{"gene":"DYNLT4","run_date":"2026-06-09T23:54:42","timeline":{"discoveries":[{"year":2013,"finding":"TCTEX1D4 (DYNLT4) interacts with PPP1CC (protein phosphatase 1) isoforms; the interaction is mediated by an N-terminal consensus PPP1 binding motif (RVSF). TCTEX1D4 and PPP1 co-localize at the microtubule organizing center (MTOC) and along microtubules in cell culture, and the PPP1 binding motif is required for PPP1 retention at the MTOC and movement along microtubules.","method":"Yeast two-hybrid screen with human testis cDNA library; overlay assays confirming interaction with PPP1CC isoforms; immunofluorescence co-localization in cell cultures; mutational analysis of the PPP1 binding motif","journal":"Biology open","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — yeast two-hybrid confirmed by overlay assay and immunofluorescence co-localization with functional consequence (MTOC retention), single lab with two orthogonal methods","pmids":["23789093"],"is_preprint":false},{"year":2013,"finding":"The PPP1 binding motif RVSF at positions 90-93 is conserved across 21 mammalian species and is sufficient for PPP1 binding; in pika (Ochotona) species where this motif is disrupted, flanking N- and C-terminal residues compensate to maintain PPP1 binding, as shown by mutational screening.","method":"Comparative sequence analysis across 21 mammalian and 7 Lagomorpha species; mutational screening validating PPP1 binding despite disrupted canonical motif","journal":"PloS one","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — mutational screening demonstrating binding maintenance with disrupted motif, single lab with functional binding validation","pmids":["24130861"],"is_preprint":false},{"year":2014,"finding":"Yeast two-hybrid screening in human testis identified 40 novel TCTEX1D4 (DYNLT4) interacting proteins, confirming its capacity to engage functionally diverse binding partners consistent with a role in sperm motility, intraflagellar transport, and acrosome reaction.","method":"Yeast two-hybrid assay with human testis cDNA library; immunofluorescence studies on spermatozoa; in silico interactome profile","journal":"Omics : a journal of integrative biology","confidence":"Low","confidence_rationale":"Tier 3 / Weak — yeast two-hybrid identifies interactors but no biochemical validation of individual interactions reported in abstract; single lab, single method for the novel interactors","pmids":["24606217"],"is_preprint":false},{"year":2026,"finding":"The E3 ubiquitin ligase Mid1 promotes ubiquitin-proteasome-dependent degradation of DYNLT4 (dynein light chain family member), and this degradation disrupts retrograde axonal transport in hippocampal neurons.","method":"RNA-sequencing, molecular biology/Western blot approaches, Mid1 silencing/knockdown, live-cell imaging-based axonal transport assays in HT-22 cells and primary hippocampal neurons","journal":"Journal of advanced research","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — genetic loss-of-function (Mid1 knockdown) with defined cellular phenotype (retrograde transport), and mechanistic pathway placement via ubiquitin-proteasome pathway; single lab","pmids":["41651028"],"is_preprint":false}],"current_model":"DYNLT4 (TCTEX1D4) is a dynein light chain family member that interacts with protein phosphatase 1 (PPP1CC) via an N-terminal RVSF motif, co-localizing with PPP1 at the MTOC and along microtubules; it engages diverse binding partners in testis relevant to sperm motility and intraflagellar transport, and its protein levels are regulated by Mid1-mediated ubiquitin-proteasome degradation, with loss of DYNLT4 disrupting retrograde axonal transport in hippocampal neurons."