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this with annotations you find in gene/protein databases, but these can be outdated or inaccurate.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.
ECM30 (systematic name YLR436C; UniProt Q06673) encodes the protein Ecm30 in Saccharomyces cerevisiae (strain ATCC 204508 / S288c). The gene was originally named "Extracellular Mutant protein 30" based on its identification in a screen for mutants with cell wall/extracellular matrix defects. Ecm30 belongs to the hid-1 protein family and contains the HID1/Ecm30 domain (IPR026705; Pfam PF12722). Ecm30 is not an enzyme itself; rather, available evidence indicates it functions as a regulatory or scaffolding component within a deubiquitinase complex and in membrane protein sorting pathways.
The best-characterized molecular function of Ecm30 is its role as a binding partner and putative regulatory subunit of the Ubp15 ubiquitin-specific protease (deubiquitinase, DUB). Benschop et al. (2010) identified and validated a physical complex between Ecm30 and Ubp15 through coprecipitation experiments, describing it as a "putative Ubp15-Ecm30 ubiquitin protease complex" (benschop2010aconsensusof pages 6-7). This complex was identified as stoichiometric, suggesting a stable and dedicated association rather than a transient interaction.
Ubp15 is a ubiquitin-specific protease of the USP/UBP family that favors K48-linked ubiquitin chains (suresh2020thestructureand pages 5-6). Ubp15 has well-documented roles in at least two functional contexts:
Because Ecm30 forms a stable complex with Ubp15, it is likely that Ecm30 modulates one or more of these Ubp15-dependent functions—most plausibly as a specificity factor or scaffold that directs Ubp15 activity toward particular substrates or cellular compartments. Consistent with this model, Costanzo et al. (2010) proposed that Ecm30 may modulate Gap1 (general amino acid permease) localization "perhaps by controlling its ubiquitination state" through its complex with Ubp15 (costanzo2010thegeneticlandscape pages 2-4).
A landmark study by Costanzo et al. (2010), which mapped the global genetic interaction network of S. cerevisiae, identified ECM30 as one of three genes (along with PAR32 and UBP15) whose genetic interaction profiles were highly similar to those of known components of the Gap1-sorting module (costanzo2010thegeneticlandscape pages 2-4, ho2015candidaglabratanew pages 3-4). When deleted, all three genes led to Gap1 sorting and transport defects, experimentally validating the computational prediction (costanzo2010thegeneticlandscape pages 2-4). Gap1 is the general amino acid permease whose trafficking between the plasma membrane, Golgi, and vacuole is tightly regulated by nitrogen availability, primarily through the TORC1-Npr1 signaling axis.
Par32 (also called Amu1) is a TORC1-Npr1-regulated phosphoprotein that controls ammonium transport and feeds back on TORC1 activity. Under conditions of nitrogen sufficiency, dephosphorylated Par32 accumulates at the cell surface and mediates inhibition of specific ammonium transport proteins (varlakhanova2018feedbackregulationof pages 20-25, varlakhanova2018feedbackregulationof pages 39-53, varlakhanova2018feedbackregulationof pages 16-20, varlakhanova2018feedbackregulationof pages 1-7). Importantly, Par32 also regulates Gap1 expression in an ammonium-dependent manner (varlakhanova2018feedbackregulationof pages 20-25, varlakhanova2018feedbackregulationof pages 39-53). While Par32's role in the TORC1 pathway has been extensively characterized, ECM30 was not directly investigated in these downstream mechanistic studies; its involvement in the Gap1-sorting module is therefore primarily supported by genetic interaction data and validated deletion phenotypes rather than by direct biochemical experiments.
