id: P47017
gene_symbol: LSM1
aliases:
- SPB8
- YJL124C
- J0714
product_type: PROTEIN
status: COMPLETE
taxon:
  id: NCBITaxon:559292
  label: Saccharomyces cerevisiae
description: LSM1 (Lsm1p) is the defining component of the cytoplasmic Lsm1-7-Pat1
  heptameric complex, which is a critical activator of mRNA decapping and a key effector
  of deadenylation-dependent mRNA decay. Unlike other Lsm proteins (Lsm2-8) that function
  in U6 snRNA splicing, LSM1 is unique and forms a complex specifically involved in
  cytoplasmic mRNA turnover. The Lsm1-7 complex binds to poly(U) tracts at the 3'
  end of deadenylated mRNAs and recruits the decapping machinery (Dcp1/Dcp2), converting
  capped mRNAs to susceptible substrates for 5' to 3' exonucleolytic degradation by
  Xrn1. The complex also functions in protective binding to mRNA 3' ends. LSM1 is
  predominantly cytoplasmic but can also localize to P-bodies and has been detected
  in the nucleus.
core_functions:
- molecular_function:
    id: GO:0003729
    label: mRNA binding
  description: LSM1 binds mRNA through its Sm domain, specifically recognizing poly(U)
    tracts at the 3' end of deadenylated mRNAs. This RNA binding is essential for
    the activation of decapping and represents a core catalytic property of LSM1.
    LSM1 functions as part of the Lsm1-7-Pat1 complex where it plays the defining
    role in mRNA decay activation through deadenylation-dependent decapping and 5'
    to 3' exonucleolytic degradation.
  directly_involved_in:
  - id: GO:0000290
    label: deadenylation-dependent decapping of nuclear-transcribed mRNA
  - id: GO:0000288
    label: nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay
  locations:
  - id: GO:0005737
    label: cytoplasm
  - id: GO:0000932
    label: P-body
existing_annotations:
- term:
    id: GO:0000290
    label: deadenylation-dependent decapping of nuclear-transcribed mRNA
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    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.
    action: ACCEPT
    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.
    supported_by:
    - reference_id: PMID:10747033
      supporting_text: 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.
    - reference_id: PMID:10761922
      supporting_text: mutations in seven yeast Lsm proteins (Lsm1-Lsm7) also lead
        to inhibition of mRNA decapping
    - reference_id: PMID:15716506
      supporting_text: The decapping of eukaryotic mRNAs is a key step in their degradation.
        The heteroheptameric Lsm1p-7p complex is a general activator of decapping
- term:
    id: GO:0003729
    label: mRNA binding
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    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.
    action: ACCEPT
    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.
    supported_by:
    - reference_id: PMID:15716506
      supporting_text: 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
    - reference_id: PMID:24139796
      supporting_text: 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.
- term:
    id: GO:1990726
    label: Lsm1-7-Pat1 complex
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    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.
    action: ACCEPT
    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.
    supported_by:
    - reference_id: PMID:10747033
      supporting_text: Lsm1p, together with Lsm2p-Lsm7p, forms a new seven-subunit
        complex...the Lsm1p-Lsm7p complex is associated with Pat1p and Xrn1p exoribonuclease
    - reference_id: PMID:24139796
      supporting_text: 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
- term:
    id: GO:0000932
    label: P-body
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    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.
    action: ACCEPT
    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.
    supported_by:
    - reference_id: PMID:12730603
      supporting_text: proteins that activate or catalyze decapping are concentrated
        in P bodies...mRNA degradation intermediates are localized to P bodies
- term:
    id: GO:0000932
    label: P-body
  evidence_type: IEA
  original_reference_id: GO_REF:0000044
  review:
    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.
    action: ACCEPT
    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.
    supported_by: []
- term:
    id: GO:0000956
    label: nuclear-transcribed mRNA catabolic process
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  review:
    summary: This parent mRNA catabolic process term is valid but broader than the
      specific decay subprocesses curated for LSM1.
    action: KEEP_AS_NON_CORE
    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.
    supported_by: []
- term:
    id: GO:0003723
    label: RNA binding
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  review:
    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.
    action: KEEP_AS_NON_CORE
    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.
    supported_by: []
- term:
    id: GO:0005634
    label: nucleus
  evidence_type: IEA
  original_reference_id: GO_REF:0000044
  review:
    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.
