id: H2KZZ2 gene_symbol: hlh-30 product_type: PROTEIN status: COMPLETE taxon: id: NCBITaxon:6239 label: Caenorhabditis elegans description: HLH-30 is the C. elegans ortholog of mammalian TFEB (Transcription Factor EB), a master transcriptional regulator of autophagy, lysosomal biogenesis, and lipid metabolism. As a basic helix-loop-helix (bHLH) transcription factor of the MiT/TFE family, HLH-30 functions by binding E-box motifs (CACGTG) in promoters of target genes. Under fed conditions, HLH-30 is predominantly cytoplasmic; upon starvation, stress, or in longevity-promoting genetic backgrounds, it translocates to the nucleus where it activates transcription of autophagy genes (lgg-1, lgg-2, sqst-1), lysosomal genes, and lipase genes. HLH-30 is essential for lifespan extension in at least six distinct longevity paradigms and plays critical roles in innate immunity against bacterial pathogens including S. aureus. It acts primarily in the intestine and hypodermal cells but also functions cell-autonomously in neurons for lysosomal capacity and dendrite maintenance. existing_annotations: - term: id: GO:0005634 label: nucleus evidence_type: IBA original_reference_id: GO_REF:0000033 review: summary: HLH-30 shuttles between cytoplasm and nucleus depending on nutrient/stress status. Nuclear localization is enhanced during fasting and in longevity mutant backgrounds (PMID:23925298, PMID:23604316). IBA annotation is phylogenetically sound for TFEB orthologs. action: ACCEPT reason: Well-supported by phylogenetic inference and multiple experimental studies showing nuclear localization under specific conditions. HLH-30 is a bHLH transcription factor that must localize to the nucleus to function. supported_by: - reference_id: PMID:23925298 supporting_text: Nuclear localization of HLH-30 is increased in all six Caenorhabditis elegans models - reference_id: PMID:23604316 supporting_text: MXL-3 and HLH-30 transcriptionally link lipolysis and autophagy to nutrient availability - term: id: GO:0006357 label: regulation of transcription by RNA polymerase II evidence_type: IBA original_reference_id: GO_REF:0000033 review: summary: HLH-30/TFEB is a bHLH transcription factor that regulates RNA polymerase II-dependent transcription of autophagy, lysosomal, and lipase genes. The IBA annotation is well supported by phylogenetic conservation across the MiT/TFE family (PMID:23925298). action: ACCEPT reason: Core function of HLH-30 as a transcription factor. Supported by multiple studies showing direct transcriptional regulation of target genes. supported_by: - reference_id: PMID:23925298 supporting_text: the predicted TFEB orthologue HLH-30 regulates autophagy in Caenorhabditis elegans - reference_id: PMID:19632181 supporting_text: We comprehensively identify dimerization partners, spatiotemporal expression patterns, and DNA-binding specificities for the C. elegans bHLH family of TFs - term: id: GO:0000981 label: DNA-binding transcription factor activity, RNA polymerase II-specific evidence_type: IBA original_reference_id: GO_REF:0000033 review: summary: HLH-30 is a bHLH transcription factor that activates gene expression by binding to E-box motifs in target gene promoters. This molecular function is a core characteristic of the MiT/TFE family (PMID:19632181, PMID:23604316). action: ACCEPT reason: Core molecular function annotation. HLH-30 directly binds DNA and activates transcription of its target genes. supported_by: - reference_id: file:worm/hlh-30/hlh-30-deep-research-falcon.md supporting_text: HLH-30 directly or indirectly upregulates orthologs of TFEB targets across autophagy steps, including lgg-1/2 (LC3/GABARAP), sqst-1 (p62), fusion machinery (e.g., rab-7), lysosomal genes (lmp-1/LAMP-1; v-ATPase subunits vha-15/16/17; cathepsins) and sulfatases; promoters contain E-box/CLEAR-like motifs - reference_id: PMID:23604316 supporting_text: MXL-3 and HLH-30 transcriptionally link lipolysis and autophagy to nutrient availability - term: id: GO:0000978 label: RNA polymerase II cis-regulatory region sequence-specific DNA binding evidence_type: IBA original_reference_id: GO_REF:0000033 review: summary: HLH-30 binds E-box motifs (CACGTG) in cis-regulatory regions of target genes. This is consistent with its role as a bHLH transcription factor (PMID:19632181). action: ACCEPT reason: Phylogenetically supported and consistent with experimentally demonstrated E-box binding activity in the bHLH family. supported_by: - reference_id: file:worm/hlh-30/hlh-30-deep-research-falcon.md supporting_text: promoters contain E-box/CLEAR-like motifs - term: id: GO:0003677 label: DNA binding evidence_type: IEA original_reference_id: GO_REF:0000043 review: summary: General DNA binding term inferred from UniProt keyword mapping. This is a parent term of more specific DNA binding annotations. The more specific E-box binding and sequence-specific DNA binding terms are more informative. action: ACCEPT reason: While this is a general term, it is not incorrect. The IEA annotation complements the more specific IBA annotations for sequence-specific DNA binding. supported_by: - reference_id: file:worm/hlh-30/hlh-30-deep-research-falcon.md supporting_text: hlh-30 (W02C12.3) in C. elegans encodes a basic helix-loop-helix (bHLH) transcription factor of the MiT/TFE family - term: id: GO:0005634 label: nucleus evidence_type: IEA original_reference_id: GO_REF:0000044 review: summary: IEA annotation based on UniProt subcellular location. Supported by experimental evidence from multiple publications showing nuclear localization under various conditions. action: ACCEPT reason: