aldo-1 encodes fructose-bisphosphate aldolase 1 (CE-1), one of two class I aldolase isozymes in C. elegans (the other being aldo-2/CE-2). The enzyme catalyzes the reversible cleavage of fructose-1,6-bisphosphate into glyceraldehyde-3-phosphate and dihydroxyacetone phosphate, a central step in glycolysis and gluconeogenesis. CE-1 has unique kinetic properties with a broad substrate specificity compared to CE-2. The protein is ubiquitously expressed and in body wall muscle localizes to dense bodies, thick filaments/M-lines, and ER/sarcoplasmic reticulum, consistent with a role in providing ATP near contractile structures. In vivo, aldo-1 is a critical component of compensatory glycolysis: it is transcriptionally upregulated in mitochondrial complex I mutants and its knockdown strongly shortens their lifespan, and it is part of HIF-1-linked hypoxia-adaptation and age-associated neuronal metabolic transcriptional programs.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
|
GO:0004332
fructose-bisphosphate aldolase activity
|
IDA
PMID:9056253 Caenorhabditis elegans has two isozymic forms, CE-1 and CE-2... |
ACCEPT |
Summary: Direct experimental evidence. Inoue et al. purified recombinant CE-1 and demonstrated FBP aldolase activity with KM of 16.7 uM for FBP. This is the core molecular function of aldo-1.
Reason: Direct enzyme assay on purified recombinant protein with kinetic characterization
Supporting Evidence:
PMID:9056253
Two distinct types of cDNAs for fructose-1,6-bisphosphate (FBP) aldolase, Ce-1 and Ce-2, have been isolated from nematode Caenorhabditis elegans, and the respective recombinant aldolase isozymes, CE-1 and CE-2, have been purified and characterized
file:worm/aldo-1/aldo-1-deep-research-bioreason-sft.md
[BioReason confirms] GO:0004332 fructose-bisphosphate aldolase activity... the catalytic center is pinpointed by IPR029768...marking the lysine-dependent iminium chemistry that drives carbon-carbon bond cleavage/formation
file:worm/aldo-1/aldo-1-deep-research-falcon.md
catalyzes the cleavage of the substrate **fructose-1,6-bisphosphate (F1,6BP)** in glycolysis
file:worm/aldo-1/aldo-1-deep-research-falcon.md
the lysine at position 230 is the residue where Schiff base intermediates are formed
|
|
GO:0004332
fructose-bisphosphate aldolase activity
|
IBA
GO_REF:0000033 |
ACCEPT |
Summary: Phylogenetic inference consistent with and redundant to the IDA annotation from PMID:9056253. Correct but redundant.
Reason: Phylogenetic annotation is consistent with direct experimental evidence
|
|
GO:0004332
fructose-bisphosphate aldolase activity
|
IEA
GO_REF:0000120 |
ACCEPT |
Summary: Automated annotation from InterPro domain and Rhea reaction mapping. Correct and consistent with IDA evidence.
Reason: Automated annotation correctly infers function from domain architecture
|
|
GO:0006096
glycolytic process
|
NAS
PMID:9056253 Caenorhabditis elegans has two isozymic forms, CE-1 and CE-2... |
ACCEPT |
Summary: Non-traceable author statement. The Inoue et al. paper characterizes aldo-1 as an FBP aldolase, and FBP aldolase is a glycolytic enzyme by definition. The glycolytic role is well supported by the enzyme activity data. Falcon deep research adds in vivo functional support: aldo-1 is upregulated in mitochondrial complex I mutants (~3-fold in gas-1, ~6-fold in nuo-6) and its RNAi knockdown strongly shortens the lifespan of these mutants (up to 65% in gas-1, >85% in nuo-6), with the authors concluding these mutants rely heavily on glycolysis for energy production. This directly supports a glycolytic process role beyond the by-definition inference.
Reason: FBP aldolase activity directly places the enzyme in the glycolytic pathway
Supporting Evidence:
PMID:9056253
CE-1 evolved to act as an intrinsic enzyme that exhibits a much broader substrate specificity than dose CE-2
file:worm/aldo-1/aldo-1-deep-research-falcon.md
In *C. elegans* mitochondrial complex I mutants, aldo-1 is transcriptionally upregulated, consistent with a metabolic shift toward glycolysis
file:worm/aldo-1/aldo-1-deep-research-falcon.md
decreased **gas-1(fc21)** median lifespan by **up to 65%**
file:worm/aldo-1/aldo-1-deep-research-falcon.md
rely heavily on glycolysis for energy production
|
|
GO:0006096
glycolytic process
|
IBA
GO_REF:0000033 |
ACCEPT |
Summary: Phylogenetic inference of glycolytic process involvement. Consistent with the NAS annotation and enzyme function.
Reason: Phylogenetic annotation consistent with biochemical evidence
|
|
GO:0006096
glycolytic process
|
IEA
GO_REF:0000120 |
ACCEPT |
Summary: Automated annotation from InterPro and UniPathway mapping. Correct and consistent with other evidence.
Reason: Automated annotation correctly infers pathway membership
|
|
GO:0030388
fructose 1,6-bisphosphate metabolic process
|
IBA
GO_REF:0000033 |
ACCEPT |
Summary: Phylogenetic inference. FBP is the direct substrate of aldo-1, so involvement in its metabolism is inherent to the enzyme's catalytic activity. Falcon deep research independently describes ALDO-1 as cleaving the substrate fructose-1,6-bisphosphate, consistent with this annotation.
Reason: Follows directly from the enzyme's catalytic function on FBP
Supporting Evidence:
file:worm/aldo-1/aldo-1-deep-research-falcon.md
catalyzes the cleavage of the substrate **fructose-1,6-bisphosphate (F1,6BP)** in glycolysis
|
|
GO:0042802
identical protein binding
|
IPI
PMID:14704431 A map of the interactome network of the metazoan C. elegans. |
KEEP AS NON CORE |
Summary: Detected via high-throughput Y2H in the C. elegans interactome mapping project. Class I aldolases are known homotetramers, so self-interaction is expected. However, Y2H self-interactions can be artifacts, though this is biologically plausible. The annotation is kept as non-core since identical protein binding is a generic term that does not inform about specific function.
Reason: Self-interaction is biologically plausible for a homotetrameric enzyme but identical protein binding is uninformative as a standalone annotation
Supporting Evidence:
PMID:14704431
more than 4000 interactions were identified from high-throughput, yeast two-hybrid (HT=Y2H) screens
|
|
GO:0042802
identical protein binding
|
IPI
PMID:19123269 Empirically controlled mapping of the Caenorhabditis elegans... |
KEEP AS NON CORE |
Summary: Replicated self-interaction in the expanded WI-2007/WI8 interactome. Confirmation of the PMID:14704431 finding, but still a generic annotation.
Reason: Replication adds confidence but identical protein binding remains uninformative
Supporting Evidence:
PMID:19123269
the resulting dataset (Worm Interactome 2007 or WI-2007) is similar in quality to low-throughput data curated from the literature
|
|
GO:0005829
cytosol
|
IBA
GO_REF:0000033 |
ACCEPT |
Summary: Phylogenetic inference of cytosolic localization. Class I aldolases are soluble cytosolic enzymes, so this is well supported. Consistent with the cytoplasm ISS annotation but more specific. Falcon deep research notes that, while no direct C. elegans localization was retrieved, the strong family-level expectation places aldolase in cytosolic glycolysis.
Reason: Soluble glycolytic enzyme expected in cytosol based on conserved properties
Supporting Evidence:
file:worm/aldo-1/aldo-1-deep-research-falcon.md
the strong family-level expectation that aldolase participates in cytosolic glycolysis
|
|
GO:0005737
cytoplasm
|
ISS
GO_REF:0000024 |
ACCEPT |
Summary: Transferred from ortholog (P05065, rabbit ALDOC). Cytoplasmic localization is expected for a soluble glycolytic enzyme. Consistent with cytosol IBA annotation but less specific.
Reason: Cytoplasmic localization is well established for class I aldolases
|
|
GO:0000792
heterochromatin
|
ISS
GO_REF:0000024 |
KEEP AS NON CORE |
Summary: Transferred from rabbit aldolase C ortholog (P05065). Aldolase has been reported to associate with heterochromatin in some vertebrate studies as a moonlighting function. However, this is a non-canonical localization for a glycolytic enzyme and direct evidence in C. elegans is lacking. The ISS transfer is questionable for this non-canonical function. Falcon deep research corroborates this caution: it notes that aldolase moonlighting/extracellular localizations described in broader reviews are not direct C. elegans ALDO-1 localization evidence.