    action: ACCEPT
    reason: LSM1 is present in both nucleus and cytoplasm. The UniProt entry states
      nuclear localization with ECO:0000269|PubMed:10761922 evidence. While the primary
      function of LSM1 is in the cytoplasm for mRNA decay, nuclear detection is documented
      and the annotation is correct.
    supported_by:
    - reference_id: PMID:10761922
      supporting_text: the Lsm1-Lsm7 proteins co-immunoprecipitate with the mRNA decapping
        enzyme (Dcp1), a decapping activator (Pat1/Mrt1) and with mRNA
- term:
    id: GO:0005737
    label: cytoplasm
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  review:
    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.
    action: ACCEPT
    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.
    supported_by: []
- term:
    id: GO:0006397
    label: mRNA processing
  evidence_type: IEA
  original_reference_id: GO_REF:0000043
  review:
    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.
    action: REMOVE
    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.
    supported_by: []
- term:
    id: GO:0032991
    label: protein-containing complex
  evidence_type: IEA
  original_reference_id: GO_REF:0000117
  review:
    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.
    action: ACCEPT
    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).
    supported_by: []
- term:
    id: GO:1990904
    label: ribonucleoprotein complex
  evidence_type: IEA
  original_reference_id: GO_REF:0000043
  review:
    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.
    action: ACCEPT
    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.
    supported_by: []
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:10688190
  review:
    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.
    action: MARK_AS_OVER_ANNOTATED
    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_replacement_terms:
    - id: GO:1990726
      label: Lsm1-7-Pat1 complex
    supported_by:
    - reference_id: PMID:10688190
      supporting_text: A comprehensive analysis of protein-protein interactions in
        Saccharomyces cerevisiae.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:10900456
  review:
    summary: IPI evidence from genome-wide protein interaction screens showing LSM1
      interactions with PAT1 and other Lsm proteins.
    action: MARK_AS_OVER_ANNOTATED
    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_replacement_terms:
    - id: GO:1990726
      label: Lsm1-7-Pat1 complex
    supported_by:
    - reference_id: PMID:10900456
      supporting_text: Genome-wide protein interaction screens reveal functional networks
        involving Sm-like proteins.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:11780629
  review:
    summary: IPI evidence showing interaction of LSM1 with Dhh1 (DEAD box helicase)
      documented in interaction studies.
    action: MARK_AS_OVER_ANNOTATED
    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.
    proposed_replacement_terms: []
    supported_by:
    - reference_id: PMID:11780629
      supporting_text: The DEAD box helicase, Dhh1p, functions in mRNA decapping and
        interacts with both the decapping and deadenylase complexes.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:11805837
  review:
    summary: IPI evidence from mass spectrometry studies of protein complexes identifying
      LSM1 in the Lsm1-7-Pat1 complex.
    action: MARK_AS_OVER_ANNOTATED
    reason: Generic protein binding annotation redundant with complex component annotation.
      The systematic protein complex identification is better represented by GO:1990726.
    proposed_replacement_terms:
    - id: GO:1990726
      label: Lsm1-7-Pat1 complex
    supported_by:
    - reference_id: PMID:11805837
      supporting_text: Systematic identification of protein complexes in Saccharomyces
        cerevisiae by mass spectrometry.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:14759368
  review:
    summary: IPI evidence from high-definition macromolecular composition of yeast
      RNA-processing complexes.
    action: MARK_AS_OVER_ANNOTATED
    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_replacement_terms:
    - id: GO:1990726
      label: Lsm1-7-Pat1 complex
    supported_by:
    - reference_id: PMID:14759368
      supporting_text: High-definition macromolecular composition of yeast RNA-processing
        complexes.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:16429126
  review:
    summary: IPI evidence from proteome survey identifying LSM1 protein interactions.
    action: MARK_AS_OVER_ANNOTATED
    reason: Generic annotation without functional specificity. LSM1 protein interactions
      are functionally significant only in the context of mRNA decay machinery assembly.
    proposed_replacement_terms:
    - id: GO:1990726
      label: Lsm1-7-Pat1 complex
    supported_by:
    - reference_id: PMID:16429126
      supporting_text: Proteome survey reveals modularity of the yeast cell machinery.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:16554755
  review:
    summary: IPI evidence from global landscape studies of yeast protein complexes.
