Israel Juarez Contreras
Postdoctoral Scholar, Biochemistry
Bio
I am a postdoctoral scholar in the lab of Rajat Rohatgi at Stanford University, where I study how membrane organization controls sterol accessibility and signaling. I earned my Ph.D. at UC San Diego with Itay Budin, where I uncovered how sterol structure and sphingolipid composition regulate membrane phase behavior in yeast and reconstituted systems. My current work translates these biophysical principles into disease-relevant contexts, with a focus on lysosomal lipid organization and sterol trafficking defects, including those associated with NPC1. Ultimately, I aim to establish an independent research program that defines how cells interpret membrane physical properties and how their dysregulation contributes to human disease.
Professional Education
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PhD, University of California, San Diego, Biochemistry and Molecular Biophysics
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MS, San Jose State University, Chemical Engineering
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BS, University of California, Merced, Bioengineering
Contact
https://orcid.org/0009-0000-8553-2791All Publications
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Coupling between sterol and sphingolipid structure in ordered membrane domains.
bioRxiv : the preprint server for biology
2026
Abstract
A hallmark of eukaryotic membranes is the pairing of lineage-specific sterols with characteristic sphingolipid species. Mammalian cell membranes are enriched in both cholesterol and long-chain sphingolipids like sphingomyelin, whereas fungi synthesize ergosterol and very long-chain sphingolipids with sugar-containing head groups. It has been proposed that these two lipid classes co-evolved to support membrane structure and organization. Here we investigated how sterol structure and sphingolipid chain length together control membrane order and phase behavior. In the yeast Saccharomyces cerevisiae , loss of very long-chain C26 sphingolipids disrupted formation of liquid-ordered ( L o ) domains in the vacuole membrane. Similarly, substitution of ergosterol synthesis for that of cholesterol also prevented vacuole L o domains. To determine a possible physical basis of these effects, we investigated synthetic membranes of defined composition containing either ergosterol or cholesterol and sphingomyelin with different chain lengths. In membranes containing egg sphingomyelin with C16 chains, ergosterol only sparsely supported L o domains, in contrast to cholesterol. Membranes containing sphingomyelin with C26 chains displayed a different pattern. Cholesterol mixtures were largely homogeneous across most compositions, with only a limited region that supported fluid domains. Ergosterol mixtures exhibited a distinct compositional window that supported fluid domains positioned between regimes of uniform membranes and gel phases. This window corresponded to stoichiometric changes in the vacuole as it phase-separates during nutritional restriction. Measurements of membrane order showed that cholesterol strongly increased membrane packing compared to ergosterol in membranes containing egg sphingomyelin, whereas this difference was lost in membranes containing C26 sphingomyelin. The results suggest that sphingolipid chain length can tune sterol interactions needed for membrane organization.Membrane phase separation into coexisting ordered and disordered fluid domains has largely been investigated using characteristic mammalian lipid components, cholesterol and long-chain saturated lipids like sphingomyelin. Under nutrient limitation, vacuole membranes in yeast organize into micron-scale domains that are important for their physiology. Compared to mammals, yeast synthesize an alternative sterol, ergosterol, and sphingolipids with very long-chains. We show that vacuole membrane domains are sensitive to both these features, which also show preferential interactions in liposomes that support membrane ordering and phase properties. In lipid mixtures containing very long-chain sphingomyelins, stoichiometric regimes that support phase separation of fluid domains are similar to those of the vacuole lipidome under nutrient limitation. This finding supports a model in which sterols and sphingolipids co-evolved to support membrane structure.
View details for DOI 10.64898/2026.04.01.715929
View details for PubMedID 41959507
View details for PubMedCentralID PMC13060081
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Transport of sphingolipids by yeast Npc2 supports phase separation of the vacuole membrane.