Expression profiling of ecm30Δ and ubp15Δ deletion mutants revealed significantly altered mRNA levels for numerous genes involved in methionine biosynthesis and amino acid metabolism, including MET2, MET3, MET14, MET17, MET10, MET16, MET1, MET28, and GAP1 (benschop2010aconsensusof pages 6-7). The similar expression profiles between ecm30Δ and ubp15Δ mutants provide strong support for the functional coupling of these two gene products within the same complex. This methionine biosynthesis connection may relate to the broader role of the Ecm30-Ubp15 complex in amino acid sensing and permease regulation, as methionine pathway genes are known to be responsive to nitrogen and amino acid availability signals.
High-throughput annotation in a genome-wide screen for negative regulators of sirtuin activity (Raisner and Madhani, 2008) listed Ecm30 as localized to the cytoplasm and annotated to "cell wall organization" based on its ECM designation (raisner2008genomewidescreenfor pages 4-5). The cytoplasmic localization is consistent with a role as a scaffolding/regulatory protein that associates with the cytosolic deubiquitinase Ubp15. However, no dedicated primary localization study using GFP-tagged Ecm30 in yeast has been identified in the present literature search, so the precise sub-compartmental distribution of Ecm30 (e.g., whether it associates with endomembranes or the Golgi apparatus as its metazoan orthologs do) remains an open question.
Ecm30 belongs to the hid-1 protein family, which is conserved from yeast to humans. The founding member of this family, HID-1 (high-temperature-induced dauer formation defective-1), was characterized in Caenorhabditis elegans as a component of the peptidergic signaling pathway (mesa2011hid1anew pages 11-12, mesa2011hid1anew pages 12-14, mesa2011hid1anew pages 2-3, mesa2011hid1anew pages 1-2). Key findings about metazoan HID-1 include:
This conservation pattern suggests that the ancestral function of the HID-1/Ecm30 family involves membrane trafficking and cargo sorting at the Golgi or post-Golgi level—consistent with Ecm30's role in Gap1 permease sorting in yeast. However, direct demonstration of Ecm30 association with the Golgi or with trafficking vesicles in yeast has not been reported.
Several high-throughput studies have linked ECM30 to pleiotropic phenotypes:
The primary pathway in which Ecm30 functions is the ubiquitin-dependent regulation of amino acid permease trafficking, specifically the sorting of Gap1. This pathway intersects with the TORC1-Npr1 nitrogen signaling axis, which governs nutrient permease stability and localization at the plasma membrane. Within this network, the Ecm30-Ubp15 complex is proposed to modulate the ubiquitination state of Gap1 or of regulatory components (such as ARTs) that govern Gap1 trafficking (costanzo2010thegeneticlandscape pages 2-4). The downstream consequence of Ecm30-Ubp15 complex activity appears to be the proper sorting of Gap1 between the plasma membrane, the Golgi, and the vacuole in response to nitrogen availability signals.
Additionally, through its complex with Ubp15, Ecm30 may indirectly participate in plasma membrane quality control via the ART-Rsp5 ubiquitin ligase network. Ubp15 deubiquitinates ART proteins, stabilizing them against proteasomal degradation and thereby supporting the ubiquitination and turnover of damaged membrane cargo (suresh2020thestructureand pages 9-9, suresh2020thestructureand pages 8-9).
Ecm30 is a cytoplasmic protein of the conserved HID-1 family that functions primarily as a regulatory partner of the Ubp15 deubiquitinase in S. cerevisiae. The Ecm30-Ubp15 complex participates in amino acid permease (Gap1) sorting and in the transcriptional regulation of methionine biosynthetic genes. Evolutionary inference from metazoan HID-1 orthologs suggests a role in membrane trafficking and cargo sorting at the Golgi or post-Golgi level, which is consistent with its yeast function in permease trafficking. Ecm30 is not known to possess enzymatic activity; it likely serves as a scaffold or specificity factor directing Ubp15 deubiquitinase activity toward appropriate substrates or subcellular compartments.
