The research report should be a detailed narrative explaining the function, biological processes, and localization of the gene product. Citations should be given for all claims.
You should prioritize authoritative reviews and primary scientific literature when conducting research. You can supplement
this with annotations you find in gene/protein databases, but these can be outdated or inaccurate.
We are specifically interested in the primary function of the gene - for enzymes, what reaction is catalyzed, and what is the substrate specificity? For transporters, what is the substrate? For structural proteins or adapters, what is the broader structural role? For signaling molecules, what is the role in the pathway.
We are interested in where in or outside the cell the gene product carries out its function.
We are also interested in the signaling or biochemical pathways in which the gene functions. We are less interested in broad pleiotropic effects, except where these elucidate the precise role.
Include evidence where possible. We are interested in both experimental evidence as well as inference from structure, evolution, or bioinformatic analysis. Precise studies should be prioritized over high-throughput, where available.
The gene symbol "LPX2" is ambiguous, and literature directly characterizing the protein product of YKL050C is extremely limited. The UniProt entry P35736 describes YKL050C as an "Uncharacterized protein" that belongs to the EIS1 protein family and contains the Eisosome1 domain (Pfam PF12757; InterPro IPR024527). It is critical to note that YKL050C is distinct from the well-characterized eisosome protein EIS1, which is encoded by the ORF YMR031C. EIS1/YMR031C has been extensively studied as a component of eisosomes involved in eisosome assembly and stability (lanze2020plasmamembranemcceisosome pages 5-6, lanze2020plasmamembranemcceisosome pages 6-7). YKL050C is not listed among the known eisosome-associated proteins in comprehensive reviews of MCC/eisosome biology (lanze2020plasmamembranemcceisosome pages 5-6, lanze2020plasmamembranemcceisosome pages 6-7). The function of the YKL050C/LPX2 gene product can therefore only be inferred from its domain and family annotations.
The YKL050C locus (alternative ORF names YKL263, YKL301) encodes a protein of unknown function in Saccharomyces cerevisiae (strain ATCC 204508 / S288c). According to its UniProt annotation (P35736), the protein belongs to the EIS1 family and contains the Eisosome1 domain (Pfam PF12757). This domain family is named after Eis1 (YMR031C), which was first identified as a new eisosome component through a systematic plasma membrane E-MAP (epistatic miniarray profile) study (aguilar2010aplasmamembraneemap pages 8-10, aguilar2010aplasmamembraneemap pages 4-8). Notably, the promoter of YKL050C has been reported to drive spore-autonomous gene expression, and it was used in a reporter construct system for tracking meiotic chromosome segregation in yeast hybrids (rogers2018sporeautonomousfluorescentprotein pages 3-5). This suggests that YKL050C may have a sporulation-specific or meiosis-related expression pattern, although its functional role during sporulation has not been characterized.
Because YKL050C contains the Eisosome1 domain, its function is most plausibly inferred from what is known about the EIS1 family protein Eis1/YMR031C and the broader biology of eisosomes. The Eisosome1 domain defines a family of proteins associated with eisosome structure and assembly.
Eis1 (YMR031C) was identified as a new eisosome component in a plasma membrane E-MAP that revealed links between the eisosome, sphingolipid metabolism, and endosomal trafficking (aguilar2010aplasmamembraneemap pages 8-10, aguilar2010aplasmamembraneemap pages 4-8). In the comprehensive catalog of MCC/eisosome proteins compiled by Lanze et al. (2020), Eis1 is listed as a peripheral eisosome protein with a function in "eisosome assembly and stability," with an estimated 5,570–12,142 copies per cell (lanze2020plasmamembranemcceisosome pages 5-6, lanze2020plasmamembranemcceisosome pages 6-7). Eis1 promotes eisosome assembly, possibly through a direct effect, since it localizes to these domains (lanze2020plasmamembranemcceisosome pages 7-8). Its role appears to be related to maintaining the integrity and proper formation of eisosome structures at the plasma membrane.
Eisosomes are large protein complexes that underlie specialized plasma membrane domains termed the MCC (Membrane Compartment of Can1) in S. cerevisiae (lanze2020plasmamembranemcceisosome pages 1-2). These domains correspond to stable furrow-like invaginations of the plasma membrane, approximately 200–300 nm long, 50 nm wide, and 50 nm deep (lanze2020plasmamembranemcceisosome pages 1-2). The core structural components of eisosomes are the BAR-domain proteins Pil1 and Lsp1, present at approximately 100,000 copies each per cell, which self-assemble into filaments that bind PI(4,5)P2-containing membranes and sculpt the membrane furrows (karotki2012structureandarchitecture pages 101-104, lanze2020plasmamembranemcceisosome pages 7-8). Crystal structure analysis of Lsp1 revealed that Pil1 and Lsp1 contain banana-shaped BAR domains known to promote membrane curvature (karotki2012structureandarchitecture pages 86-86, lanze2020plasmamembranemcceisosome pages 7-8). The "half-pipe" model proposes that aligned filaments of Pil1 and Lsp1 create the characteristic plasma membrane invaginations (lanze2020plasmamembranemcceisosome pages 7-8).
