IRE-1 is a conserved ER transmembrane stress sensor with dual enzymatic activities: a serine/threonine protein kinase and an endoribonuclease. The core function is sensing unfolded proteins in the ER lumen and transducing this signal to the cytosol through trans-autophosphorylation of its kinase domain, which activates its RNase domain to catalyze unconventional cytoplasmic splicing of xbp-1 mRNA, generating the active XBP-1s transcription factor that induces UPR target genes. IRE-1 also executes Regulated IRE1-Dependent Decay (RIDD) of select mRNAs including daf-7. The protein localizes to the ER membrane as a type I single-pass transmembrane protein with a luminal stress-sensing domain and cytosolic kinase-RNase effector domains. IRE-1 acts in one of three parallel UPR-ER branches (with PEK-1 and ATF-6), showing synthetic lethality with loss of a second branch. Neuronal IRE-1 also mediates cell-nonautonomous signaling including germline apoptosis regulation and anticipatory stress responses.
Summary: IRE-1 is an ER-localized protein. UniProt and experimental evidence from PMID:11779465 confirm ER membrane localization. This annotation is correct but the more specific term GO:0005789 (endoplasmic reticulum membrane) would be more accurate as IRE-1 is a transmembrane protein.
Reason: IRE-1 localizes to the ER as confirmed by multiple sources including UniProt subcellular location annotation. While GO:0005789 (ER membrane) is more precise, this broader term is acceptable for IBA-level evidence. The protein is a type I single-pass ER transmembrane sensor.
Supporting Evidence:
UniProt:Q09499
SUBCELLULAR LOCATION: Endoplasmic reticulum membrane {ECO:0000269|PubMed:11779465}; Single-pass type I membrane protein {ECO:0000269|PubMed:11779465}
file:worm/ire-1/ire-1-deep-research-falcon.md
model: Edison Scientific Literature
GO:0036498 IRE1-mediated unfolded protein response
IBA GO_REF:0000033
ACCEPT
Summary: This is the core biological process for IRE-1. The protein is the eponymous component of the IRE1-mediated UPR branch. In C. elegans, IRE-1 mediates xbp-1 mRNA splicing to generate XBP-1s transcription factor for UPR gene transcription (PMID:11779465, PMID:11780124).
Reason: This is the definitive core function of IRE-1. The annotation is well-supported by multiple studies demonstrating that C. elegans requires ire-1-mediated splicing of xbp-1 mRNA for UPR gene transcription and survival upon ER stress.
Summary: IRE-1 has an endoribonuclease domain that cleaves xbp-1 mRNA in a non-conventional cytoplasmic splicing reaction. The RNase activity also mediates RIDD (Regulated IRE1-Dependent Decay) of select mRNAs including daf-7.
Reason: RNA endonuclease activity is a core catalytic function of IRE-1. The RNase domain has two known outputs: (1) unconventional splicing of xbp-1 mRNA, and (2) RIDD of select mRNAs. This activity requires kinase domain activation.
Purified mouse IRE1 accurately cleaved XBP-1 mRNA in vitro, indicating that XBP-1 mRNA is a direct target of IRE1 endonucleolytic activity
file:worm/ire-1/ire-1-bioreason-rl-predictions.md
IRE-1's RNase has two outputs: (i) non-conventional cytoplasmic splicing of xbp-1 mRNA to produce XBP-1s; and (ii) regulated IRE1-dependent decay (RIDD) of select ER-targeted mRNAs
GO:0004674 protein serine/threonine kinase activity
IBA GO_REF:0000033
ACCEPT
Summary: IRE-1 contains a cytosolic serine/threonine protein kinase domain that undergoes trans-autophosphorylation to activate the endoribonuclease domain. Kinase activity is essential for RNase function.
Reason: The kinase domain is a core catalytic function of IRE-1. Trans-autophosphorylation of the kinase domain is required for activation of the endoribonuclease. The kinase-dead G723R mutation abolishes both xbp-1 splicing and RIDD activity.
