The structure of the human LACTB filament reveals the mechanisms of assembly and membrane binding

Abstract

Mitochondria are complex organelles that play a central role in metabolism. Dynamic membrane-associated processes regulate mitochondrial morphology and biogenesis in response to cellular demand. In tumor cells, metabolic reprogramming requires active mitochondrial metabolism for providing key metabolites and building blocks for tumor growth and rapid proliferation. To counter this, the mitochondrial serine beta-lactamase-like protein (LACTB) alters mitochondrial lipid metabolism and potently inhibits the proliferation of a variety of tumor cells. Mammalian LACTB is localized in the mitochondrial intermembrane space, where it assembles into filaments to regulate mitochondrial membrane organization and the efficiency of essential metabolic processes. However, the structural basis of LACTB polymerization and regulation remains incompletely understood. Here, we describe how human LACTB self-assembles into micron-scale filaments that increase their catalytic activity. The electron cryo-microscopy (cryoEM) structure defines the mechanism of assembly and reveals how highly ordered filament bundles stabilize the active state of the enzyme. We identify and characterize residues that are located at the filament-forming interface, and further show that mutations that disrupt filamentation reduce enzyme activity. Furthermore, our results provide evidence that LACTB filaments can bind lipid membranes. These data reveal the detailed molecular organization and polymerization-based regulation of human LACTB and provide new insights into the mechanism of mitochondrial membrane organization that modulates tumor suppression.

LACTB exerts tumor suppressor properties in epithelial ovarian cancer through regulation of Slug

“…We confirmed the RNA-seq results by RT–PCR in two different cell lines (PEO4 and EFO27), which showed a common strong down-regulation of different EMT-related factors (SLUG, CD44, TGM2, WNT5A, INHBA, LAMA3, GLIPR1, SERPINE2) upon LACTB induction for 3 d ( Fig 5E ). LACTB was previously shown to be associated with lipids and/or lipid metabolism ( 27 Preprint , 28 , 29 , 30 , 31 , 32 ). This was supported by our own results where we showed that in breast cancer model, LACTB exerts its tumor suppressive effect through down-regulation of mitochondrial lipid–synthesizing enzyme phosphatidyl serine decarboxylase (PISD) which is partially responsible for the resulting breast cancer cell differentiation ( 18 ).…”

“…The connection of LACTB and lipid metabolism was further supported by studies in hepatocellular carcinoma where it was shown that LACTB expression influences the expression and activity of important enzymes involved in lipid metabolism (such as carnitine palmitoyltransferase 1A, acyl-coenzyme A dehydrogenase) (28). Furthermore, recent study by Bennett et al (2022) provides evidence that LACTB filaments can bind liposomes that closely mimic the lipid composition of mitochondrial inner membranes (28). We hypothesize that the interaction of LACTB polymers with inner mitochondrial membranes might modulate the presence and/or activity of proteins/enzymes embedded in this membrane (such as PISD).…”