A landmark cryo-EM study by Kefauver et al. (2024) solved the near-native structure of eisosomes as helical tubules composed of Pil1/Lsp1 lattices bound to plasma membrane lipids (kefauver2024cryoemarchitectureof pages 1-2, kefauver2024cryoemarchitectureof pages 2-3). This work revealed that individual PI(4,5)P2, phosphatidylserine (PS), and sterol molecules are specifically sequestered beneath the Pil1/Lsp1 coat (kefauver2024cryoemarchitectureof pages 1-2, kefauver2024cryoemarchitectureof pages 5-5). Key residues in the Pil1 lipid-binding pocket include R126, K130, and R133 for PI(4,5)P2 interaction, K66 and R70 for PS binding, and hydrophobic residues F33, Y40, F42, and F50 for sterol coordination (kefauver2024cryoemarchitectureof pages 5-6, kefauver2024cryoemarchitectureof pages 5-5). Three-dimensional variability analysis revealed dynamic stretching of the Pil1/Lsp1 lattice that affects lipid sequestration, providing the molecular basis for mechanosensing (kefauver2024cryoemarchitectureof pages 1-2, kefauver2024cryoemarchitectureof pages 5-6).
The protein product of YKL050C has not been definitively localized in published studies available in the literature surveyed. However, based on domain homology:
While YKL050C's specific pathway involvement is unknown, the EIS1 family context places it within the eisosome-centered signaling network, which includes several critical pathways:
Eisosomes serve as mechanosensitive membrane domains that sense changes in membrane tension. Under conditions of increased membrane tension (e.g., hypoosmotic shock, sphingolipid depletion), the eisosome furrows flatten and release sequestered proteins such as Slm1 and Slm2 (lanze2020plasmamembranemcceisosome pages 11-12, lanze2020plasmamembranemcceisosome pages 12-13). Released Slm1/2 proteins relocate to the TORC2-containing membrane compartment (MCT), where they promote TORC2 activation (athanasopoulos2019fungalplasmamembrane pages 21-22, athanasopoulos2019fungalplasmamembrane pages 8-9). TORC2 then phosphorylates the kinase Ypk1, which in turn phosphorylates and inactivates the Orm1/2 repressors of sphingolipid biosynthesis, thereby stimulating de novo sphingolipid production and restoring membrane homeostasis (lanze2020plasmamembranemcceisosome pages 11-12, lanze2020plasmamembranemcceisosome pages 12-13, lanze2020plasmamembranemcceisosome pages 9-11, athanasopoulos2019fungalplasmamembrane pages 21-22).
The Ser/Thr kinases Pkh1 and Pkh2 localize to eisosomes and phosphorylate Pil1 and Lsp1 on multiple sites, regulating eisosome assembly and disassembly (lanze2020plasmamembranemcceisosome pages 8-9, lanze2020plasmamembranemcceisosome pages 6-7). Full activation of Ypk1 requires dual phosphorylation by both TORC2 and Pkh1/2 (athanasopoulos2019fungalplasmamembrane pages 21-22). The transmembrane protein Nce102 acts as a sphingolipid sensor: under sphingolipid-replete conditions, Nce102 resides in the MCC and inhibits Pkh1/2, promoting eisosome stability; upon sphingolipid depletion, Nce102 relocates, de-repressing Pkh1/2 and triggering eisosome remodeling (frohlich2010analysisofsphingolipidsignaling pages 35-38, athanasopoulos2019fungalplasmamembrane pages 8-9).
During the post-diauxic shift (glucose depletion), the 5'–3' exoribonuclease Xrn1 is sequestered at eisosomes, separating it from its mRNA substrates and thereby protecting mRNAs from degradation (courtin2023xrn1biochemicallyassociates pages 1-5, athanasopoulos2019fungalplasmamembrane pages 17-18, lanze2020plasmamembranemcceisosome pages 15-16). This sequestration is reversible upon glucose restoration and represents a mechanism for preserving mRNAs during nutrient starvation, enabling faster recovery when conditions improve (athanasopoulos2019fungalplasmamembrane pages 17-18).