Supporting Evidence:
UniProt:Q09499
The kinase domain is activated by trans- autophosphorylation. Kinase activity is required for activation of the endoribonuclease domain (By similarity)
Summary: IRE-1 senses unfolded proteins in the ER lumen via its N-terminal luminal domain, which leads to enzyme auto-activation. This sensing function is fundamental to UPR activation.
Reason: GO:0051082 is now formally obsolete. IRE-1 senses unfolded proteins in the ER lumen to trigger UPR signaling, but this is not chaperone-type unfolded protein binding. The sensing function is captured by the endoribonuclease and kinase activities plus UPR biological process annotations.
Supporting Evidence:
UniProt:Q09499
Senses unfolded proteins in the lumen of the endoplasmic reticulum via its N-terminal domain which leads to enzyme auto- activation (PubMed:11779465)
GO:0070059 intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress
IBA GO_REF:0000033
KEEP AS NON CORE
Summary: IRE-1 mediates ER stress-induced apoptosis through an XBP-1-independent pathway. In C. elegans, IRE-1 regulates germline apoptosis cell non-autonomously from sensory neurons. This pro-apoptotic role is distinct from the adaptive UPR response.
Reason: While the adaptive UPR response is the core function, IRE-1 also has pro-apoptotic signaling functions under severe or prolonged ER stress. In C. elegans, this is notably cell non-autonomous, with neuronal IRE-1 regulating germline apoptosis. This is a secondary function that occurs under specific stress conditions.
Summary: IRE-1 binds ATP for its kinase activity. This is a parent term of ATP binding which is more specific.
Reason: Correct annotation as the kinase domain requires nucleotide (ATP) binding for catalytic activity. The more specific term GO:0005524 (ATP binding) is also present and is preferred, but this broader term is acceptable for IEA evidence.
Summary: IRE-1 has dual catalytic activities - kinase and endoribonuclease. This is a very general parent term.
Reason: While very general, this accurately reflects that IRE-1 is a bifunctional enzyme. More specific child terms for both kinase and RNase activities are also annotated.
Summary: Duplicate annotation of RNA endonuclease activity from InterPro mapping. Same as the IBA annotation above.
Reason: Valid annotation via InterPro domain mapping. The KEN domain (IPR010513) and RNase_Ire1 (cd10422) domains support this function. Duplicates are acceptable when from different evidence sources.
Summary: Parent term of RNA endonuclease activity. IRE-1 cleaves RNA endonucleolytically, not exonucleolytically.
Reason: Accurate general term for the RNase activity of IRE-1. The more specific child term GO:0004521 (RNA endonuclease activity) is also annotated and preferred.
Summary: IRE-1 has protein kinase activity via its cytosolic kinase domain. This is a parent term of protein serine/threonine kinase activity.
Reason: Accurate annotation from InterPro domain mapping. The Pkinase domain (PF00069) is present. More specific child term for Ser/Thr kinase is also annotated.
Supporting Evidence:
UniProt:Q09499
InterPro; IPR000719; Prot_kinase_dom
GO:0004674 protein serine/threonine kinase activity
IEA GO_REF:0000120
ACCEPT
Summary: Duplicate annotation of protein serine/threonine kinase activity from combined automated methods.
Reason: Valid annotation consistent with the kinase domain function. The IBA annotation is also present. Duplicates from different evidence sources are acceptable.
Summary: IRE-1 kinase domain binds ATP as substrate for phosphotransfer reactions.
Reason: Core molecular function required for kinase activity. ATP binding is essential for the trans-autophosphorylation that activates the RNase domain.
Summary: IRE-1 processes xbp-1 mRNA through unconventional cytoplasmic splicing, removing a small intron to generate the active XBP-1s form.
Reason: Valid annotation reflecting the mRNA splicing function. The term captures the processing of xbp-1 mRNA, though the more specific IRE1-mediated UPR term is preferred for capturing the biological context.
The unfolded protein response (UPR) is a transcriptional and translational intracellular signaling pathway activated by the accumulation of unfolded proteins in the lumen of the endoplasmic reticulum (ER)
Summary: IRE-1 regulates gene expression by activating XBP-1s transcription factor through xbp-1 mRNA splicing.
