Regulation and Function of Mitochondria–Lysosome Membrane Contact Sites in Cellular Homeostasis

Although endolysosomal trafficking is well defined, how it is regulated and coordinates with cellular metabolism is unclear. To identify genes governing endolysosomal dynamics, we conducted a global fluorescence-based screen to reveal endomembrane effector genes. Screening implicated Phox (PX) domain–containing protein Mdm1 in endomembrane dynamics. Surprisingly, we demonstrate that Mdm1 is a novel interorganelle tethering protein that localizes to endoplasmic reticulum (ER)–vacuole/lysosome membrane contact sites (MCSs). We show that Mdm1 is ER anchored and contacts the vacuole surface in trans via its lipid-binding PX domain. Strikingly, overexpression of Mdm1 induced ER–vacuole hypertethering, underscoring its role as an interorganelle tether. We also show that Mdm1 and its paralogue Ydr179w-a (named Nvj3 in this study) localize to ER–vacuole MCSs independently of established tether Nvj1. Finally, we find that Mdm1 truncations analogous to neurological disease–associated SNX14 alleles fail to tether the ER and vacuole and perturb sphingolipid metabolism. Our work suggests that human Mdm1 homologues may play previously unappreciated roles in interorganelle communication and lipid metabolism.

Download Full-text

The formation and function of ER-endosome membrane contact sites

Biochimica et Biophysica Acta (BBA) - Molecular and Cell Biology of Lipids ◽

10.1016/j.bbalip.2016.01.020 ◽

2016 ◽

Vol 1861 (8) ◽

pp. 874-879 ◽

Cited By ~ 39

Author(s):

Emily R. Eden

Keyword(s):

Membrane Contact Sites ◽

Contact Sites ◽

Membrane Contact ◽

And Function

Download Full-text

Organization and function of membrane contact sites

Biochimica et Biophysica Acta (BBA) - Molecular Cell Research ◽

10.1016/j.bbamcr.2013.01.028 ◽

2013 ◽

Vol 1833 (11) ◽

pp. 2526-2541 ◽

Cited By ~ 266

Author(s):

Sebastian C.J. Helle ◽

Gil Kanfer ◽

Katja Kolar ◽

Alexander Lang ◽

Agnès H. Michel ◽

...

Keyword(s):

Membrane Contact Sites ◽

Contact Sites ◽

Membrane Contact ◽

And Function

Download Full-text

Stitching Organelles: Organization and Function of Specialized Membrane Contact Sites in Plants

Trends in Cell Biology ◽

10.1016/j.tcb.2016.05.007 ◽

2016 ◽

Vol 26 (9) ◽

pp. 705-717 ◽

Cited By ~ 62

Author(s):

Jessica Pérez-Sancho ◽

Jens Tilsner ◽

A. Lacey Samuels ◽

Miguel A. Botella ◽

Emmanuelle M. Bayer ◽

...

Keyword(s):

Membrane Contact Sites ◽

Contact Sites ◽

Membrane Contact ◽

And Function

Download Full-text

SAC1 Degrades its Lipid Substrate PtdIns4P in the Endoplasmic Reticulum to Maintain a Steep Chemical Gradient with Donor Membranes

10.1101/258087 ◽

2018 ◽

Author(s):

James P. Zewe ◽

Rachel C. Wills ◽

Sahana Sangappa ◽

Brady D. Goulden ◽

Gerald R. V. Hammond

Keyword(s):

Endoplasmic Reticulum ◽

Lipid Homeostasis ◽

Chemical Gradient ◽

Vesicular Traffic ◽

Membrane Contact Sites ◽

Contact Sites ◽

Catalytic Domains ◽

In Trans ◽

Membrane Contact ◽

And Function

AbstractGradients of PtdIns4P between organelle membranes and the endoplasmic reticulum (ER) are thought to drive counter-transport of other lipids via non-vesicular traffic. This novel pathway requires the SAC1 phosphatase to degrade PtdIns4P in a “cis” configuration at the ER to maintain the gradient. However, SAC1 has also been proposed to act in “trans” at membrane contact sites, which could oppose lipid traffic. It is therefore crucial to determine which mode SAC1 uses in living cells. We report that acute inhibition of SAC1 causes accumulation of PtdIns4P in the ER, that SAC1 does not enrich at membrane contact sites, and that SAC1 has little activity in “trans”, unless a linker is added between its ER-anchored and catalytic domains. The data reveal an obligate “cis” activity of SAC1, supporting its role in non-vesicular lipid traffic and implicating lipid traffic more broadly in inositol lipid homeostasis and function.

Download Full-text

CRISPR screens for lipid regulators reveal a role for ER-bound SNX13 in lysosomal cholesterol export

The Journal of Cell Biology ◽

10.1083/jcb.202105060 ◽

2021 ◽

Vol 221 (2) ◽

Author(s):

Albert Lu ◽

Frank Hsieh ◽

Bikal R. Sharma ◽

Sydney R. Vaughn ◽

Carlos Enrich ◽

...

