NleB1 (Non-LEE-encoded type III effector B1) is a protein-arginine N-acetylglucosaminyltransferase that is secreted by the type III secretion system (T3SS) into host cells during EHEC infection. The enzyme catalyzes the transfer of N-acetylglucosamine (GlcNAc) from UDP-GlcNAc to the guanidino nitrogen of arginine residues on host target proteins, primarily death domain-containing proteins such as FADD (Arg117), TRADD (Arg235), and RIPK1 (Arg603). This unusual post-translational modification disrupts homotypic and heterotypic death domain interactions required for death receptor signaling complex assembly, thereby inhibiting TNF/TRAIL/Fas-mediated apoptosis, necroptosis, and NF-kappaB activation. NleB1 also glycosylates GAPDH at Arg197/Arg200, preventing GAPDH-TRAF2 interaction. The enzyme requires Mn2+ as a cofactor and contains a GT-A fold with a characteristic DXD motif and HEN catalytic triad. NleB1 undergoes auto-GlcNAcylation which is required for activity toward death domain-containing substrates. Importantly, NleB1 is a signaling modulator/effector that manipulates host cell processes rather than a classical toxin that directly kills cells (nleB1-deep-research-falcon.md).
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
|
GO:0005576
extracellular region
|
IEA
GO_REF:0000044 |
ACCEPT |
Summary: NleB1 is secreted via the type III secretion system into the extracellular milieu and then translocated directly into host cells. The annotation reflects that the protein leaves the bacterial cytoplasm and enters the extracellular space transiently before entering host cells (PMID:30619781, PMID:28522607).
Reason: This annotation is correct as NleB1 is a T3SS effector that is secreted from the bacterium. UniProt confirms the subcellular location as "Secreted" with subsequent translocation to "Host cytoplasm" via T3SS. The IEA annotation based on UniProt subcellular location vocabulary mapping is appropriate.
Supporting Evidence:
PMID:30619781
The enteropathogenic and enterohemorrhagic Escherichia coli NleB proteins as well as the Salmonella enterica SseK proteins are type III secretion system effectors that function as glycosyltransferase enzymes
|
|
GO:0016740
transferase activity
|
IEA
GO_REF:0000043 |
ACCEPT |
Summary: NleB1 is a glycosyltransferase that transfers GlcNAc from UDP-GlcNAc to arginine residues on protein substrates. This broad transferase activity annotation is correct but less specific than GO:0106362 (protein-arginine N-acetylglucosaminyltransferase activity) which is also annotated.
Reason: This is a correct parent term annotation. While more specific annotations exist (GO:0016757, GO:0106362), having parent terms from IEA mappings is acceptable and does not conflict with more specific annotations. The UniProt record explicitly lists EC=2.4.1.- confirming transferase activity.
Supporting Evidence:
PMID:30619781
The kinetic parameters of NleB1 (150 nM at 30°C) were calculated as follows: Vmax: 2,975.3 ± 125 RLU/min/μg protein; Km: 379 ± 43 μM; Kcat (s-1): 50, Kcat/Km (s-1, M-1): 130,703.4
|
|
GO:0016757
glycosyltransferase activity
|
IEA
GO_REF:0000043 |
ACCEPT |
Summary: NleB1 catalyzes the transfer of N-acetylglucosamine (GlcNAc) from UDP-GlcNAc to arginine residues on host proteins. Multiple publications confirm glycosyltransferase activity (PMID:28522607, PMID:30619781). The protein belongs to the glycosyltransferase NleB family and has a GT-A fold.
Reason: This annotation is experimentally validated. PMID:28522607 states "NleB is a glycosyltransferase that modifies host proteins with N-acetyl-d-glucosamine". PMID:30619781 further characterizes the kinetic parameters. This is an appropriate intermediate-level MF annotation.