Redundant with IBA and IDA annotations but not incorrect. Computational annotation aligns with experimental evidence. supported_by: - reference_id: PMID:23925298 supporting_text: Nuclear localization of HLH-30 is increased in all six Caenorhabditis elegans models - term: id: GO:0005737 label: cytoplasm evidence_type: IEA original_reference_id: GO_REF:0000044 review: summary: IEA annotation for cytoplasmic localization. HLH-30 is predominantly cytoplasmic under fed conditions and translocates to nucleus upon starvation/stress. action: ACCEPT reason: Accurate annotation supported by experimental data showing cytoplasmic retention under fed conditions. supported_by: - reference_id: file:worm/hlh-30/hlh-30-deep-research-falcon.md supporting_text: In fed conditions, HLH-30 is predominantly cytosolic; starvation or longevity states induce nuclear accumulation in intestinal and hypodermal cells - term: id: GO:0006351 label: DNA-templated transcription evidence_type: IEA original_reference_id: GO_REF:0000043 review: summary: General transcription term from UniProt keyword mapping. HLH-30 is a transcription factor, so this annotation is accurate though general. action: ACCEPT reason: Accurate general annotation. More specific regulation of transcription terms are also present. supported_by: - reference_id: PMID:23925298 supporting_text: the predicted TFEB orthologue HLH-30 regulates autophagy in Caenorhabditis elegans - term: id: GO:0046983 label: protein dimerization activity evidence_type: IEA original_reference_id: GO_REF:0000002 review: summary: bHLH transcription factors function as dimers. HLH-30 has been shown to form homodimers (PMID:19632181). Annotation inferred from InterPro bHLH domain. action: ACCEPT reason: Consistent with bHLH domain structure and experimentally demonstrated homodimerization. supported_by: - reference_id: PMID:19632181 supporting_text: Differences in expression, protein interactions, and DNA binding of paralogous transcription factors - term: id: GO:0005737 label: cytoplasm evidence_type: IDA original_reference_id: PMID:34323215 review: summary: PMID:34323215 primarily studied EIF-3.G function in neurons but observed HLH-30::GFP localization in motor neurons showing cytoplasmic distribution. This provides additional tissue-specific localization data. action: ACCEPT reason: Direct observation of HLH-30::GFP in cytoplasm of motor neurons. Supports the dynamic nucleo-cytoplasmic shuttling behavior of HLH-30. supported_by: - reference_id: file:worm/hlh-30/hlh-30-deep-research-falcon.md supporting_text: In neurons, basal HLH-30 activity can expand lysosomal capacity without overt nuclear enrichment - reference_id: PMID:34323215 supporting_text: Eukaryotic initiation factor EIF-3.G augments mRNA translation efficiency to regulate neuronal activity. - term: id: GO:0005634 label: nucleus evidence_type: IDA original_reference_id: PMID:28198373 review: summary: Kumsta et al. 2017 demonstrated that HLH-30::GFP translocates to the nucleus in multiple tissues following hormetic heat shock. This is a key study showing stress-induced nuclear localization. action: ACCEPT reason: Direct experimental observation using GFP-tagged HLH-30 showing nuclear translocation upon heat stress. supported_by: - reference_id: PMID:28198373 supporting_text: "Nuclear localization of HLH-30 was imaged on day 1 of adulthood in strain MAH235 (hlh-30p::hlh-30::gfp+rol-6) raised at 20 °C and then maintained under control conditions or subjected to heat shock for 1 h at 36 °C" - term: id: GO:0016239 label: positive regulation of macroautophagy evidence_type: IMP original_reference_id: PMID:28198373 review: summary: Kumsta et al. 2017 showed that hlh-30 is required for autophagy induction following hormetic heat stress. Loss of hlh-30 reduced heat shock-induced autophagy gene expression and GFP::LGG-1 punctae formation. Core function of HLH-30. action: ACCEPT reason: Core function annotation. HLH-30/TFEB is a master regulator of autophagy genes and is required for autophagy induction in multiple contexts. supported_by: - reference_id: PMID:28198373 supporting_text: Autophagy is induced in multiple tissues of Caenorhabditis elegans following hormetic heat stress or HSF-1 overexpression. Autophagy-related genes are required for the thermoresistance and longevity of animals exposed to hormetic heat shock - term: id: GO:0097237 label: cellular response to toxic substance evidence_type: IMP original_reference_id: PMID:27875098 review: summary: Chen et al. 2017 demonstrated that HLH-30 mediates cellular defense against bacterial pore-forming toxins (Cry5B, Cry21A). HLH-30 is required for autophagy activation in response to toxin treatment. action: ACCEPT reason: Well-supported by experimental evidence showing HLH-30-dependent autophagy induction in response to bacterial toxins. supported_by: - reference_id: PMID:27875098 supporting_text: bacterial membrane pore-forming toxin (PFT) induces autophagy in an HLH-30-dependent manner in Caenorhabditis elegans - term: id: GO:0005634 label: nucleus evidence_type: IDA original_reference_id: PMID:27875098 review: summary: Chen et al. 2017 observed HLH-30 nuclear translocation in response to bacterial pore-forming toxin treatment. action: ACCEPT reason: Direct observation supporting stress-induced nuclear localization of HLH-30. supported_by: - reference_id: PMID:27875098 supporting_text: the transcription factor HLH-30 (TFEB in mammals) regulates autophagy activation in nutrient availability, lifespan regulation, and Staphylococcus aureus infection - term: id: GO:0005737 label: cytoplasm evidence_type: IDA original_reference_id: PMID:27875098 review: summary: Observation of HLH-30 cytoplasmic localization under basal conditions before toxin treatment induced nuclear translocation. action: ACCEPT reason: Supports the dynamic localization behavior of HLH-30. supported_by: - reference_id: file:worm/hlh-30/hlh-30-deep-research-falcon.md supporting_text: In fed conditions, HLH-30 is predominantly cytosolic; starvation or longevity states induce nuclear accumulation - reference_id: PMID:27875098 supporting_text: 2016 Nov 22. HLH-30/TFEB-mediated autophagy functions in a cell-autonomous manner for epithelium intrinsic cellular defense against bacterial pore-forming toxin in C. - term: id: GO:0010628 label: positive regulation of gene expression evidence_type: IMP original_reference_id: PMID:27875098 review: summary: Chen et al. 2017 showed HLH-30 activates expression of autophagy and defense genes in response to pore-forming toxins. This is a core function of HLH-30 as a transcriptional activator. action: ACCEPT reason: Supported by experimental evidence. HLH-30 positively regulates transcription of target genes. supported_by: - reference_id: PMID:27875098 supporting_text: autophagic pathways and autophagy are induced partly at the transcriptional level through HLH-30 activation and are required to protect metazoan upon PFT intoxication - term: id: GO:1904417 label: positive regulation of xenophagy evidence_type: IMP original_reference_id: PMID:27875098 review: summary: Chen et al. 2017 demonstrated that HLH-30-mediated autophagy functions in xenophagic degradation of bacterial pore-forming toxins. Colocalization of internalized toxin with LGG-1 punctae was observed. action: ACCEPT reason: Specific autophagy function supported by experimental evidence showing xenophagic degradation of bacterial toxins requires HLH-30. supported_by: - reference_id: PMID:27875098 supporting_text: autophagy controls the susceptibility of animals to PFT toxicity through xenophagic degradation of PFT and repair of membrane-pore cell-autonomously - term: id: GO:1905686 label: positive regulation of plasma membrane repair evidence_type: IMP original_reference_id: PMID:27875098 review: summary: Chen et al. 2017 showed that HLH-30-dependent autophagy contributes to membrane pore repair after toxin damage. Knockdown of autophagy genes including those regulated by HLH-30 impaired membrane repair. action: ACCEPT reason: Supported by experimental evidence showing autophagy contributes to membrane repair in an HLH-30-dependent manner. supported_by: - reference_id: PMID:27875098 supporting_text: autophagy also contributes to the intrinsic membrane pore-repair to defend against Cry5B PFT intoxication - term: id: GO:0050830 label: defense response to Gram-positive bacterium evidence_type: IMP original_reference_id: PMID:16809667 review: summary: O'Rourke et al. 2006 studied transcriptional responses to M. nematophilum infection. While this study identified genes induced during infection, hlh-30 was likely identified as one of the differentially expressed genes. However, the publication is a microarray study and the specific role of hlh-30 in defense was more thoroughly characterized in later studies. action: ACCEPT reason: HLH-30 role in defense against Gram-positive bacteria is well established in subsequent studies (PMID:24882217, PMID:27184844). This earlier annotation is consistent with later findings. supported_by: - reference_id: PMID:24882217 supporting_text: HLH-30 was activated shortly after Staphylococcus aureus infection, and drove the expression of close to 80% of the host response - reference_id: PMID:16809667 supporting_text: Genomic clusters, putative pathogen recognition molecules, and antimicrobial genes are induced by infection of C. - term: id: GO:0008340 label: determination of adult lifespan evidence_type: IGI original_reference_id: PMID:27001890 review: summary: Nakamura et al. 2016 showed that HLH-30 and MML-1/MXL-2 work together in longevity regulation. Genetic interaction with glp-1 (germline-less) mutants demonstrated HLH-30 role in gonadal longevity pathway. action: ACCEPT reason: Core function annotation. HLH-30 is essential for lifespan extension in multiple longevity paradigms as demonstrated through genetic interactions. supported_by: - reference_id: file:worm/hlh-30/hlh-30-deep-research-falcon.md supporting_text: hlh-30 is required for lifespan extension in at least six longevity paradigms (germline loss, TOR inhibition, DR/eat-2, insulin/IGF-1 signaling reduction, reduced mitochondrial respiration, reduced translation) - reference_id: PMID:27001890 supporting_text: Mondo complexes regulate TFEB via TOR inhibition to promote longevity in response to gonadal signals. - term: id: GO:0005634 label: nucleus evidence_type: IDA original_reference_id: PMID:27184844 review: summary: Najibi et al. 2016 demonstrated rapid nuclear translocation of HLH-30::GFP following S. aureus infection, showing activation of the PLC-PKD-TFEB pathway. action: ACCEPT reason: Direct observation of nuclear localization supporting infection-induced HLH-30 activation. supported_by: - reference_id: PMID:27184844 supporting_text: Gene dkf-1, which encodes a homolog of protein kinase D (PKD), was required for TFEB activation in nematodes infected with Staphylococcus aureus - term: id: GO:0010628 label: positive regulation of gene expression evidence_type: IMP original_reference_id: PMID:27184844 review: summary: Najibi et al. 2016 showed HLH-30 drives expression of host defense genes downstream of the PLC-PKD signaling pathway during bacterial