LSM1

Existing Annotations Review

GO Term	Evidence	Action	Reason
GO:0000290 deadenylation-dependent decapping of nuclear-transcribed mRNA	IBA GO_REF:0000033	ACCEPT	Summary: Phylogenetic annotation indicating that LSM1 is involved in deadenylation-dependent decapping of nuclear-transcribed mRNA based on ortholog inference. This annotation is well-supported by experimental evidence from multiple sources, including IMP annotations with PMIDs 10761922 and 15716506, which directly demonstrate the role of Lsm1p in mRNA decapping. Reason: This is a core function of LSM1. The annotation is correct and represents the primary mechanistic role of the Lsm1-7-Pat1 complex. Bouveret et al. (2000) demonstrated that Lsm1p-Lsm7p complex activates the decapping step of mRNA degradation, with deletion mutants showing accumulation of capped mRNAs and blocks in mRNA decay. This is a conserved function across eukaryotes and LSM1 is the defining member of this pathway. Supporting Evidence: PMID:10747033 Deletions of LSM1, 6, 7 and PAT1 genes increased the half-life of reporter mRNAs. Interestingly, accumulating mRNAs were capped, suggesting a block in mRNA decay at the decapping step. PMID:10761922 mutations in seven yeast Lsm proteins (Lsm1-Lsm7) also lead to inhibition of mRNA decapping PMID:15716506 The decapping of eukaryotic mRNAs is a key step in their degradation. The heteroheptameric Lsm1p-7p complex is a general activator of decapping file:yeast/LSM1/LSM1-deep-research-falcon.md The Lsm1-7 ring plus Pat1 is a key module that links 3' end status to decapping: Pat1/Lsm1-7 binds oligoadenylated 3' ends and helps recruit/activate the decapping enzyme.
GO:0003729 mRNA binding	IBA GO_REF:0000033	ACCEPT	Summary: Phylogenetic inference of mRNA binding capacity. This is mechanistically accurate as the Lsm1-7 complex binds to oligo-U tracts at the 3' end of deadenylated mRNAs, which is essential for its decapping activation function. The annotation is supported by IDA evidence (PMID:23222640) that demonstrates LSM1 association with yeast mRNPs. Reason: LSM1 is a core component of the Lsm1-7 complex that binds to poly(U) tracts of mRNA 3' ends as part of its mechanism for mRNA decay activation. The mRNA binding is functionally relevant to the decapping activation role. The complex specifically recognizes RNA motifs via the ring-structured Sm domain. Supporting Evidence: PMID:15716506 Mutations affecting the predicted RNA-binding and inter-subunit interaction residues of Lsm1p led to impairment of mRNA decay, suggesting that the integrity of the Lsm1p-7p complex and the ability of the Lsm1p-7p complex to interact with mRNA are important for mRNA decay function PMID:24139796 The 3.7 Å resolution structure of Lsm1-7 bound to the C-terminal domain of Pat1 reveals...A distinct structural feature of the cytoplasmic Lsm ring is the C-terminal extension of Lsm1, which plugs the exit site of the central channel and approaches the RNA binding pockets.
GO:1990726 Lsm1-7-Pat1 complex	IBA GO_REF:0000033	ACCEPT	Summary: Phylogenetic annotation indicating LSM1 is a component of the Lsm1-7-Pat1 complex. This is well-supported by IDA evidence (PMID:24139796) that provides crystal structure of the complex, confirming LSM1 as a core subunit. Reason: LSM1 is the defining member of the Lsm1-7-Pat1 complex, forming the heptameric ring that recruits Pat1 for mRNA decay activation. Sharif & Conti (2013) resolved the 2.3 Ångström crystal structure showing Lsm1-2-3-6-5-7-4 topology with LSM1 as the unique subunit. This is factual component annotation. Supporting Evidence: PMID:10747033 Lsm1p, together with Lsm2p-Lsm7p, forms a new seven-subunit complex...the Lsm1p-Lsm7p complex is associated with Pat1p and Xrn1p exoribonuclease PMID:24139796 The 2.3 Å resolution structure of S. cerevisiae Lsm1-7 shows the presence of a heptameric ring with Lsm1-2-3-6-5-7-4 topology
