LYS-1 is one of the protist-type (Entamoeba-type) lysozymes of Caenorhabditis elegans, a nematode that carries an unusually large and divergent lysozyme family (15 genes split into protist-type lys and invertebrate-type ilys classes). Structurally it is a glycoside hydrolase family 25 (GH25) protein with an N-terminal signal peptide. LYS-1 functions as an infection-inducible antibacterial effector of the intestinal innate immune response: it is one of the most strongly induced genes upon infection by the Gram-negative bacterium Serratia marcescens, and its overexpression increases resistance to that pathogen, while RNAi knockdown reduces survival on the Gram-positive bacterium Staphylococcus aureus. It is also transcriptionally upregulated by Bacillus thuringiensis and is part of the ELT-2/GATA-controlled intestinal infection-response program, and it is a DAF-16/FOXO target that links the immune response to the dauer developmental decision. The protein localizes to vesicles in the apical region of intestinal cells and is expressed in the intestine and a subset of head neurons. Although the GH25 fold implies muramidase (peptidoglycan-hydrolysing) activity, this catalytic activity has never been demonstrated for LYS-1 at the protein level, and the sequence lacks the conserved active-site residues, so its actual enzymatic function is uncertain.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
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GO:0007165
signal transduction
|
IBA
GO_REF:0000033 |
REMOVE |
Summary: This IBA is a phylogenetic propagation from a PANTHER subfamily seeded by non-lysozyme members (including a Dictyostelium protein). Lysozymes are secreted antibacterial hydrolases/effectors, not signal-transducing proteins, and there is no evidence that LYS-1 transduces any signal.
Reason: Over-broad phylogenetic inference inconsistent with the biology of a lysozyme-family antibacterial effector. No experimental or sequence feature supports a signal transduction role for LYS-1; the specific, experimentally supported role is antibacterial defense (captured by the defense-response terms below).
Propagation Review
Root cause:
PROPAGATION BAD
Failure modes:
FUNCTIONAL DIVERGENCE
GRANULARITY MISMATCH
Sources checked:
PANTHER:PTN000574946
· PTN000574946 (PANTHER ancestral node)
SOURCE WEAK OR INFERRED
Ancestral node whose GO:0007165 assignment was seeded from dictyBase:DDB_G0273175 (a Dictyostelium protein). "Signal transduction" is not a function of a GH25 lysozyme-family antibacterial effector; the propagation transfers an unrelated, overly generic process to LYS-1.
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GO:0045087
innate immune response
|
IBA
GO_REF:0000033 |
KEEP AS NON CORE |
Summary: The innate-immune-response assignment is correct for LYS-1, but this IBA is redundant with the stronger experimental IMP (PMID:21209831) and HEP (PMID:16968778) annotations to the same term. Retained as valid biological process context rather than as a distinct line of evidence.
Reason: Correct process but redundant with experimental annotations to the same term; the more specific defense-response-to-Gram-positive/Gram-negative terms carry the core biology.
|
|
GO:0003796
lysozyme activity
|
IEA
GO_REF:0000002 |
UNDECIDED |
Summary: This is a family/domain-based (InterPro IPR002053, GH25) inference of muramidase activity. It has never been demonstrated for LYS-1: no C. elegans lysozyme has been characterized at the protein level, and UniProt flags a CAUTION that LYS-1 "Lacks conserved active site residues, suggesting it has no catalytic activity." The activity therefore cannot be confirmed, and there is positive sequence evidence that it may be absent.
Reason: Cannot verify: no biochemical/enzymatic assay of purified LYS-1 exists, and the UniProt active-site CAUTION suggests possible loss of catalytic activity. Per guidelines this is an author-flagged unresolved MF, not a confident REMOVE (family activity cannot be definitively excluded without biochemistry). This is the central molecular-function knowledge gap for this gene.
Supporting Evidence:
PMID:21931778
All available data is based on genetic analysis, whereas none of the lysozymes have been characterized at the protein level.
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|
GO:0006950
response to stress
|
IEA
GO_REF:0000117 |
MARK AS OVER ANNOTATED |
Summary: A very generic ARBA machine-learned assignment. The specific infection/defense-response terms below describe LYS-1's biology far more informatively; a bare response-to-stress term adds little.
Reason: Too general to be informative and subsumed by the specific defense response / innate immune response annotations that are experimentally supported.
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GO:0009253
peptidoglycan catabolic process
|
IEA
GO_REF:0000002 |
UNDECIDED |
Summary: The biological-process counterpart of the unverified lysozyme activity (InterPro/GH25 inference). Because peptidoglycan hydrolysis by LYS-1 has not been demonstrated and the sequence may lack catalytic residues, this process cannot be confirmed for this paralog.
Reason: Depends on an unverified catalytic (muramidase) activity; no direct evidence LYS-1 cleaves peptidoglycan. Tied to the lysozyme-activity knowledge gap.
Supporting Evidence:
PMID:21931778
All available data is based on genetic analysis, whereas none of the lysozymes have been characterized at the protein level.
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|
GO:0016998
cell wall macromolecule catabolic process
|
IEA
GO_REF:0000002 |
UNDECIDED |
Summary: A more general parent of peptidoglycan catabolism, from the same family-based InterPro inference; same caveat that the underlying catalytic activity is undemonstrated for LYS-1.
Reason: Same unverified-catalysis basis as the peptidoglycan/lysozyme-activity annotations; cannot confirm cell-wall macromolecule catabolism for LYS-1.
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GO:0060205
cytoplasmic vesicle lumen
|
IEA
GO_REF:0000044 |
KEEP AS NON CORE |
Summary: UniProt Subcellular Location keyword propagation matching the curated localization of LYS-1 to the lumen of apical intestinal vesicles. Redundant with the EXP annotation from PMID:12176330.
Reason: Correct location but electronically propagated and redundant with the experimental EXP/IDA vesicle annotations.
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GO:0060205
cytoplasmic vesicle lumen
|
EXP
PMID:12176330 Inducible antibacterial defense system in C. elegans. |
ACCEPT |
Summary: Experimentally curated localization of LYS-1 to the lumen of vesicles in the apical region of intestinal cells, from the primary characterization of the inducible antibacterial defense system.
Reason: Curator-assigned experimental localization consistent with a secreted intestinal antibacterial effector stored in apical vesicles.
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GO:0045087
innate immune response
|
HEP
PMID:16968778 A conserved role for a GATA transcription factor in regulati... |
KEEP AS NON CORE |
Summary: High-throughput expression evidence: lys-1 is part of the intestinal ELT-2/GATA-regulated infection-response gene program identified in a genome-wide study of epithelial innate immunity. Consistent with its infection-inducible antibacterial role.
Reason: Expression-based support for involvement in the innate immune response; corroborates the experimental IMP annotation but is itself expression- level evidence.
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|
GO:0045087
innate immune response
|
IMP
PMID:21209831 RNAi screen of DAF-16/FOXO target genes in C. elegans links ... |
ACCEPT |
Summary: RNAi knockdown of lys-1 significantly reduces C. elegans survival on the pathogen Staphylococcus aureus (TD50 4.7 vs 6.8 days for control, p<0.0001), demonstrating that lys-1 is required for a normal innate immune/pathogen-resistance response.
Reason: Direct loss-of-function (RNAi) phenotype establishing a functional role in the innate immune response; core immune-defense biology of the gene.
Supporting Evidence:
PMID:21209831
Two genes, lys-1 and clc-1, were required for normal resistance to S. aureus.
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|
GO:0050830
defense response to Gram-positive bacterium
|
IMP
PMID:21209831 RNAi screen of DAF-16/FOXO target genes in C. elegans links ... |
ACCEPT |
Summary: Staphylococcus aureus is a Gram-positive bacterium, and lys-1 RNAi reduces survival on it (TD50 4.7 vs 6.8 days, p<0.0001), directly supporting a role in defense against Gram-positive bacteria. This is the most specific, experimentally supported process term for the gene.
Reason: Specific, experimentally demonstrated defense function against a Gram-positive pathogen; a core biological process of LYS-1.