Key outstanding questions include: (1) the precise subcellular localization of Ecm30 at high resolution in yeast; (2) whether Ecm30 directly contacts Gap1 or other permease substrates; (3) the specific substrates of the Ecm30-Ubp15 complex beyond what can be inferred from genetic interaction data; and (4) whether Ecm30 retains the membrane-trafficking functions of its metazoan HID-1 orthologs or has diverged to function primarily in the cytosolic ubiquitin regulatory pathway.
| Gene name | Systematic name | Protein name | Organism | UniProt accession | Protein family/domain | Subcellular localization | Physical interactors | Predicted function | Key pathways/processes | GO / functional annotations | Key references |
|---|---|---|---|---|---|---|---|---|---|---|---|
| ECM30 | YLR436C | Protein ECM30 / Extracellular mutant protein 30 | Saccharomyces cerevisiae strain ATCC 204508 / S288c | Q06673 | Belongs to the hid-1 family; contains HID1/Ecm30 domain (IPR026705) / Hid1 (PF12722); family-level evidence from metazoan HID-1 supports a membrane-trafficking role (mesa2011hid1anew pages 11-12, mesa2011hid1anew pages 17-21) | Reported as cytoplasmic in a genome-wide screen table; no strong direct primary localization study for yeast ECM30 was retrieved, so localization remains only modestly supported in yeast-specific literature (raisner2008genomewidescreenfor pages 7-8, raisner2008genomewidescreenfor pages 4-5) | Forms a stoichiometric complex with Ubp15; physical association validated by coprecipitation (benschop2010aconsensusof pages 6-7, costanzo2010thegeneticlandscape pages 2-4) | Best-supported model: regulatory/scaffold-like factor associated with the Ubp15 deubiquitinase, contributing to Gap1 permease sorting/localization and broader control of amino acid metabolism; may modulate cargo ubiquitination state indirectly through the Ubp15 complex rather than acting as an enzyme itself (costanzo2010thegeneticlandscape pages 2-4, benschop2010aconsensusof pages 6-7) | Gap1 sorting module; amino acid uptake and nitrogen-responsive trafficking; linked to methionine biosynthesis / amino acid metabolic gene regulation via expression profiling of ecm30Δ and ubp15Δ; possible connection to plasma-membrane quality control through Ubp15’s role in ART/Rsp5 regulation, though ECM30 itself has not been directly shown in that mechanism (costanzo2010thegeneticlandscape pages 2-4, benschop2010aconsensusof pages 6-7, suresh2020thestructureand pages 9-9, suresh2020thestructureand pages 8-9) | Annotated/associated with cell wall organization in one screen; predicted involvement in Gap1 sorting from genetic interaction mapping; also recovered in a screen for negative regulators of sirtuin activity, but this is likely a pleiotropic phenotype rather than the primary molecular function (raisner2008genomewidescreenfor pages 4-5, ho2015candidaglabratanew pages 3-4, raisner2008genomewidescreenfor pages 6-7) | Costanzo et al., Science (2010), published Jan 22 2010, https://doi.org/10.1126/science.1180823 (costanzo2010thegeneticlandscape pages 2-4); Benschop et al., Molecular Cell (2010), published Jun 25 2010, https://doi.org/10.1016/j.molcel.2010.06.002 (benschop2010aconsensusof pages 6-7); Raisner & Madhani, Genetics (2008), published Aug 2008, https://doi.org/10.1534/genetics.108.088443 (raisner2008genomewidescreenfor pages 4-5) |