    action: MARK_AS_OVER_ANNOTATED
    reason: Generic protein binding term redundant with more specific complex component
      annotation.
    proposed_replacement_terms:
    - id: GO:1990726
      label: Lsm1-7-Pat1 complex
    supported_by:
    - reference_id: PMID:16554755
      supporting_text: Global landscape of protein complexes in the yeast Saccharomyces
        cerevisiae.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:18719252
  review:
    summary: IPI evidence from high-quality binary protein interaction mapping.
    action: MARK_AS_OVER_ANNOTATED
    reason: Binary protein interactions documented but better represented by complex
      component annotation.
    proposed_replacement_terms:
    - id: GO:1990726
      label: Lsm1-7-Pat1 complex
    supported_by:
    - reference_id: PMID:18719252
      supporting_text: High-quality binary protein interaction map of the yeast interactome
        network.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:23267104
  review:
    summary: IPI evidence from proteome-wide protein interaction measurements.
    action: MARK_AS_OVER_ANNOTATED
    reason: Generic binding annotation without functional context.
    proposed_replacement_terms:
    - id: GO:1990726
      label: Lsm1-7-Pat1 complex
    supported_by:
    - reference_id: PMID:23267104
      supporting_text: Proteome-wide protein interaction measurements of bacterial
        proteins of unknown function.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:37070168
  review:
    summary: IPI evidence from RNA-dependent interactome analysis.
    action: MARK_AS_OVER_ANNOTATED
    reason: Generic protein binding term lacks functional specificity for RNA-binding
      protein annotation.
    proposed_replacement_terms:
    - id: GO:1990726
      label: Lsm1-7-Pat1 complex
    supported_by:
    - reference_id: PMID:37070168
      supporting_text: RNA-dependent interactome allows network-based assignment of
        RNA-binding protein function.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:37968396
  review:
    summary: IPI evidence from social and structural architecture study of yeast protein
      interactome.
    action: MARK_AS_OVER_ANNOTATED
    reason: Generic annotation not informative for molecular function annotation.
    proposed_replacement_terms:
    - id: GO:1990726
      label: Lsm1-7-Pat1 complex
    supported_by:
    - reference_id: PMID:37968396
      supporting_text: The social and structural architecture of the yeast protein
        interactome.
- term:
    id: GO:0000290
    label: deadenylation-dependent decapping of nuclear-transcribed mRNA
  evidence_type: IMP
  original_reference_id: PMID:15716506
  review:
    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.
    action: ACCEPT
    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.
    supported_by:
    - reference_id: PMID:15716506
      supporting_text: 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
- term:
    id: GO:0000932
    label: P-body
  evidence_type: IDA
  original_reference_id: PMID:12730603
  review:
    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.
    action: ACCEPT
    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.
    supported_by:
    - reference_id: PMID:12730603
      supporting_text: proteins that activate or catalyze decapping are concentrated
        in P bodies
- term:
    id: GO:0005737
    label: cytoplasm
  evidence_type: HDA
  original_reference_id: PMID:22842922
  review:
    summary: HDA (high-throughput direct assay) evidence showing cytoplasmic localization
      from DNA damage response studies detecting LSM1 in cytoplasm.
    action: ACCEPT
    reason: Cytoplasmic localization is well-established and essential for LSM1 function.
      HDA evidence is high-confidence direct observation. Consistent with other localization
      evidence.
    supported_by:
    - reference_id: PMID:22842922
      supporting_text: Dissecting DNA damage response pathways by analysing protein
        localization and abundance changes during DNA replication stress
- term:
    id: GO:1990726
    label: Lsm1-7-Pat1 complex
  evidence_type: IDA
  original_reference_id: PMID:24139796
  review:
    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.
    action: ACCEPT
    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.
    supported_by:
    - reference_id: PMID:24139796
      supporting_text: The 2.3 Å resolution structure of S. cerevisiae Lsm1-7 shows
        the presence of a heptameric ring
- term:
    id: GO:0003729
    label: mRNA binding
  evidence_type: IDA
  original_reference_id: PMID:23222640
  review:
    summary: IDA evidence from global analysis of yeast mRNPs (messenger ribonucleoprotein
      particles) showing LSM1 associated with mRNA.
    action: ACCEPT
    reason: Direct evidence of LSM1 in mRNP complexes confirms functional mRNA binding.