Supporting Evidence:
PMID:28522607
NleB is a glycosyltransferase that modifies host proteins with N-acetyl-d-glucosamine to inhibit antibacterial and inflammatory host responses
PMID:30619781
The NleB1/NleB2 (enteropathogenic and enterohemorrhagic E. coli; EPEC and EHEC) and SseK1/SseK2/SseK3 (Salmonella enterica) T3SS effectors are glycosyltransferases that modify protein substrates on arginine residues
|
|
GO:0030430
host cell cytoplasm
|
IEA
GO_REF:0000044 |
ACCEPT |
Summary: NleB1 is translocated into host cells via the T3SS where it functions in the host cell cytoplasm to modify death domain-containing proteins. This localization is essential for its function in disrupting host signaling pathways.
Reason: Correct localization annotation. The deep research report confirms "NleB1 is secreted by the T3SS into host cells, where it acts in the host cytosol to modify death-domain proteins." UniProt also lists "Host cytoplasm" as the subcellular location with evidence by similarity to related effectors.
Supporting Evidence:
PMID:28522607
Many Gram-negative bacterial pathogens use a syringe-like apparatus called a type III secretion system to inject virulence factors into host cells
|
|
GO:0046872
metal ion binding
|
IEA
GO_REF:0000043 |
ACCEPT |
Summary: NleB1 requires manganese (Mn2+) as a cofactor for its glycosyltransferase activity. The DXD motif (residues 221-223) coordinates the metal ion. Mutation of the DXD motif to AAA abolishes activity (PMID:30619781).
Reason: Correct annotation supported by experimental evidence. While GO:0030145 (manganese ion binding) is more specific and also annotated with IDA evidence, this broader term is acceptable as an IEA annotation. The DXD motif essential for Mn2+ coordination is confirmed in the UniProt feature table.
Supporting Evidence:
PMID:30619781
an inactive form of NleB1 (NleB1-AAA) in which the aspartic acid residues required for Mn2+ stabilization were mutated to alanines
|
|
GO:0090729
toxin activity
|
IEA
GO_REF:0000043 |
REMOVE |
Summary: This annotation derives from the UniProt keyword "Toxin" (KW-0800) mapping to GO. However, the GO definition of toxin activity requires "Interacting selectively with one or more biological molecules in another (target) organism, initiating pathogenesis (leading to an abnormal, generally detrimental state)." While NleB1 is a virulence factor, it is fundamentally different from classical toxins. NleB1 is a signaling modulator that manipulates host cell processes by enzymatically modifying host proteins - it does NOT directly kill or damage cells like true toxins (e.g., Shiga toxin which inhibits protein synthesis, hemolysin which lyses cells by pore formation). NleB1 actually INHIBITS cell death (apoptosis, necroptosis) rather than causing it (nleB1-deep-research-falcon.md).
Reason: This is a clear case of SPKW over-annotation. The UniProt keyword "Toxin" is applied broadly to bacterial virulence factors, but the GO term "toxin activity" has a specific definition that does not fit NleB1. Key distinctions: 1) True toxins (Shiga toxin, diphtheria toxin, hemolysins) directly damage/kill cells 2) NleB1 is a T3SS effector that MODULATES host signaling without direct cytotoxicity 3) NleB1 actually SUPPRESSES host cell death pathways (apoptosis, necroptosis) 4) The mechanism is enzymatic modification of host proteins to subvert signaling,
not direct cellular damage
5) PMID:30619781 explicitly notes that inhibitors of NleB1 "were not significantly
toxic to mammalian cells" and did not cause "significant macrophage death"
The appropriate GO terms for NleB1's function are process terms like GO:0052041 (symbiont-mediated suppression of host programmed cell death), GO:0085034 (symbiont-mediated suppression of host NF-kappaB cascade), and GO:0140403 (effector-mediated suppression of host innate immune response).
Supporting Evidence:
PMID:28522607
NleB is a glycosyltransferase that modifies host proteins with N-acetyl-d-glucosamine to inhibit antibacterial and inflammatory host responses
PMID:30619781
We also failed to observe significant macrophage death in our studies
|
|
GO:0106362
protein-arginine N-acetylglucosaminyltransferase activity
|
IEA
GO_REF:0000002 |
ACCEPT |
Summary: This is the most precise molecular function annotation for NleB1. The enzyme specifically catalyzes the transfer of GlcNAc to the guanidino nitrogen of arginine residues on protein substrates. This activity is directly demonstrated in PMID:28522607 and PMID:30619781.