},"narrative":{"mechanistic_narrative":"DYNLT4 (TCTEX1D4) is a dynein light chain family member that functions as a microtubule-associated adaptor coupling protein phosphatase 1 to the microtubule cytoskeleton and supporting dynein-based transport [PMID:23789093, PMID:41651028]. It binds PPP1CC isoforms through an N-terminal RVSF consensus motif at positions 90-93, and this interaction recruits and retains PPP1 at the microtubule organizing center and along microtubules; the motif is required for PPP1 retention and movement [PMID:23789093]. The RVSF motif is conserved across mammals, and where it is disrupted, flanking residues compensate to preserve PPP1 binding [PMID:24130861]. DYNLT4 protein levels are controlled by Mid1-mediated ubiquitin-proteasome degradation, and loss of DYNLT4 disrupts retrograde axonal transport in hippocampal neurons, linking it to dynein-dependent cargo movement [PMID:41651028]. A testis-enriched interactome consistent with roles in sperm motility and intraflagellar transport has been catalogued [PMID:24606217], but beyond the PPP1 interaction and the Mid1 degradation axis, the biochemical detail of these partnerships has not been characterized in the available corpus.","teleology":[{"year":2013,"claim":"Established that DYNLT4 is not merely a dynein component but a direct adaptor for protein phosphatase 1, defining a molecular link between the phosphatase and the microtubule cytoskeleton.","evidence":"Yeast two-hybrid screen of human testis cDNA, overlay assays against PPP1CC isoforms, immunofluorescence co-localization, and mutational analysis of the RVSF motif in cell culture","pmids":["23789093"],"confidence":"Medium","gaps":["Functional consequence of PPP1 retention at the MTOC for cell physiology not defined","Substrates dephosphorylated by the DYNLT4-PPP1 complex unidentified","No structural model of the interaction"]},{"year":2013,"claim":"Showed the PPP1-binding RVSF motif is evolutionarily conserved and that binding is robust to motif disruption via compensatory flanking residues, indicating PPP1 engagement is a constrained, functionally important feature of DYNLT4.","evidence":"Comparative sequence analysis across 21 mammalian and 7 Lagomorpha species with mutational screening of binding","pmids":["24130861"],"confidence":"Medium","gaps":["Physiological role of conservation not tested in vivo","Whether compensatory binding is functionally equivalent unknown"]},{"year":2014,"claim":"Expanded the candidate interactome of DYNLT4 in testis, raising the possibility of roles in sperm motility, intraflagellar transport, and the acrosome reaction.","evidence":"Yeast two-hybrid screen of human testis cDNA, immunofluorescence on spermatozoa, and in silico interactome profiling","pmids":["24606217"],"confidence":"Low","gaps":["No biochemical validation of the 40 novel interactors beyond yeast two-hybrid","Functional roles in sperm/cilia not demonstrated","Single method, single lab"]},{"year":2026,"claim":"Placed DYNLT4 in a regulated degradation pathway and tied its abundance to a concrete transport phenotype, establishing functional importance in neuronal cargo trafficking.","evidence":"RNA-sequencing, Mid1 knockdown, Western blot, and live-cell axonal transport imaging in HT-22 cells and primary hippocampal neurons","pmids":["41651028"],"confidence":"Medium","gaps":["Direct ubiquitination of DYNLT4 by Mid1 not biochemically reconstituted","Mechanism linking DYNLT4 level to retrograde transport machinery unresolved","Single lab"]},{"year":null,"claim":"How DYNLT4's PPP1-scaffolding activity, its testis interactome, and its Mid1-regulated role in axonal transport integrate into a unified cellular function remains unresolved.","evidence":"","pmids":[],"confidence":"Low","gaps":["No structural data on the DYNLT4-dynein or DYNLT4-PPP1 assembly","Substrates of the targeted phosphatase activity unknown","Whether the testis and neuronal roles share a common mechanism untested"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[0]},{"term_id":"GO:0008092","term_label":"cytoskeletal protein binding","supporting_discovery_ids":[0]}],"localization":[{"term_id":"GO:0005815","term_label":"microtubule organizing center","supporting_discovery_ids":[0]},{"term_id":"GO:0005856","term_label":"cytoskeleton","supporting_discovery_ids":[0]}],"pathway":[],"complexes":[],"partners":["PPP1CC","MID1"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q5JR98","full_name":"Dynein light chain Tctex-type 4","aliases":["Protein N22.1","Tctex-2-beta","Tctex1 domain-containing protein 