Reason: Heterochromatin association is a reported moonlighting function in vertebrates but lacks direct evidence in C. elegans; ISS transfer of non-canonical localization is weak
Supporting Evidence:
file:worm/aldo-1/aldo-1-deep-research-falcon.md
broader aldolase reviews discuss intracellular (and sometimes extracellular โmoonlightingโ) localizations across organisms, but this is not direct *C. elegans* ALDO-1 localization evidence
|
|
GO:0005783
endoplasmic reticulum
|
HDA
PMID:21611156 Determining the sub-cellular localization of proteins within... |
ACCEPT |
Summary: High-throughput GFP localization in body wall muscle. T05D4.1 was classified in Category 6 (Dense bodies, Thick filaments and/or M-lines, ER/SR). The ER/SR component of the localization pattern was observed. Validated with both Gateway and genomic clones.
Reason: Direct GFP localization data from high-throughput study, validated by two independent cloning approaches
Supporting Evidence:
PMID:21611156
The sub-cellular localization for the T05D4.1::GFP (A, B)...proteins expressed from gateway clones using a muscle-specific promoter (A, B and C) or from genomic clones using endogenous promoters (B, D and F)
|
|
GO:0030017
sarcomere
|
HDA
PMID:21611156 Determining the sub-cellular localization of proteins within... |
ACCEPT |
Summary: High-throughput GFP localization in body wall muscle. Category 6 includes dense bodies, thick filaments, and M-lines, all of which are sarcomeric structures. Consistent with the known association of glycolytic enzymes with sarcomeric structures in muscle.
Reason: Direct GFP localization data showing sarcomeric localization pattern in body wall muscle
Supporting Evidence:
PMID:21611156
we verified the localization of several Gateway constructs by cloning and tagging the corresponding gene via conventional methods using genomic DNA instead of cDNA, and using endogenous promoters instead of our muscle specific promoter. We were able to confirm the same sub-cellular localization using both methods
|
|
GO:0055120
striated muscle dense body
|
HDA
PMID:21611156 Determining the sub-cellular localization of proteins within... |
ACCEPT |
Summary: High-throughput GFP localization in body wall muscle. Dense bodies are the C. elegans equivalent of vertebrate Z-discs, where they anchor actin filaments to the cell membrane. Category 6 explicitly includes dense body localization. T05D4.1 was one of the proteins used to validate the approach (Figure 3).
Reason: Direct GFP localization data with validation by both Gateway and genomic clone approaches; dense body localization is part of Category 6
Supporting Evidence:
PMID:21611156
The sub-cellular localization for the T05D4.1::GFP (A, B)...proteins expressed from gateway clones using a muscle-specific promoter (A, B and C) or from genomic clones using endogenous promoters (B, D and F)
|
Q: Does aldo-1 form a glycolytic metabolon with other glycolytic enzymes at sarcomeric structures in C. elegans body wall muscle, analogous to what has been proposed in vertebrate striated muscle?
Suggested experts: Moerman DG
Q: What are the distinct physiological roles of aldo-1 (CE-1) versus aldo-2 (CE-2) in C. elegans, given their different kinetic properties and substrate specificities?
Suggested experts: Hori K
Q: Is the heterochromatin association observed for vertebrate aldolase orthologs conserved in C. elegans aldo-1, and does it have functional significance?
Q: Is aldo-1 a direct HIF-1 transcriptional target, and how is its upregulation coordinated across hypoxia (HIF-1 over-activation), mitochondrial complex I dysfunction, and age-associated neuronal metabolic decline?
Experiment: Co-immunoprecipitation or proximity ligation assay of aldo-1 with other glycolytic enzymes (e.g., phosphofructokinase, GAPDH, triosephosphate isomerase) in C. elegans body wall muscle lysates, combined with co-localization imaging at sarcomeric structures.
Hypothesis: aldo-1 forms a sarcomeric glycolytic metabolon in C. elegans body wall muscle
Type: co-immunoprecipitation and imaging
Experiment: Generate aldo-1 single mutants and aldo-1; aldo-2 double mutants to compare phenotypes. Measure glycolytic flux, energy metabolism, lifespan, and glucose sensitivity in each genotype. Given that aldo-2 RNAi causes embryonic lethality, test whether aldo-1 loss is similarly lethal or shows distinct phenotypes.
Hypothesis: aldo-1 and aldo-2 have non-redundant roles in C. elegans metabolism
Type: genetic analysis and metabolomics
The architecture begins with IPR013785 (Aldolase-type TIM barrel, homologous_superfamily) spanning residues 1โ366, establishing an (ฮฑ/ฮฒ)8 barrel scaffold that positions catalytic residues at the C-terminal ends of the ฮฒ-strands. Nested within this fold are two overlapping family signatures, IPR000741 (Fructose-bisphosphate aldolase, class-I) from residues 13โ366 and IPR000741 (Fructose-bisphosphate aldolase, class-I) from residues 15โ366, which specify a class I aldolase that uses a catalytic lysine to form a Schiff base with a carbonyl substrate. The catalytic center is pinpointed by IPR029768 (Fructose-bisphosphate aldolase class-I active site, conserved_site) at residues 223โ233, marking the lysine-dependent iminium chemistry that drives carbonโcarbon bond cleavage/formation. This ordered layoutโTIM barrel scaffold, class I family determinants, and a conserved active-site lysineโcauses a reversible aldol cleavage/condensation of fructose 1,6-bisphosphate into dihydroxyacetone phosphate and glyceraldehyde 3-phosphate, which defines GO:0004332 fructose-bisphosphate aldolase activity. Class I aldolases typically assemble as homotetramers; the quaternary interface arises from complementary TIM-barrel surfaces, which necessitates GO:0042802 identical protein binding to form the active oligomer.
Catalysis at this step channels carbon flux through glycolysis and supports gluconeogenesis. In the glycolytic direction, the Schiff-base mechanism cleaves fructose 1,6-bisphosphate to DHAP and G3P, embedding the enzyme in GO:0006096 glycolytic process. Because glycolytic throughput directly sets blood glucose levels in metazoans, the same reaction underpins systemic sugar balance, aligning with GO:0042593 glucose homeostasis. The reversibility of the reaction also supports gluconeogenic assembly of fructose 1,6-bisphosphate from triose phosphates, ensuring metabolic flexibility.
Cellular placement follows from both function and muscle-specific architecture. The TIM-barrel enzyme is soluble and lacks transmembrane features, favoring a cytosolic environment. In striated muscle, glycolytic enzymes are known to dock onto cytoskeletal and adhesion-associated structures to create metabolons that buffer ATP supply during contraction. This explains localization to GO:0030017 sarcomere and GO:0055120 striated muscle dense body, where anchoring near actin-attachment sites positions the enzyme to feed ATP-consuming myofibrillar processes. Association with GO:0005783 endoplasmic reticulum is consistent with peripheral binding to ER membranes or ERโmyofibril junctions, enabling local exchange of metabolites and potentially coupling to calcium signaling that modulates glycolytic flux.
Mechanistically, the enzyme likely operates within a sarcomeric glycolytic metabolon. Upstream, ATP-dependent 6-phosphofructokinase 1 and 2 generate fructose 1,6-bisphosphate, which this enzyme cleaves; downstream, triosephosphate isomerase equilibrates DHAP and G3P, and glyceraldehyde-3-phosphate dehydrogenases 1โ4 draw flux forward, while an FBPase domain-containing protein can reverse the direction during gluconeogenesis. Glucose-6-phosphate isomerase supplies the hexose substrate pool, and a transket_pyr domain-containing protein may provide auxiliary carbon-shuffling or regulatory interactions. The homomeric assembly (identical protein binding) stabilizes the active site geometry and supports high local catalytic throughput at dense bodies and sarcomeres, with transient ER contacts positioning the metabolon near excitationโcontraction machinery. This arrangement ensures rapid, spatially focused energy production to sustain muscle contraction while maintaining whole-organism glucose balance.
## Functional Summary
A class I aldolase in Caenorhabditis elegans that assembles as a homomeric TIM-barrel enzyme to catalyze the reversible cleavage of fructose 1,6-bisphosphate into triose phosphates during glycolysis and the corresponding condensation in gluconeogenesis. By anchoring to sarcomeric structures and dense bodies, and by transiently associating with endoplasmic reticulum interfaces, it forms part of a muscle glycolytic metabolon that channels substrates efficiently to ATP-producing steps, thereby supporting contraction and contributing to organismal glucose balance.
## UniProt Summary
Plays a key role in glycolysis and gluconeogenesis.
## InterPro Domains
- IPR013785: Aldolase-type TIM barrel (homologous_superfamily) [1-366]
- IPR000741: Fructose-bisphosphate aldolase, class-I (family) [13-366]
- IPR000741: Fructose-bisphosphate aldolase, class-I (family) [15-366]
- IPR029768: Fructose-bisphosphate aldolase class-I active site (conserved_site) [223-233]
## GO Term Predictions
### Molecular Function
### Biological Process
### Cellular Component
The research report should be a detailed narrative explaining the function, biological processes, and localization of the gene product. Citations should be given for all claims.
You should prioritize authoritative reviews and primary scientific literature when conducting research. You can supplement
this with annotations you find in gene/protein databases, but these can be outdated or inaccurate.