Reason: Correct and appropriate annotation. This GO term precisely describes NleB1's enzymatic activity. UniProt lists this exact term with IDA evidence from PMID:28522607 and PMID:30619781. The IEA annotation from InterPro is consistent with experimental evidence.
Supporting Evidence:
PMID:28522607
EHEC NleB1 glycosylated two GAPDH arginine residues, Arg197 and Arg200
PMID:30619781
This modification is unusual because it occurs on the guanidinium groups of arginines, which are poor nucleophiles
|
|
GO:0005515
protein binding
|
IPI
PMID:27018634 Quantitative Mass Spectrometry Identifies Novel Host Binding... |
MODIFY |
Summary: PMID:27018634 identified ensconsin (MAP7) as a binding partner for NleB1 using quantitative mass spectrometry. The study confirmed that NleB1 interacted with ensconsin in a region corresponding to its microtubule binding domain. However, "protein binding" is an uninformative annotation per GO curation guidelines.
Reason: While the interaction with ensconsin/MAP7 is experimentally validated, the GO term "protein binding" (GO:0005515) is considered too vague to be informative. Per GO curation guidelines, more specific binding terms should be used. The interaction with MAP7 led to disruption of intracellular trafficking (see GO:0052038 annotation). A more informative annotation would describe the functional consequence or use a specific binding term if available.
Proposed replacements:
effector-mediated perturbation of host process by symbiont
Supporting Evidence:
PMID:27018634
we confirmed that NleB1 and EspL interacted with ensconsin in a region that corresponded to its microtubule binding domain
|
|
GO:0030145
manganese ion binding
|
IDA
PMID:30619781 High-Throughput Screening for Bacterial Glycosyltransferase ... |
ACCEPT |
Summary: NleB1 requires Mn2+ as a cofactor for its glycosyltransferase activity. The DXD motif (residues 221-223) is essential for Mn2+ coordination. PMID:30619781 demonstrated that mutation of the DXD motif to AAA (NleB1-AAA) abolished enzymatic activity, confirming the requirement for metal coordination.
Reason: This is a well-supported annotation with direct experimental evidence. The kinetic assays in PMID:30619781 used 25 mM MnCl2 and showed that the DXD->AAA mutant lacked activity. UniProt features annotate residues 223, 320, and 322 as Mn2+ binding sites.
Supporting Evidence:
PMID:30619781
UDP-Glo luminescence assays were performed in 96 well-microplates, containing 250 nM NleB1 in 125 mM Tris pH 7.4, 25 mM MnCl2, 2.5 mM DTT, and 100 μM UDP-GlcNAc
PMID:30619781
an inactive form of NleB1 (NleB1-AAA) in which the aspartic acid residues required for Mn2+ stabilization were mutated to alanines
|
|
GO:0106362
protein-arginine N-acetylglucosaminyltransferase activity
|
IDA
PMID:28522607 NleB/SseK effectors from Citrobacter rodentium, Escherichia ... |
ACCEPT |
Summary: PMID:28522607 directly demonstrated that EHEC NleB1 glycosylates host proteins GAPDH (at Arg197 and Arg200) and FADD on arginine residues using in vitro glycosylation assays and mass spectrometry.
Reason: This is the primary experimental evidence for NleB1's enzymatic activity. The study used in vitro assays and cell culture experiments to demonstrate arginine-specific N-acetylglucosaminyltransferase activity. The specific modification sites were identified by mass spectrometry.
Supporting Evidence:
PMID:28522607
We also found that EHEC NleB1 glycosylated two GAPDH arginine residues, Arg197 and Arg200, and that these two residues were essential for GAPDH-mediated activation of TNF receptor-associated factor 2 ubiquitination
PMID:28522607
C. rodentium NleB, EHEC NleB1, EPEC NleB1, and SseK2 glycosylated the FADD (Fas-associated death domain protein)
|
|
GO:0106362
protein-arginine N-acetylglucosaminyltransferase activity
|
IDA
PMID:30619781 High-Throughput Screening for Bacterial Glycosyltransferase ... |
ACCEPT |
Summary: PMID:30619781 characterized the kinetic parameters of NleB1's glycosyltransferase activity (Km = 379 uM for UDP-GlcNAc, kcat = 50 s-1) and developed high-throughput screening assays to identify inhibitors. The study used purified recombinant NleB1 and demonstrated activity against GAPDH and TRADD substrates.