Supporting Evidence:
PMID:21209831
The TD50 (time required for 50% of the nematodes to die) for lys-1 was 4.7 days (p<0.0001)
|
|
GO:0031410
cytoplasmic vesicle
|
IDA
PMID:12176330 Inducible antibacterial defense system in C. elegans. |
ACCEPT |
Summary: Direct-assay localization of LYS-1 to cytoplasmic vesicles in intestinal cells, from the primary characterization paper.
Reason: Experimentally observed subcellular localization consistent with storage of the effector in intestinal vesicles.
|
|
GO:0045177
apical part of cell
|
IDA
PMID:12176330 Inducible antibacterial defense system in C. elegans. |
ACCEPT |
Summary: LYS-1 localizes to the apical region of intestinal cells (apically positioned vesicles), consistent with secretion toward the gut lumen where ingested bacteria are encountered.
Reason: Experimentally supported apical localization appropriate for a gut-luminal antibacterial effector.
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GO:0050829
defense response to Gram-negative bacterium
|
IEP
PMID:12176330 Inducible antibacterial defense system in C. elegans. |
ACCEPT |
Summary: lys-1 is among the most robustly induced genes upon infection by the Gram-negative bacterium Serratia marcescens, and its overexpression augments resistance to that pathogen, supporting a role in defense against Gram-negative bacteria. The evidence code is IEP (expression), reinforced by the overexpression gain-of-resistance phenotype.
Reason: Infection-inducible expression plus overexpression-conferred resistance establish a defense role against a Gram-negative pathogen; a core biological process of LYS-1.
Supporting Evidence:
PMID:12176330
overexpression of the lysozyme gene lys-1 augments the resistance of C. elegans to S. marcescens.
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Q: Does purified LYS-1 protein possess muramidase/bacteriolytic activity, or has this GH25 protist-type lysozyme lost catalytic function and act by a non-enzymatic antibacterial mechanism?
Suggested experts: Schulenburg H
Q: What is the phenotype of a lys-1 loss-of-function null, and to what extent is lys-1 redundant with other protist-type lysozymes in defense against ingested pathogens?
Suggested experts: Schulenburg H, Ewbank JJ
Experiment: Express and purify recombinant LYS-1, then assay (i) muramidase activity on Micrococcus luteus cell walls and defined peptidoglycan substrates, (ii) bacteriolytic/growth-inhibitory activity against S. aureus and S. marcescens, and (iii) direct binding to bacterial cell-surface components; pair with active-site mutagenesis and, if possible, structure determination.
Hypothesis: LYS-1 either hydrolyzes bacterial peptidoglycan (canonical lysozyme mechanism) or, lacking active-site residues, kills/inhibits bacteria by a non-catalytic binding/permeabilizing mechanism.
Type: biochemistry / enzymology / structural biology
Experiment: Generate a lys-1 null allele (CRISPR) and test survival and intestinal pathogen load on a panel of Gram-negative and Gram-positive pathogens (S. marcescens, S. aureus, B. thuringiensis, P. aeruginosa), comparing single mutant, paralog combinations, and rescue/overexpression lines.
Hypothesis: lys-1 contributes non-redundantly to intestinal antibacterial defense in vivo.
Type: genetics / host-pathogen survival and CFU assays
What is not known โ curated, literature-grounded statements of the open unknowns (the inverse of core functions).
Gap: It is not known whether LYS-1 has any muramidase / lysozyme (peptidoglycan-hydrolysing) enzymatic activity. All functional evidence is genetic (infection-inducible expression, RNAi, overexpression); the protein has never been purified or assayed, and its sequence lacks the conserved GH25 active-site residues, raising the possibility that it is a pseudo-muramidase.
OPEN BIOLOGY MF_DARK
What is known: What is firmly established is that LYS-1 is a GH25 protist-type lysozyme whose gene is infection-inducible and functionally required for normal antibacterial defense (S. marcescens, S. aureus). What is unknown is the biochemical activity of the protein: whether it cleaves peptidoglycan, permeabilizes/agglutinates bacteria by another mechanism, or acts non-catalytically.
Significance: Whether LYS-1 kills bacteria enzymatically (like canonical lysozymes) or by a non-catalytic mechanism determines the correct molecular-function annotation and whether the current InterPro-based lysozyme-activity / peptidoglycan-catabolism annotations should stand. This is a recurring issue across the expanded, divergent C. elegans lysozyme family.
What would resolve it: Express and purify recombinant LYS-1 and assay muramidase / bacteriolytic activity (e.g. on Micrococcus cell walls and defined peptidoglycan) and its ability to bind/permeabilize target bacteria; complement with active-site residue mutagenesis and structural analysis.
Provenance (the field's own admissions):
Gap: The molecular substrate or microbial target of LYS-1 is undefined: it is unknown which bacterial surface molecule(s) LYS-1 acts on, and whether its antibacterial spectrum extends beyond S. marcescens, S. aureus and B. thuringiensis.
OPEN BIOLOGY MF_DARK
What is known: LYS-1 is known to be required for resistance to S. aureus and to protect against S. marcescens when overexpressed, and it is transcriptionally induced by these plus B. thuringiensis. What is unknown is the direct biochemical target/substrate and the full microbial spectrum.
Significance: Identifying the target molecule would clarify the mechanism (enzymatic versus binding/permeabilizing) and the range of pathogens LYS-1 counters, informing both its MF annotation and its place in the surveillance-immunity effector repertoire.
What would resolve it: Biochemical target/substrate identification with purified protein (peptidoglycan/cell-wall degradation assays, pull-downs of bacterial ligands) and broader pathogen-panel survival/CFU assays with defined lys-1 loss- and gain-of-function strains.
Provenance (the field's own admissions):
Gap: Whether lys-1 is individually necessary in vivo or is functionally redundant within the 15-member C. elegans lysozyme family is unresolved. The defense phenotypes rest on RNAi knockdown and overexpression rather than a characterized single-gene null, and many lysozyme paralogs share overlapping infection-induction profiles.
OPEN BIOLOGY BP_DARK
What is known: lys-1 RNAi reduces S. aureus survival and lys-1 overexpression increases S. marcescens resistance, establishing a contribution to defense. What is unknown is the phenotype of a clean lys-1 loss-of-function null and the degree of redundancy with paralogs such as lys-2, lys-3 and lys-7.
Significance: Redundancy determines whether lys-1 is a non-redundant defense gene or one of several partially interchangeable effectors, which affects how strongly its individual loss impacts host survival and how its biological role should be weighted.
What would resolve it: Generate and phenotype a lys-1 null allele (and higher-order lysozyme combinatorial mutants) across a pathogen panel, quantifying survival and pathogen load relative to wild type and to single-paralog mutants.
Provenance (the field's own admissions):
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 lys-1 gene (ORF Y22F5A.4) in Caenorhabditis elegans encodes Lysozyme-Like Protein 1 (LYS-1), a member of the glycosyl hydrolase family 25 (GH25). The C. elegans genome encodes 10 protist-type lysozymes (lys-1 through lys-10), all belonging to the GH25 family, as well as six invertebrate-type lysozymes (ilys-1 through ilys-6) (simonsen2012strengthinnumbers pages 4-5, schulenburg2004evolutionofthe pages 7-8). The protist-type lysozymes in C. elegans are structurally most similar to lysozymes found in the amoeboid protozoon Entamoeba histolytica, rather than to the chicken-type (GH22) or insect-type lysozyme families that are well-characterized in vertebrates and arthropods (schulenburg2004evolutionofthe pages 7-8, mallo2002inducibleantibacterialdefense pages 2-3). This phylogenetic relationship suggests an ancient protist-type lysozyme lineage retained in nematodes.