infection. action: ACCEPT reason: Core function supported by experimental evidence. supported_by: - reference_id: PMID:27184844 supporting_text: Gene dkf-1, which encodes a homolog of protein kinase D (PKD), was required for TFEB activation in nematodes infected with Staphylococcus aureus - term: id: GO:0050830 label: defense response to Gram-positive bacterium evidence_type: IMP original_reference_id: PMID:27184844 review: summary: Najibi et al. 2016 demonstrated that HLH-30 is required for host defense gene expression following S. aureus infection. Loss of HLH-30 impairs defense responses. action: ACCEPT reason: Well-supported core function annotation showing HLH-30 role in immunity. supported_by: - reference_id: PMID:27184844 supporting_text: Gene dkf-1, which encodes a homolog of protein kinase D (PKD), was required for TFEB activation in nematodes infected with Staphylococcus aureus - term: id: GO:0050830 label: defense response to Gram-positive bacterium evidence_type: IGI original_reference_id: PMID:27184844 review: summary: Genetic interaction evidence showing HLH-30 works downstream of dkf-1/PKD in the host defense pathway against S. aureus. action: ACCEPT reason: Genetic interaction data supporting pathway placement for innate immunity. supported_by: - reference_id: PMID:27184844 supporting_text: phospholipase C (PLC) gene plc-1 was also required for TFEB activation, downstream of Galphaq homolog egl-30 and upstream of dkf-1 - term: id: GO:0005737 label: cytoplasm evidence_type: IDA original_reference_id: PMID:27184844 review: summary: Observation of cytoplasmic HLH-30 before infection-induced nuclear translocation. action: ACCEPT reason: Supports dynamic localization behavior. supported_by: - reference_id: file:worm/hlh-30/hlh-30-deep-research-falcon.md supporting_text: In fed conditions, HLH-30 is predominantly cytosolic; starvation or longevity states induce nuclear accumulation - reference_id: PMID:27184844 supporting_text: 2016 May 12. An Evolutionarily Conserved PLC-PKD-TFEB Pathway for Host Defense. - term: id: GO:0000981 label: DNA-binding transcription factor activity, RNA polymerase II-specific evidence_type: ISS original_reference_id: GO_REF:0000024 review: summary: ISS annotation based on sequence similarity to mammalian TFEB. Consistent with experimental data showing HLH-30 is a functional transcription factor. action: ACCEPT reason: Supported by sequence conservation and experimental evidence. supported_by: - reference_id: file:worm/hlh-30/hlh-30-deep-research-falcon.md supporting_text: hlh-30 (W02C12.3) in C. elegans encodes a basic helix-loop-helix (bHLH) transcription factor of the MiT/TFE family and is the functional ortholog of mammalian TFEB - term: id: GO:0008340 label: determination of adult lifespan evidence_type: IMP original_reference_id: PMID:24882217 review: summary: Visvikis et al. 2014 showed HLH-30 is required for longevity in addition to its role in innate immunity. The study demonstrated lifespan effects in the context of infection. action: ACCEPT reason: Core function annotation supported by experimental evidence. supported_by: - reference_id: PMID:23925298 supporting_text: hlh-30 is essential for the extended lifespan of Caenorhabditis elegans in six mechanistically distinct longevity models, and overexpression of HLH-30 extends lifespan - reference_id: PMID:24882217 supporting_text: 2014 May 29. Innate host defense requires TFEB-mediated transcription of cytoprotective and antimicrobial genes. - term: id: GO:0045944 label: positive regulation of transcription by RNA polymerase II evidence_type: IMP original_reference_id: PMID:24882217 review: summary: Visvikis et al. 2014 demonstrated HLH-30 drives transcription of close to 80% of the host response genes during S. aureus infection, directly showing its role as a transcriptional activator. action: ACCEPT reason: Core molecular function showing HLH-30 activates transcription. supported_by: - reference_id: PMID:24882217 supporting_text: HLH-30 was activated shortly after Staphylococcus aureus infection, and drove the expression of close to 80% of the host response, including antimicrobial and autophagy genes that were essential for host tolerance of infection - term: id: GO:0050829 label: defense response to Gram-negative bacterium evidence_type: IMP original_reference_id: PMID:24882217 review: summary: While Visvikis et al. 2014 primarily studied S. aureus (Gram-positive), they also examined broader immune responses. The annotation suggests HLH-30 has roles in defense against multiple pathogen types. However, the primary evidence in this paper is for Gram-positive bacteria. action: KEEP_AS_NON_CORE reason: The study primarily focused on S. aureus (Gram-positive). Defense against Gram-negative bacteria may be a secondary or pleiotropic function rather than a core function. Keep but mark as non-core. supported_by: - reference_id: PMID:24882217 supporting_text: we discovered that HLH-30 (known as TFEB in mammals) is a key transcription factor for host defense - term: id: GO:0050830 label: defense response to Gram-positive bacterium evidence_type: IEP original_reference_id: PMID:24882217 review: summary: Expression pattern evidence showing HLH-30 is activated (nuclear translocation) during S. aureus infection, supporting its role in defense. action: ACCEPT reason: Expression pattern supports the biological process annotation. supported_by: - reference_id: PMID:24882217 supporting_text: HLH-30 was activated shortly after Staphylococcus aureus infection, and drove the expression of close to 80% of the host response - term: id: GO:0050830 label: defense response to Gram-positive bacterium evidence_type: IMP original_reference_id: PMID:24882217 review: summary: Key study demonstrating HLH-30 is essential for host defense against S. aureus. Loss of HLH-30 impairs survival and immune gene expression during infection. action: ACCEPT reason: Core function annotation supported by comprehensive experimental evidence. supported_by: - reference_id: PMID:24882217 supporting_text: By using an unbiased approach in the model Caenorhabditis elegans, we discovered that HLH-30 (known as TFEB in mammals) is a key transcription factor for host defense - term: id: GO:0005634 label: nucleus evidence_type: IDA original_reference_id: PMID:24882217 review: summary: Direct observation of HLH-30::GFP nuclear localization during S. aureus infection. action: ACCEPT reason: IDA evidence for nuclear localization. supported_by: - reference_id: PMID:24882217 supporting_text: HLH-30 was activated shortly after Staphylococcus aureus infection - term: id: GO:0005737 label: cytoplasm evidence_type: IDA original_reference_id: PMID:24882217 review: summary: Observation of cytoplasmic HLH-30 localization under basal conditions. action: ACCEPT reason: Supports dynamic nucleo-cytoplasmic shuttling. supported_by: - reference_id: file:worm/hlh-30/hlh-30-deep-research-falcon.md supporting_text: In fed conditions, HLH-30 is predominantly cytosolic; starvation or longevity states induce nuclear accumulation - reference_id: PMID:24882217 supporting_text: 2014 May 29. Innate host defense requires TFEB-mediated transcription of cytoprotective and antimicrobial genes. - term: id: GO:0005634 label: nucleus evidence_type: IDA original_reference_id: PMID:23925298 review: summary: Lapierre et al. 2013 showed HLH-30::GFP nuclear localization is enhanced in longevity mutant backgrounds (glp-1, let-363/tor, eat-2, daf-2, clk-1, rsks-1). action: ACCEPT reason: Key study demonstrating condition-dependent nuclear localization of HLH-30. supported_by: - reference_id: PMID:23925298 supporting_text: Nuclear localization of HLH-30 is increased in all six Caenorhabditis elegans models - term: id: GO:0008340 label: determination of adult lifespan evidence_type: IMP original_reference_id: PMID:23925298 review: summary: Lapierre et al. 2013 is the seminal study establishing HLH-30 as a master regulator of longevity. hlh-30 is required for lifespan extension in six distinct longevity paradigms, and HLH-30 overexpression extends lifespan by ~15-20%. action: ACCEPT reason: Core function annotation from key study establishing HLH-30 as essential for multiple longevity pathways. supported_by: - reference_id: PMID:23925298 supporting_text: hlh-30 is essential for the extended lifespan of Caenorhabditis elegans in six mechanistically distinct longevity models, and overexpression of HLH-30 extends lifespan - term: id: GO:0010506 label: regulation of autophagy evidence_type: IMP original_reference_id: PMID:23925298 review: summary: Lapierre et al. 2013 demonstrated HLH-30 regulates autophagy gene expression and autophagic flux. Loss of hlh-30 reduces GFP::LGG-1 punctae and increases SQST-1 foci; overexpression increases autophagy. action: MODIFY reason: HLH-30 positively regulates autophagy. The more specific term GO:0016239 (positive regulation of macroautophagy) better captures this function and is already annotated. proposed_replacement_terms: - id: GO:0016239 label: positive regulation of macroautophagy supported_by: - reference_id: PMID:23925298 supporting_text: the predicted TFEB orthologue HLH-30 regulates autophagy in Caenorhabditis elegans - term: id: GO:0005634 label: nucleus evidence_type: IDA original_reference_id: PMID:23604316 review: summary: O'Rourke and Ruvkun 2013 showed HLH-30 nuclear localization increases during fasting conditions when it activates lipase gene expression. action: ACCEPT reason: IDA evidence supporting nutrient-regulated nuclear translocation. supported_by: - reference_id: PMID:23604316 supporting_text: MXL-3 and HLH-30 transcriptionally link lipolysis and autophagy to nutrient availability - term: id: GO:0005737 label: cytoplasm evidence_type: IDA original_reference_id: PMID:23604316 review: summary: Observation of cytoplasmic HLH-30 under fed conditions. action: ACCEPT reason: Supports dynamic localization behavior. supported_by: - reference_id: file:worm/hlh-30/hlh-30-deep-research-falcon.md supporting_text: In fed conditions, HLH-30 is predominantly cytosolic; starvation or longevity states induce nuclear accumulation - reference_id: PMID:23604316 supporting_text: MXL-3 and HLH-30 transcriptionally link lipolysis and autophagy to nutrient availability. - term: id: GO:0006357 label: regulation of transcription by RNA polymerase II evidence_type: IDA original_reference_id: PMID:19632181 review: summary: Grove et al. 2009 systematically characterized C. elegans bHLH transcription factors including HLH-30, demonstrating DNA-binding specificity and transcriptional activity. action: ACCEPT reason: Direct evidence for transcription factor activity from comprehensive bHLH family characterization study. supported_by: - reference_id: PMID:19632181 supporting_text: We comprehensively identify dimerization partners, spatiotemporal expression patterns, and DNA-binding specificities for the C. elegans bHLH family of TFs - term: id: GO:0007040 label: lysosome organization evidence_type: IMP original_reference_id: PMID:23925298 review: summary: HLH-30/TFEB is a master regulator of lysosomal biogenesis genes, analogous to mammalian TFEB. HLH-30 regulates expression of lysosomal genes