4"],"length_aa":221,"mass_kda":23.4,"function":"","subcellular_location":"Cell projection, cilium, flagellum; Cytoplasmic vesicle, secretory vesicle, acrosome; Cytoplasm, cytoskeleton, cilium axoneme; Cytoplasm; Nucleus; Cytoplasm, cytoskeleton, microtubule organizing center","url":"https://www.uniprot.org/uniprotkb/Q5JR98/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/DYNLT4","classification":"Not Classified","n_dependent_lines":10,"n_total_lines":1208,"dependency_fraction":0.008278145695364239},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/DYNLT4","total_profiled":1310},"omim":[{"mim_id":"612257","title":"MICROTUBULE-ASSOCIATED SERINE/THREONINE KINASE 2; MAST2","url":"https://www.omim.org/entry/612257"},{"mim_id":"611713","title":"DYNEIN, LIGHT CHAIN, TCTEX-TYPE 4; DYNLT4","url":"https://www.omim.org/entry/611713"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Vesicles","reliability":"Supported"}],"tissue_specificity":"Group enriched","tissue_distribution":"Detected in many","driving_tissues":[{"tissue":"choroid plexus","ntpm":22.9},{"tissue":"fallopian tube","ntpm":6.5}],"url":"https://www.proteinatlas.org/search/DYNLT4"},"hgnc":{"alias_symbol":[],"prev_symbol":["TCTEX1D4"]},"alphafold":{"accession":"Q5JR98","domains":[{"cath_id":"3.30.1140.40","chopping":"121-220","consensus_level":"high","plddt":94.5883,"start":121,"end":220}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q5JR98","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q5JR98-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q5JR98-F1-predicted_aligned_error_v6.png","plddt_mean":73.31},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=DYNLT4","jax_strain_url":"https://www.jax.org/strain/search?query=DYNLT4"},"sequence":{"accession":"Q5JR98","fasta_url":"https://rest.uniprot.org/uniprotkb/Q5JR98.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q5JR98/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q5JR98"}},"corpus_meta":[{"pmid":"23789093","id":"PMC_23789093","title":"TCTEX1D4, a novel protein phosphatase 1 interactor: connecting the phosphatase to the microtubule network.","date":"2013","source":"Biology open","url":"https://pubmed.ncbi.nlm.nih.gov/23789093","citation_count":16,"is_preprint":false},{"pmid":"24606217","id":"PMC_24606217","title":"TCTEX1D4 interactome in human testis: unraveling the function of dynein light chain in spermatozoa.","date":"2014","source":"Omics : a journal of integrative biology","url":"https://pubmed.ncbi.nlm.nih.gov/24606217","citation_count":6,"is_preprint":false},{"pmid":"24130861","id":"PMC_24130861","title":"An intriguing shift occurs in the novel protein phosphatase 1 binding partner, TCTEX1D4: evidence of positive selection in a pika model.","date":"2013","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/24130861","citation_count":2,"is_preprint":false},{"pmid":"41428483","id":"PMC_41428483","title":"Multi-ancestry exome-wide study identifies variants associated with Alzheimer's disease protection.","date":"2025","source":"Journal of Alzheimer's disease : JAD","url":"https://pubmed.ncbi.nlm.nih.gov/41428483","citation_count":0,"is_preprint":false},{"pmid":"41651028","id":"PMC_41651028","title":"VPA targets Mid1 to improve disrupted retrograde axonal transport in hippocampal neurons and alleviate lithium manganate-induced learning and memory dysfunction.","date":"2026","source":"Journal of advanced research","url":"https://pubmed.ncbi.nlm.nih.gov/41651028","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":5193,"output_tokens":1160,"usd":0.01649,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":7717,"output_tokens":1858,"usd":0.042517,"stage2_stop_reason":"end_turn"},"total_usd":0.059007,"stage1_batch_id":"msgbatch_01AsR7g8dGTEiEw9U83bJeWn","stage2_batch_id":"msgbatch_01YV5ZyxtFNUZEjxRcpd9jzb","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2013,\n      \"finding\": \"TCTEX1D4 (DYNLT4) interacts with PPP1CC (protein phosphatase 1) isoforms; the interaction is mediated by an N-terminal consensus PPP1 binding motif (RVSF). TCTEX1D4 and PPP1 co-localize at the microtubule organizing center (MTOC) and along microtubules in cell culture, and the PPP1 binding motif is required for PPP1 retention at the MTOC and movement along microtubules.