GO:0000932 P-body	IBA GO_REF:0000033	ACCEPT	Summary: Phylogenetic inference that LSM1 is active in or localized to P-bodies. This is accurate as Lsm1-7 is a core component of P-bodies where mRNA decapping and decay occur. Multiple IDA and IMP annotations (PMIDs 12730603, 18611963) directly support localization and function in P-bodies. Reason: LSM1 and the Lsm1-7-Pat1 complex are core P-body components. Sheth & Parker (2003) demonstrated that proteins involved in mRNA decapping are concentrated in P-bodies, and that mRNA degradation intermediates localize to these structures. The complex is active_in P-bodies as the primary site of its mRNA decay function. Supporting Evidence: PMID:12730603 proteins that activate or catalyze decapping are concentrated in P bodies...mRNA degradation intermediates are localized to P bodies
GO:0000932 P-body	IEA GO_REF:0000044	ACCEPT	Summary: UniProt subcellular location mapping indicates P-body localization based on automated annotation. This is consistent with experimental evidence but is weaker than IBA inference or direct experimental evidence. Reason: P-body localization is correct and well-supported. While this IEA annotation is lower confidence than the IBA and IDA annotations, it is not incorrect and represents the same underlying biological reality. All annotations for P-body are consistent across different evidence types, confirming LSM1 localization to this critical mRNA decay compartment.
GO:0000956 nuclear-transcribed mRNA catabolic process	IEA GO_REF:0000002	KEEP AS NON CORE	Summary: This parent mRNA catabolic process term is valid but broader than the specific decay subprocesses curated for LSM1. Reason: Changed from MODIFY to KEEP_AS_NON_CORE because the review rationale supports retaining the broad parent term as non-core rather than replacing it.
GO:0003723 RNA binding	IEA GO_REF:0000120	KEEP AS NON CORE	Summary: IEA annotation based on InterPro Sm domain and RNA-binding keywords. While LSM1 does bind RNA via its Sm domain, this is a generic parent term that is superseded by GO:0003729 (mRNA binding) which is more specific. Reason: GO:0003723 (RNA binding) is technically correct but overly general compared to GO:0003729 (mRNA binding), which specifies the actual substrate and mechanism. LSM1 specifically binds mRNA (particularly poly(U) tracts) rather than other RNA types like snRNAs. The more specific mRNA binding term is already present with IBA and IDA evidence. This general RNA binding term is redundant and less informative.
GO:0005634 nucleus	IEA GO_REF:0000044	KEEP AS NON CORE	Summary: UniProt subcellular location mapping to nucleus. LSM1 has been detected in the nucleus according to the UniProt record, and there is IDA evidence (PMID:23706738) supporting nuclear localization. Reason: LSM1 is present in both nucleus and cytoplasm. The UniProt entry states nuclear localization with ECO:0000269\|PubMed:10761922 evidence, so the annotation is correct, but the primary site of LSM1 function is the cytoplasm and the nuclear pool reflects a secondary shuttling role. Retained as non-core, consistent with the IDA nucleus entry from PMID:23706738. Supporting Evidence: PMID:10761922 the Lsm1-Lsm7 proteins co-immunoprecipitate with the mRNA decapping enzyme (Dcp1), a decapping activator (Pat1/Mrt1) and with mRNA
GO:0005737 cytoplasm	IEA GO_REF:0000120	ACCEPT	Summary: IEA annotation indicating cytoplasmic localization based on automated inference. This is correct and reflects the primary location of LSM1 where the mRNA decay machinery operates. Reason: LSM1 is predominantly localized to the cytoplasm where it functions in mRNA decay and P-body assembly. This is well-documented by multiple IDA annotations and is essential to its biological function.
GO:0006397 mRNA processing	IEA GO_REF:0000043	REMOVE	Summary: UniProt keyword mapping indicates LSM1 involvement in mRNA processing. However, this is misleading because mRNA processing typically refers to 5' capping, 3' polyadenylation, and splicing of nascent transcripts. Reason: This annotation is mechanistically incorrect for LSM1. GO:0006397 (mRNA processing) encompasses 5' capping, 3' polyadenylation, and splicing during transcription. LSM1 functions in mRNA decay/degradation, not mRNA processing. The Lsm1-7 complex removes the 5' cap as part of decay, but this is degradation, not processing. The specific mRNA decay processes (GO:0000288, GO:0000290) are the correct annotations. This IEA annotation appears to result from incorrect keyword mapping and should not be retained.