LYS-1 is classified as a muramidase (EC 3.2.1.17) based on its membership in the GH25 family. GH25 muramidases catalyze the hydrolysis of the ฮฒ-1,4-glycosidic bond between N-acetylmuramic acid (MurNAc/NAM) and N-acetylglucosamine (GlcNAc/NAG) in the carbohydrate backbone of bacterial peptidoglycan (moroz2021fungalgh25muramidases pages 1-2). Characterized GH25 enzymes exhibit both ฮฒ-1,4-N-acetyl- and ฮฒ-1,4-N,6-O-diacetylmuramidase activities (moroz2021fungalgh25muramidases pages 1-2). The catalytic mechanism of GH25 muramidases involves substrate-assisted catalysis: an aspartate residue acts as a general acid, donating a proton to the glycosidic oxygen, while the N-acetyl group of the substrate itself acts as the enzymatic nucleophile to stabilize the oxocarbenium ion-like transition state (moroz2021fungalgh25muramidases pages 13-16). This mechanism is shared with family GH20 chitobiases.
While no direct biochemical characterization of recombinant LYS-1 has been published, its enzymatic activity as a peptidoglycan-degrading muramidase is strongly inferred from its GH25 family membership and conserved domain architecture (simonsen2012strengthinnumbers pages 4-5, moroz2021fungalgh25muramidases pages 1-2). As antimicrobial proteins, lysozymes function by breaking down peptidoglycan, the major structural component of bacterial cell walls, causing bacterial cell lysis (simonsen2012strengthinnumbers pages 4-5). In E. histolytica, the related protist-type lysozymes are known to act synergistically with amoebapores to break up bacteria, and a similar synergistic action with C. elegans amoebapore-like peptides (SPP family) has been hypothesized (mallo2002inducibleantibacterialdefense pages 2-3).
LYS-1 is primarily expressed in intestinal cells throughout the length of the nematode body, consistent with its role as an antimicrobial effector at the primary site of pathogen encounter (mallo2002inducibleantibacterialdefense pages 3-4, alper2007specificityandcomplexity pages 3-4). Using lys-1::GFP reporter constructs, expression has been detected at multiple positions along the intestine, including mid-body, anterior-to-mid-body, and posterior regions (alper2007specificityandcomplexity pages 3-4). In addition to intestinal expression, lys-1::GFP is also expressed in specific neuronal populations, including the six IL1 and six IL2 neurons, a few additional neurons in the head ganglia, and two posterior phasmid chemosensory neurons (mallo2002inducibleantibacterialdefense pages 3-4, alper2007specificityandcomplexity pages 3-4, mallo2002inducibleantibacterialdefense pages 2-3). The functional significance of neuronal expression remains unclear.
At the subcellular level, LYS-1::GFP localizes to vesicles within intestinal cells. These vesicles are distinct from secondary lysosomes and show a high concentration at the apical surface of intestinal cells, suggesting trafficking toward the intestinal lumen (mallo2002inducibleantibacterialdefense pages 3-4, schulenburg2004evolutionofthe pages 7-8). This localization pattern is reminiscent of the granular exocytosis mechanisms described in E. histolytica and secretory lysosomes in cytotoxic T lymphocytes (schulenburg2004evolutionofthe pages 7-8). The apical/luminal secretion is consistent with LYS-1 acting directly on bacteria present in the intestinal lumen, the primary site where S. marcescens and other pathogens colonize (mallo2002inducibleantibacterialdefense pages 3-4).
The expression of lys-1 is regulated by multiple conserved innate immune signaling pathways:
TIR-1/NSY-1 (SARM-MAPKKK) pathway: RNAi-mediated knockdown of either nsy-1 (a MAPKKK) or tir-1 (a TIR domain adaptor protein upstream of NSY-1) leads to strong reduction of lys-1 expression, demonstrating that this pathway is a major positive regulator of constitutive lys-1 transcription (alper2007specificityandcomplexity pages 5-7, alper2007specificityandcomplexity pages 4-5). The effects of tir-1 and nsy-1 knockdown on lys-1 are nearly identical, consistent with their action in the same signaling cascade.
PMK-1/p38 MAPK pathway: Several studies have confirmed that lys-1 is a PMK-1-dependent immune gene. In studies of probiotic-mediated immune stimulation, upregulation of lys-1 by heat-inactivated Lactobacillus curvatus was abolished in pmk-1 mutants, demonstrating PMK-1 dependence (dinic2021probioticmediatedp38mapk pages 4-5). Additionally, the bZIP transcription factor ZIP-11, which acts in a feedback loop with the PMK-1/p38 pathway, was shown to regulate lys-1 among other PMK-1-dependent immune genes (zheng2021thebziptranscription pages 6-8).
TGF-ฮฒ/DBL-1 pathway and PMK-1 dual regulation: One study explicitly noted that "the lysozyme-like protein Lys-1 is regulated by both TGF-ฮฒ and PMK-1 signaling pathways" (liu2013componentsofthe pages 4-5, liu2013componentsofthe pages 2-2).
DAF-2/DAF-16 insulin-like signaling pathway: lys-1 has been identified as a putative target of the DAF-16/FOXO transcription factor. In a genetic screen for DAF-16 target genes, RNAi knockdown of lys-1 resulted in a synthetic dauer-constitutive (SynDaf) phenotype in a sensitized background, linking lys-1 to the insulin-like signaling network that regulates both immunity and dauer formation (jensen2010rnaiscreenof pages 2-3, jensen2010rnaiscreenof pages 4-5).
The transcriptional induction of lys-1 exhibits pathogen specificity. In the original study by Mallo et al. (2002), lys-1 was identified as one of the most robustly induced genes following infection with the Gram-negative bacterium Serratia marcescens, confirmed by both microarray and Northern blot analyses at 24 and 48 hours post-infection (mallo2002inducibleantibacterialdefense pages 2-3, mallo2002inducibleantibacterialdefense pages 1-2). Subsequent work by Alper et al. (2007) found that lys-1 was induced by Pseudomonas aeruginosa but not by S. marcescens in their experimental conditions, highlighting that quantitative differences in induction can depend on experimental context, timing, and bacterial strain (alper2007specificityandcomplexity pages 5-7). More recent studies have confirmed lys-1 upregulation in the context of Staphylococcus aureus infection (jensen2010rnaiscreenof pages 2-3) and various other pathogenic and probiotic bacterial challenges (dinic2021probioticmediatedp38mapk pages 4-5).
Overexpression: Transgenic C. elegans overexpressing the lys-1::GFP fusion construct showed significantly increased survival when challenged with the protease-deficient S. marcescens strain Db1140, providing direct evidence that LYS-1 contributes to antibacterial defense (mallo2002inducibleantibacterialdefense pages 1-2, mallo2002inducibleantibacterialdefense pages 3-4). Importantly, overexpression did not confer protection against the more virulent wild-type Db11 strain, likely because bacterial proteases produced by virulent S. marcescens can counteract LYS-1's protective effects (mallo2002inducibleantibacterialdefense pages 3-4, schulenburg2004evolutionofthe pages 6-7). Overexpression of lys-1 has also been noted to augment resistance to S. marcescens in other reports (mallo2002inducibleantibacterialdefense pages 1-2).
Knockdown: RNAi knockdown of lys-1 in wild-type worms had little effect on survival against S. marcescens, suggesting that multiple redundant defense factors contribute to antibacterial immunity in C. elegans (mallo2002inducibleantibacterialdefense pages 3-4, schulenburg2004evolutionofthe pages 6-7). However, in a sensitized RNAi-hypersensitive background (rrf-3), lys-1 RNAi significantly reduced survival upon S. aureus challenge, indicating that LYS-1 does contribute to pathogen resistance when other defense mechanisms are limiting (jensen2010rnaiscreenof pages 2-3, jensen2010rnaiscreenof pages 4-5).
An intriguing link has been established between lys-1-mediated innate immunity and the developmental decision to enter the dauer larval stage. Jensen et al. (2010) showed that lys-1 knockdown causes a synthetic dauer-constitutive phenotype when combined with the sdf-9 mutation, suggesting that infection-induced stress or compromised immunity can feed back into the dauer signaling circuit (jensen2010rnaiscreenof pages 2-3, jensen2010rnaiscreenof pages 4-5). This is consistent with the broader model that pathogen exposure increases dauer pheromone production and promotes dauer entry as a behavioral response to pathogenic environments (jensen2010rnaiscreenof pages 3-4).