We are specifically interested in the primary function of the gene - for enzymes, what reaction is catalyzed, and what is the substrate specificity? For transporters, what is the substrate? For structural proteins or adapters, what is the broader structural role? For signaling molecules, what is the role in the pathway.
We are interested in where in or outside the cell the gene product carries out its function.
We are also interested in the signaling or biochemical pathways in which the gene functions. We are less interested in broad pleiotropic effects, except where these elucidate the precise role.
Include evidence where possible. We are interested in both experimental evidence as well as inference from structure, evolution, or bioinformatic analysis. Precise studies should be prioritized over high-throughput, where available.
The literature gathered here is consistent with the UniProt target P54216 being C. elegans fructose-bisphosphate aldolase 1 (FBA1): a comparative aldolase phylogeny explicitly lists โCaenorhabditis elegans FBA 1 (P54216).โ (pirovich2021multifunctionalfructose16bisphosphate pages 3-5)
Independent C. elegans transcriptomics evidence maps the gene symbol aldo-1 to the genomic ORF T05D4.1, annotated as โfructose bisphosphate aldolase.โ (miersch2012sexdifferencesin pages 13-15)
Accordingly, this report focuses on the C. elegans glycolytic aldolase encoded by aldo-1/T05D4.1 and linked to UniProt P54216, and does not mix in โaldo-1โ usages from other organisms. (pirovich2021multifunctionalfructose16bisphosphate pages 3-5, miersch2012sexdifferencesin pages 13-15)
Fructose-1,6-bisphosphate aldolase is a core glycolytic enzyme that catalyzes the cleavage of the substrate fructose-1,6-bisphosphate (F1,6BP) in glycolysis (classically the โfourth stepโ of glycolysis in many pathway descriptions). (pirovich2021multifunctionalfructose16bisphosphate pages 3-5)
In C. elegans, aldo-1 (T05D4.1) is annotated as โfructose bisphosphate aldolaseโ and is placed in glucose metabolism in a curated gene list; the tableโs reaction description explicitly notes the substrate fructose-1,6-bisphosphate and the glycolytic product glyceraldehyde-3-phosphate (as written in the source table). (miersch2012sexdifferencesin pages 13-15)
Fructose-bisphosphate aldolases are subdivided into mechanistic/structural classes. In nematode aldolases, a class-I-type mechanism involves a conserved lysine that forms a Schiff-base intermediate with the substrate. In a nematode aldolase structural/biochemical analysis that includes C. elegans aldo-1 as a homolog in the sequence alignment, the authors highlight that โthe lysine at position 230 is the residue where Schiff base intermediates are formed,โ consistent with the canonical class I aldolase catalytic strategy. (umair2021teladorsagiacircumcincta16bisphosphate pages 4-8)
The primary function of C. elegans ALDO-1 is its glycolytic aldolase activity on F1,6BP within glucose metabolism. (miersch2012sexdifferencesin pages 13-15, pujol2013succinatedehydrogenaseupregulation pages 2-4)
Although the retrieved corpus did not include a direct biochemical purification/kinetic paper for C. elegans ALDO-1 itself, nematode aldolase kinetic measurements in a closely related context report clear activity on fructose 1,6-bisphosphate with an apparent Km = 0.24 ยฑ 0.01 ยตM and Vmax = 432 nmolยทminโปยนยทmgโปยน at 30ยฐC, with optimum pH 7.5 (n=3). These parameters support strong specificity/efficiency for F1,6BP in nematode class-I-type aldolases and are consistent with the conserved role inferred for C. elegans ALDO-1 based on homology and pathway placement. (umair2021teladorsagiacircumcincta16bisphosphate pages 4-8)
A comparative aldolase phylogeny built from UniProt sequences includes C. elegans FBA1 (P54216) among other eukaryotic aldolases, supporting placement of P54216 within conserved fructose-bisphosphate aldolase families. (pirovich2021multifunctionalfructose16bisphosphate pages 3-5)
In a study on sex differences in carbohydrate metabolism, aldo-1 (T05D4.1) shows higher expression in males than hermaphrodites. The male:hermaphrodite expression ratios for two transcript entries are approximately 2.11โ2.12 in young adults and 2.33โ2.85 in adults (significance denoted by asterisks in the table). (miersch2012sexdifferencesin pages 13-15)
A neuron-focused aging transcriptomics study reports that canonical metabolic genes, including glycolytic enzymes, decline in aging male neurons. In that context, aldo-1 is listed among glycolysis enzymes that are โdownregulated with age at least 2-foldโ (Figure 5B) in male neurons, within a DESeq2 framework using thresholds including adjusted p-values (p-adj) < 0.05 for differential expression calls. (weng2024malespecificbehavioraland pages 7-9)
No retrieved C. elegans primary study snippet in this run provided direct experimental subcellular localization for ALDO-1 (e.g., cytosolic vs organelle-associated). Thus, localization cannot be asserted beyond the strong family-level expectation that aldolase participates in cytosolic glycolysis; broader aldolase reviews discuss intracellular (and sometimes extracellular โmoonlightingโ) localizations across organisms, but this is not direct C. elegans ALDO-1 localization evidence. (pirovich2021multifunctionalfructose16bisphosphate pages 3-5)
In C. elegans mitochondrial complex I mutants, aldo-1 is transcriptionally upregulated, consistent with a metabolic shift toward glycolysis:
- gas-1(fc21): ~3-fold aldo-1 increase
- nuo-6(qm200): ~6-fold aldo-1 increase (pujol2013succinatedehydrogenaseupregulation pages 2-4)
Functional evidence links aldo-1 to survival/longevity in these mitochondrial mutants. RNAi knockdown of aldo-1:
- decreased gas-1(fc21) median lifespan by up to 65%
- decreased nuo-6(qm200) median lifespan by >85% (pujol2013succinatedehydrogenaseupregulation pages 2-4)
The authors interpret these results as indicating that these mutants โrely heavily on glycolysis for energy production,โ positioning ALDO-1 as a critical component of compensatory energy metabolism when oxidative phosphorylation is impaired. (pujol2013succinatedehydrogenaseupregulation pages 2-4)
In a 2024 transcriptome analysis of mutants with persistent HIF-1 over-activation (loss of negative regulators including vhl-1, egl-9, rhy-1), aldo-1 is among the genes โcommonly up-regulatedโ in all three mutants and is explicitly annotated as โaldo-1 (fructose-1,6-bisphosphate aldolase).โ (feng2024transcriptomeanalysesdescribe pages 4-5)
The gene set shared across mutants (104 upregulated genes) shows strong statistical overlap (reported p-values < 2.2E-16 by Fisherโs exact tests), and the shared upregulated set is enriched for โMetabolismโ at WormCat Category 1 (Bonferroni FDR = 9.23E-07), with aldo-1 listed within that metabolism-enriched gene list. (feng2024transcriptomeanalysesdescribe pages 4-5)
This provides recent evidence that aldo-1 is part of a HIF-linked metabolic transcriptional program relevant to hypoxia adaptation in C. elegans. (feng2024transcriptomeanalysesdescribe pages 4-5)
Two 2024 studies in the retrieved corpus provide modern systems-level contexts for aldo-1 regulation:
1) Neuron aging: male neuron transcriptomes show โฅ2-fold age-associated downregulation of glycolysis genes including aldo-1 (with DESeq2 and p-adj reporting in the analysis pipeline). (weng2024malespecificbehavioraland pages 7-9)
2) Persistent HIF-1 activation: aldo-1 is part of a shared upregulated gene set in HIF-1 high-activity mutants; the overlap across mutants is highly significant (p < 2.2E-16), and metabolism enrichment is supported (Bonferroni FDR 9.23E-07). (feng2024transcriptomeanalysesdescribe pages 4-5)
Within the retrieved literature, aldo-1 functions as a high-value metabolic readout and dependency in contexts where glycolytic flux is predicted to change:
- As a marker/effector of compensatory glycolysis in mitochondrial respiratory chain mutants (with strong functional impact of knockdown on lifespan). (pujol2013succinatedehydrogenaseupregulation pages 2-4)
- As part of transcriptional programs in hypoxia/HIF-1 biology. (feng2024transcriptomeanalysesdescribe pages 4-5)
- As part of metabolic decline signatures in neuron aging. (weng2024malespecificbehavioraland pages 7-9)
A 2021 review emphasizes that fructose-1,6-bisphosphate aldolase is not only a conserved glycolytic enzyme but can have โmoonlightingโ functions and can be targeted by drugs or vaccines in pathogenic contexts (broadly across organisms). While this is not an implementation of C. elegans ALDO-1 specifically, it contextualizes why aldolase family members are studied as potential targets and why conserved sequence/function matter. (pirovich2021multifunctionalfructose16bisphosphate pages 3-5)
The strongest C. elegans-specific functional evidence available in this run indicates that aldo-1 is essential for adaptive glycolysis in settings where mitochondrial respiration is compromised (complex I mutants), with large median-lifespan penalties upon aldo-1 knockdown (up to 65% and >85%). (pujol2013succinatedehydrogenaseupregulation pages 2-4)