GO:0032991 protein-containing complex	IEA GO_REF:0000117	ACCEPT	Summary: ARBA machine learning annotation indicating LSM1 is part of a protein-containing complex. This is correct as LSM1 is a core member of the Lsm1-7-Pat1 complex. Reason: LSM1 is an obligate component of the heptameric Lsm1-7-Pat1 complex. This is a generic parent term but accurate. More specific component annotations exist (GO:1990726 for the specific complex).
GO:1990904 ribonucleoprotein complex	IEA GO_REF:0000043	ACCEPT	Summary: UniProt keyword mapping indicates LSM1 is part of a ribonucleoprotein complex. The Lsm1-7 complex is indeed a ribonucleoprotein that binds and processes RNA. Reason: The Lsm1-7-Pat1 complex is a ribonucleoprotein complex containing RNA-binding Sm domains and functionally interacting with mRNA. This annotation is accurate though the more specific complex identifier (GO:1990726) is more informative.
GO:0005515 protein binding	IPI PMID:10688190 A comprehensive analysis of protein-protein interactions in ...	MARK AS OVER ANNOTATED	Summary: IPI evidence from comprehensive protein-protein interaction study. LSM1 interacts with LSM2, LSM3, LSM4, LSM5, LSM6, LSM7 as core members of the Lsm1-7 complex. Reason: While LSM1 does bind proteins as part of the Lsm1-7 complex, the generic GO:0005515 (protein binding) term is not informative for functional annotation. The specific protein-protein interactions and the biological role (complex assembly for mRNA decay) are better captured by GO:1990726 (Lsm1-7-Pat1 complex). Generic "protein binding" annotations lack functional specificity and should be replaced with mechanistically informative terms that describe what the binding accomplishes. Proposed replacements: Lsm1-7-Pat1 complex Supporting Evidence: PMID:10688190 A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae.
GO:0005515 protein binding	IPI PMID:10900456 Genome-wide protein interaction screens reveal functional ne...	MARK AS OVER ANNOTATED	Summary: IPI evidence from genome-wide protein interaction screens showing LSM1 interactions with PAT1 and other Lsm proteins. Reason: Generic protein binding annotation without functional context. LSM1 interacts with other Lsm proteins and PAT1, but this is comprehensively described by the complex component annotation GO:1990726. The generic term provides no insight into the biological significance of these interactions. Proposed replacements: Lsm1-7-Pat1 complex Supporting Evidence: PMID:10900456 Genome-wide protein interaction screens reveal functional networks involving Sm-like proteins.
GO:0005515 protein binding	IPI PMID:11780629 The DEAD box helicase, Dhh1p, functions in mRNA decapping an...	MARK AS OVER ANNOTATED	Summary: IPI evidence showing interaction of LSM1 with Dhh1 (DEAD box helicase) documented in interaction studies. Reason: Generic protein binding term without mechanistic context. While LSM1 does interact with Dhh1, the biological significance and functional consequence are not captured by this vague annotation. The mRNA decay process annotations better describe what these interactions accomplish. Supporting Evidence: PMID:11780629 The DEAD box helicase, Dhh1p, functions in mRNA decapping and interacts with both the decapping and deadenylase complexes.
GO:0005515 protein binding	IPI PMID:11805837 Systematic identification of protein complexes in Saccharomy...	MARK AS OVER ANNOTATED	Summary: IPI evidence from mass spectrometry studies of protein complexes identifying LSM1 in the Lsm1-7-Pat1 complex. Reason: Generic protein binding annotation redundant with complex component annotation. The systematic protein complex identification is better represented by GO:1990726. Proposed replacements: Lsm1-7-Pat1 complex Supporting Evidence: PMID:11805837 Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry.