      Consistent with IBA annotation and structural data showing RNA binding pocket.
    supported_by:
    - reference_id: PMID:23222640
      supporting_text: Global analysis of yeast mRNPs
- term:
    id: GO:0003682
    label: chromatin binding
  evidence_type: IDA
  original_reference_id: PMID:23706738
  review:
    summary: IDA evidence from localization study reporting LSM1 chromatin binding.
      However, this annotation may reflect contamination or indirect association rather
      than true chromatin binding.
    action: REMOVE
    reason: LSM1 is an mRNA decay protein, not primarily a chromatin-binding protein.
      The Lsm1-7 complex functions in the cytoplasm and at P-bodies on mRNA transcripts,
      not at chromatin. The annotation from PMID:23706738 appears to report LSM1 in
      nuclei and potentially binding to chromatin during the "Gene expression is circular"
      studies, but this is not a core function. LSM1 does not have characteristic
      chromatin-binding domains. This annotation likely represents mislocalization
      or experimental artifact and should not be retained.
    supported_by:
    - reference_id: PMID:23706738
      supporting_text: 'Gene expression is circular: factors for mRNA degradation
        also foster mRNA synthesis.'
- term:
    id: GO:0005634
    label: nucleus
  evidence_type: IDA
  original_reference_id: PMID:23706738
  review:
    summary: IDA evidence showing nuclear localization from the "Gene expression is
      circular" study. LSM1 is detected in both nucleus and cytoplasm.
    action: ACCEPT
    reason: Consistent with UniProt annotation showing nuclear localization. While
      cytoplasmic mRNA decay is the primary function, nuclear detection is documented.
      Acceptable to retain.
    supported_by:
    - reference_id: PMID:23706738
      supporting_text: 'Gene expression is circular: factors for mRNA degradation
        also foster mRNA synthesis.'
- term:
    id: GO:0005737
    label: cytoplasm
  evidence_type: IDA
  original_reference_id: PMID:23706738
  review:
    summary: IDA evidence confirming cytoplasmic localization from direct observation
      studies.
    action: ACCEPT
    reason: Cytoplasm is the primary site of LSM1 function. Direct observation confirms
      expected localization.
    supported_by:
    - reference_id: PMID:23706738
      supporting_text: 'Gene expression is circular: factors for mRNA degradation
        also foster mRNA synthesis.'
- term:
    id: GO:0000288
    label: nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay
  evidence_type: IMP
  original_reference_id: PMID:10747033
  review:
    summary: IMP evidence from Bouveret et al. (2000) directly demonstrating LSM1
      involvement in deadenylation-dependent mRNA decay through deletion analysis.
    action: ACCEPT
    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.
    supported_by:
    - reference_id: PMID:10747033
      supporting_text: 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.
- term:
    id: GO:0000290
    label: deadenylation-dependent decapping of nuclear-transcribed mRNA
  evidence_type: IMP
  original_reference_id: PMID:10761922
  review:
    summary: IMP evidence from Tharun et al. (2000) showing LSM1-Lsm7 mutations inhibit
      mRNA decapping and demonstrating interaction with decapping machinery.
    action: ACCEPT
    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.
    supported_by:
    - reference_id: PMID:10761922
      supporting_text: mutations in seven yeast Lsm proteins (Lsm1-Lsm7) also lead
        to inhibition of mRNA decapping
- term:
    id: GO:0000932
    label: P-body
  evidence_type: IMP
  original_reference_id: PMID:12730603
  review:
    summary: IMP evidence showing P-body function in mRNA decay where LSM1 acts as
      part of the decapping and decay machinery.
    action: ACCEPT
    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.
    supported_by:
    - reference_id: PMID:12730603
      supporting_text: A major pathway of eukaryotic messenger RNA (mRNA) turnover
        begins with deadenylation, followed by decapping and 5' to 3' exonucleolytic
        decay
- term:
    id: GO:0000932
    label: P-body
  evidence_type: IDA
  original_reference_id: PMID:18611963
  review:
    summary: IDA evidence showing LSM1 localization to P-bodies in studies of Q/N-rich
      aggregation-prone regions required for P-body localization.
    action: ACCEPT
    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.