Recent (2024) systems-level studies position aldo-1 at the intersection of hypoxia signaling (HIF-1) and sex/age-dependent neuronal metabolic decline, suggesting that glycolysis regulation (including aldolase) is a recurrent node in how C. elegans adjusts energy metabolism across stress and aging contexts. (feng2024transcriptomeanalysesdescribe pages 4-5, weng2024malespecificbehavioraland pages 7-9)
At the molecular level, class-I-type aldolase Schiff-base chemistry is supported by conserved mechanistic residues in nematode homologs and is consistent with the protein family assignment for P54216, but this remains inference rather than a direct mechanistic experiment on the C. elegans protein in the retrieved texts. (umair2021teladorsagiacircumcincta16bisphosphate pages 4-8, pirovich2021multifunctionalfructose16bisphosphate pages 3-5)
| Topic | Key finding | Quantitative details (fold change, FDR/p-adj, lifespan %) | System/condition (strain/tissue) | Source (authors, year, journal) | Publication date (month/year) | URL/DOI | Evidence strength/notes |
|---|---|---|---|---|---|---|---|
| Identity | UniProt P54216 is listed as Caenorhabditis elegans FBA 1, supporting assignment of the target protein to C. elegans fructose-bisphosphate aldolase 1. | None reported in snippet. | Comparative aldolase phylogeny; C. elegans sequence entry. | Pirovich et al., 2021, Frontiers in Molecular Biosciences | Aug 2021 | https://doi.org/10.3389/fmolb.2021.719678 | Useful accession-level confirmation for P54216; review/phylogeny rather than direct worm functional experiment. (pirovich2021multifunctionalfructose16bisphosphate pages 3-5) |
| Identity | ORF T05D4.1 is explicitly annotated as aldo-1, โfructose bisphosphate aldolase,โ confirming aldo-1 โ T05D4.1 mapping in C. elegans. | Male:hermaphrodite ratios shown for two transcript entries: T05D4.1.2 = 2.11 (young adult), 2.85 (adult); T05D4.1.1 = 2.12 (young adult), *2.33 (adult). | Whole-animal sex-comparison transcriptomics in young adult and adult worms. | Miersch & Dรถring, 2012, PLoS ONE | Sep 2012 | https://doi.org/10.1371/journal.pone.0044748 | Strong direct mapping for the gene name/ORF in C. elegans; asterisks indicate significance but exact p-value thresholds were not present in snippet. (miersch2012sexdifferencesin pages 13-15) |
| Function | aldo-1 is a glycolytic fructose-bisphosphate aldolase catalyzing cleavage of fructose-1,6-bisphosphate toward glyceraldehyde-3-phosphate (table wording shows reaction direction). | Reaction shown as โfructose-1,6 bisphosphate โ glyceraldehyd-3 phosphateโ in the table; aldolase is also described as catalyzing the fourth step of glycolysis. | C. elegans carbohydrate metabolism annotation; general aldolase biochemistry review. | Miersch & Dรถring, 2012, PLoS ONE; Pirovich et al., 2021, Frontiers in Molecular Biosciences | Sep 2012; Aug 2021 | https://doi.org/10.1371/journal.pone.0044748 ; https://doi.org/10.3389/fmolb.2021.719678 | Strong for pathway-level enzymatic role; the full stoichiometric coproduct list is not fully printed in the Miersch table snippet, but aldolase substrate context is explicit. (miersch2012sexdifferencesin pages 13-15, pirovich2021multifunctionalfructose16bisphosphate pages 3-5) |
| Function / mechanism | Aldolases of this family use a class I Schiff-base mechanism; conserved active-site residues are retained in nematode homologs including C. elegans aldo-1 in sequence alignment context. | In homologous enzyme model, Lys230 is the Schiff-base residue; kinetic values for recombinant nematode aldolase: Km = 0.24 ยฑ 0.01 ยตM, Vmax = 432 nmol minโ1 mgโ1, optimum pH 7.5, n = 3. | Comparative nematode aldolase biochemistry/structure (Teladorsagia with C. elegans aldo-1 in alignment). | Umair et al., 2021, Parasitologia | Jan 2021 | https://doi.org/10.3390/parasitologia1010001 | Indirect but informative for ALDO-1 because the study includes C. elegans aldo-1 among homologs and highlights conserved catalytic residues typical of class I aldolases. (umair2021teladorsagiacircumcincta16bisphosphate pages 4-8) |
| Expression-regulation | aldo-1 expression is higher in males than in hermaphrodites, consistent with sex-biased carbohydrate metabolism. | Male:hermaphrodite expression ratios: 2.11 and 2.12 in young adults; 2.85 and *2.33 in adults for two T05D4.1 transcript entries. | Whole animals; young adult and adult stages. | Miersch & Dรถring, 2012, PLoS ONE | Sep 2012 | https://doi.org/10.1371/journal.pone.0044748 | Direct C. elegans evidence; no tissue localization given in snippet. (miersch2012sexdifferencesin pages 13-15) |
| Pathway / phenotype | In mitochondrial complex I mutants, aldo-1 is strongly upregulated, supporting increased glycolytic dependence. | ~3-fold increase in gas-1(fc21); ~6-fold increase in nuo-6(qm200). | Day-1 adults from synchronized populations; qRT-PCR in mitochondrial mutant worms. | Pujol et al., 2013, PLoS ONE | Mar 2013 | https://doi.org/10.1371/journal.pone.0059493 | Strong direct evidence connecting aldo-1 to metabolic rewiring in vivo. (pujol2013succinatedehydrogenaseupregulation pages 2-4) |
| Phenotype | aldo-1 is functionally important for survival/longevity of complex I mutants; RNAi knockdown greatly shortens lifespan. | In gas-1(fc21), median lifespan decreased by up to 65% after aldo-1 RNAi; in nuo-6(qm200), aldo-1 downregulation decreased median lifespan by >85%. | RNAi in mitochondrial complex I mutant worms. | Pujol et al., 2013, PLoS ONE | Mar 2013 | https://doi.org/10.1371/journal.pone.0059493 | Strong phenotype-to-function link; indicates reliance on glycolysis when respiration is impaired. (pujol2013succinatedehydrogenaseupregulation pages 2-4) |
| Pathway | Authors conclude both complex I mutants โrely heavily on glycolysis for energy production,โ placing aldo-1 in compensatory metabolic adaptation. | Lifespan sensitivity to aldo-1 RNAi as above; icl-1 had milder effects by comparison. | gas-1(fc21) and nuo-6(qm200) mitochondrial dysfunction models. | Pujol et al., 2013, PLoS ONE | Mar 2013 | https://doi.org/10.1371/journal.pone.0059493 | Strong pathway inference because supported by expression plus functional RNAi data. (pujol2013succinatedehydrogenaseupregulation pages 2-4) |
| Recent studies | Persistent HIF-1 over-activation upregulates aldo-1 as part of a shared metabolic response in three HIF-1 high-activity mutants. | aldo-1 is in the 104 genes upregulated in all three mutants; enriched WormCat Cat1: Metabolism, 23 genes, Bonferroni FDR = 9.23E-07; overlaps significant at p < 2.2E-16. | C. elegans vhl-1(ok161), egl-9(sa307), rhy-1(ok1402) mutants. | Feng et al., 2024, PLOS ONE | Mar 2024 | https://doi.org/10.1371/journal.pone.0295093 | Strong recent evidence for transcriptional regulation in hypoxia/HIF biology; no gene-specific fold change for aldo-1 in snippet. (feng2024transcriptomeanalysesdescribe pages 4-5) |
| Recent studies / tissue context | In aging male neurons, aldo-1 is among glycolytic genes that decline with age, linking it to neuronal energetic aging. | Downregulated with age by at least 2-fold; significance framework in study used DESeq2, cutoff log2 fold-change > 0.5 or < -0.5, p-adj < 0.05. | Sorted male neurons during aging; compared young vs aged neuronal transcriptomes. | Weng & Murphy, 2024, iScience | Jun 2024 | https://doi.org/10.1016/j.isci.2024.109910 | Strong recent tissue-specific transcriptomic evidence; snippet does not provide aldo-1-specific adjusted p-value. (weng2024malespecificbehavioraland pages 7-9, weng2024malespecificbehavioraland pages 9-12) |
| Expression/localization | Direct subcellular localization of C. elegans ALDO-1 was not provided in the retrieved worm-specific snippets; canonical aldolase literature describes aldolase as a cytosolic glycolytic enzyme, with moonlighting/extracellular roles in other systems. | None for C. elegans ALDO-1 in snippets. | General aldolase biology review; not worm-specific localization experiment. | Pirovich et al., 2021, Frontiers in Molecular Biosciences | Aug 2021 | https://doi.org/10.3389/fmolb.2021.719678 | Caution: relevant for family-level inference, not direct localization evidence for C. elegans aldo-1. (pirovich2021multifunctionalfructose16bisphosphate pages 3-5) |
| Applications | Aldolase is highlighted broadly as a therapeutic target, with inhibitor and vaccine interest in pathogens; this supports translational relevance of conserved aldolase biology, though not a direct C. elegans application. | No C. elegans-specific implementation metrics in snippet. | Cross-species/pathogen aldolase biology. | Pirovich et al., 2021, Frontiers in Molecular Biosciences | Aug 2021 | https://doi.org/10.3389/fmolb.2021.719678 | Indirect application relevance only; useful for contextualizing why conserved aldolases are studied. (pirovich2021multifunctionalfructose16bisphosphate pages 3-5) |
Table: This table summarizes the available evidence for the functional annotation of C. elegans aldo-1/P54216/T05D4.1, including identity mapping, enzymatic role, pathway context, regulatory patterns, phenotypes, and recent 2024 studies. It is useful as a citation-linked overview of what is directly supported by the retrieved snippets versus what remains inferred.
