Conserved SMP domains of the ERMES complex bind phospholipids and mediate tether assembly

Abstract

Membrane contact sites (MCS) between organelles are proposed as nexuses for the exchange of lipids, small molecules, and other signals crucial to cellular function and homeostasis. Various protein complexes, such as the endoplasmic reticulum-mitochondrial encounter structure (ERMES), function as dynamic molecular tethers between organelles. Here, we report the reconstitution and characterization of subcomplexes formed by the cytoplasm-exposed synaptotagmin-like mitochondrial lipid-binding protein (SMP) domains present in three of the five ERMES subunits-the soluble protein Mdm12, the endoplasmic reticulum (ER)-resident membrane protein Mmm1, and the mitochondrial membrane protein Mdm34. SMP domains are conserved lipid-binding domains found exclusively in proteins at MCS. We show that the SMP domains of Mdm12 and Mmm1 associate into a tight heterotetramer with equimolecular stoichiometry. Our 17-Å-resolution EM structure of the complex reveals an elongated crescent-shaped particle in which two Mdm12 subunits occupy symmetric but distal positions at the opposite ends of a central ER-anchored Mmm1 homodimer. Rigid body fitting of homology models of these SMP domains in the density maps reveals a distinctive extended tubular structure likely traversed by a hydrophobic tunnel. Furthermore, these two SMP domains bind phospholipids and display a strong preference for phosphatidylcholines, a class of phospholipids whose exchange between the ER and mitochondria is essential. Last, we show that the three SMP-containing ERMES subunits form a ternary complex in which Mdm12 bridges Mmm1 to Mdm34. Our findings highlight roles for SMP domains in ERMES assembly and phospholipid binding and suggest a structure-based mechanism for the facilitated transport of phospholipids between organelles.interorganelle tether | phospholipid exchange | membrane contact sites | membrane protein complex | electron microscopy

Lipid synthesis and membrane contact sites: a crossroads for cellular physiology

“…The SMP domains of Mdm12 and Mmm1 both exhibit PL binding activity with preference for PC (89). In addition, a ternary complex was described in which cytosolic Mdm12 bridges the integral ER Mmm1 to the mitochondrial Mdm34 (89). The structural and biochemical characterization of the three SMP domain-containing components of the ERMES complex provides evidence of the involvement of these proteins in the mechanical tethering of both compartments and supports their plausible role in mediating lipid transfer.…”

“…Structural analyses of the SMP domains of Mdm12 and Mmm1 revealed that they assemble into a heterotetramer forming an elongated crescent shape in which Mmm1 forms a central homodimer and a monomer of Mdm12 binds to each end of this dimer. A hydrophobic channel traverses this elongated heterotetramer (89). The SMP domains of Mdm12 and Mmm1 both exhibit PL binding activity with preference for PC (89).…”

“…A hydrophobic channel traverses this elongated heterotetramer (89). The SMP domains of Mdm12 and Mmm1 both exhibit PL binding activity with preference for PC (89). In addition, a ternary complex was described in which cytosolic Mdm12 bridges the integral ER Mmm1 to the mitochondrial Mdm34 (89).…”

Extended synaptotagmins are Ca 2+ -dependent lipid transfer proteins at membrane contact sites

“…S1) (15)(16)(17)(18)(19). The SMP domain exhibits a β-barrel structure, which is common to the tubular lipid binding superfamily (20), and harbors lipids in its hydrophobic cavity (21)(22)(23). C2 domains are autonomously folded structures that bind to lipids and Ca 2+ (12,24,25).…”

The ubiquitous and ancient ER membrane protein complex (EMC): tether or not?

“…The ER-mitochondria encounter structure (ERMES), also involved in ER-mitochondria tethering, is a multifunctional protein complex implicated in both lipid transfer and mitochondrial outer membrane protein assembly ( AhYoung et al , 2015; Kornmann et al , 2009; Meisinger et al , 2006, Meisinger et al , 2007; Wideman et al , 2013; Wideman et al , 2010). However, ERMES as an ER-mitochondria tether is limited to a subset of eukaryote taxa ( Wideman et al , 2013), suggesting that a universal ER-mitochondria tethering complex might exist.…”