\",\n      \"method\": \"Yeast two-hybrid screen with human testis cDNA library; overlay assays confirming interaction with PPP1CC isoforms; immunofluorescence co-localization in cell cultures; mutational analysis of the PPP1 binding motif\",\n      \"journal\": \"Biology open\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — yeast two-hybrid confirmed by overlay assay and immunofluorescence co-localization with functional consequence (MTOC retention), single lab with two orthogonal methods\",\n      \"pmids\": [\"23789093\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"The PPP1 binding motif RVSF at positions 90-93 is conserved across 21 mammalian species and is sufficient for PPP1 binding; in pika (Ochotona) species where this motif is disrupted, flanking N- and C-terminal residues compensate to maintain PPP1 binding, as shown by mutational screening.\",\n      \"method\": \"Comparative sequence analysis across 21 mammalian and 7 Lagomorpha species; mutational screening validating PPP1 binding despite disrupted canonical motif\",\n      \"journal\": \"PloS one\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — mutational screening demonstrating binding maintenance with disrupted motif, single lab with functional binding validation\",\n      \"pmids\": [\"24130861\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"Yeast two-hybrid screening in human testis identified 40 novel TCTEX1D4 (DYNLT4) interacting proteins, confirming its capacity to engage functionally diverse binding partners consistent with a role in sperm motility, intraflagellar transport, and acrosome reaction.\",\n      \"method\": \"Yeast two-hybrid assay with human testis cDNA library; immunofluorescence studies on spermatozoa; in silico interactome profile\",\n      \"journal\": \"Omics : a journal of integrative biology\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — yeast two-hybrid identifies interactors but no biochemical validation of individual interactions reported in abstract; single lab, single method for the novel interactors\",\n      \"pmids\": [\"24606217\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"The E3 ubiquitin ligase Mid1 promotes ubiquitin-proteasome-dependent degradation of DYNLT4 (dynein light chain family member), and this degradation disrupts retrograde axonal transport in hippocampal neurons.\",\n      \"method\": \"RNA-sequencing, molecular biology/Western blot approaches, Mid1 silencing/knockdown, live-cell imaging-based axonal transport assays in HT-22 cells and primary hippocampal neurons\",\n      \"journal\": \"Journal of advanced research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — genetic loss-of-function (Mid1 knockdown) with defined cellular phenotype (retrograde transport), and mechanistic pathway placement via ubiquitin-proteasome pathway; single lab\",\n      \"pmids\": [\"41651028\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"DYNLT4 (TCTEX1D4) is a dynein light chain family member that interacts with protein phosphatase 1 (PPP1CC) via an N-terminal RVSF motif, co-localizing with PPP1 at the MTOC and along microtubules; it engages diverse binding partners in testis relevant to sperm motility and intraflagellar transport, and its protein levels are regulated by Mid1-mediated ubiquitin-proteasome degradation, with loss of DYNLT4 disrupting retrograde axonal transport in hippocampal neurons.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"DYNLT4 (TCTEX1D4) is a dynein light chain family member that functions as a microtubule-associated adaptor coupling protein phosphatase 1 to the microtubule cytoskeleton and supporting dynein-based transport [#0, #3]. It binds PPP1CC isoforms through an N-terminal RVSF consensus motif at positions 90-93, and this interaction recruits and retains PPP1 at the microtubule organizing center and along microtubules; the motif is required for PPP1 retention and movement [#0]. The RVSF motif is conserved across mammals, and where it is disrupted, flanking residues compensate to preserve PPP1 binding [#1]. DYNLT4 protein levels are controlled by Mid1-mediated ubiquitin-proteasome degradation, and loss of DYNLT4 disrupts retrograde axonal transport in hippocampal neurons, linking it to dynein-dependent cargo movement [#3]. A testis-enriched interactome consistent with roles in sperm motility and intraflagellar transport has been catalogued [#2], but beyond the PPP1 interaction and the Mid1 degradation axis, the biochemical detail of these partnerships has not been characterized in the available corpus.