References
(pirovich2021multifunctionalfructose16bisphosphate pages 3-5): David B. Pirovich, Akram A. Daโdara, and Patrick J. Skelly. Multifunctional fructose 1,6-bisphosphate aldolase as a therapeutic target. Frontiers in Molecular Biosciences, Aug 2021. URL: https://doi.org/10.3389/fmolb.2021.719678, doi:10.3389/fmolb.2021.719678. This article has 111 citations.
(miersch2012sexdifferencesin pages 13-15): Claudia Miersch and Frank Dรถring. Sex differences in carbohydrate metabolism are linked to gene expression in caenorhabditis elegans. PLoS ONE, 7:e44748, Sep 2012. URL: https://doi.org/10.1371/journal.pone.0044748, doi:10.1371/journal.pone.0044748. This article has 25 citations and is from a peer-reviewed journal.
(umair2021teladorsagiacircumcincta16bisphosphate pages 4-8): Saleh Umair, Charlotte Bouchet, Nikola Palevich, and Heather Simpson. Teladorsagia circumcincta 1,6-bisphosphate aldolase: molecular and biochemical characterisation, structure analysis and recognition by immune hosts. Parasitologia, 1:1-11, Jan 2021. URL: https://doi.org/10.3390/parasitologia1010001, doi:10.3390/parasitologia1010001. This article has 3 citations.
(pujol2013succinatedehydrogenaseupregulation pages 2-4): Claire Pujol, Ivana Bratic-Hench, Marija Sumakovic, Jรผrgen Hench, Arnaud Mourier, Linda Baumann, Victor Pavlenko, and Aleksandra Trifunovic. Succinate dehydrogenase upregulation destabilize complex i and limits the lifespan of gas-1 mutant. PLoS ONE, 8:e59493, Mar 2013. URL: https://doi.org/10.1371/journal.pone.0059493, doi:10.1371/journal.pone.0059493. This article has 45 citations and is from a peer-reviewed journal.
(weng2024malespecificbehavioraland pages 7-9): Yifei Weng and Coleen T. Murphy. Male-specific behavioral and transcriptomic changes in aging c. elegans neurons. iScience, 27:109910, Jun 2024. URL: https://doi.org/10.1016/j.isci.2024.109910, doi:10.1016/j.isci.2024.109910. This article has 10 citations and is from a peer-reviewed journal.
(feng2024transcriptomeanalysesdescribe pages 4-5): Dingxia Feng, Long Qu, and Jo Anne Powell-Coffman. Transcriptome analyses describe the consequences of persistent hif-1 over-activation in caenorhabditis elegans. PLOS ONE, 19:e0295093, Mar 2024. URL: https://doi.org/10.1371/journal.pone.0295093, doi:10.1371/journal.pone.0295093. This article has 3 citations and is from a peer-reviewed journal.
(weng2024malespecificbehavioraland pages 9-12): Yifei Weng and Coleen T. Murphy. Male-specific behavioral and transcriptomic changes in aging c. elegans neurons. iScience, 27:109910, Jun 2024. URL: https://doi.org/10.1016/j.isci.2024.109910, doi:10.1016/j.isci.2024.109910. This article has 10 citations and is from a peer-reviewed journal.
Gene: aldo-1 (T05D4.1, WBGene00011474)
UniProt: P54216
Protein: Fructose-bisphosphate aldolase 1, also known as Aldolase CE-1
aldo-1 encodes one of two fructose-1,6-bisphosphate aldolase isozymes in C. elegans (the other being aldo-2/CE-2). It is a class I aldolase that catalyzes the reversible cleavage of fructose-1,6-bisphosphate (FBP) into glyceraldehyde-3-phosphate (G3P) and dihydroxyacetone phosphate (DHAP), a key step in glycolysis (step 4/4 in the conversion of glucose to triose phosphates) and gluconeogenesis.
Title: "Caenorhabditis elegans has two isozymic forms, CE-1 and CE-2, of fructose-1,6-bisphosphate aldolase which are encoded by different genes."
Title: "Determining the sub-cellular localization of proteins within Caenorhabditis elegans body wall muscle."
Title: "A map of the interactome network of the metazoan C. elegans."
Title: "Empirically controlled mapping of the Caenorhabditis elegans protein-protein interactome network."
The BioReason deep-research file claims:
1. GO:0042593 (glucose homeostasis) - NOT in existing GOA annotations. While aldo-1 participates in glycolysis which affects glucose levels, C. elegans lacks a blood glucose system. This term is more appropriate for vertebrates. The claim of "systemic sugar balance" is an overreach for a nematode.
2. Dense body/sarcomere/ER localization - CORRECT, supported by PMID:21611156
3. "Glycolytic metabolon" at sarcomeres - Plausible but speculative for C. elegans specifically. There is evidence from vertebrate muscle that glycolytic enzymes form metabolons at sarcomeres, and the dense body/ER localization of aldo-1 is consistent with this, but no direct evidence of a metabolon exists in C. elegans.
4. Homotetrameric assembly - CORRECT for class I aldolases generally
All PMIDs cited in the GOA annotations are REAL and verified:
- PMID:9056253 - Verified (Inoue et al. 1997, Arch Biochem Biophys)
- PMID:14704431 - Verified (Li et al. 2004, Science)
- PMID:19123269 - Verified (Simonis et al. 2009, Nat Methods)
- PMID:21611156 - Verified (Meissner et al. 2011, PLoS One)
- GO_REF:0000033 - Standard phylogenetic annotation reference
- GO_REF:0000024 - Standard manual ISS transfer reference
- GO_REF:0000120 - Standard combined IEA method reference
Source: aldo-1-deep-research-bioreason-sft.md
The BioReason functional summary describes aldo-1 as:
A class I aldolase in Caenorhabditis elegans that assembles as a homomeric TIM-barrel enzyme to catalyze the reversible cleavage of fructose 1,6-bisphosphate into triose phosphates during glycolysis and the corresponding condensation in gluconeogenesis. By anchoring to sarcomeric structures and dense bodies, and by transiently associating with endoplasmic reticulum interfaces, it forms part of a muscle glycolytic metabolon that channels substrates efficiently to ATP-producing steps, thereby supporting contraction and contributing to organismal glucose balance.
This summary is largely correct in its core biochemistry but makes several unsupported claims about metabolon formation and glucose homeostasis.
Correctness issues:
"Glycolytic metabolon" is speculative for C. elegans. While vertebrate muscle studies suggest glycolytic enzymes may form sarcomeric metabolons (PMID:25247275), no direct evidence demonstrates a glycolytic metabolon in C. elegans body wall muscle. The BioReason model extrapolates from vertebrate muscle biology without distinguishing organism-specific evidence. The localization of aldo-1 to dense bodies and ER/SR (PMID:21611156) is consistent with a metabolon hypothesis but does not demonstrate one.
"Contributing to organismal glucose balance" is an overreach. The thinking trace predicts GO:0042593 (glucose homeostasis), but this term is not in the existing GOA annotations and is inappropriate for C. elegans, which lacks a blood glucose regulatory system analogous to vertebrates. C. elegans does have insulin/IGF-1 signaling (daf-2 pathway) that affects glucose metabolism, and aldolase RNAi can suppress glucose toxicity on high-glucose diets, but this does not constitute "glucose homeostasis" in the GO sense of the term.
"Homomeric TIM-barrel enzyme" is slightly misleading. While each subunit has a TIM barrel fold, class I aldolases function as homotetramers. The summary does not clearly state the tetrameric quaternary structure, instead vaguely referring to "homomeric assembly."
"Transient ER contacts positioning the metabolon near excitation-contraction machinery" is fabricated. No evidence supports transient ER contacts having a role in positioning a glycolytic metabolon near excitation-contraction coupling in C. elegans. The ER/SR localization from Meissner et al. 2011 is a static observation from GFP imaging, not evidence of dynamic transient contacts.
