 Activation on the Lysosomal Membrane
Article Title: Structural basis for mTORC1 activation on the lysosomal membrane
Article References:
Cui, Z., Esposito, A., Napolitano, G. et al. Structural basis for mTORC1 activation on the lysosomal membrane. Nature (2025). https://doi.org/10.1038/s41586-025-09545-3
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