The following table summarizes the key properties of LYS-1:
| Property | Summary | Evidence |
|---|---|---|
| Gene name | lys-1; encodes lysozyme-like protein 1 in Caenorhabditis elegans | (mallo2002inducibleantibacterialdefense pages 2-3, alper2007specificityandcomplexity pages 1-2) |
| ORF | Y22F5A.4 | (mallo2002inducibleantibacterialdefense pages 2-3) |
| UniProt ID | O62415 | (mallo2002inducibleantibacterialdefense pages 2-3) |
| Protein family | Protist-type lysozyme; glycosyl hydrolase family 25 (GH25), one of 10 C. elegans protist-type lysozymes (lys-1 to lys-10) | (simonsen2012strengthinnumbers pages 4-5, schulenburg2004evolutionofthe pages 7-8, mallo2002inducibleantibacterialdefense pages 2-3) |
| Enzymatic activity | Predicted muramidase/lysozyme that hydrolyzes bacterial peptidoglycan; direct biochemical activity has not been shown for LYS-1 itself, but inferred from GH25 family membership | (simonsen2012strengthinnumbers pages 4-5, moroz2021fungalgh25muramidases pages 1-2, moroz2021fungalgh25muramidases pages 13-16) |
| Substrate | Bacterial peptidoglycan, specifically the ฮฒ-1,4 glycosidic bond between MurNAc/NAM and GlcNAc/NAG in the glycan backbone | (vollmer2008bacterialpeptidoglycan(murein) pages 6-7, moroz2021fungalgh25muramidases pages 1-2) |
| Catalytic mechanism | Inferred GH25 mechanism: substrate-assisted catalysis with an Asp acting as general acid; the substrate N-acetyl group contributes to catalysis | (moroz2021fungalgh25muramidases pages 13-16) |
| Tissue expression | Strongly expressed in intestinal cells; also reported in IL1/IL2 neurons, head ganglia neurons, and posterior phasmid chemosensory neurons in reporter analyses | (mallo2002inducibleantibacterialdefense pages 2-3, mallo2002inducibleantibacterialdefense pages 3-4, alper2007specificityandcomplexity pages 3-4) |
| Subcellular localization | Vesicular localization in intestinal cells, with vesicles concentrated near the apical surface; distinct from secondary lysosomes and suggestive of trafficking toward the intestinal lumen | (schulenburg2004evolutionofthe pages 7-8, mallo2002inducibleantibacterialdefense pages 3-4) |
| Likely site of action | Likely acts in or toward the intestinal lumen, consistent with defense against ingested bacteria and luminal pathogens | (schulenburg2004evolutionofthe pages 7-8, mallo2002inducibleantibacterialdefense pages 3-4) |
| Signaling pathways regulating expression | Expression requires TIR-1/NSY-1 innate immune signaling; lys-1 is also reported to be regulated by PMK-1/p38 MAPK and TGF-ฮฒ/DBL-1 pathways; lys-1 is additionally described as a DAF-16/FOXO target in the insulin-like signaling network | (alper2007specificityandcomplexity pages 5-7, alper2007specificityandcomplexity pages 4-5, liu2013componentsofthe pages 4-5, jensen2010rnaiscreenof pages 2-3, dinic2021probioticmediatedp38mapk pages 4-5) |
| Pathogen induction | Reported as induced during infection by Serratia marcescens and Pseudomonas aeruginosa; one study found induction by P. aeruginosa but not S. marcescens, indicating pathogen- and condition-specific regulation across assays | (mallo2002inducibleantibacterialdefense pages 2-3, mallo2002inducibleantibacterialdefense pages 1-2, alper2007specificityandcomplexity pages 5-7) |
| Functional evidence: overexpression | Transgenic overexpression/lys-1::GFP animals showed increased resistance to the less virulent S. marcescens strain Db1140, but not to the more virulent strain Db11 | (mallo2002inducibleantibacterialdefense pages 1-2, mallo2002inducibleantibacterialdefense pages 3-4) |
| Functional evidence: knockdown | lys-1 RNAi abolished reporter expression but had little effect on survival against S. marcescens Db1140, suggesting redundancy; in a separate study, lys-1 RNAi increased sensitivity to Staphylococcus aureus and promoted dauer-related phenotypes in a sensitized background | (schulenburg2004evolutionofthe pages 6-7, jensen2010rnaiscreenof pages 2-3, jensen2010rnaiscreenof pages 4-5, mallo2002inducibleantibacterialdefense pages 3-4) |
| Biological role | Antibacterial innate immune effector positioned at host-environment interfaces, especially the intestine; likely contributes to bacterial cell-wall degradation and host defense in combination with other effectors | (schulenburg2004evolutionofthe pages 7-8, alper2007specificityandcomplexity pages 1-2, simonsen2012strengthinnumbers pages 4-5) |
| Evolutionary relationships | LYS-1 is evolutionarily closer to protist/Entamoeba histolytica lysozymes than to classical vertebrate chicken-type or insect lysozymes; this supports an ancient protist-type lysozyme lineage in nematodes | (mallo2002inducibleantibacterialdefense pages 2-3, schulenburg2004evolutionofthe pages 7-8) |
Table: This table summarizes the main annotated and experimentally supported properties of C. elegans LYS-1, including molecular identity, inferred enzymatic activity, localization, regulation, pathogen responsiveness, and functional evidence. It is useful as a compact evidence map for gene functional annotation.
In summary, C. elegans LYS-1 is a protist-type lysozyme of the glycosyl hydrolase family 25 that functions as an antimicrobial effector in the nematode's innate immune system. Based on its GH25 family membership, LYS-1 is predicted to catalyze the hydrolysis of the ฮฒ-1,4-glycosidic bond between MurNAc and GlcNAc in bacterial peptidoglycan, using a substrate-assisted catalytic mechanism (moroz2021fungalgh25muramidases pages 1-2, moroz2021fungalgh25muramidases pages 13-16). The protein is expressed constitutively in intestinal cells, where it localizes to vesicles that traffic toward the apical surface for likely secretion into the intestinal lumenโthe primary site of bacterial encounter (mallo2002inducibleantibacterialdefense pages 3-4, schulenburg2004evolutionofthe pages 7-8). Its expression is transcriptionally regulated by the TIR-1/NSY-1 SARM-MAPKKK pathway and the PMK-1/p38 MAPK cascade, as well as by the TGF-ฮฒ/DBL-1 and DAF-2/DAF-16 insulin-like signaling pathways (alper2007specificityandcomplexity pages 5-7, alper2007specificityandcomplexity pages 4-5, liu2013componentsofthe pages 4-5, jensen2010rnaiscreenof pages 2-3, dinic2021probioticmediatedp38mapk pages 4-5). Functionally, overexpression of LYS-1 enhances resistance to bacterial pathogens, while its knockdown increases susceptibility, particularly to Staphylococcus aureus (mallo2002inducibleantibacterialdefense pages 1-2, jensen2010rnaiscreenof pages 2-3, mallo2002inducibleantibacterialdefense pages 3-4). The redundancy of the lysozyme family in C. elegans, with at least 16 lysozyme genes across two distinct families, likely reflects the central importance of peptidoglycan degradation in the nematode's bacterivorous lifestyle and innate immune defense (simonsen2012strengthinnumbers pages 4-5, schulenburg2004evolutionofthe pages 7-8).
References
(simonsen2012strengthinnumbers pages 4-5): Karina T. Simonsen, Sandra F. Gallego, Nils J. Fรฆrgeman, and Birgitte H. Kallipolitis. Strength in numbers. Virulence, 3:477-484, Oct 2012. URL: https://doi.org/10.4161/viru.21906, doi:10.4161/viru.21906. This article has 36 citations and is from a peer-reviewed journal.
(schulenburg2004evolutionofthe pages 7-8): Hinrich Schulenburg, C. Lรฉopold Kurz, and Jonathan J. Ewbank. Evolution of the innate immune system: the worm perspective. Immunological Reviews, 198:36-58, Apr 2004. URL: https://doi.org/10.1111/j.0105-2896.2004.0125.x, doi:10.1111/j.0105-2896.2004.0125.x. This article has 317 citations and is from a domain leading peer-reviewed journal.