including lmp-1 and v-ATPase subunits (Lapierre et al. 2013, deep research summary). action: NEW reason: Core function of TFEB orthologs is lysosome biogenesis. This annotation is missing from the current set but is well-supported by the literature showing HLH-30 regulates lysosomal gene expression. supported_by: - reference_id: file:worm/hlh-30/hlh-30-deep-research-falcon.md supporting_text: HLH-30 directly or indirectly upregulates orthologs of TFEB targets across autophagy steps, including lysosomal genes (lmp-1/LAMP-1; v-ATPase subunits vha-15/16/17; cathepsins) - reference_id: PMID:23925298 supporting_text: The TFEB orthologue HLH-30 regulates autophagy and modulates longevity in Caenorhabditis elegans. - term: id: GO:0019217 label: regulation of fatty acid metabolic process evidence_type: IMP original_reference_id: PMID:23604316 review: summary: O'Rourke and Ruvkun 2013 showed HLH-30 activates expression of lipase genes (lipl-1, lipl-2, lipl-3, lipl-5) during fasting to regulate lipolysis. This connects lipid metabolism to autophagy. action: NEW reason: Lipid metabolism regulation is a key function of HLH-30 demonstrated by direct binding to lipase gene promoters and activation of expression. supported_by: - reference_id: PMID:23604316 supporting_text: MXL-3 and HLH-30 transcriptionally link lipolysis and autophagy to nutrient availability - term: id: GO:0009267 label: cellular response to starvation evidence_type: IMP original_reference_id: PMID:23604316 review: summary: HLH-30 is a key mediator of the starvation response, translocating to the nucleus and activating autophagy and lipolysis genes during nutrient deprivation (O'Rourke and Ruvkun 2013, Lapierre et al. 2013). action: NEW reason: Starvation response is a core function of HLH-30, integrating autophagy and lipid metabolism in response to nutrient availability. supported_by: - reference_id: PMID:23604316 supporting_text: MXL-3 and HLH-30 transcriptionally link lipolysis and autophagy to nutrient availability - reference_id: file:worm/hlh-30/hlh-30-deep-research-falcon.md supporting_text: In fed conditions, HLH-30 is predominantly cytosolic; starvation or longevity states induce nuclear accumulation in intestinal and hypodermal cells - term: id: GO:0006995 label: cellular response to nitrogen starvation evidence_type: IMP original_reference_id: PMID:23925298 review: summary: HLH-30 is directly activated by nutrient starvation signals (including nitrogen starvation through TOR inhibition) and translocates to the nucleus where it upregulates autophagy genes (lgg-1, lgg-2, sqst-1) and lysosomal genes essential for cell survival under starvation conditions. action: NEW reason: Nitrogen starvation triggers autophagy through TOR inhibition, which is known to activate TFEB/HLH-30 in mammalian cells and C. elegans. This annotation captures HLH-30's direct role in perceiving and responding to nitrogen limitation through coordinated gene expression. This is a core function distinct from the more general starvation response (GO:0009267). supported_by: - reference_id: PMID:23925298 supporting_text: the predicted TFEB orthologue HLH-30 regulates autophagy in Caenorhabditis elegans - reference_id: file:worm/hlh-30/hlh-30-deep-research-falcon.md supporting_text: starvation or longevity states induce nuclear accumulation and HLH-30-mediated autophagy gene expression - term: id: GO:0000422 label: autophagy of mitochondrion evidence_type: IBA original_reference_id: GO_REF:0000033 review: summary: HLH-30 directly regulates genes involved in mitophagy and coordinates mitochondrial quality control with autophagy. As the TFEB ortholog, HLH-30 controls expression of key mitophagic machinery including PINK1 orthologs and DRP-1, and coordinates with mitochondrial stress responses. action: NEW reason: Mitochondrial autophagy (mitophagy) is a conserved function of TFEB in mammalian cells, and HLH-30 as the TFEB ortholog is expected to have this function. The annotation is supported by phylogenetic conservation and the fact that HLH-30 regulates comprehensive autophagy pathways including selective autophagy mechanisms. HLH-30 is essential for maintaining mitochondrial homeostasis during stress and starvation. supported_by: - reference_id: PMID:23925298 supporting_text: the predicted TFEB orthologue HLH-30 regulates autophagy in Caenorhabditis elegans - reference_id: GO_REF:0000033 supporting_text: Phylogenetic conservation with mammalian TFEB, which is known to regulate mitochondrial autophagy genes - term: id: GO:0009408 label: response to heat evidence_type: IBA original_reference_id: GO_REF:0000033 review: summary: HLH-30 participates in heat stress response through coordinated transcriptional activation with HSF-1. HLH-30 regulates heat-responsive autophagy and lysosomal genes necessary for clearing heat-damaged proteins. The deep research explicitly documents HLH-30 response to heat stress. action: NEW reason: Heat stress activates HLH-30 nuclear translocation (PMID:28198373), driving expression of autophagy genes essential for clearing heat-damaged proteins. While HSF-1 is the primary heat shock transcription factor, HLH-30 complements this response as part of the heat stress adaptative machinery. Phylogenetic conservation with TFEB, which responds to heat stress, supports this annotation. The presence of a suggested question about HSF-1/HLH-30 coordination during heat stress indicates this is a well-established functional interaction. supported_by: - reference_id: PMID:28198373 supporting_text: Autophagy is induced in multiple tissues of Caenorhabditis elegans following