Keyword(s):

Lipid Droplet ◽

Negative Regulator ◽

Gene Products ◽

Membrane Contact Sites ◽

Contact Sites ◽

Genome Wide ◽

Lipid Regulators ◽

Membrane Contact ◽

Lysosome Membrane ◽

Insight Into

We report here two genome-wide CRISPR screens performed to identify genes that, when knocked out, alter levels of lysosomal cholesterol or bis(monoacylglycero)phosphate. In addition, these screens were also performed under conditions of NPC1 inhibition to identify modifiers of NPC1 function in lysosomal cholesterol export. The screens confirm tight coregulation of cholesterol and bis(monoacylglycero)phosphate in cells and reveal an unexpected role for the ER-localized SNX13 protein as a negative regulator of lysosomal cholesterol export and contributor to ER–lysosome membrane contact sites. In the absence of NPC1 function, SNX13 knockdown redistributes lysosomal cholesterol and is accompanied by triacylglycerol-rich lipid droplet accumulation and increased lysosomal bis(monoacylglycero)phosphate. These experiments provide unexpected insight into the regulation of lysosomal lipids and modification of these processes by novel gene products.

Download Full-text

IP3 Receptor Properties and Function at Membrane Contact Sites

Advances in Experimental Medicine and Biology - Membrane Dynamics and Calcium Signaling ◽

10.1007/978-3-319-55858-5_7 ◽

2017 ◽

pp. 149-178 ◽

Cited By ~ 10

Author(s):

Gemma Roest ◽

Rita M. La Rovere ◽

Geert Bultynck ◽

Jan B. Parys

Keyword(s):

Ip3 Receptor ◽

Membrane Contact Sites ◽

Contact Sites ◽

Membrane Contact ◽

And Function

Download Full-text

GRAM domain proteins specialize functionally distinct ER-PM contact sites in human cells

eLife ◽

10.7554/elife.31019 ◽

2018 ◽

Vol 7 ◽

Cited By ~ 45

Author(s):

Marina Besprozvannaya ◽

Eamonn Dickson ◽

Hao Li ◽

Kenneth S Ginburg ◽

Donald M Bers ◽

...

Keyword(s):

Human Cells ◽

Lipid Homeostasis ◽

Dependent Manner ◽

Membrane Contact Sites ◽

Contact Sites ◽

Membrane Contact ◽

And Function ◽

Pleiotropic Functions ◽

Human Family

Endoplasmic reticulum (ER) membrane contact sites (MCSs) are crucial regulatory hubs in cells, playing roles in signaling, organelle dynamics, and ion and lipid homeostasis. Previous work demonstrated that the highly conserved yeast Ltc/Lam sterol transporters localize and function at ER MCSs. Our analysis of the human family members, GRAMD1a and GRAMD2a, demonstrates that they are ER-PM MCS proteins, which mark separate regions of the plasma membrane (PM) and perform distinct functions in vivo. GRAMD2a, but not GRAMD1a, co-localizes with the E-Syt2/3 tethers at ER-PM contacts in a PIP lipid-dependent manner and pre-marks the subset of PI(4,5)P2-enriched ER-PM MCSs utilized for STIM1 recruitment. Data from an analysis of cells lacking GRAMD2a suggest that it is an organizer of ER-PM MCSs with pleiotropic functions including calcium homeostasis. Thus, our data demonstrate the existence of multiple ER-PM domains in human cells that are functionally specialized by GRAM-domain containing proteins.

Download Full-text

Rod-shaped tricalbins contribute to PM asymmetry at curved ER-PM contact sites

10.1101/579128 ◽

2019 ◽

Cited By ~ 2

Author(s):

Patrick C. Hoffmann ◽

Tanmay A. M. Bharat ◽

Michael R. Wozny ◽

Elizabeth A. Miller ◽

Wanda Kukulski

Keyword(s):

Protein Composition ◽

Lipid Transfer ◽

Cellular Lipid ◽

Membrane Contact Sites ◽

Contact Sites ◽

Membrane Morphology ◽

Structural Framework ◽

Structural Functions ◽

Membrane Contact ◽

And Function

AbstractLipid flow between cellular organelles occurs via membrane contact sites that form dynamic conduits. Extended-synaptotagmins, known as tricalbins in yeast, mediate lipid transfer between the endoplasmic reticulum (ER) and plasma membrane (PM). How these proteins regulate the membrane architecture to transport lipids across the aqueous space between bilayers remains unknown. Using correlative microscopy, electron cryo-tomography and high-throughput genetics we address this interplay of architecture and function in budding yeast. We find that ER-PM contacts are diverse in protein composition and membrane morphology, not in intermembrane distance. In situ cryo-EM of tricalbins reveals their molecular organisation that suggests an unexpected structural framework for lipid transfer. Genetic analysis identifies functional redundancies, both for tricalbin domains and cellular lipid routes, and points to tricalbin function in maintenance of PM asymmetry. These results uncover a modularity of molecular and structural functions of tricalbins, and of their roles within the network of cellular lipid fluxes.

Download Full-text