bims-raghud 2026-04-05 papers

Issue of 2026–04–05
four papers selected by
Irene Sambri, TIGEM

Trends Biochem Sci. 2026 Mar 30. pii: S0968-0004(26)00037-X. [Epub ahead of print]

Molecular and structural mechanisms of nutrient sensing in the mTORC1 pathway.

Primary nutrient sensors directly bind metabolites and undergo conformational changes that signal through core pathways to coordinate metabolic and cellular outcomes. Sensing of amino acids, lipids, sugars, and nucleotides is critical for the master growth regulatory Ser/Thr kinase, mechanistic target of rapamycin complex 1 (mTORC1), to promote growth and proliferation. Systematic proteomic and bioinformatic studies have accelerated the discovery of primary nutrient sensors upstream of mTORC1, whereas structural biology has shed light on how binding to their cognate metabolites triggers mTORC1-dependent signaling responses. This review focuses on recently reported amino acid and lipid sensors upstream of mTORC1 and highlights structural and functional features of these sensors that illuminate fundamental principles of nutrient detection and signal transduction.

Keywords: CASTOR1; LYCHOS; amino acid sensors; cholesterol sensors; metabolites; primary nutrient sensor

DOI: https://doi.org/10.1016/j.tibs.2026.02.009

Nat Commun. 2026 Apr 01.

TFEB degradation is regulated by an IKK/β-TrCP2 phosphorylation-ubiquitination cascade.

Yan Xiong, Jaiprakash Sharma, Meggie N Young, Wen Xiong, Ali Jazayeri, Karl F Poncha, Ma Xenia G Ilagan, Qing Wang, Bei Gao, Hui Zheng, Nicolas L Young, Marco Sardiello.

Transcription factor EB (TFEB) is a master regulator of lysosomal biogenesis and cellular clearance pathways. TFEB activity is tightly controlled by multiple post-translational mechanisms, but the exact molecular mechanism controlling its stability has remained elusive. Here, we identify the IκB kinase (IKK) complex as a key regulator of TFEB protein stability through a phosphorylation-ubiquitination cascade. A high-content kinase inhibitor screen reveals that IKK inhibition increases TFEB protein levels, and genetic ablation of IKK components increases TFEB stability, upregulates lysosomal genes, and enhances lysosomal biogenesis and degradative capacity. Mechanistically, we show that IKK phosphorylates TFEB on a cluster of serine residues (423SPFPSLS429), generating a phosphodegron recognized by the E3 ligase β-TrCP2, which in turn targets TFEB for proteasomal degradation via ubiquitination of adjacent lysine residues (K430 and K431). Mutation of either the phosphosites or the ubiquitination sites stabilizes TFEB without impairing its ability to translocate to the nucleus, activate target gene expression, or promote tau clearance in a cell model of tauopathy. These findings establish IKK-β-TrCP2 as a core regulatory axis controlling TFEB protein turnover and levels and reveal a mechanistically distinct layer of TFEB regulation that may be leveraged to enhance lysosomal function in disease contexts.

DOI: https://doi.org/10.1038/s41467-026-71001-1

Autophagy. 2026 Mar 30. 1-3

Dual pathways of TFEB activation under lysosomal stress: ATG conjugation-dependent and -independent modes.

Takayuki Shima, Shuhei Nakamura.

TFEB (transcription factor EB) regulates the expression of autophagy and lysosomal genes, is activated by various cellular stresses, and plays a key role in maintaining cellular homeostasis. Recent work demonstrates that TFEB is activated during lysosomal damage through two distinct mechanisms: ATG conjugation-dependent and -independent. TFEB activation proceeds sequentially through two modes. In the early ATG conjugation-independent mode (Mode I), APEX1 interacts with TFEB in the nucleus, maintaining its transcriptional activity and protein stability. In the later ATG conjugation-dependent mode (Mode II), CCT7 and TRIP6 translocate to lysosomes and interact with TFEB, modulating its phosphorylation and nuclear localization. Moreover, TFEB regulation induced by other cellular stresses-such as oxidative stress, proteasome inhibition, mitochondrial damage, and DNA damage-also involves either Mode I or Mode II. Our findings provide new insights into a unified understanding of TFEB regulation under diverse cellular stress conditions.

Keywords: Damage; TFEB; lysosome; mitochondria; organelle

DOI: https://doi.org/10.1080/15548627.2026.2642336

J Clin Invest. 2026 Apr 01. pii: e199845. [Epub ahead of print]136(7):

Lysosomal homeostasis at the crossroads of neurodegeneration.

Stefano De Tito, Sharon A Tooze.

Lysosomes function as metabolic control centers that integrate degradation, nutrient sensing, and stress signaling. In neurons, which must maintain proteostasis and energetic balance throughout life, lysosomal homeostasis determines cellular resilience. Emerging evidence identifies lysosomal injury and defective repair as common denominators across neurodegenerative diseases. Damage to the lysosomal membrane caused by oxidative stress, lipid imbalance, or genetic mutations triggers a hierarchical quality control cascade. Early lesions recruit the endosomal sorting complex required for transport (ESCRT) machinery for mechanical resealing, while larger ruptures activate lipid-centered recovery modules. When repair fails, lysophagy eliminates irreparable organelles and a TFEB-dependent transcriptional program regenerates the lysosomal pool. These tightly coupled responses safeguard neurons from catastrophic proteostatic collapse. Their impairment, through mutations in lysosomal proteins, or through aging, produces the lysosomal fragility that underlies Alzheimer disease, Parkinson disease, amyotrophic lateral sclerosis/frontotemporal dementia, and Huntington disease. Crosstalk between lysosomes, mitochondria, and ER integrates local damage with systemic metabolic adaptation, while dysregulated lysosomal exocytosis and inflammation propagate pathology. Understanding how ESCRT complexes, lipid transport, and transcriptional renewal cooperate to preserve lysosomal integrity reveals unifying principles of neurodegeneration and defines molecular targets for intervention. Restoring lysosomal repair and renewal offers a rational path toward preventing neuronal loss.

DOI: https://doi.org/10.1172/JCI199845