Reason: This provides additional IDA evidence for the same molecular function. The study provides quantitative kinetic characterization of the enzyme. Having multiple IDA annotations from different publications strengthens the evidence base.
Supporting Evidence:
PMID:30619781
The kinetic parameters of NleB1 (150 nM at 30°C) were calculated as follows: Vmax: 2,975.3 ± 125 RLU/min/μg protein; Km: 379 ± 43 μM; Kcat (s-1): 50, Kcat/Km (s-1, M-1): 130,703.4
|
|
GO:0052038
symbiont-mediated perturbation of host intracellular transport
|
IMP
PMID:27018634 Quantitative Mass Spectrometry Identifies Novel Host Binding... |
ACCEPT |
Summary: PMID:27018634 demonstrated that NleB1 and EspL interact with ensconsin (MAP7), an essential cofactor of kinesin-1 required for intracellular trafficking. The study showed that intracellular trafficking was severely disrupted during wild-type EPEC infections but not during infections with ΔnleB1 or ΔespL mutants.
Reason: This is a well-supported annotation with genetic evidence (IMP). The phenotype was observed in wild-type but not mutant infections, providing direct evidence that NleB1 contributes to perturbation of host intracellular transport through its interaction with the microtubule-associated protein ensconsin.
Supporting Evidence:
PMID:27018634
Ensconsin is an essential cofactor of kinesin-1 that is required for intracellular trafficking, and we demonstrated that intracellular trafficking was severely disrupted during wild type EPEC infections but not during infections with ΔnleB1 or ΔespL mutants
|
|
GO:0085034
symbiont-mediated suppression of host NF-kappaB cascade
|
IDA
PMID:28522607 NleB/SseK effectors from Citrobacter rodentium, Escherichia ... |
NEW |
Summary: NleB1 blocks TNF-mediated NF-kappaB pathway activation by glycosylating death domain proteins FADD, TRADD, and RIPK1, preventing their assembly into signaling complexes. This is a core function of NleB1. PMID:28522607 directly demonstrated that EHEC NleB1 blocked TNF-mediated NF-kappaB pathway activation.
Reason: This annotation is strongly supported by the literature and represents a core biological function of NleB1. The mechanism (arginine glycosylation of death domain proteins preventing signaling complex assembly) is well characterized.
Supporting Evidence:
PMID:28522607
SseK1, SseK3, EHEC NleB1, EPEC NleB1, and Crodentium NleB blocked TNF-mediated NF-κB pathway activation
PMID:30619781
This modification is biologically important because the glycosylation of arginines on protein substrates disrupts the normal functioning of the innate immune system
|
|
GO:0033668
symbiont-mediated suppression of host apoptosis
|
IDA
PMID:28522607 NleB/SseK effectors from Citrobacter rodentium, Escherichia ... |
NEW |
Summary: NleB1 inhibits host apoptosis by glycosylating death domain proteins (FADD, TRADD, RIPK1) which prevents death receptor signaling complex assembly. This blocks TNF/TRAIL/Fas-mediated apoptotic signaling pathways (nleB1-deep-research-falcon.md).
Reason: This is a well-documented function of NleB1. The enzyme specifically targets death domain-containing proteins that are essential for death receptor-mediated apoptosis. By glycosylating these proteins, NleB1 prevents their interaction and blocks apoptotic signaling.