(mallo2002inducibleantibacterialdefense pages 2-3): Gustavo V. Mallo, C.Lรฉopold Kurz, Carole Couillault, Nathalie Pujol, Samuel Granjeaud, Yuji Kohara, and Jonathan J. Ewbank. Inducible antibacterial defense system in c. elegans. Current Biology, 12:1209-1214, Jul 2002. URL: https://doi.org/10.1016/s0960-9822(02)00928-4, doi:10.1016/s0960-9822(02)00928-4. This article has 614 citations and is from a highest quality peer-reviewed journal.
(moroz2021fungalgh25muramidases pages 1-2): Olga V. Moroz, Elena Blagova, Edward Taylor, Johan P. Turkenburg, Lars K. Skov, Garry P. Gippert, Kirk M. Schnorr, Li Ming, Liu Ye, Mikkel Klausen, Marianne T. Cohn, Esben G. W. Schmidt, Sรธren Nymand-Grarup, Gideon J. Davies, and Keith S. Wilson. Fungal gh25 muramidases: new family members with applications in animal nutrition and a crystal structure at 0.78รฅ resolution. PLOS ONE, 16:e0248190, Mar 2021. URL: https://doi.org/10.1371/journal.pone.0248190, doi:10.1371/journal.pone.0248190. This article has 12 citations and is from a peer-reviewed journal.
(moroz2021fungalgh25muramidases pages 13-16): Olga V. Moroz, Elena Blagova, Edward Taylor, Johan P. Turkenburg, Lars K. Skov, Garry P. Gippert, Kirk M. Schnorr, Li Ming, Liu Ye, Mikkel Klausen, Marianne T. Cohn, Esben G. W. Schmidt, Sรธren Nymand-Grarup, Gideon J. Davies, and Keith S. Wilson. Fungal gh25 muramidases: new family members with applications in animal nutrition and a crystal structure at 0.78รฅ resolution. PLOS ONE, 16:e0248190, Mar 2021. URL: https://doi.org/10.1371/journal.pone.0248190, doi:10.1371/journal.pone.0248190. This article has 12 citations and is from a peer-reviewed journal.
(mallo2002inducibleantibacterialdefense pages 3-4): Gustavo V. Mallo, C.Lรฉopold Kurz, Carole Couillault, Nathalie Pujol, Samuel Granjeaud, Yuji Kohara, and Jonathan J. Ewbank. Inducible antibacterial defense system in c. elegans. Current Biology, 12:1209-1214, Jul 2002. URL: https://doi.org/10.1016/s0960-9822(02)00928-4, doi:10.1016/s0960-9822(02)00928-4. This article has 614 citations and is from a highest quality peer-reviewed journal.
(alper2007specificityandcomplexity pages 3-4): Scott Alper, Sandra J. McBride, Brad Lackford, Jonathan H. Freedman, and David A. Schwartz. Specificity and complexity of the caenorhabditis elegans innate immune response. Aug 2007. URL: https://doi.org/10.1128/mcb.02070-06, doi:10.1128/mcb.02070-06. This article has 232 citations and is from a domain leading peer-reviewed journal.
(alper2007specificityandcomplexity pages 5-7): Scott Alper, Sandra J. McBride, Brad Lackford, Jonathan H. Freedman, and David A. Schwartz. Specificity and complexity of the caenorhabditis elegans innate immune response. Aug 2007. URL: https://doi.org/10.1128/mcb.02070-06, doi:10.1128/mcb.02070-06. This article has 232 citations and is from a domain leading peer-reviewed journal.
(alper2007specificityandcomplexity pages 4-5): Scott Alper, Sandra J. McBride, Brad Lackford, Jonathan H. Freedman, and David A. Schwartz. Specificity and complexity of the caenorhabditis elegans innate immune response. Aug 2007. URL: https://doi.org/10.1128/mcb.02070-06, doi:10.1128/mcb.02070-06. This article has 232 citations and is from a domain leading peer-reviewed journal.
(dinic2021probioticmediatedp38mapk pages 4-5): Miroslav Diniฤ, Stefan Jakovljeviฤ, Jelena ฤokiฤ, Nikola Popoviฤ, Duลกan Radojeviฤ, Ivana Strahiniฤ, and Nataลกa Goliฤ. Probiotic-mediated p38 mapk immune signaling prolongs the survival of caenorhabditis elegans exposed to pathogenic bacteria. Scientific Reports, Oct 2021. URL: https://doi.org/10.1038/s41598-021-00698-5, doi:10.1038/s41598-021-00698-5. This article has 45 citations and is from a peer-reviewed journal.
(zheng2021thebziptranscription pages 6-8): Zhongfan Zheng, Yilixiati Aihemaiti, Junqiang Liu, Muhammad Irfan Afridi, Shengmei Yang, Xiumei Zhang, Yongfu Xu, Chunhong Chen, and Haijun Tu. The bzip transcription factor zip-11 is required for the innate immune regulation in caenorhabditis elegans. Frontiers in Immunology, Nov 2021. URL: https://doi.org/10.3389/fimmu.2021.744454, doi:10.3389/fimmu.2021.744454. This article has 8 citations and is from a peer-reviewed journal.
(liu2013componentsofthe pages 4-5): Jinghua Liu, Jeff Hafting, Alan T. Critchley, Arjun H. Banskota, and Balakrishnan Prithiviraj. Components of the cultivated red seaweed chondrus crispus enhance the immune response of caenorhabditis elegans to pseudomonas aeruginosa through the pmk-1 , daf-2/daf-16 , and skn-1 pathways. Applied and Environmental Microbiology, 79:7343-7350, Dec 2013. URL: https://doi.org/10.1128/aem.01927-13, doi:10.1128/aem.01927-13. This article has 85 citations and is from a peer-reviewed journal.
(liu2013componentsofthe pages 2-2): Jinghua Liu, Jeff Hafting, Alan T. Critchley, Arjun H. Banskota, and Balakrishnan Prithiviraj. Components of the cultivated red seaweed chondrus crispus enhance the immune response of caenorhabditis elegans to pseudomonas aeruginosa through the pmk-1 , daf-2/daf-16 , and skn-1 pathways. Applied and Environmental Microbiology, 79:7343-7350, Dec 2013. URL: https://doi.org/10.1128/aem.01927-13, doi:10.1128/aem.01927-13. This article has 85 citations and is from a peer-reviewed journal.
(jensen2010rnaiscreenof pages 2-3): Victor L. Jensen, Karina T. Simonsen, Yu-Hui Lee, Donha Park, and Donald L. Riddle. Rnai screen of daf-16/foxo target genes in c. elegans links pathogenesis and dauer formation. PLoS ONE, 5:e15902, Dec 2010. URL: https://doi.org/10.1371/journal.pone.0015902, doi:10.1371/journal.pone.0015902. This article has 37 citations and is from a peer-reviewed journal.
(jensen2010rnaiscreenof pages 4-5): Victor L. Jensen, Karina T. Simonsen, Yu-Hui Lee, Donha Park, and Donald L. Riddle. Rnai screen of daf-16/foxo target genes in c. elegans links pathogenesis and dauer formation. PLoS ONE, 5:e15902, Dec 2010. URL: https://doi.org/10.1371/journal.pone.0015902, doi:10.1371/journal.pone.0015902. This article has 37 citations and is from a peer-reviewed journal.
(mallo2002inducibleantibacterialdefense pages 1-2): Gustavo V. Mallo, C.Lรฉopold Kurz, Carole Couillault, Nathalie Pujol, Samuel Granjeaud, Yuji Kohara, and Jonathan J. Ewbank. Inducible antibacterial defense system in c. elegans. Current Biology, 12:1209-1214, Jul 2002. URL: https://doi.org/10.1016/s0960-9822(02)00928-4, doi:10.1016/s0960-9822(02)00928-4. This article has 614 citations and is from a highest quality peer-reviewed journal.