GO:0005515 protein binding	IPI PMID:14759368 High-definition macromolecular composition of yeast RNA-proc...	MARK AS OVER ANNOTATED	Summary: IPI evidence from high-definition macromolecular composition of yeast RNA-processing complexes. Reason: This annotation documents LSM1 protein interactions from complex characterization studies, but the generic "protein binding" term is uninformative. The complex assembly and function are better captured by specific GO terms. Proposed replacements: Lsm1-7-Pat1 complex Supporting Evidence: PMID:14759368 High-definition macromolecular composition of yeast RNA-processing complexes.
GO:0005515 protein binding	IPI PMID:16429126 Proteome survey reveals modularity of the yeast cell machine...	MARK AS OVER ANNOTATED	Summary: IPI evidence from proteome survey identifying LSM1 protein interactions. Reason: Generic annotation without functional specificity. LSM1 protein interactions are functionally significant only in the context of mRNA decay machinery assembly. Proposed replacements: Lsm1-7-Pat1 complex Supporting Evidence: PMID:16429126 Proteome survey reveals modularity of the yeast cell machinery.
GO:0005515 protein binding	IPI PMID:16554755 Global landscape of protein complexes in the yeast Saccharom...	MARK AS OVER ANNOTATED	Summary: IPI evidence from global landscape studies of yeast protein complexes. Reason: Generic protein binding term redundant with more specific complex component annotation. Proposed replacements: Lsm1-7-Pat1 complex Supporting Evidence: PMID:16554755 Global landscape of protein complexes in the yeast Saccharomyces cerevisiae.
GO:0005515 protein binding	IPI PMID:18719252 High-quality binary protein interaction map of the yeast int...	MARK AS OVER ANNOTATED	Summary: IPI evidence from high-quality binary protein interaction mapping. Reason: Binary protein interactions documented but better represented by complex component annotation. Proposed replacements: Lsm1-7-Pat1 complex Supporting Evidence: PMID:18719252 High-quality binary protein interaction map of the yeast interactome network.
GO:0005515 protein binding	IPI PMID:23267104 Proteome-wide protein interaction measurements of bacterial ...	MARK AS OVER ANNOTATED	Summary: IPI evidence from proteome-wide protein interaction measurements. Reason: Generic binding annotation without functional context. Proposed replacements: Lsm1-7-Pat1 complex Supporting Evidence: PMID:23267104 Proteome-wide protein interaction measurements of bacterial proteins of unknown function.
GO:0005515 protein binding	IPI PMID:37070168 RNA-dependent interactome allows network-based assignment of...	MARK AS OVER ANNOTATED	Summary: IPI evidence from RNA-dependent interactome analysis. Reason: Generic protein binding term lacks functional specificity for RNA-binding protein annotation. Proposed replacements: Lsm1-7-Pat1 complex Supporting Evidence: PMID:37070168 RNA-dependent interactome allows network-based assignment of RNA-binding protein function.
GO:0005515 protein binding	IPI PMID:37968396 The social and structural architecture of the yeast protein ...	MARK AS OVER ANNOTATED	Summary: IPI evidence from social and structural architecture study of yeast protein interactome. Reason: Generic annotation not informative for molecular function annotation. Proposed replacements: Lsm1-7-Pat1 complex Supporting Evidence: PMID:37968396 The social and structural architecture of the yeast protein interactome.
GO:0000290 deadenylation-dependent decapping of nuclear-transcribed mRNA	IMP PMID:15716506 Mutations in the Saccharomyces cerevisiae LSM1 gene that aff...	ACCEPT	Summary: IMP evidence from mutagenesis study directly testing LSM1 function in mRNA decapping. Tharun et al. (2005) used point mutations of LSM1 to show impaired mRNA decay and defective decapping. Reason: This is strong experimental evidence that LSM1 is required for mRNA decapping activation. The mutagenesis study demonstrates that RNA-binding residues are critical for function, confirming the mechanistic role. Duplicate annotation with different evidence codes is appropriate. Supporting Evidence: PMID:15716506 Mutations affecting the predicted RNA-binding and inter-subunit interaction residues of Lsm1p led to impairment of mRNA decay, suggesting that the integrity of the Lsm1p-7p complex and the ability of the Lsm1p-7p complex to interact with mRNA are important for mRNA decay function