MCC/eisosomes act as coordinating hubs for diverse stress responses, including osmotic stress, alkaline pH stress, nutrient limitation, cell wall integrity, oxidative stress, and copper toxicity (lanze2020plasmamembranemcceisosome pages 13-14, lanze2020plasmamembranemcceisosome pages 9-11, lanze2020plasmamembranemcceisosome pages 1-2). In each case, eisosome flattening under increased membrane tension or altered lipid composition triggers release of specific protein subsets that activate downstream signaling pathways (lanze2020plasmamembranemcceisosome pages 13-14, lanze2020plasmamembranemcceisosome pages 9-11).
The following table summarizes the known MCC/eisosome proteins and the placement of YKL050C/LPX2 based on domain inference:
| Protein | Localization/domain context | Reported or inferred function | Estimated copies per cell | Notes | Citation |
|---|---|---|---|---|---|
| Pil1 | Eisosome; BAR-domain scaffold | Core structural eisosome component; essential for eisosome formation; binds PI(4,5)P2 and helps sculpt plasma-membrane furrows | Western: 115,000; MS: 48,996; GFP: 38,869 | Major structural scaffold; phosphorylation regulates assembly/disassembly | (lanze2020plasmamembranemcceisosome pages 5-6, lanze2020plasmamembranemcceisosome pages 7-8, lanze2020plasmamembranemcceisosome pages 6-7, kefauver2024cryoemarchitectureof pages 1-2) |
| Lsp1 | Eisosome; BAR-domain scaffold | Core eisosome component; forms filaments with Pil1 and contributes to membrane curvature and furrow architecture | Western: 104,000; MS: 41,516; GFP: 6,109 | Highly similar to Pil1; important for stress-dependent eisosome remodeling | (lanze2020plasmamembranemcceisosome pages 5-6, lanze2020plasmamembranemcceisosome pages 7-8, lanze2020plasmamembranemcceisosome pages 6-7, kefauver2024cryoemarchitectureof pages 1-2) |
| Eis1 (YMR031C) | Eisosome | Eisosome assembly and stability | Western: 5,570; MS: 12,142; GFP: 7,173 | Well-characterized eisosome protein; distinct from YKL050C/LPX2 | (lanze2020plasmamembranemcceisosome pages 5-6, lanze2020plasmamembranemcceisosome pages 7-8, lanze2020plasmamembranemcceisosome pages 6-7) |
| Seg1 | Eisosome | Eisosome assembly and stability; facilitates initiation/nucleation and promotes furrow length | Western: ND; MS: 4,834; GFP: 3,890 | Loss reduces eisosome formation efficiency; overproduction lengthens furrows | (lanze2020plasmamembranemcceisosome pages 5-6, lanze2020plasmamembranemcceisosome pages 7-8, lanze2020plasmamembranemcceisosome pages 6-7) |
| Pkh1 | Eisosome; Ser/Thr kinase | Regulates eisosome assembly via Pil1/Lsp1 phosphorylation; part of sphingolipid/endocytosis/cell-wall signaling | Western: ND; MS: 1,786; GFP: 1,262 | Redundant with Pkh2; linked to Pkh-Ypk signaling | (lanze2020plasmamembranemcceisosome pages 5-6, lanze2020plasmamembranemcceisosome pages 6-7) |
| Pkh2 | Eisosome; Ser/Thr kinase | Regulates eisosome assembly via Pil1/Lsp1 phosphorylation; part of sphingolipid/endocytosis/cell-wall signaling | Western: ND; MS: 1,080; GFP: 1,336 | Redundant with Pkh1 | (lanze2020plasmamembranemcceisosome pages 5-6, lanze2020plasmamembranemcceisosome pages 6-7) |
| Slm1 | Eisosome; BAR/PH-domain protein | Stress-responsive eisosome protein; exits eisosomes under membrane tension and promotes TORC2 signaling | Western: 5,190; MS: 4,116; GFP: 3,289 | Binds PI(4,5)P2; links eisosomes to TORC2-Ypk1-Orm1/2 signaling | (lanze2020plasmamembranemcceisosome pages 5-6, lanze2020plasmamembranemcceisosome pages 6-7, lanze2020plasmamembranemcceisosome pages 11-12, lanze2020plasmamembranemcceisosome pages 12-13) |
| Slm2 | Eisosome; BAR/PH-domain protein | Stress-responsive eisosome protein; functionally related to Slm1 in TORC2 signaling and membrane-stress response | Western: 2,610; MS: 980; GFP: ND | Can exit eisosomes during increased membrane tension | (lanze2020plasmamembranemcceisosome pages 5-6, lanze2020plasmamembranemcceisosome pages 6-7, lanze2020plasmamembranemcceisosome pages 11-12, lanze2020plasmamembranemcceisosome pages 12-13) |