Reason: Valid annotation as IRE-1 ultimately regulates expression of UPR target genes through XBP-1s. However, this is a very broad term; more specific terms like GO:0045944 (positive regulation of transcription by RNA polymerase II) are also annotated and more informative.
Supporting Evidence:
UniProt:Q09499
The active endoribonuclease domain splices xbp-1 precursor mRNA to produce the mature form which then induces transcription of UPR target genes (PubMed:11779465)
Summary: General parent term for the endoribonuclease activity which hydrolyzes phosphodiester bonds in RNA.
Reason: Valid but general annotation. More specific RNA nuclease terms are preferred.
Supporting Evidence:
UniProt:Q09499
Endoribonuclease; EC=3.1.26.-
GO:0030968 endoplasmic reticulum unfolded protein response
IEA GO_REF:0000002
ACCEPT
Summary: IRE-1 is one of three sensors mediating the ER-UPR in metazoans. This term captures the broader UPR pathway.
Reason: Core biological process annotation. IRE-1 is a major and highly conserved ER stress sensor that activates the UPR. The child term GO:0036498 (IRE1-mediated UPR) is more specific.
C. elegans requires ire-1-mediated splicing of xbp-1 mRNA for UPR gene transcription and survival upon ER stress
GO:0080090 regulation of primary metabolic process
IEA GO_REF:0000117
MARK AS OVER ANNOTATED
Summary: Very broad term that encompasses IRE-1's regulatory role in protein folding homeostasis.
Reason: While technically accurate as UPR affects protein and lipid metabolism, this term is too broad to be informative about IRE-1's specific function. More specific UPR-related terms are preferred.
Summary: IRE-1 autophosphorylates on serine residues. This is more specific than protein Ser/Thr kinase activity.
Reason: Valid annotation based on Rhea mapping. UniProt indicates autophosphorylation mainly on serine residues.
Supporting Evidence:
UniProt:Q09499
PTM: Autophosphorylated mainly on serine residues
GO:0036498 IRE1-mediated unfolded protein response
IMP PMID:20733002 Protein misfolding induces hypoxic preconditioning via a sub...
ACCEPT
Summary: Mao & Crowder 2010 showed that IRE-1 is required for hypoxic preconditioning in C. elegans, linking UPR activation to adaptive protection.
Reason: Valid experimental evidence. The study demonstrated that non-lethal hypoxia activates the UPR through IRE-1, and this confers adaptive protection to subsequent hypoxia.
the pharmacological induction of misfolded proteins is itself sufficient to stimulate a delayed protective response to hypoxic injury that requires the UPR pathway proteins IRE-1, XBP-1, and ATF-6
GO:0045944 positive regulation of transcription by RNA polymerase II
IMP PMID:18216284 APY-1, a novel Caenorhabditis elegans apyrase involved in un...
KEEP AS NON CORE
Summary: Uccelletti et al. 2008 showed that IRE-1 is required for transcriptional upregulation of apy-1 and other UPR target genes upon ER stress.
Reason: Valid annotation showing IRE-1's downstream effect on transcription through XBP-1s activation. However, this is an indirect effect of the core xbp-1 splicing function rather than a direct transcriptional role.
ER stress induced by tunicamycin or high temperature resulted in increased transcription of apy-1. This increase was not observed in C. elegans mutants defective in ire-1 or atf-6
GO:0045944 positive regulation of transcription by RNA polymerase II
IGI PMID:18216284 APY-1, a novel Caenorhabditis elegans apyrase involved in un...
KEEP AS NON CORE
Summary: Same study showing genetic interaction for transcriptional regulation of UPR target genes.
Reason: Valid genetic interaction evidence. The G723R kinase-dead mutation prevents transcriptional upregulation of apy-1 upon ER stress. This demonstrates the role of IRE-1 in UPR gene induction.
Supporting Evidence:
UniProt:Q09499
G->R: In zc14; loss of adaptive protection conferred by non-lethal hypoxia treatment. Prevents transcriptional up-regulation of apy-1 upon ER stress
GO:0036498 IRE1-mediated unfolded protein response
IGI PMID:22125500 Physiological IRE-1-XBP-1 and PEK-1 signaling in Caenorhabdi...