\",\n  \"teleology\": [\n    {\n      \"year\": 2013,\n      \"claim\": \"Established that DYNLT4 is not merely a dynein component but a direct adaptor for protein phosphatase 1, defining a molecular link between the phosphatase and the microtubule cytoskeleton.\",\n      \"evidence\": \"Yeast two-hybrid screen of human testis cDNA, overlay assays against PPP1CC isoforms, immunofluorescence co-localization, and mutational analysis of the RVSF motif in cell culture\",\n      \"pmids\": [\"23789093\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Functional consequence of PPP1 retention at the MTOC for cell physiology not defined\", \"Substrates dephosphorylated by the DYNLT4-PPP1 complex unidentified\", \"No structural model of the interaction\"]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"Showed the PPP1-binding RVSF motif is evolutionarily conserved and that binding is robust to motif disruption via compensatory flanking residues, indicating PPP1 engagement is a constrained, functionally important feature of DYNLT4.\",\n      \"evidence\": \"Comparative sequence analysis across 21 mammalian and 7 Lagomorpha species with mutational screening of binding\",\n      \"pmids\": [\"24130861\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Physiological role of conservation not tested in vivo\", \"Whether compensatory binding is functionally equivalent unknown\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Expanded the candidate interactome of DYNLT4 in testis, raising the possibility of roles in sperm motility, intraflagellar transport, and the acrosome reaction.\",\n      \"evidence\": \"Yeast two-hybrid screen of human testis cDNA, immunofluorescence on spermatozoa, and in silico interactome profiling\",\n      \"pmids\": [\"24606217\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No biochemical validation of the 40 novel interactors beyond yeast two-hybrid\", \"Functional roles in sperm/cilia not demonstrated\", \"Single method, single lab\"]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"Placed DYNLT4 in a regulated degradation pathway and tied its abundance to a concrete transport phenotype, establishing functional importance in neuronal cargo trafficking.\",\n      \"evidence\": \"RNA-sequencing, Mid1 knockdown, Western blot, and live-cell axonal transport imaging in HT-22 cells and primary hippocampal neurons\",\n      \"pmids\": [\"41651028\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct ubiquitination of DYNLT4 by Mid1 not biochemically reconstituted\", \"Mechanism linking DYNLT4 level to retrograde transport machinery unresolved\", \"Single lab\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How DYNLT4's PPP1-scaffolding activity, its testis interactome, and its Mid1-regulated role in axonal transport integrate into a unified cellular function remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No structural data on the DYNLT4-dynein or DYNLT4-PPP1 assembly\", \"Substrates of the targeted phosphatase activity unknown\", \"Whether the testis and neuronal roles share a common mechanism untested\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [0]},\n      {\"term_id\": \"GO:0008092\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005815\", \"supporting_discovery_ids\": [0]},\n      {\"term_id\": \"GO:0005856\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"pathway\": [],\n    \"complexes\": [],\n    \"partners\": [\"PPP1CC\", \"MID1\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"faith_supported":3,"faith_total":4,"faith_pct":75.0}}