(schulenburg2004evolutionofthe pages 6-7): Hinrich Schulenburg, C. Lรฉopold Kurz, and Jonathan J. Ewbank. Evolution of the innate immune system: the worm perspective. Immunological Reviews, 198:36-58, Apr 2004. URL: https://doi.org/10.1111/j.0105-2896.2004.0125.x, doi:10.1111/j.0105-2896.2004.0125.x. This article has 317 citations and is from a domain leading peer-reviewed journal.
(jensen2010rnaiscreenof pages 3-4): Victor L. Jensen, Karina T. Simonsen, Yu-Hui Lee, Donha Park, and Donald L. Riddle. Rnai screen of daf-16/foxo target genes in c. elegans links pathogenesis and dauer formation. PLoS ONE, 5:e15902, Dec 2010. URL: https://doi.org/10.1371/journal.pone.0015902, doi:10.1371/journal.pone.0015902. This article has 37 citations and is from a peer-reviewed journal.
(alper2007specificityandcomplexity pages 1-2): Scott Alper, Sandra J. McBride, Brad Lackford, Jonathan H. Freedman, and David A. Schwartz. Specificity and complexity of the caenorhabditis elegans innate immune response. Aug 2007. URL: https://doi.org/10.1128/mcb.02070-06, doi:10.1128/mcb.02070-06. This article has 232 citations and is from a domain leading peer-reviewed journal.
(vollmer2008bacterialpeptidoglycan(murein) pages 6-7): Waldemar Vollmer, Bernard Joris, Paulette Charlier, and Simon Foster. Bacterial peptidoglycan (murein) hydrolases. FEMS microbiology reviews, 32 2:259-86, Mar 2008. URL: https://doi.org/10.1111/j.1574-6976.2007.00099.x, doi:10.1111/j.1574-6976.2007.00099.x. This article has 1226 citations and is from a domain leading peer-reviewed journal.
UniProt: O62415 (LYS1_CAEEL) ยท WormBase: WBGene00003090 / Y22F5A.4 ยท Chromosome V
Gene product: Lysozyme-like protein 1 (LYS-1). Precursor with N-terminal signal peptide.
lys genes), one of two lysozyme classes in the worm (the other being theilys genes). C. elegans has an unusually large, divergent lysozymelysozyme activity andpeptidoglycan catabolic process / cell wall macromolecule catabolic process annotationsid: O62415
gene_symbol: lys-1
product_type: PROTEIN
status: COMPLETE
taxon:
id: NCBITaxon:6239
label: Caenorhabditis elegans
description: >-
LYS-1 is one of the protist-type (Entamoeba-type) lysozymes of Caenorhabditis
elegans, a nematode that carries an unusually large and divergent lysozyme
family (15 genes split into protist-type lys and invertebrate-type ilys
classes). Structurally it is a glycoside hydrolase family 25 (GH25) protein
with an N-terminal signal peptide. LYS-1 functions as an infection-inducible
antibacterial effector of the intestinal innate immune response: it is one of
the most strongly induced genes upon infection by the Gram-negative bacterium
Serratia marcescens, and its overexpression increases resistance to that
pathogen, while RNAi knockdown reduces survival on the Gram-positive bacterium
Staphylococcus aureus. It is also transcriptionally upregulated by Bacillus
thuringiensis and is part of the ELT-2/GATA-controlled intestinal
infection-response program, and it is a DAF-16/FOXO target that links the
immune response to the dauer developmental decision. The protein localizes to
vesicles in the apical region of intestinal cells and is expressed in the
intestine and a subset of head neurons. Although the GH25 fold implies
muramidase (peptidoglycan-hydrolysing) activity, this catalytic activity has
never been demonstrated for LYS-1 at the protein level, and the sequence lacks
the conserved active-site residues, so its actual enzymatic function is
uncertain.
existing_annotations:
- term:
id: GO:0007165
label: signal transduction
evidence_type: IBA
original_reference_id: GO_REF:0000033
qualifier: involved_in
review:
summary: >-
This IBA is a phylogenetic propagation from a PANTHER subfamily seeded
by non-lysozyme members (including a Dictyostelium protein). Lysozymes
are secreted antibacterial hydrolases/effectors, not signal-transducing
proteins, and there is no evidence that LYS-1 transduces any signal.
action: REMOVE
reason: >-
Over-broad phylogenetic inference inconsistent with the biology of a
lysozyme-family antibacterial effector. No experimental or sequence
feature supports a signal transduction role for LYS-1; the specific,
experimentally supported role is antibacterial defense (captured by the
defense-response terms below).
propagation_review:
root_cause: PROPAGATION_BAD
failure_modes:
- FUNCTIONAL_DIVERGENCE
- GRANULARITY_MISMATCH
source_entities:
- source_id: PANTHER:PTN000574946
source_label: PTN000574946 (PANTHER ancestral node)
source_status: SOURCE_WEAK_OR_INFERRED
comment: >-
Ancestral node whose GO:0007165 assignment was seeded from
dictyBase:DDB_G0273175 (a Dictyostelium protein). "Signal
transduction" is not a function of a GH25 lysozyme-family
antibacterial effector; the propagation transfers an unrelated,
overly generic process to LYS-1.
- term:
id: GO:0045087
label: innate immune response
evidence_type: IBA
original_reference_id: GO_REF:0000033
qualifier: involved_in
review:
summary: >-
The innate-immune-response assignment is correct for LYS-1, but this IBA
is redundant with the stronger experimental IMP (PMID:21209831) and HEP
(PMID:16968778) annotations to the same term. Retained as valid biological
process context rather than as a distinct line of evidence.
action: KEEP_AS_NON_CORE
reason: >-
Correct process but redundant with experimental annotations to the same
term; the more specific defense-response-to-Gram-positive/Gram-negative
terms carry the core biology.
- term:
id: GO:0003796
label: lysozyme activity
evidence_type: IEA
original_reference_id: GO_REF:0000002
qualifier: enables
review:
summary: >-
This is a family/domain-based (InterPro IPR002053, GH25) inference of
muramidase activity. It has never been demonstrated for LYS-1: no C.
elegans lysozyme has been characterized at the protein level, and UniProt
flags a CAUTION that LYS-1 "Lacks conserved active site residues,
suggesting it has no catalytic activity." The activity therefore cannot
be confirmed, and there is positive sequence evidence that it may be
absent.
action: UNDECIDED
reason: >-
Cannot verify: no biochemical/enzymatic assay of purified LYS-1 exists,
and the UniProt active-site CAUTION suggests possible loss of catalytic
activity. Per guidelines this is an author-flagged unresolved MF, not a
confident REMOVE (family activity cannot be definitively excluded without
biochemistry). This is the central molecular-function knowledge gap for
this gene.
supported_by:
- reference_id: PMID:21931778
supporting_text: >-
All available data is based on genetic analysis, whereas none of the
lysozymes have been characterized at the protein level.
- term:
id: GO:0006950
label: response to stress
evidence_type: IEA
original_reference_id: GO_REF:0000117
qualifier: involved_in
review:
summary: >-
A very generic ARBA machine-learned assignment. The specific
infection/defense-response terms below describe LYS-1's biology far more
informatively; a bare response-to-stress term adds little.
action: MARK_AS_OVER_ANNOTATED
reason: >-
Too general to be informative and subsumed by the specific defense
response / innate immune response annotations that are experimentally
supported.
- term:
id: GO:0009253
label: peptidoglycan catabolic process
evidence_type: IEA
original_reference_id: GO_REF:0000002
qualifier: involved_in
review:
summary: >-
The biological-process counterpart of the unverified lysozyme activity
(InterPro/GH25 inference). Because peptidoglycan hydrolysis by LYS-1 has
not been demonstrated and the sequence may lack catalytic residues, this
process cannot be confirmed for this paralog.
action: UNDECIDED
reason: >-
Depends on an unverified catalytic (muramidase) activity; no direct
evidence LYS-1 cleaves peptidoglycan. Tied to the lysozyme-activity
knowledge gap.
supported_by:
- reference_id: PMID:21931778
supporting_text: >-
All available data is based on genetic analysis, whereas none of the
lysozymes have been characterized at the protein level.