The Journal of biological chemistry
2026: 111370
Abstract
The yeast vacuole membrane forms ordered microdomains that facilitate micro-lipophagy under nutrient limitation. We previously found that this process involves the intracellular sorting of sphingolipids to the vacuole. While multiple vacuole protein pathways have been identified, corresponding mechanisms for lipid sorting remain undefined. Here we use a range of approaches to identify how endocytic sorting and intraluminal transport of sphingolipids contribute to the formation of vacuole domains. To visualize sphingolipid trafficking, we employed the ceramide analogue BODIPY C12-ceramide (BODIPY-Cer), which is internalized by cells and stains the vacuole. We observed that cells lacking Vps29 and Vps30, proteins involved in endosomal sorting, show altered vacuole domains and accumulate BODIPY-Cer at sites proximal to the plasma membrane. Subsequent incorporation of endocytic-derived ceramide into the vacuole is dependent on the Niemann-Pick Type C 2 protein (Npc2). Loss of Npc2 reduces domain formation and causes BODIPY-Cer to accumulate within the vacuole lumen. Both intra-vacuole trafficking of BODIPY-Cer and membrane phase separation were not dependent on Npc2's canonical receptor, Ncr1. Lipidomics of isolated vacuoles confirmed that Npc2 independently mediates sphingolipid sorting under micro-lipophagy conditions. In liposome assays, yeast Npc2 - but not its human homologue - robustly transports an analogue of inositol phosphorylceramide, a complex sphingolipid that is enriched in phase-separated vacuoles. We propose that the enlarged binding cavity of yeast Npc2 is specialized for the incorporation of sphingolipids into the vacuole membrane to support its phase separation.
View details for DOI 10.1016/j.jbc.2026.111370
View details for PubMedID 41850403
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Structural dissection of ergosterol metabolism reveals a pathway optimized for membrane phase separation.
Science advances
2025; 11 (17): eadu7190
Abstract
Sterols are among the most abundant lipids in eukaryotic cells yet are synthesized through notoriously long metabolic pathways. It has been proposed that the molecular evolution of such pathways must have required each step to increase the capacity of its product to condense and order phospholipids. Here, we carry out a systematic analysis of the ergosterol pathway that leverages the yeast vacuole's capacity to phase separate into ordered membrane domains. In the post-synthetic steps specific to ergosterol biosynthesis, we find that successive modifications act to oscillate ordering capacity, settling on a level that supports phase separation while retaining fluidity of the resulting domains. Simulations carried out with each intermediate showed how conformers in the sterol's alkyl tail are capable of modulating long-range ordering of phospholipids, which could underlie changes in phase behavior. Our results indicate that the complexity of sterol metabolism could have resulted from the need to balance lipid interactions required for membrane organization.
View details for DOI 10.1126/sciadv.adu7190
View details for PubMedID 40267201
View details for PubMedCentralID PMC12017304
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Using the yeast vacuole as a system to test the lipidic drivers of membrane heterogeneity in living cells.
Methods in enzymology
2024; 700: 77-104
Abstract
The biophysical drivers of membrane lateral heterogeneity, often termed lipid rafts, have been largely explored using synthetic liposomes or mammalian plasma membrane-derived giant vesicles. Yeast vacuoles, an organelle comparable to mammalian lysosomes, is the only in vivo system that shows stable micrometer scale phase separation in unperturbed cells. The ease of manipulating lipid metabolism in yeast makes this a powerful system for identifying lipids involved in the onset of vacuole membrane heterogeneity. Vacuole domains are induced by stationary stage growth and nutritional starvation, during which they serve as a docking and internalization site for lipid droplet energy stores. Here we describe methods for characterizing vacuole phase separation, its physiological function, and its lipidic drivers. First, we detail methodologies for robustly inducing vacuole domain formation and quantitatively characterizing during live cell imaging experiments. Second, we detail a new protocol for biochemical isolation of stationary stage vacuoles, which allows for lipidomic dissection of membrane phase separation. Third, we describe biochemical techniques for analyzing lipid droplet internalization in vacuole domains. When combined with genetic or chemical perturbations to lipid metabolism, these methods allow for systematic dissection of lipid composition in the structure and function of ordered membrane domains in living cells.
View details for DOI 10.1016/bs.mie.2024.02.015
View details for PubMedID 38971613
View details for PubMedCentralID PMC12083250