GO:0000932 P-body	IDA PMID:12730603 Decapping and decay of messenger RNA occur in cytoplasmic pr...	ACCEPT	Summary: IDA evidence from immunofluorescence and localization studies showing LSM1 in P-bodies. Sheth & Parker (2003) demonstrated that decapping enzymes and LSM proteins localize to P-bodies. Reason: Direct observation of LSM1 localization to P-bodies where mRNA decay occurs. This is consistent with IBA and IMP annotations and represents core cellular compartmentalization of LSM1 function. Supporting Evidence: PMID:12730603 proteins that activate or catalyze decapping are concentrated in P bodies
GO:0005737 cytoplasm	HDA PMID:22842922 Dissecting DNA damage response pathways by analysing protein...	ACCEPT	Summary: HDA (high-throughput direct assay) evidence showing cytoplasmic localization from DNA damage response studies detecting LSM1 in cytoplasm. Reason: Cytoplasmic localization is well-established and essential for LSM1 function. HDA evidence is high-confidence direct observation. Consistent with other localization evidence. Supporting Evidence: PMID:22842922 Dissecting DNA damage response pathways by analysing protein localization and abundance changes during DNA replication stress
GO:1990726 Lsm1-7-Pat1 complex	IDA PMID:24139796 Architecture of the Lsm1-7-Pat1 complex: a conserved assembl...	ACCEPT	Summary: IDA evidence from crystal structure showing LSM1 as core subunit of the Lsm1-7-Pat1 complex. Sharif & Conti (2013) provided 2.3 Å structure demonstrating complex architecture. Reason: The crystal structure provides definitive evidence of LSM1 as a core component of the Lsm1-7-Pat1 complex. This is the highest quality structural evidence and confirms mechanistic details of complex assembly. Supporting Evidence: PMID:24139796 The 2.3 Å resolution structure of S. cerevisiae Lsm1-7 shows the presence of a heptameric ring
GO:0003729 mRNA binding	IDA PMID:23222640 Global analysis of yeast mRNPs.	ACCEPT	Summary: IDA evidence from global analysis of yeast mRNPs (messenger ribonucleoprotein particles) showing LSM1 associated with mRNA. Reason: Direct evidence of LSM1 in mRNP complexes confirms functional mRNA binding. Consistent with IBA annotation and structural data showing RNA binding pocket. Supporting Evidence: PMID:23222640 Global analysis of yeast mRNPs
GO:0003682 chromatin binding	IDA PMID:23706738 Gene expression is circular: factors for mRNA degradation al...	KEEP AS NON CORE	Summary: IDA evidence for a nuclear "moonlighting" role of LSM1. Haimovich et al. (2013) report that cytoplasmic mRNA-decay ("decaysome") components shuttle to the nucleus and associate with chromatin just upstream of transcription start sites, where they stimulate transcription. This is a separate activity from LSM1's well-established cytoplasmic decapping-activation function. Reason: The SGD curator made this an experimental (IDA) annotation from the full text, and the cached abstract independently describes decaysome components associating with chromatin near transcription start sites, so there is no basis for removing it by second-guessing the curator without full-text access. The nuclear chromatin association is nonetheless a secondary role distinct from LSM1's core cytoplasmic mRNA-decay function, so it is retained as non-core rather than accepted as core. Supporting Evidence: PMID:23706738 these components shuttle between the cytoplasm and the nucleus, in a manner dependent on proper mRNA degradation. In the nucleus, they associate with chromatin-preferentially ∼30 bp upstream of transcription start-sites-and directly stimulate transcription initiation and elongation.
GO:0005634 nucleus	IDA PMID:23706738 Gene expression is circular: factors for mRNA degradation al...	KEEP AS NON CORE	Summary: IDA evidence showing nuclear localization from the "Gene expression is circular" study. LSM1 is detected in both nucleus and cytoplasm. Reason: Nuclear localization is documented and consistent with the UniProt record, but it reflects the same secondary shuttling/chromatin-association phenomenon as the GO:0003682 annotation from this paper, not LSM1's core site of action. Retained as non-core for consistency with the chromatin binding entry and with core_functions, which lists only cytoplasm and P-body locations. Supporting Evidence: PMID:23706738 these components shuttle between the cytoplasm and the nucleus, in a manner dependent on proper mRNA degradation