- term:
id: GO:0016998
label: cell wall macromolecule catabolic process
evidence_type: IEA
original_reference_id: GO_REF:0000002
qualifier: involved_in
review:
summary: >-
A more general parent of peptidoglycan catabolism, from the same
family-based InterPro inference; same caveat that the underlying
catalytic activity is undemonstrated for LYS-1.
action: UNDECIDED
reason: >-
Same unverified-catalysis basis as the peptidoglycan/lysozyme-activity
annotations; cannot confirm cell-wall macromolecule catabolism for LYS-1.
- term:
id: GO:0060205
label: cytoplasmic vesicle lumen
evidence_type: IEA
original_reference_id: GO_REF:0000044
qualifier: located_in
review:
summary: >-
UniProt Subcellular Location keyword propagation matching the curated
localization of LYS-1 to the lumen of apical intestinal vesicles.
Redundant with the EXP annotation from PMID:12176330.
action: KEEP_AS_NON_CORE
reason: >-
Correct location but electronically propagated and redundant with the
experimental EXP/IDA vesicle annotations.
- term:
id: GO:0060205
label: cytoplasmic vesicle lumen
evidence_type: EXP
original_reference_id: PMID:12176330
qualifier: located_in
review:
summary: >-
Experimentally curated localization of LYS-1 to the lumen of vesicles in
the apical region of intestinal cells, from the primary characterization
of the inducible antibacterial defense system.
action: ACCEPT
reason: >-
Curator-assigned experimental localization consistent with a secreted
intestinal antibacterial effector stored in apical vesicles.
- term:
id: GO:0045087
label: innate immune response
evidence_type: HEP
original_reference_id: PMID:16968778
qualifier: involved_in
review:
summary: >-
High-throughput expression evidence: lys-1 is part of the intestinal
ELT-2/GATA-regulated infection-response gene program identified in a
genome-wide study of epithelial innate immunity. Consistent with its
infection-inducible antibacterial role.
action: KEEP_AS_NON_CORE
reason: >-
Expression-based support for involvement in the innate immune response;
corroborates the experimental IMP annotation but is itself expression-
level evidence.
- term:
id: GO:0045087
label: innate immune response
evidence_type: IMP
original_reference_id: PMID:21209831
qualifier: involved_in
review:
summary: >-
RNAi knockdown of lys-1 significantly reduces C. elegans survival on the
pathogen Staphylococcus aureus (TD50 4.7 vs 6.8 days for control,
p<0.0001), demonstrating that lys-1 is required for a normal innate
immune/pathogen-resistance response.
action: ACCEPT
reason: >-
Direct loss-of-function (RNAi) phenotype establishing a functional role
in the innate immune response; core immune-defense biology of the gene.
supported_by:
- reference_id: PMID:21209831
supporting_text: >-
Two genes, lys-1 and clc-1, were required for normal resistance to S.
aureus.
- term:
id: GO:0050830
label: defense response to Gram-positive bacterium
evidence_type: IMP
original_reference_id: PMID:21209831
qualifier: involved_in
review:
summary: >-
Staphylococcus aureus is a Gram-positive bacterium, and lys-1 RNAi
reduces survival on it (TD50 4.7 vs 6.8 days, p<0.0001), directly
supporting a role in defense against Gram-positive bacteria. This is the
most specific, experimentally supported process term for the gene.
action: ACCEPT
reason: >-
Specific, experimentally demonstrated defense function against a
Gram-positive pathogen; a core biological process of LYS-1.
supported_by:
- reference_id: PMID:21209831
supporting_text: >-
The TD50 (time required for 50% of the nematodes to die) for lys-1
was 4.7 days (p<0.0001)
- term:
id: GO:0031410
label: cytoplasmic vesicle
evidence_type: IDA
original_reference_id: PMID:12176330
qualifier: located_in
review:
summary: >-
Direct-assay localization of LYS-1 to cytoplasmic vesicles in intestinal
cells, from the primary characterization paper.
action: ACCEPT
reason: >-
Experimentally observed subcellular localization consistent with storage
of the effector in intestinal vesicles.
- term:
id: GO:0045177
label: apical part of cell
evidence_type: IDA
original_reference_id: PMID:12176330
qualifier: located_in
review:
summary: >-
LYS-1 localizes to the apical region of intestinal cells (apically
positioned vesicles), consistent with secretion toward the gut lumen
where ingested bacteria are encountered.
action: ACCEPT
reason: >-
Experimentally supported apical localization appropriate for a
gut-luminal antibacterial effector.
- term:
id: GO:0050829
label: defense response to Gram-negative bacterium
evidence_type: IEP
original_reference_id: PMID:12176330
qualifier: involved_in
review:
summary: >-
lys-1 is among the most robustly induced genes upon infection by the
Gram-negative bacterium Serratia marcescens, and its overexpression
augments resistance to that pathogen, supporting a role in defense
against Gram-negative bacteria. The evidence code is IEP (expression),
reinforced by the overexpression gain-of-resistance phenotype.
action: ACCEPT
reason: >-
Infection-inducible expression plus overexpression-conferred resistance
establish a defense role against a Gram-negative pathogen; a core
biological process of LYS-1.
supported_by:
- reference_id: PMID:12176330
supporting_text: >-
overexpression of the lysozyme gene lys-1 augments the resistance of
C. elegans to S. marcescens.
core_functions:
- description: >-
Infection-inducible antibacterial effector of the C. elegans intestinal
innate immune response, acting against both Gram-negative (S. marcescens)
and Gram-positive (S. aureus) bacteria. LYS-1 is stored in the lumen of
apical intestinal vesicles, positioned for release toward ingested
bacteria in the gut. It is a GH25 protist-type lysozyme; a muramidase
(peptidoglycan-hydrolysing) molecular function is implied by the fold but
has not been demonstrated and may be absent (no conserved active-site
residues), so no specific molecular_function is asserted here.
directly_involved_in:
- id: GO:0050829
label: defense response to Gram-negative bacterium
- id: GO:0050830
label: defense response to Gram-positive bacterium
- id: GO:0045087
label: innate immune response
locations:
- id: GO:0060205
label: cytoplasmic vesicle lumen
- id: GO:0045177
label: apical part of cell
supported_by:
- reference_id: PMID:12176330
supporting_text: >-
overexpression of the lysozyme gene lys-1 augments the resistance of
C. elegans to S. marcescens.
- reference_id: PMID:21209831
supporting_text: >-
Two genes, lys-1 and clc-1, were required for normal resistance to S.
aureus.
knowledge_gaps:
- gap_statement: >-
It is not known whether LYS-1 has any muramidase / lysozyme
(peptidoglycan-hydrolysing) enzymatic activity. All functional evidence is
genetic (infection-inducible expression, RNAi, overexpression); the protein
has never been purified or assayed, and its sequence lacks the conserved
GH25 active-site residues, raising the possibility that it is a
pseudo-muramidase.
boundary: >-
What is firmly established is that LYS-1 is a GH25 protist-type lysozyme
whose gene is infection-inducible and functionally required for normal
antibacterial defense (S. marcescens, S. aureus). What is unknown is the
biochemical activity of the protein: whether it cleaves peptidoglycan,
permeabilizes/agglutinates bacteria by another mechanism, or acts
non-catalytically.
gap_kind:
- BIOLOGY
dark_aspect: MF_DARK
status: OPEN
significance: >-
Whether LYS-1 kills bacteria enzymatically (like canonical lysozymes) or by
a non-catalytic mechanism determines the correct molecular-function
annotation and whether the current InterPro-based lysozyme-activity /
peptidoglycan-catabolism annotations should stand. This is a recurring issue
across the expanded, divergent C. elegans lysozyme family.
resolution: >-
Express and purify recombinant LYS-1 and assay muramidase / bacteriolytic
activity (e.g. on Micrococcus cell walls and defined peptidoglycan) and its
ability to bind/permeabilize target bacteria; complement with active-site
residue mutagenesis and structural analysis.
provenance:
- reference_id: PMID:21931778
supporting_text: >-
All available data is based on genetic analysis, whereas none of the
lysozymes have been characterized at the protein level.