| Context from family orthologs (not yeast ECM30 directly) | — | HID-1 orthologs | Conserved from nematodes to mammals | — | HID-1 family proteins are membrane-associated trafficking factors; metazoan HID-1 localizes partly to the trans-Golgi network and dense-core vesicle related compartments and functions in early secretory vesicle biogenesis/maturation (mesa2011hid1anew pages 11-12, mesa2011hid1anew pages 17-21, mesa2011hid1anew pages 14-15) | TGN / post-Golgi / dense-core vesicle-associated in metazoans (mesa2011hid1anew pages 17-21, mesa2011hid1anew pages 14-15) | — | Supports inference that ECM30 may participate in membrane trafficking or cargo-sorting events, but this remains inference, not direct demonstration in budding yeast (mesa2011hid1anew pages 11-12, mesa2011hid1anew pages 14-15) | Secretory trafficking / vesicle maturation in orthologous systems (mesa2011hid1anew pages 11-12, mesa2011hid1anew pages 14-15) | Family-level evolutionary support only | Mesa et al., Genetics (2011), published Feb 2011, https://doi.org/10.1534/genetics.110.121996 (mesa2011hid1anew pages 11-12) |
| Phenotypic / systems-level observations | YLR436C | ECM30 | S. cerevisiae | Q06673 | As above | Cytoplasmic annotation from screen table (raisner2008genomewidescreenfor pages 4-5) | Linked functionally to PAR32 and UBP15 by genetic interaction profile similarity in the Gap1-sorting module (costanzo2010thegeneticlandscape pages 2-4) | Deletion causes Gap1 sorting and transport defects; a truncated/frameshifted ECM30 variant was suggested as a contributor in experimentally evolved high-temperature-tolerant yeast, implying that altering ECM30 function can affect stress adaptation (costanzo2010thegeneticlandscape pages 2-4, huang2018experimentalevolutionof pages 5-6) | Nutrient permease trafficking; stress adaptation / thermotolerance (costanzo2010thegeneticlandscape pages 2-4, huang2018experimentalevolutionof pages 5-6) | Functional-genomics prediction; stress-related phenotype rather than direct biochemical activity | Huang et al., Molecular Biology and Evolution (2018), published Aug 2018, https://doi.org/10.1093/molbev/msy077 (huang2018experimentalevolutionof pages 5-6); Costanzo et al., Science (2010), https://doi.org/10.1126/science.1180823 (costanzo2010thegeneticlandscape pages 2-4) |
Table: This table summarizes the key properties, evidence-supported functions, localization, interactions, and pathway associations of yeast ECM30/YLR436C. It is useful as a concise evidence map distinguishing direct yeast data from family-based functional inference.
References
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(mesa2011hid1anew pages 17-21): Rosana Mesa, Shuo Luo, Christopher M Hoover, Kenneth Miller, Alicia Minniti, Nibaldo Inestrosa, and Michael L Nonet. Hid-1, a new component of the peptidergic signaling pathway. Genetics, 187:467-483, Feb 2011. URL: https://doi.org/10.1534/genetics.110.121996, doi:10.1534/genetics.110.121996. This article has 36 citations and is from a domain leading peer-reviewed journal.
(mesa2011hid1anew pages 14-15): Rosana Mesa, Shuo Luo, Christopher M Hoover, Kenneth Miller, Alicia Minniti, Nibaldo Inestrosa, and Michael L Nonet. Hid-1, a new component of the peptidergic signaling pathway. Genetics, 187:467-483, Feb 2011. URL: https://doi.org/10.1534/genetics.110.121996, doi:10.1534/genetics.110.121996. This article has 36 citations and is from a domain leading peer-reviewed journal.
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(raisner2008genomewidescreenfor pages 7-8): Ryan M Raisner and Hiten D Madhani. Genomewide screen for negative regulators of sirtuin activity in saccharomyces cerevisiae reveals 40 loci and links to metabolism. Genetics, 179:1933-1944, Aug 2008. URL: https://doi.org/10.1534/genetics.108.088443, doi:10.1534/genetics.108.088443. This article has 24 citations and is from a domain leading peer-reviewed journal.
(raisner2008genomewidescreenfor pages 6-7): Ryan M Raisner and Hiten D Madhani. Genomewide screen for negative regulators of sirtuin activity in saccharomyces cerevisiae reveals 40 loci and links to metabolism. Genetics, 179:1933-1944, Aug 2008. URL: https://doi.org/10.1534/genetics.108.088443, doi:10.1534/genetics.108.088443. This article has 24 citations and is from a domain leading peer-reviewed journal.