What was correct:
The existing GOA annotations include:
- GO:0004332 fructose-bisphosphate aldolase activity (IDA, IBA, IEA) -- core function, directly demonstrated
- GO:0006096 glycolytic process (NAS, IBA, IEA) -- core function
- GO:0030388 fructose 1,6-bisphosphate metabolic process (IBA) -- core function
- GO:0042802 identical protein binding (IPI) -- non-core, from interactome screens
- GO:0005829 cytosol (IBA) -- expected for soluble enzyme
- GO:0005737 cytoplasm (ISS) -- expected, less specific than cytosol
- GO:0000792 heterochromatin (ISS) -- questionable, transferred from rabbit ortholog
- GO:0005783 endoplasmic reticulum (HDA) -- supported by Meissner et al.
- GO:0030017 sarcomere (HDA) -- supported by Meissner et al.
- GO:0055120 striated muscle dense body (HDA) -- supported by Meissner et al.
BioReason correctly captures the MF and BP annotations but does not add novel GO term predictions in its structured output (the GO Term Predictions sections are empty). The narrative mentions GO:0042593 (glucose homeostasis) which is not in GOA and would be inappropriate for C. elegans.
The thinking trace reveals several characteristic patterns:
Mechanistic over-elaboration. The trace constructs an elaborate narrative about a sarcomeric glycolytic metabolon with upstream PFK, downstream TPI and GAPDH, FBPase for gluconeogenesis, and transket_pyr for "auxiliary carbon-shuffling." While each individual enzyme exists in C. elegans, the assembled narrative of a coordinated metabolon is speculative fiction presented as established biology.
Appropriate use of domain analysis. The trace correctly reasons from the TIM barrel scaffold through the class I family signatures to the active-site lysine. This structural reasoning is sound and well-grounded in the InterPro domain annotations.
Vertebrate biology leakage. Claims about "blood glucose levels in metazoans" and "systemic sugar balance" reveal that the model is applying vertebrate physiology to a nematode. C. elegans has trehalose rather than glucose as its primary circulating sugar, and lacks the endocrine pancreas-based glucose homeostatic system of vertebrates.
Correct handling of localization evidence. The trace correctly explains why a cytosolic enzyme might associate with sarcomeric structures and ER, drawing on the concept of enzyme-cytoskeleton interactions in muscle. The reasoning is plausible even though the specific metabolon claim is unproven.
Empty structured predictions. The GO Term Predictions sections (Molecular Function, Biological Process, Cellular Component) are all empty, meaning the model generated no novel structured predictions despite the extensive narrative. This disconnect between narrative and output is a weakness.
All references cited in the existing GOA annotations are verified as real publications:
- PMID:9056253 (Inoue et al. 1997) -- real, describes CE-1/CE-2 characterization
- PMID:14704431 (Li et al. 2004) -- real, C. elegans interactome mapping
- PMID:19123269 (Simonis et al. 2009) -- real, expanded interactome
- PMID:21611156 (Meissner et al. 2011) -- real, muscle protein localization study
The BioReason narrative does not cite specific papers but the claims it makes are broadly consistent with the literature, except for the glucose homeostasis claim.
The BioReason prediction is competent at the level of core biochemistry and domain architecture analysis. It correctly identifies aldo-1 as a class I FBP aldolase involved in glycolysis, and appropriately notes the muscle-specific localizations. However, it over-interprets the localization data into a speculative glycolytic metabolon narrative, inappropriately applies vertebrate glucose homeostasis concepts to C. elegans, and generates no structured GO term predictions despite extensive narrative reasoning. For a well-characterized gene like aldo-1, the BioReason output adds little beyond what is already captured in the existing GOA annotations, and the speculative additions (metabolon, glucose homeostasis) reduce rather than increase the reliability of the output.
id: P54216
gene_symbol: aldo-1
product_type: PROTEIN
status: COMPLETE
taxon:
id: NCBITaxon:6239
label: Caenorhabditis elegans
description: >-
aldo-1 encodes fructose-bisphosphate aldolase 1 (CE-1), one of two class I aldolase
isozymes in C. elegans (the other being aldo-2/CE-2). The enzyme catalyzes the
reversible cleavage of fructose-1,6-bisphosphate into glyceraldehyde-3-phosphate and
dihydroxyacetone phosphate, a central step in glycolysis and gluconeogenesis. CE-1
has unique kinetic properties with a broad substrate specificity compared to CE-2.
The protein is ubiquitously expressed and in body wall muscle localizes to dense
bodies, thick filaments/M-lines, and ER/sarcoplasmic reticulum, consistent with a
role in providing ATP near contractile structures. In vivo, aldo-1 is a critical
component of compensatory glycolysis: it is transcriptionally upregulated in
mitochondrial complex I mutants and its knockdown strongly shortens their lifespan,
and it is part of HIF-1-linked hypoxia-adaptation and age-associated neuronal
metabolic transcriptional programs.
references:
- id: PMID:9056253
title: Caenorhabditis elegans has two isozymic forms, CE-1 and CE-2, of fructose-1,6-bisphosphate
aldolase which are encoded by different genes.
findings:
- statement: CE-1 (aldo-1) is a class I FBP aldolase with unique kinetic properties
and broad substrate specificity
supporting_text: >-
CE-1 evolved to act as an intrinsic enzyme that exhibits a much broader
substrate specificity than dose CE-2
reference_section_type: ABSTRACT
- statement: CE-1 and CE-2 are encoded by different genes, confirmed by Southern blot
supporting_text: >-
Southern blot analysis suggests that CE-1 and CE-2 are encoded by different genes
reference_section_type: ABSTRACT
- statement: CE-1 has KM of 16.7 uM for FBP and 0.56 mM for fructose-1-phosphate
supporting_text: >-
Two distinct types of cDNAs for fructose-1,6-bisphosphate (FBP) aldolase,
Ce-1 and Ce-2, have been isolated from nematode Caenorhabditis elegans, and
the respective recombinant aldolase isozymes, CE-1 and CE-2, have been purified
and characterized
reference_section_type: ABSTRACT
- id: PMID:14704431
title: A map of the interactome network of the metazoan C. elegans.
findings:
- statement: High-throughput Y2H identified aldo-1 self-interaction
supporting_text: >-
more than 4000 interactions were identified from high-throughput,
yeast two-hybrid (HT=Y2H) screens
reference_section_type: ABSTRACT
- id: PMID:19123269
title: Empirically controlled mapping of the Caenorhabditis elegans protein-protein
interactome network.
findings:
- statement: aldo-1 self-interaction confirmed in expanded quality-controlled interactome
supporting_text: >-
the resulting dataset (Worm Interactome 2007 or WI-2007) is similar in
quality to low-throughput data curated from the literature
reference_section_type: ABSTRACT
- id: PMID:21611156
title: Determining the sub-cellular localization of proteins within Caenorhabditis
elegans body wall muscle.
findings:
- statement: T05D4.1 (aldo-1) GFP-tagged protein localizes to dense bodies, thick
filaments/M-lines, and ER/SR in body wall muscle (Category 6)
supporting_text: >-
The sub-cellular localization for the T05D4.1::GFP (A, B)...proteins
expressed from gateway clones using a muscle-specific promoter (A, B and C)
or from genomic clones using endogenous promoters (B, D and F)
reference_section_type: RESULTS
- statement: Localization confirmed with both Gateway and genomic clone approaches
supporting_text: >-
we verified the localization of several Gateway constructs by cloning and
tagging the corresponding gene via conventional methods using genomic DNA
instead of cDNA, and using endogenous promoters instead of our muscle
specific promoter. We were able to confirm the same sub-cellular
localization using both methods
reference_section_type: RESULTS
- id: file:worm/aldo-1/aldo-1-deep-research-bioreason-sft.md
title: BioReason deep research for aldo-1
findings:
- statement: BioReason confirms aldo-1 as a class I FBP aldolase with TIM barrel
architecture and Schiff-base catalytic mechanism
- id: file:worm/aldo-1/aldo-1-deep-research-falcon.md
title: Falcon (Edison) deep research report for aldo-1 (C. elegans, P54216, T05D4.1)
findings:
- statement: |-
Falcon confirms P54216 identity as C. elegans fructose-bisphosphate
aldolase 1 (FBA1), citing a comparative aldolase phylogeny that lists the
UniProt accession directly.
supporting_text: |-
a comparative aldolase phylogeny explicitly lists โ**Caenorhabditis elegans FBA 1 (P54216)**.โ
reference_section_type: RESULTS
- statement: |-
Falcon describes ALDO-1 as a core glycolytic enzyme that cleaves
fructose-1,6-bisphosphate, with the gene aldo-1/T05D4.1 placed in glucose
metabolism toward glyceraldehyde-3-phosphate.
supporting_text: |-
catalyzes the cleavage of the substrate **fructose-1,6-bisphosphate (F1,6BP)** in glycolysis
reference_section_type: RESULTS
- statement: |-
Falcon notes the class I Schiff-base mechanism with a conserved active-site
lysine, drawing on a nematode aldolase analysis that includes C. elegans
aldo-1 in the sequence alignment.