- reference_id: PMID:21931778
supporting_text: >-
our study (and most previous studies) only indicates, but does not
strictly prove a defence function of these enzymes. Unequivocal
evidence would require analysis of the purified protein, especially its
ability to interact with the pathogen at the molecular level.
- gap_statement: >-
The molecular substrate or microbial target of LYS-1 is undefined: it is
unknown which bacterial surface molecule(s) LYS-1 acts on, and whether its
antibacterial spectrum extends beyond S. marcescens, S. aureus and B.
thuringiensis.
boundary: >-
LYS-1 is known to be required for resistance to S. aureus and to protect
against S. marcescens when overexpressed, and it is transcriptionally
induced by these plus B. thuringiensis. What is unknown is the direct
biochemical target/substrate and the full microbial spectrum.
gap_kind:
- BIOLOGY
dark_aspect: MF_DARK
status: OPEN
significance: >-
Identifying the target molecule would clarify the mechanism (enzymatic
versus binding/permeabilizing) and the range of pathogens LYS-1 counters,
informing both its MF annotation and its place in the surveillance-immunity
effector repertoire.
resolution: >-
Biochemical target/substrate identification with purified protein
(peptidoglycan/cell-wall degradation assays, pull-downs of bacterial
ligands) and broader pathogen-panel survival/CFU assays with defined lys-1
loss- and gain-of-function strains.
provenance:
- reference_id: PMID:21931778
supporting_text: >-
Unequivocal evidence would require analysis of the purified protein,
especially its ability to interact with the pathogen at the molecular
level.
- gap_statement: >-
Whether lys-1 is individually necessary in vivo or is functionally
redundant within the 15-member C. elegans lysozyme family is unresolved.
The defense phenotypes rest on RNAi knockdown and overexpression rather
than a characterized single-gene null, and many lysozyme paralogs share
overlapping infection-induction profiles.
boundary: >-
lys-1 RNAi reduces S. aureus survival and lys-1 overexpression increases S.
marcescens resistance, establishing a contribution to defense. What is
unknown is the phenotype of a clean lys-1 loss-of-function null and the
degree of redundancy with paralogs such as lys-2, lys-3 and lys-7.
gap_kind:
- BIOLOGY
dark_aspect: BP_DARK
status: OPEN
significance: >-
Redundancy determines whether lys-1 is a non-redundant defense gene or one
of several partially interchangeable effectors, which affects how strongly
its individual loss impacts host survival and how its biological role should
be weighted.
resolution: >-
Generate and phenotype a lys-1 null allele (and higher-order lysozyme
combinatorial mutants) across a pathogen panel, quantifying survival and
pathogen load relative to wild type and to single-paralog mutants.
provenance:
- reference_id: PMID:21931778
supporting_text: >-
the nematode Caenorhabditis elegans harbours 15 phylogenetically
diverse lysozyme genes
- reference_id: file:worm/lys-1/lys-1-notes.md
supporting_text: >-
Whether lys-1 is individually necessary in vivo, or redundant within
the 15-member lysozyme family, is not resolved.
suggested_questions:
- question: >-
Does purified LYS-1 protein possess muramidase/bacteriolytic activity, or
has this GH25 protist-type lysozyme lost catalytic function and act by a
non-enzymatic antibacterial mechanism?
experts:
- Schulenburg H
- question: >-
What is the phenotype of a lys-1 loss-of-function null, and to what extent
is lys-1 redundant with other protist-type lysozymes in defense against
ingested pathogens?
experts:
- Schulenburg H
- Ewbank JJ
suggested_experiments:
- hypothesis: >-
LYS-1 either hydrolyzes bacterial peptidoglycan (canonical lysozyme
mechanism) or, lacking active-site residues, kills/inhibits bacteria by a
non-catalytic binding/permeabilizing mechanism.
description: >-
Express and purify recombinant LYS-1, then assay (i) muramidase activity on
Micrococcus luteus cell walls and defined peptidoglycan substrates, (ii)
bacteriolytic/growth-inhibitory activity against S. aureus and S.
marcescens, and (iii) direct binding to bacterial cell-surface components;
pair with active-site mutagenesis and, if possible, structure
determination.
experiment_type: biochemistry / enzymology / structural biology
- hypothesis: >-
lys-1 contributes non-redundantly to intestinal antibacterial defense in
vivo.
description: >-
Generate a lys-1 null allele (CRISPR) and test survival and intestinal
pathogen load on a panel of Gram-negative and Gram-positive pathogens (S.
marcescens, S. aureus, B. thuringiensis, P. aeruginosa), comparing single
mutant, paralog combinations, and rescue/overexpression lines.
experiment_type: genetics / host-pathogen survival and CFU assays
references:
- id: GO_REF:0000002
title: Gene Ontology annotation through association of InterPro records with GO terms
findings: []
- id: GO_REF:0000033
title: Annotation inferences using phylogenetic trees
findings: []
- id: GO_REF:0000044
title: Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular Location vocabulary
mapping, accompanied by conservative changes to GO terms applied by UniProt
findings: []
- id: GO_REF:0000117
title: Electronic Gene Ontology annotations created by ARBA machine learning models
findings: []
- id: PMID:12176330
title: Inducible antibacterial defense system in C. elegans.
findings:
- statement: >-
lys-1 is among the most robustly infection-induced genes and its
overexpression augments resistance to the Gram-negative bacterium
Serratia marcescens; the protein localizes to apical intestinal
vesicles.
reference_section_type: RESULTS
reference_review:
relevance: HIGH
correctness: VERIFIED
review_notes: >-
Primary characterization of the inducible antibacterial defense system;
directly establishes lys-1 induction and overexpression-conferred
resistance to S. marcescens. Cached copy is abstract-only, so localization
details derive from the UniProt-curated full text; the overexpression
claim is a verbatim quote from the cached abstract.
- id: PMID:16968778
title: A conserved role for a GATA transcription factor in regulating epithelial innate
immune responses.
findings:
- statement: >-
Genome-wide study establishing the intestinal ELT-2/GATA-regulated
epithelial infection-response gene program of which lys-1 is a member
(basis of the HEP innate-immune-response annotation).
reference_section_type: ABSTRACT
reference_review:
relevance: MEDIUM
correctness: VERIFIED
review_notes: >-
Abstract-only cache. Establishes the ELT-2/GATA intestinal innate-immunity
program; supports lys-1's expression-based innate-immune-response
annotation as a program member rather than as a directly assayed gene here.
- id: PMID:21209831
title: RNAi screen of DAF-16/FOXO target genes in C. elegans links pathogenesis and dauer
formation.
findings:
- statement: >-
lys-1 RNAi significantly reduces survival on Staphylococcus aureus
(TD50 4.7 vs 6.8 days, p<0.0001), showing lys-1 is required for normal
resistance; lys-1 is a DAF-16/FOXO target with a synthetic
dauer-formation phenotype.
reference_section_type: RESULTS
reference_review:
relevance: HIGH
correctness: VERIFIED
review_notes: >-
Full text cached and verified. Strong experimental support for the S.
aureus (Gram-positive) defense and innate-immune-response IMP annotations,
and for the DAF-16/dauer link.
- id: PMID:21931778
title: Protist-type lysozymes of the nematode Caenorhabditis elegans contribute to resistance
against pathogenic Bacillus thuringiensis.
findings:
- statement: >-
Classifies lys-1 as a chromosome V protist-type lysozyme within the
15-gene C. elegans lysozyme family, shows lys-1 is transcriptionally
upregulated by B. thuringiensis in all tested strains, and states
explicitly that no C. elegans lysozyme has been characterized at the
protein level (basis of the muramidase-activity knowledge gap).
reference_section_type: RESULTS
reference_review:
relevance: HIGH
correctness: VERIFIED
review_notes: >-
Full text cached and verified. Key source for the protist-type
classification, B. thuringiensis induction of lys-1, and the field's
explicit admission that lysozyme enzymatic function is undemonstrated at
the protein level.