| Sur7 | MCC (membrane compartment of Can1) | Tetraspan membrane protein associated with MCC/eisosome architecture and stress responses | Western: 17,000; MS: 4,045; GFP: 14,332 | Localizes near tops/rims of furrows; one of the longest-lived yeast proteins | (lanze2020plasmamembranemcceisosome pages 5-6, lanze2020plasmamembranemcceisosome pages 6-7) |
| Nce102 | MCC | Tetraspan protein implicated in eisosome assembly and sphingolipid sensing; influences furrow depth | Western: ND; MS: 7,567; GFP: 55,428 | Proposed sphingolipid sensor; exits MCC/eisosome under stress | (lanze2020plasmamembranemcceisosome pages 5-6, lanze2020plasmamembranemcceisosome pages 7-8, lanze2020plasmamembranemcceisosome pages 11-12, athanasopoulos2019fungalplasmamembrane pages 8-9) |
| Can1 | MCC | Arginine/H+ symporter protected in MCC/eisosomes from endocytosis under steady-state conditions | Western: ND; MS: 1,812; GFP: 8,324 | Nutrient transporter resident of MCC; can exit under substrate/stress conditions | (lanze2020plasmamembranemcceisosome pages 5-6, lanze2020plasmamembranemcceisosome pages 1-2) |
| Xrn1 | Eisosome under post-diauxic shift | 5'-3' exoribonuclease; sequestration at eisosomes during nutrient limitation reduces mRNA degradation | Western: 11,700; MS: 14,753; GFP: 14,897 | Recruited to eisosomes after post-diauxic shift; not a constitutive structural eisosome protein | (lanze2020plasmamembranemcceisosome pages 6-7, courtin2023xrn1biochemicallyassociates pages 1-5, lanze2020plasmamembranemcceisosome pages 15-16) |
| YKL050C / LPX2 | Not established; UniProt P35736; EIS1-family protein with Eisosome1 domain | Uncharacterized protein; inferred family relationship to EIS1/eisosome-associated proteins | Not reported in Lanze et al. Table 1 | Distinct from EIS1/YMR031C; literature is limited; YKL050C promoter supports spore-autonomous expression in a reporter context | (rogers2018sporeautonomousfluorescentprotein pages 3-5) |
Table: This table summarizes major S. cerevisiae MCC/eisosome proteins, their functions, and copy-number estimates compiled primarily from Lanze et al. 2020 Table 1, with added recent functional context and a clarification that YKL050C/LPX2 is distinct from the canonical eisosome protein EIS1/YMR031C.
The YKL050C gene (also referred to as LPX2; UniProt P35736) encodes an uncharacterized protein in S. cerevisiae that belongs to the EIS1 protein family and contains the Eisosome1 domain (Pfam PF12757). Despite this domain annotation, YKL050C is not the canonical EIS1 protein (which is YMR031C), and it is not listed among the recognized eisosome components in major published studies of eisosome composition (lanze2020plasmamembranemcceisosome pages 5-6, lanze2020plasmamembranemcceisosome pages 6-7). Its function therefore remains experimentally uncharacterized.
By inference from its EIS1 family membership, YKL050C may have a role related to eisosome biology—potentially in eisosome assembly, stability, or membrane organization at the plasma membrane. The observation that the YKL050C promoter drives spore-autonomous expression (rogers2018sporeautonomousfluorescentprotein pages 3-5) suggests that this gene may have a specialized role during meiosis and sporulation, possibly in organizing membrane domains during prospore membrane formation or spore wall assembly. However, no direct experimental evidence supports this hypothesis.
Given the current state of knowledge, future studies employing GFP tagging, deletion phenotyping, and protein interaction analysis would be required to determine whether YKL050C/LPX2 functions as an eisosome component, acts during sporulation, or has another as-yet-undiscovered function. The presence of the Eisosome1 domain provides the strongest clue to its likely biological role, placing it within the broader context of plasma membrane microdomain organization in yeast.
References
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(lanze2020plasmamembranemcceisosome pages 13-14): Carla E. Lanze, Rafael M. Gandra, Jenna E. Foderaro, Kara A. Swenson, Lois M. Douglas, and James B. Konopka. Plasma membrane mcc/eisosome domains promote stress resistance in fungi. Nov 2020. URL: https://doi.org/10.1128/mmbr.00063-19, doi:10.1128/mmbr.00063-19. This article has 68 citations and is from a domain leading peer-reviewed journal.