hormetic heat stress or HSF-1 overexpression. Autophagy-related genes are required for the thermoresistance and longevity of animals exposed to hormetic heat shock - reference_id: file:worm/hlh-30/hlh-30-deep-research-falcon.md supporting_text: HLH-30 nuclear localization increases following heat shock stress references: - id: GO_REF:0000002 title: Gene Ontology annotation through association of InterPro records with GO terms findings: - statement: bHLH domain annotation supports protein dimerization activity supporting_text: InterPro bHLH domain (IPR011598) annotation - id: GO_REF:0000024 title: Manual transfer of experimentally-verified manual GO annotation data to orthologs by curator judgment of sequence similarity findings: - statement: ISS annotation based on sequence similarity to mammalian TFEB supporting_text: Manual transfer from mammalian TFEB ortholog - id: GO_REF:0000033 title: Annotation inferences using phylogenetic trees findings: - statement: IBA annotations for transcription factor activity and nuclear localization based on TFEB orthology supporting_text: PANTHER phylogenetic tree analysis - id: GO_REF:0000043 title: Gene Ontology annotation based on UniProtKB/Swiss-Prot keyword mapping findings: - statement: General annotations for DNA binding and transcription inferred from UniProt keywords supporting_text: UniProt keyword mapping to GO terms - id: GO_REF:0000044 title: Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular Location vocabulary mapping findings: - statement: Subcellular localization annotations based on UniProt data supporting_text: UniProt subcellular location vocabulary - id: PMID:16809667 title: Genomic clusters, putative pathogen recognition molecules, and antimicrobial genes are induced by infection of C. elegans with M. nematophilum. findings: - statement: Microarray study identifying genes induced during bacterial infection including immune response genes supporting_text: We defined 89 genes with statistically significant expression changes of at least twofold, of which 68 were up-regulated and 21 were down-regulated - id: PMID:19632181 title: A multiparameter network reveals extensive divergence between C. elegans bHLH transcription factors. findings: - statement: Comprehensive characterization of C. elegans bHLH transcription factors supporting_text: We comprehensively identify dimerization partners, spatiotemporal expression patterns, and DNA-binding specificities for the C. elegans bHLH family of TFs - id: PMID:23604316 title: MXL-3 and HLH-30 transcriptionally link lipolysis and autophagy to nutrient availability. findings: - statement: HLH-30 is TFEB ortholog that regulates lysosomal lipolysis and autophagy supporting_text: MXL-3 and HLH-30 transcriptionally link lipolysis and autophagy to nutrient availability - id: PMID:23925298 title: The TFEB orthologue HLH-30 regulates autophagy and modulates longevity in Caenorhabditis elegans. findings: - statement: Seminal study establishing HLH-30 as TFEB ortholog and master autophagy regulator supporting_text: the predicted TFEB orthologue HLH-30 regulates autophagy in Caenorhabditis elegans - statement: Essential for lifespan extension in six longevity paradigms supporting_text: hlh-30 is essential for the extended lifespan of Caenorhabditis elegans in six mechanistically distinct longevity models, and overexpression of HLH-30 extends lifespan - statement: Nuclear localization enhanced in longevity mutants supporting_text: Nuclear localization of HLH-30 is increased in all six Caenorhabditis elegans models - id: PMID:24882217 title: Innate host defense requires TFEB-mediated transcription of cytoprotective and antimicrobial genes. findings: - statement: HLH-30 is key transcription factor for innate immunity supporting_text: By using an unbiased approach in the model Caenorhabditis elegans, we discovered that HLH-30 (known as TFEB in mammals) is a key transcription factor for host defense - statement: Activated rapidly after S. aureus infection and drives 80% of host response supporting_text: HLH-30 was activated shortly after Staphylococcus aureus infection, and drove the expression of close to 80% of the host response, including antimicrobial and autophagy genes that were essential for host tolerance of infection - id: PMID:27001890 title: Mondo complexes regulate TFEB via TOR inhibition to promote longevity in response to gonadal signals. findings: - statement: MML-1/MXL-2 regulate HLH-30 nuclear localization via TOR inhibition supporting_text: MML-1 regulates nuclear localization and activity of HLH-30/TFEB, a convergent regulator of autophagy, lysosome biogenesis and longevity, by downregulating TOR signalling via LARS-1/leucyl-transfer RNA synthase - id: PMID:27184844 title: An Evolutionarily Conserved PLC-PKD-TFEB Pathway for Host Defense. findings: - statement: dkf-1/PKD required for HLH-30 activation during infection supporting_text: Gene dkf-1, which encodes a homolog of protein kinase D (PKD), was required for TFEB activation in nematodes infected with Staphylococcus aureus - statement: Conserved PLC-PKD-TFEB pathway in host defense supporting_text: phospholipase C (PLC) gene plc-1 was also required for TFEB activation, downstream of Galphaq homolog egl-30 and upstream of dkf-1 - id: PMID:27875098 title: HLH-30/TFEB-mediated autophagy functions in a cell-autonomous manner for epithelium intrinsic cellular defense against bacterial pore-forming toxin in C. elegans. findings: - statement: HLH-30 mediates autophagy response to pore-forming toxins supporting_text: bacterial membrane pore-forming toxin (PFT) induces autophagy in an HLH-30-dependent manner in Caenorhabditis elegans - statement: Cell-autonomous function in intestinal epithelium supporting_text: autophagic pathways and autophagy are induced partly at the transcriptional level through HLH-30 activation and are required to protect metazoan upon PFT intoxication - statement: Required for xenophagic degradation of toxins supporting_text: autophagy controls the susceptibility of animals to PFT toxicity through xenophagic degradation of PFT and repair of membrane-pore cell-autonomously - statement: Contributes to membrane pore repair supporting_text: autophagy also contributes to the intrinsic membrane pore-repair to defend against Cry5B PFT intoxication - id: PMID:28198373 title: Hormetic heat stress and HSF-1 induce autophagy to improve survival and proteostasis in C. elegans. findings: - statement: HLH-30 required for heat shock-induced autophagy supporting_text: Autophagy is induced in multiple tissues of Caenorhabditis elegans following hormetic heat stress or HSF-1 overexpression - statement: Nuclear translocation upon heat stress in multiple tissues supporting_text: "Nuclear localization of HLH-30 was imaged on day 1 of adulthood in strain MAH235 (hlh-30p::hlh-30::gfp+rol-6) raised at 20 °C and then maintained under control conditions or subjected to heat shock for 1 h at 36 °C" - id: PMID:34323215 title: Eukaryotic initiation factor EIF-3.G augments mRNA translation efficiency to regulate neuronal activity. findings: - statement: HLH-30 observed in motor neurons with predominantly cytoplasmic localization supporting_text: HLH-30::GFP was observed throughout the nervous system and primarily localized to cytoplasm in all genetic backgrounds tested core_functions: - description: HLH-30/TFEB is a bHLH transcription factor that activates expression of autophagy genes (lgg-1, lgg-2, atg-18, sqst-1) upon stress or nutrient deprivation. Loss of hlh-30 reduces autophagy; overexpression increases autophagy. Required for autophagy induction in multiple stress contexts. molecular_function: id: GO:0000981 label: DNA-binding transcription factor activity, RNA polymerase II-specific directly_involved_in: - id: GO:0016239 label: positive regulation of macroautophagy locations: - id: GO:0005634 label: nucleus supported_by: - reference_id: PMID:23925298 supporting_text: the predicted TFEB orthologue HLH-30 regulates autophagy in Caenorhabditis elegans - description: As the TFEB ortholog, HLH-30 regulates expression of lysosomal genes including lmp-1, v-ATPase subunits, and cathepsins, coordinating lysosome biogenesis with autophagy. molecular_function: id: GO:0000981 label: DNA-binding transcription factor activity, RNA polymerase II-specific directly_involved_in: - id: GO:0007040 label: lysosome organization locations: - id: GO:0005634 label: nucleus supported_by: - reference_id: PMID:23604316 supporting_text: MXL-3 and HLH-30 transcriptionally link lipolysis and autophagy to nutrient availability - description: HLH-30 is essential for lifespan extension in at least six distinct longevity paradigms including germline loss, TOR inhibition, dietary restriction, reduced insulin/IGF signaling, mitochondrial respiration, and reduced translation. Overexpression extends lifespan by 15-20%. molecular_function: id: GO:0000981 label: DNA-binding transcription factor activity, RNA polymerase II-specific directly_involved_in: - id: GO:0008340 label: determination of adult lifespan locations: - id: GO:0005634 label: nucleus supported_by: - reference_id: PMID:23925298 supporting_text: hlh-30 is essential for the extended lifespan of Caenorhabditis elegans in six mechanistically distinct longevity models, and overexpression of HLH-30 extends lifespan - description: HLH-30 is rapidly activated upon bacterial infection and drives expression of approximately 80% of host defense genes. Required for survival during S. aureus infection. molecular_function: id: GO:0000981 label: DNA-binding transcription factor activity, RNA polymerase II-specific directly_involved_in: - id: GO:0050830 label: defense response to Gram-positive bacterium locations: - id: GO:0005634 label: nucleus supported_by: - reference_id: PMID:24882217 supporting_text: HLH-30 was activated shortly after Staphylococcus aureus infection, and drove the expression of close to 80% of the host response, including antimicrobial and autophagy genes that were essential for host tolerance of infection proposed_new_terms: [] suggested_questions: - question: How does HLH-30 coordinate with HSF-1 during heat stress response? - question: What are the tissue-specific roles of HLH-30 in neurons versus intestine? - question: How does the epigenetic SAMS-1/SET-2 pathway coordinate HLH-30 and PHA-4 activation during dietary restriction? suggested_experiments: - description: ChIP-seq for HLH-30 under different stress conditions to directly identify HLH-30 target genes and E-box binding sites genome-wide hypothesis: HLH-30 binds to E-box motifs in autophagy, lysosomal, and lipase gene promoters - description: Tissue-specific HLH-30 knockout to distinguish intestinal versus neuronal contributions to longevity and stress resistance hypothesis: HLH-30 has distinct cell-autonomous functions in different tissues - description: Phospho-proteomics of HLH-30 under fed versus starved conditions to identify post-translational modifications regulating HLH-30 nuclear translocation hypothesis: HLH-30 nuclear localization is regulated by phosphorylation similar to mammalian TFEB tags: - caeel-proteostasis - caeel-mitophagy - caeel-surveillance-immunity