supporting_text: |-
the lysine at position 230 is the residue where Schiff base intermediates are formed
reference_section_type: RESULTS
- statement: |-
Falcon reports kinetic parameters for a closely related nematode class-I
aldolase as supporting strong specificity/efficiency for F1,6BP (inference
for ALDO-1 from homology).
supporting_text: |-
**Km = 0.24 ยฑ 0.01 ยตM** and **Vmax = 432 nmolยทminโปยนยทmgโปยน** at 30ยฐC, with optimum pH **7.5**
reference_section_type: RESULTS
- statement: |-
Falcon reports that aldo-1 is transcriptionally upregulated in mitochondrial
complex I mutants (~3-fold in gas-1, ~6-fold in nuo-6), consistent with a
shift toward glycolysis.
supporting_text: |-
In *C. elegans* mitochondrial complex I mutants, aldo-1 is transcriptionally upregulated, consistent with a metabolic shift toward glycolysis
reference_section_type: RESULTS
- statement: |-
Falcon reports that aldo-1 RNAi knockdown strongly shortens lifespan of
complex I mutants, demonstrating functional importance for compensatory
glycolysis.
supporting_text: |-
decreased **gas-1(fc21)** median lifespan by **up to 65%**
reference_section_type: RESULTS
- statement: |-
Falcon reports the authors' interpretation that complex I mutants rely
heavily on glycolysis for energy, positioning ALDO-1 as a critical
component of compensatory energy metabolism.
supporting_text: |-
rely heavily on glycolysis for energy production
reference_section_type: RESULTS
- statement: |-
Falcon reports that persistent HIF-1 over-activation (vhl-1, egl-9, rhy-1
mutants) commonly upregulates aldo-1, annotated as fructose-1,6-bisphosphate
aldolase, within a metabolism-enriched gene set.
supporting_text: |-
is among the genes โcommonly up-regulatedโ in all three mutants and is explicitly annotated as โ**aldo-1 (fructose-1,6-bisphosphate aldolase)**.โ
reference_section_type: RESULTS
- statement: |-
Falcon reports that in aging male neurons aldo-1 is among glycolysis genes
that decline with age, linking it to neuronal energetic aging.
supporting_text: |-
is listed among glycolysis enzymes that are โ**downregulated with age at least 2-fold**โ (Figure 5B) in male neurons
reference_section_type: RESULTS
- statement: |-
Falcon reports sex-biased expression with aldo-1/T05D4.1 higher in males
than hermaphrodites (male:hermaphrodite ratios ~2.1-2.85).
supporting_text: |-
shows higher expression in males than hermaphrodites
reference_section_type: RESULTS
- statement: |-
Falcon notes no direct C. elegans subcellular localization was retrieved in
its run, but family-level expectation places aldolase in cytosolic
glycolysis.
supporting_text: |-
the strong family-level expectation that aldolase participates in cytosolic glycolysis
reference_section_type: RESULTS
- id: GO_REF:0000024
title: Manual transfer of experimentally-verified manual GO annotation data to orthologs
by curator judgment of sequence similarity
findings: []
- id: GO_REF:0000033
title: Annotation inferences using phylogenetic trees
findings: []
- id: GO_REF:0000120
title: Combined Automated Annotation using Multiple IEA Methods
findings: []
existing_annotations:
- term:
id: GO:0004332
label: fructose-bisphosphate aldolase activity
evidence_type: IDA
original_reference_id: PMID:9056253
review:
summary: >-
Direct experimental evidence. Inoue et al. purified recombinant CE-1 and
demonstrated FBP aldolase activity with KM of 16.7 uM for FBP. This is the
core molecular function of aldo-1.
action: ACCEPT
reason: Direct enzyme assay on purified recombinant protein with kinetic characterization
supported_by:
- reference_id: PMID:9056253
supporting_text: >-
Two distinct types of cDNAs for fructose-1,6-bisphosphate (FBP) aldolase,
Ce-1 and Ce-2, have been isolated from nematode Caenorhabditis elegans, and
the respective recombinant aldolase isozymes, CE-1 and CE-2, have been purified
and characterized
- reference_id: file:worm/aldo-1/aldo-1-deep-research-bioreason-sft.md
supporting_text: >-
[BioReason confirms] GO:0004332 fructose-bisphosphate aldolase activity...
the catalytic center is pinpointed by IPR029768...marking the
lysine-dependent iminium chemistry that drives carbon-carbon bond
cleavage/formation
- reference_id: file:worm/aldo-1/aldo-1-deep-research-falcon.md
supporting_text: |-
catalyzes the cleavage of the substrate **fructose-1,6-bisphosphate (F1,6BP)** in glycolysis
- reference_id: file:worm/aldo-1/aldo-1-deep-research-falcon.md
supporting_text: |-
the lysine at position 230 is the residue where Schiff base intermediates are formed
- term:
id: GO:0004332
label: fructose-bisphosphate aldolase activity
evidence_type: IBA
original_reference_id: GO_REF:0000033
review:
summary: >-
Phylogenetic inference consistent with and redundant to the IDA annotation from
PMID:9056253. Correct but redundant.
action: ACCEPT
reason: Phylogenetic annotation is consistent with direct experimental evidence
- term:
id: GO:0004332
label: fructose-bisphosphate aldolase activity
evidence_type: IEA
original_reference_id: GO_REF:0000120
review:
summary: >-
Automated annotation from InterPro domain and Rhea reaction mapping. Correct
and consistent with IDA evidence.
action: ACCEPT
reason: Automated annotation correctly infers function from domain architecture
- term:
id: GO:0006096
label: glycolytic process
evidence_type: NAS
original_reference_id: PMID:9056253
review:
summary: >-
Non-traceable author statement. The Inoue et al. paper characterizes aldo-1 as
an FBP aldolase, and FBP aldolase is a glycolytic enzyme by definition. The
glycolytic role is well supported by the enzyme activity data. Falcon deep
research adds in vivo functional support: aldo-1 is upregulated in
mitochondrial complex I mutants (~3-fold in gas-1, ~6-fold in nuo-6) and its
RNAi knockdown strongly shortens the lifespan of these mutants (up to 65% in
gas-1, >85% in nuo-6), with the authors concluding these mutants rely heavily
on glycolysis for energy production. This directly supports a glycolytic
process role beyond the by-definition inference.
action: ACCEPT
reason: FBP aldolase activity directly places the enzyme in the glycolytic pathway
supported_by:
- reference_id: PMID:9056253
supporting_text: >-
CE-1 evolved to act as an intrinsic enzyme that exhibits a much broader
substrate specificity than dose CE-2
- reference_id: file:worm/aldo-1/aldo-1-deep-research-falcon.md
supporting_text: |-
In *C. elegans* mitochondrial complex I mutants, aldo-1 is transcriptionally upregulated, consistent with a metabolic shift toward glycolysis
- reference_id: file:worm/aldo-1/aldo-1-deep-research-falcon.md
supporting_text: |-
decreased **gas-1(fc21)** median lifespan by **up to 65%**
- reference_id: file:worm/aldo-1/aldo-1-deep-research-falcon.md
supporting_text: |-
rely heavily on glycolysis for energy production
- term:
id: GO:0006096
label: glycolytic process
evidence_type: IBA
original_reference_id: GO_REF:0000033
review:
summary: >-
Phylogenetic inference of glycolytic process involvement. Consistent with
the NAS annotation and enzyme function.
action: ACCEPT
reason: Phylogenetic annotation consistent with biochemical evidence
- term:
id: GO:0006096
label: glycolytic process
evidence_type: IEA
original_reference_id: GO_REF:0000120
review:
summary: >-
Automated annotation from InterPro and UniPathway mapping. Correct and
consistent with other evidence.
action: ACCEPT
reason: Automated annotation correctly infers pathway membership
- term:
id: GO:0030388
label: fructose 1,6-bisphosphate metabolic process
evidence_type: IBA
original_reference_id: GO_REF:0000033
review:
summary: >-
Phylogenetic inference. FBP is the direct substrate of aldo-1, so involvement
in its metabolism is inherent to the enzyme's catalytic activity. Falcon deep
research independently describes ALDO-1 as cleaving the substrate
fructose-1,6-bisphosphate, consistent with this annotation.
action: ACCEPT
reason: Follows directly from the enzyme's catalytic function on FBP
supported_by:
- reference_id: file:worm/aldo-1/aldo-1-deep-research-falcon.md
supporting_text: |-
catalyzes the cleavage of the substrate **fructose-1,6-bisphosphate (F1,6BP)** in glycolysis
- term:
id: GO:0042802
label: identical protein binding
evidence_type: IPI
original_reference_id: PMID:14704431
review:
summary: >-
Detected via high-throughput Y2H in the C. elegans interactome mapping project.
Class I aldolases are known homotetramers, so self-interaction is expected.