GO:0005737 cytoplasm	IDA PMID:23706738 Gene expression is circular: factors for mRNA degradation al...	ACCEPT	Summary: IDA evidence confirming cytoplasmic localization from direct observation studies. Reason: Cytoplasm is the primary site of LSM1 function. Direct observation confirms expected localization. Supporting Evidence: PMID:23706738 most yeast mRNAs are degraded by the cytoplasmic 5'-to-3' pathway (the "decaysome")
GO:0000288 nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay	IMP PMID:10747033 A Sm-like protein complex that participates in mRNA degradat...	ACCEPT	Summary: IMP evidence from Bouveret et al. (2000) directly demonstrating LSM1 involvement in deadenylation-dependent mRNA decay through deletion analysis. Reason: LSM1 deletion mutants showed increased mRNA half-life and accumulation of capped mRNAs, demonstrating a block in the decapping step. This is the seminal paper identifying the Lsm1-7 complex role in mRNA decay. Core functional annotation. Supporting Evidence: PMID:10747033 Deletions of LSM1, 6, 7 and PAT1 genes increased the half-life of reporter mRNAs. Interestingly, accumulating mRNAs were capped, suggesting a block in mRNA decay at the decapping step.
GO:0000290 deadenylation-dependent decapping of nuclear-transcribed mRNA	IMP PMID:10761922 Yeast Sm-like proteins function in mRNA decapping and decay.	ACCEPT	Summary: IMP evidence from Tharun et al. (2000) showing LSM1-Lsm7 mutations inhibit mRNA decapping and demonstrating interaction with decapping machinery. Reason: Tharun et al. demonstrated that lsm mutations specifically block mRNA decapping, and that Lsm proteins co-immunoprecipitate with Dcp1 and mRNA. This establishes the mechanistic link between LSM1 and decapping activation. Duplicate IMP annotation with different PMID is appropriate as it provides additional mechanistic detail. Supporting Evidence: PMID:10761922 mutations in seven yeast Lsm proteins (Lsm1-Lsm7) also lead to inhibition of mRNA decapping
GO:0000932 P-body	IMP PMID:12730603 Decapping and decay of messenger RNA occur in cytoplasmic pr...	ACCEPT	Summary: IMP evidence showing P-body function in mRNA decay where LSM1 acts as part of the decapping and decay machinery. Reason: While primarily a localization annotation (IDA also exists for same PMID), the IMP evidence demonstrates that P-body function in mRNA decay is dependent on the decapping machinery where LSM1 operates. Both evidence types are valid and appropriate. Supporting Evidence: PMID:12730603 A major pathway of eukaryotic messenger RNA (mRNA) turnover begins with deadenylation, followed by decapping and 5' to 3' exonucleolytic decay
GO:0000932 P-body	IDA PMID:18611963 A role for Q/N-rich aggregation-prone regions in P-body loca...	ACCEPT	Summary: IDA evidence showing LSM1 localization to P-bodies in studies of Q/N-rich aggregation-prone regions required for P-body localization. Reason: Direct observation of LSM1 in P-bodies. This annotation is consistent with other P-body localization evidence. Duplicate IDA annotations with different PMIDs are acceptable as they represent independent observations. Supporting Evidence: PMID:18611963 A role for Q/N-rich aggregation-prone regions in P-body localization
GO:0005737 cytoplasm	IDA PMID:18029398 Requirements for nuclear localization of the Lsm2-8p complex...	ACCEPT	Summary: IDA evidence from studies of Lsm2-8 nuclear complex showing that LSM1-7 cytoplasmic complex has different localization than its U6-binding counterpart. Reason: Direct evidence of LSM1-7 cytoplasmic localization, demonstrating distinction from nuclear Lsm2-8 complex. Consistent with other cytoplasmic localization evidence. Supporting Evidence: PMID:18029398 Requirements for nuclear localization of the Lsm2-8p complex and competition between nuclear and cytoplasmic Lsm complexes

Gene Description

Existing Annotations Review

Core Functions

References

Deep Research

Falcon

📚 Additional Documentation

Notes

Curation Summary

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