ACCEPT
Summary: Richardson et al. 2011 demonstrated genetic interactions between ire-1, xbp-1, pek-1, and atf-6 in UPR signaling during development and immunity.
Reason: Valid genetic interaction evidence showing functional IRE-1 pathway in physiological conditions. XBP-1 deficiency causes constitutive ER stress with elevated IRE-1 activity.
Reason: Valid ISS annotation based on conserved kinase domain. The protein kinase domain (aa 518-778) is well-conserved with mammalian IRE1.
Supporting Evidence:
UniProt:Q09499
Belongs to the protein kinase superfamily. Ser/Thr protein kinase family
GO:0030968 endoplasmic reticulum unfolded protein response
IMP PMID:25340700 It's all in your mind: determining germ cell fate by neurona...
ACCEPT
Summary: Levi-Ferber et al. 2014 demonstrated IRE-1 function in ER stress response including cell non-autonomous signaling from neurons to germline.
Reason: Valid IMP evidence. The study showed ire-1 mutants fail to respond to ER stress conditions that increase germline apoptosis in wild-type animals.
IMP PMID:23791175 XBP-1 is a cell-nonautonomous regulator of stress resistance...
KEEP AS NON CORE
Summary: Taylor & Dillin 2013 showed neuronal IRE-1/XBP-1 signaling with cell non-autonomous effects on stress resistance and longevity.
Reason: Valid annotation reflecting neuronal localization and function. IRE-1 in neurons mediates cell non-autonomous signaling. However, neuronal cell body is a specific subcellular localization within neurons; the primary localization is ER membrane.
Neuronally derived XBP-1s was sufficient to rescue stress resistance, increase longevity, and activate the UPR(ER) in distal, non-neuronal cell types through a cell-nonautonomous mechanism
ire-1/xbp-1 acts with pek-1, a protein kinase that mediates translation attenuation, in complementary pathways that are essential for worm development and survival
GO:0030968 endoplasmic reticulum unfolded protein response
IMP PMID:11780124 IRE1 couples endoplasmic reticulum load to secretory capacit...
ACCEPT
Summary: Calfon et al. 2002 (Nature) demonstrated that ire-1 and xbp-1 mutations abolish the UPR in C. elegans.
Reason: Key experimental evidence from Nature paper establishing IRE-1-XBP-1 pathway conservation in metazoans.
ISS PMID:11779465 Complementary signaling pathways regulate the unfolded prote...
ACCEPT
Summary: Sequence similarity evidence for ER membrane localization based on conserved topology and transmembrane domain.
Reason: Valid ISS annotation. The protein has a conserved type I transmembrane topology with luminal sensor domain and cytosolic effector domains.
Supporting Evidence:
UniProt:Q09499
SUBCELLULAR LOCATION: Endoplasmic reticulum membrane {ECO:0000269|PubMed:11779465}; Single-pass type I membrane protein
GO:0035966 response to topologically incorrect protein
IMP PMID:23335331 A novel interaction between aging and ER overload in a prote...
KEEP AS NON CORE
Summary: Schipanski et al. 2013 showed that UPR pathways including IRE-1 modulate protein aggregation in a neuroserpin disease model.
Reason: Valid annotation showing IRE-1's role in responding to misfolded/aggregated proteins. This is related to but distinct from the canonical unfolded protein response.
IGI PMID:11779465 Complementary signaling pathways regulate the unfolded prote...
KEEP AS NON CORE
Summary: Shen et al. 2001 showed that ire-1 and pek-1 are redundant genes essential for larval development.
Reason: Valid developmental phenotype annotation. Single mutants are viable but double mutants (ire-1 with pek-1 or atf-6) arrest at early larval stages. This is a downstream consequence of UPR function rather than a direct developmental regulatory role.
Supporting Evidence:
UniProt:Q09499
In combination with RNAi-mediated knockdown of atf-6, causes sluggish movement, arrested development at the L2 larval stage, and lethality soon thereafter
Core Functions
IRE-1 cleaves xbp-1 mRNA in an unconventional cytoplasmic splicing reaction, removing a 23-nucleotide intron to generate the active XBP-1s transcription factor. The RNase domain also executes RIDD (Regulated IRE1-Dependent Decay) of select mRNAs including daf-7.