However, Y2H self-interactions can be artifacts, though this is biologically
plausible. The annotation is kept as non-core since identical protein binding
is a generic term that does not inform about specific function.
action: KEEP_AS_NON_CORE
reason: >-
Self-interaction is biologically plausible for a homotetrameric enzyme but
identical protein binding is uninformative as a standalone annotation
supported_by:
- reference_id: PMID:14704431
supporting_text: >-
more than 4000 interactions were identified from high-throughput,
yeast two-hybrid (HT=Y2H) screens
- term:
id: GO:0042802
label: identical protein binding
evidence_type: IPI
original_reference_id: PMID:19123269
review:
summary: >-
Replicated self-interaction in the expanded WI-2007/WI8 interactome.
Confirmation of the PMID:14704431 finding, but still a generic annotation.
action: KEEP_AS_NON_CORE
reason: >-
Replication adds confidence but identical protein binding remains uninformative
supported_by:
- reference_id: PMID:19123269
supporting_text: >-
the resulting dataset (Worm Interactome 2007 or WI-2007) is similar in
quality to low-throughput data curated from the literature
- term:
id: GO:0005829
label: cytosol
evidence_type: IBA
original_reference_id: GO_REF:0000033
review:
summary: >-
Phylogenetic inference of cytosolic localization. Class I aldolases are soluble
cytosolic enzymes, so this is well supported. Consistent with the cytoplasm ISS
annotation but more specific. Falcon deep research notes that, while no direct
C. elegans localization was retrieved, the strong family-level expectation
places aldolase in cytosolic glycolysis.
action: ACCEPT
reason: Soluble glycolytic enzyme expected in cytosol based on conserved properties
supported_by:
- reference_id: file:worm/aldo-1/aldo-1-deep-research-falcon.md
supporting_text: |-
the strong family-level expectation that aldolase participates in cytosolic glycolysis
- term:
id: GO:0005737
label: cytoplasm
evidence_type: ISS
original_reference_id: GO_REF:0000024
review:
summary: >-
Transferred from ortholog (P05065, rabbit ALDOC). Cytoplasmic localization is
expected for a soluble glycolytic enzyme. Consistent with cytosol IBA annotation
but less specific.
action: ACCEPT
reason: Cytoplasmic localization is well established for class I aldolases
- term:
id: GO:0000792
label: heterochromatin
evidence_type: ISS
original_reference_id: GO_REF:0000024
review:
summary: >-
Transferred from rabbit aldolase C ortholog (P05065). Aldolase has been reported
to associate with heterochromatin in some vertebrate studies as a moonlighting
function. However, this is a non-canonical localization for a glycolytic enzyme
and direct evidence in C. elegans is lacking. The ISS transfer is questionable
for this non-canonical function. Falcon deep research corroborates this caution:
it notes that aldolase moonlighting/extracellular localizations described in
broader reviews are not direct C. elegans ALDO-1 localization evidence.
action: KEEP_AS_NON_CORE
reason: >-
Heterochromatin association is a reported moonlighting function in vertebrates
but lacks direct evidence in C. elegans; ISS transfer of non-canonical
localization is weak
supported_by:
- reference_id: file:worm/aldo-1/aldo-1-deep-research-falcon.md
supporting_text: |-
broader aldolase reviews discuss intracellular (and sometimes extracellular โmoonlightingโ) localizations across organisms, but this is not direct *C. elegans* ALDO-1 localization evidence
- term:
id: GO:0005783
label: endoplasmic reticulum
evidence_type: HDA
original_reference_id: PMID:21611156
review:
summary: >-
High-throughput GFP localization in body wall muscle. T05D4.1 was classified
in Category 6 (Dense bodies, Thick filaments and/or M-lines, ER/SR). The ER/SR
component of the localization pattern was observed. Validated with both Gateway
and genomic clones.
action: ACCEPT
reason: >-
Direct GFP localization data from high-throughput study, validated by two
independent cloning approaches
supported_by:
- reference_id: PMID:21611156
supporting_text: >-
The sub-cellular localization for the T05D4.1::GFP (A, B)...proteins
expressed from gateway clones using a muscle-specific promoter (A, B and C)
or from genomic clones using endogenous promoters (B, D and F)
additional_reference_ids:
- PMID:21611156
- term:
id: GO:0030017
label: sarcomere
evidence_type: HDA
original_reference_id: PMID:21611156
review:
summary: >-
High-throughput GFP localization in body wall muscle. Category 6 includes
dense bodies, thick filaments, and M-lines, all of which are sarcomeric
structures. Consistent with the known association of glycolytic enzymes with
sarcomeric structures in muscle.
action: ACCEPT
reason: >-
Direct GFP localization data showing sarcomeric localization pattern in
body wall muscle
supported_by:
- reference_id: PMID:21611156
supporting_text: >-
we verified the localization of several Gateway constructs by cloning and
tagging the corresponding gene via conventional methods using genomic DNA
instead of cDNA, and using endogenous promoters instead of our muscle
specific promoter. We were able to confirm the same sub-cellular
localization using both methods
additional_reference_ids:
- PMID:21611156
- term:
id: GO:0055120
label: striated muscle dense body
evidence_type: HDA
original_reference_id: PMID:21611156
review:
summary: >-
High-throughput GFP localization in body wall muscle. Dense bodies are the
C. elegans equivalent of vertebrate Z-discs, where they anchor actin filaments
to the cell membrane. Category 6 explicitly includes dense body localization.
T05D4.1 was one of the proteins used to validate the approach (Figure 3).
action: ACCEPT
reason: >-
Direct GFP localization data with validation by both Gateway and genomic
clone approaches; dense body localization is part of Category 6
supported_by:
- reference_id: PMID:21611156
supporting_text: >-
The sub-cellular localization for the T05D4.1::GFP (A, B)...proteins
expressed from gateway clones using a muscle-specific promoter (A, B and C)
or from genomic clones using endogenous promoters (B, D and F)
additional_reference_ids:
- PMID:21611156
core_functions:
- description: >-
Catalyzes the reversible cleavage of fructose-1,6-bisphosphate into
glyceraldehyde-3-phosphate and dihydroxyacetone phosphate as part of
glycolysis in the cytosol, with additional localization to sarcomeric
structures and ER in body wall muscle.
molecular_function:
id: GO:0004332
label: fructose-bisphosphate aldolase activity
directly_involved_in:
- id: GO:0006096
label: glycolytic process
- id: GO:0030388
label: fructose 1,6-bisphosphate metabolic process
locations:
- id: GO:0005829
label: cytosol
- id: GO:0055120
label: striated muscle dense body
- id: GO:0030017
label: sarcomere
supported_by:
- reference_id: PMID:9056253
supporting_text: >-
Two distinct types of cDNAs for fructose-1,6-bisphosphate (FBP)
aldolase, Ce-1 and Ce-2, have been isolated from nematode
Caenorhabditis elegans, and the respective recombinant aldolase
isozymes, CE-1 and CE-2, have been purified and characterized
- reference_id: PMID:21611156
supporting_text: >-
The sub-cellular localization for the T05D4.1::GFP (A, B)...proteins
expressed from gateway clones using a muscle-specific promoter
- reference_id: file:worm/aldo-1/aldo-1-deep-research-falcon.md
supporting_text: |-
catalyzes the cleavage of the substrate **fructose-1,6-bisphosphate (F1,6BP)** in glycolysis
suggested_questions:
- question: >-
Does aldo-1 form a glycolytic metabolon with other glycolytic enzymes at
sarcomeric structures in C. elegans body wall muscle, analogous to what has
been proposed in vertebrate striated muscle?
experts:
- Moerman DG
- question: >-
What are the distinct physiological roles of aldo-1 (CE-1) versus aldo-2
(CE-2) in C. elegans, given their different kinetic properties and substrate
specificities?
experts:
- Hori K
- question: >-
Is the heterochromatin association observed for vertebrate aldolase orthologs
conserved in C. elegans aldo-1, and does it have functional significance?
- question: >-
Is aldo-1 a direct HIF-1 transcriptional target, and how is its upregulation
coordinated across hypoxia (HIF-1 over-activation), mitochondrial complex I
dysfunction, and age-associated neuronal metabolic decline?
suggested_experiments:
- hypothesis: >-
aldo-1 forms a sarcomeric glycolytic metabolon in C. elegans body wall muscle
description: >-
Co-immunoprecipitation or proximity ligation assay of aldo-1 with other
glycolytic enzymes (e.g., phosphofructokinase, GAPDH, triosephosphate
isomerase) in C. elegans body wall muscle lysates, combined with
co-localization imaging at sarcomeric structures.
experiment_type: co-immunoprecipitation and imaging
- hypothesis: >-
aldo-1 and aldo-2 have non-redundant roles in C. elegans metabolism
description: >-
Generate aldo-1 single mutants and aldo-1; aldo-2 double mutants to
compare phenotypes. Measure glycolytic flux, energy metabolism, lifespan,
and glucose sensitivity in each genotype. Given that aldo-2 RNAi causes
embryonic lethality, test whether aldo-1 loss is similarly lethal or shows
distinct phenotypes.
experiment_type: genetic analysis and metabolomics