tlcd4b encodes a TLC (TRAM/LAG1/CLN8) domain-containing multi-pass integral membrane protein in Dictyostelium discoideum. The protein belongs to the TLCD4 subfamily of TLC domain proteins, which are distinct from the ceramide synthase branch of the TLC family. Based on recent characterization of TLCD family members as phospholipid acyltransferases (Sheokand et al. 2025), tlcd4b likely functions in membrane phospholipid remodeling. No experimental studies have been performed directly on this protein; all functional annotations are inferred from phylogeny or domain architecture.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0005783 endoplasmic reticulum | IBA GO_REF:0000033 | ACCEPT | Summary: IBA annotation based on phylogenetic inference. TLC domain proteins, including ceramide synthases (CerS) and other TLCD family members, are characteristically localized to the ER. The S. pombe homolog Tlc4 was localized at the nuclear envelope and ER. TLCD1 also localizes to ER membranes. The ER localization is consistent with the protein's predicted multi-pass transmembrane topology and the known biology of the TLC domain family. Reason: ER localization is well-established across the TLC domain family. CerS proteins, TLCD1, and CLN8 all localize to the ER. Phylogenetic inference to ER is appropriate and consistent with the transmembrane topology of tlcd4b. Supporting Evidence: PMID:37078207 Tlc4 was localized at the NE and endoplasmic reticulum, similar to CerS proteins PMID:39970228 poorly understood TRAM-LAG1-CLN8 domain (TLCD)-containing proteins are phospholipid remodeling enzymes |
| GO:0055088 lipid homeostasis | IBA GO_REF:0000033 | ACCEPT | Summary: IBA annotation for lipid homeostasis based on phylogenetic inference. This is a broad term that encompasses the function of TLC domain proteins. Recent work shows TLCD family members are phospholipid acyltransferases that regulate cellular phospholipid composition, which falls under lipid homeostasis. However, the term is quite general and does not specify whether the protein acts through sphingolipid or phospholipid metabolism. Reason: Lipid homeostasis is an appropriate broad annotation for a TLCD family member. TLCD1 regulates cellular phospholipid composition and CLN8 catalyzes phospholipid biosynthesis -- both are forms of lipid homeostasis. The term is conservative and appropriate given the lack of direct experimental data on tlcd4b. Supporting Evidence: PMID:39970228 TLCD1 is an evolutionarily conserved lysophosphatidylethanolamine acyltransferase, which regulates cellular phospholipid composition |
| GO:0016020 membrane | IEA GO_REF:0000120 | ACCEPT | Summary: IEA annotation based on InterPro domain IPR006634 (TLC domain) and UniProt subcellular location. The protein has six predicted transmembrane helices and is annotated as a multi-pass membrane protein by UniProt. This annotation is correct. Reason: The membrane annotation is correct given the six predicted transmembrane helices and multi-pass topology documented in UniProt. A MODIFY to GO:0016021 (integral component of membrane) was previously proposed, but GO has merged GO:0016021 into GO:0016020 membrane, so this term is already the most specific available. |
| GO:0003674 molecular_function | ND GO_REF:0000015 | ACCEPT | Summary: ND annotation indicating no experimental data for molecular function. This is appropriate as no direct experimental characterization of tlcd4b enzymatic activity has been performed. Based on the TLCD family context, lysophospholipid acyltransferase activity is a plausible prediction but remains unconfirmed for this specific protein. Reason: No experimental molecular function data exists for this protein. The ND annotation correctly reflects the current state of knowledge. |
| GO:0008150 biological_process | ND GO_REF:0000015 | ACCEPT | Summary: ND annotation indicating no experimental data for biological process. While the IBA annotation for lipid homeostasis provides a phylogenetic inference, no direct experimental evidence exists for tlcd4b biological process. Reason: The ND annotation from dictyBase correctly indicates the absence of direct experimental evidence. The IBA lipid homeostasis annotation provides complementary inferred information. |
| GO:0071617 lysophospholipid acyltransferase activity | ISS PMID:39970228 TRAM-LAG1-CLN8 family proteins are acyltransferases regulati... | NEW | Summary: Proposed new annotation based on the 2025 discovery that non-CerS TLCD family members are phospholipid acyltransferases. TLCD1 was demonstrated to be a lysophosphatidylethanolamine acyltransferase. As tlcd4b belongs to the same TLCD branch of the TLC family, lysophospholipid acyltransferase activity is the most parsimonious predicted molecular function. The BioReason deep research trace incorrectly predicted ceramidase activity instead. Reason: Based on the characterization of TLCD family members as phospholipid acyltransferases (Sheokand et al. 2025), this is the best-supported predicted molecular function for a TLCD4 subfamily member. Supporting Evidence: PMID:39970228 poorly understood TRAM-LAG1-CLN8 domain (TLCD)-containing proteins are phospholipid remodeling enzymes file:DICDI/tlcd4b/tlcd4b-deep-research-bioreason-sft.md [BioReason incorrectly predicted ceramidase activity; actual TLCD family function is phospholipid acyltransferase] |
| GO:0006644 phospholipid metabolic process | ISS PMID:39970228 TRAM-LAG1-CLN8 family proteins are acyltransferases regulati... | NEW | Summary: Proposed new annotation for phospholipid metabolic process, based on the demonstrated phospholipid remodeling activity of TLCD family members. More specific than lipid homeostasis (GO:0055088) for describing the biological process. Reason: TLCD family members regulate cellular phospholipid composition through acyltransferase activity. Phospholipid metabolic process is the appropriate biological process term for a phospholipid acyltransferase. Supporting Evidence: PMID:39970228 TLCD1 is an evolutionarily conserved lysophosphatidylethanolamine acyltransferase, which regulates cellular phospholipid composition |
Loading supporting content…
Download this section (compressed HTML)Q: Does D. discoideum tlcd4b possess lysophospholipid acyltransferase activity like its mammalian TLCD family relatives TLCD1 and CLN8?
Suggested experts: Kasparas Petkevicius
Q: What is the substrate specificity of tlcd4b -- does it act on lysophosphatidylethanolamine, lysophosphatidylglycerol, or other lysophospholipid species?
Suggested experts: Kasparas Petkevicius, Michael P Murphy
Experiment: Express and purify recombinant D. discoideum tlcd4b in a cell-free system or yeast expression system and test for lysophospholipid acyltransferase activity using radiolabeled or fluorescent acyl-CoA substrates and various lysophospholipid acceptors.
Hypothesis: tlcd4b possesses lysophospholipid acyltransferase activity consistent with the TLCD family.
Type: in vitro enzymatic assay
Experiment: Generate a tlcd4b knockout in D. discoideum and perform lipidomic profiling to identify changes in phospholipid and sphingolipid composition compared to wild-type.
Hypothesis: Loss of tlcd4b alters membrane phospholipid acyl chain composition, consistent with a role in phospholipid remodeling.
Type: lipidomics
Experiment: Tag tlcd4b with GFP in D. discoideum and determine subcellular localization by confocal microscopy, comparing with ER markers and other organelle markers.
Hypothesis: tlcd4b localizes to the ER membrane, consistent with the IBA annotation and the known localization of other TLC domain proteins.
Type: fluorescence microscopy
Loading supporting content…
Download this section (compressed HTML)Loading supporting content…
Download this section (compressed HTML)Loading supporting content…
Download this section (compressed HTML)Loading supporting content…
Download this section (compressed HTML)Loading supporting content…
Download this section (compressed HTML)