Purified mouse IRE1 accurately cleaved XBP-1 mRNA in vitro, indicating that XBP-1 mRNA is a direct target of IRE1 endonucleolytic activity
The cytosolic kinase domain undergoes trans-autophosphorylation upon ER stress, which is required for activation of the endoribonuclease domain. Kinase-dead mutations (G723R) abolish both xbp-1 splicing and RIDD.
The kinase domain is activated by trans- autophosphorylation. Kinase activity is required for activation of the endoribonuclease domain (By similarity)
The luminal N-terminal domain senses accumulation of unfolded proteins in the ER lumen, triggering IRE-1 oligomerization and activation of cytosolic effector domains. No molecular-function term is asserted for sensing. GO:0051082 is obsolete (and the IBA annotation to it is removed in this review), and the signalling output is captured by the kinase and endoribonuclease core functions.
Q: What are the specific RIDD substrates beyond daf-7 in C. elegans, and how does RIDD contribute to tissue-specific IRE-1 functions? Recent work identified daf-7 as a neuronal RIDD substrate, but the full spectrum of RIDD targets in different tissues remains to be characterized.
Q: How does IRE-1 achieve different activation thresholds for xbp-1 splicing versus RIDD? Studies show RIDD can occur at lower stress levels than xbp-1 splicing, suggesting distinct regulatory mechanisms.
Suggested Experiments
Experiment: RNA-seq or CLIP-seq to identify IRE-1 RIDD substrates in different C. elegans tissues under varying stress conditions. This would reveal the full complement of RIDD targets and tissue-specific regulation.
Experiment: Structure-function analysis of IRE-1 domains required for cell non-autonomous signaling versus canonical UPR. This would help distinguish the molecular requirements for neuronal IRE-1 signaling to germline versus canonical xbp-1-dependent UPR.
Tags
caeel-upr-stress
External Prediction Reviews
These computational predictions are reviewed separately from the GOA annotation set used for this review. The assessments below are from this project and do not constitute official GO annotations or endorsement by GO/UniProt. They are not included in the existing annotation review above.
Focused review of the GO-GPT/BioReason-Pro prediction that ire-1 has hydrolase activity acting on ester bonds. The prediction is not a useful new annotation: the direct activity is the already curated RNA endonuclease activity of the IRE-1 KEN domain, and GO:0016788 is both less informative and off the current ontology branch for GO:0004521 RNA endonuclease activity.
Review rationale: IRE-1 cleaves phosphodiester bonds in xbp-1 mRNA, so the prediction is chemically adjacent to the true activity but less precise than the accepted GO:0004521 RNA endonuclease activity already present on the review. In the current GO structure, GO:0016788 is not an asserted ancestor of RNA endonuclease activity, while IRE-1 already carries the more precise RNA nuclease and RNA endonuclease terms. LSP is preferred over NPI or UNC because the broad ester-hydrolase chemistry is adjacent to the curated nuclease activity, but the proposed term is off-branch and redundant.
Supporting Evidence:
PMID:11780124: "Purified mouse IRE1 accurately cleaved XBP-1 mRNA in vitro, indicating that XBP-1 mRNA is a direct target of IRE1 endonucleolytic activity"
PMID:11779465: "C. elegans requires ire-1-mediated splicing of xbp-1 mRNA for UPR gene transcription and survival upon ER stress"
WormBase gene description for ire-1 (worm)WormBase
WormBase gene description for ire-1 (worm)
ire-1 encodes a transmembrane serine/threonine protein kinase and site-specific endoribonuclease orthologous to Saccharomyces cerevisiae inositol-requiring 1 protein kinase (Ire1) and human endoplasmic reticulum-to-nucleus signaling 1 (ERN1, OMIM:604033); IRE-1 is required for the unfolded protein response (UPR) that counteracts cellular stress induced by accumulation of unfolded proteins in the endoplasmic reticulum (ER); in response to ER stress, IRE-1 cleaves xbp-1 mRNA to produce transcriptionally active XBP-1 that positively regulates UPR gene expression in order to maintain ER homeostasis.