    supported_by:
    - reference_id: PMID:18611963
      supporting_text: A role for Q/N-rich aggregation-prone regions in P-body localization
- term:
    id: GO:0005737
    label: cytoplasm
  evidence_type: IDA
  original_reference_id: PMID:18029398
  review:
    summary: IDA evidence from studies of Lsm2-8 nuclear complex showing that LSM1-7
      cytoplasmic complex has different localization than its U6-binding counterpart.
    action: ACCEPT
    reason: Direct evidence of LSM1-7 cytoplasmic localization, demonstrating distinction
      from nuclear Lsm2-8 complex. Consistent with other cytoplasmic localization
      evidence.
    supported_by:
    - reference_id: PMID:18029398
      supporting_text: Requirements for nuclear localization of the Lsm2-8p complex
        and competition between nuclear and cytoplasmic Lsm complexes
references:
- id: GO_REF:0000002
  title: Gene Ontology annotation through association of InterPro records with GO
    terms
  findings: []
- id: GO_REF:0000033
  title: Annotation inferences using phylogenetic trees
  findings: []
- id: GO_REF:0000043
  title: Gene Ontology annotation based on UniProtKB/Swiss-Prot keyword mapping
  findings: []
- id: GO_REF:0000044
  title: Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular Location
    vocabulary mapping, accompanied by conservative changes to GO terms applied by
    UniProt
  findings: []
- id: GO_REF:0000117
  title: Electronic Gene Ontology annotations created by ARBA machine learning models
  findings: []
- id: GO_REF:0000120
  title: Combined Automated Annotation using Multiple IEA Methods
  findings: []
- id: PMID:10688190
  title: A comprehensive analysis of protein-protein interactions in Saccharomyces
    cerevisiae.
  findings: []
- id: PMID:10747033
  title: A Sm-like protein complex that participates in mRNA degradation.
  findings: []
- id: PMID:10761922
  title: Yeast Sm-like proteins function in mRNA decapping and decay.
  findings: []
- id: PMID:10900456
  title: Genome-wide protein interaction screens reveal functional networks involving
    Sm-like proteins.
  findings: []
- id: PMID:11780629
  title: The DEAD box helicase, Dhh1p, functions in mRNA decapping and interacts with
    both the decapping and deadenylase complexes.
  findings: []
- id: PMID:11805837
  title: Systematic identification of protein complexes in Saccharomyces cerevisiae
    by mass spectrometry.
  findings: []
- id: PMID:12730603
  title: Decapping and decay of messenger RNA occur in cytoplasmic processing bodies.
  findings: []
- id: PMID:14759368
  title: High-definition macromolecular composition of yeast RNA-processing complexes.
  findings: []
- id: PMID:15716506
  title: Mutations in the Saccharomyces cerevisiae LSM1 gene that affect mRNA decapping
    and 3' end protection.
  findings: []
- id: PMID:16429126
  title: Proteome survey reveals modularity of the yeast cell machinery.
  findings: []
- id: PMID:16554755
  title: Global landscape of protein complexes in the yeast Saccharomyces cerevisiae.
  findings: []
- id: PMID:18029398
  title: Requirements for nuclear localization of the Lsm2-8p complex and competition
    between nuclear and cytoplasmic Lsm complexes.
  findings: []
- id: PMID:18611963
  title: A role for Q/N-rich aggregation-prone regions in P-body localization.
  findings: []
- id: PMID:18719252
  title: High-quality binary protein interaction map of the yeast interactome network.
  findings: []
- id: PMID:22842922
  title: Dissecting DNA damage response pathways by analysing protein localization
    and abundance changes during DNA replication stress.
  findings: []
- id: PMID:23222640
  title: Global analysis of yeast mRNPs.
  findings: []
- id: PMID:23267104
  title: Proteome-wide protein interaction measurements of bacterial proteins of unknown
    function.
  findings: []
- id: PMID:23706738
  title: 'Gene expression is circular: factors for mRNA degradation also foster mRNA
    synthesis.'
  findings: []
- id: PMID:24139796
  title: 'Architecture of the Lsm1-7-Pat1 complex: a conserved assembly in eukaryotic
    mRNA turnover.'
  findings: []
- id: PMID:37070168
  title: RNA-dependent interactome allows network-based assignment of RNA-binding
    protein function.
  findings: []
- id: PMID:37968396
  title: The social and structural architecture of the yeast protein interactome.
  findings: []