Supporting Evidence:
PMID:28522607
NleB is a glycosyltransferase that modifies host proteins with N-acetyl-d-glucosamine to inhibit antibacterial and inflammatory host responses
PMID:30619781
Several death domain-containing proteins have been described as substrates of some of the NleB/SseK orthologs, including the Fas-associated protein with death domain (FADD), tumor necrosis factor receptor type 1-associated DEATH domain protein (TRADD), and the receptor-interacting serine/threonine-protein kinase 1 (RIPK1)
|
Q: Should UniProt keyword "Toxin" be applied to T3SS effectors that modulate host signaling without direct cytotoxic activity? The current mapping leads to inappropriate GO annotations.
Q: What is the relative importance of different NleB1 substrates (FADD, TRADD, RIPK1, GAPDH) for virulence during natural infection?
Experiment: Comparative analysis of NleB1 activity on different death domain proteins to establish substrate hierarchy and physiological relevance during infection.
Hypothesis: FADD may be the primary physiological target based on structural and kinetic data
Experiment: Structural characterization of NleB1-substrate complexes to understand substrate recognition and guide inhibitor development.
Hypothesis: Substrate recognition involves specific interactions with death domain fold
provider: falcon
model: Edison Scientific Literature
cached: false
start_time: '2026-01-31T14:04:00.210520'
end_time: '2026-01-31T14:12:00.625182'
duration_seconds: 480.41
template_file: templates/gene_research_go_focused.md
template_variables:
organism: ECO57
gene_id: nleB1
gene_symbol: nleB1
uniprot_accession: Q8XBX8
protein_description: 'RecName: Full=Protein-arginine N-acetylglucosaminyltransferase
NleB1 {ECO:0000305}; Short=Arginine GlcNAcyltransferase NleB1 {ECO:0000305}; EC=2.4.1.-
{ECO:0000269|PubMed:30619781}; AltName: Full=Non-LEE-encoded type III effector
B1 {ECO:0000303|PubMed:30619781};'
gene_info: Name=nleB1 {ECO:0000303|PubMed:30619781}; OrderedLocusNames=ECs3857 {ECO:0000312|EMBL:BAB37280.1};
organism_full: Escherichia coli O157:H7.
protein_family: Belongs to the glycosyltransferase NleB family.
protein_domains: SseK_NleB. (IPR057545); SseK_NleB (PF24688)
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citation_count: 17
BEFORE YOU BEGIN RESEARCH: You MUST verify you are researching the CORRECT gene/protein. Gene symbols can be ambiguous, especially for less well-characterized genes from non-model organisms.
DO NOT PROCEED WITH RESEARCH ON A DIFFERENT GENE. Instead:
- State clearly: "The gene symbol 'nleB1' is ambiguous or literature is limited for this specific protein"
- Explain what you found (e.g., "Found extensive literature on a different gene with the same symbol in a different organism")
- Describe the protein based ONLY on the UniProt information provided above
- Suggest that the protein function can be inferred from domain/family information
Please provide a comprehensive research report on the gene nleB1 (gene ID: nleB1, UniProt: Q8XBX8) in ECO57.
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.
Question: You are an expert researcher providing comprehensive, well-cited information.
Provide detailed information focusing on:
1. Key concepts and definitions with current understanding
2. Recent developments and latest research (prioritize 2023-2024 sources)
3. Current applications and real-world implementations
4. Expert opinions and analysis from authoritative sources
5. Relevant statistics and data from recent studies
Format as a comprehensive research report with proper citations. Include URLs and publication dates where available.
Always prioritize recent, authoritative sources and provide specific citations for all major claims.
BEFORE YOU BEGIN RESEARCH: You MUST verify you are researching the CORRECT gene/protein. Gene symbols can be ambiguous, especially for less well-characterized genes from non-model organisms.
DO NOT PROCEED WITH RESEARCH ON A DIFFERENT GENE. Instead:
- State clearly: "The gene symbol 'nleB1' is ambiguous or literature is limited for this specific protein"
- Explain what you found (e.g., "Found extensive literature on a different gene with the same symbol in a different organism")
- Describe the protein based ONLY on the UniProt information provided above
- Suggest that the protein function can be inferred from domain/family information
Please provide a comprehensive research report on the gene nleB1 (gene ID: nleB1, UniProt: Q8XBX8) in ECO57.
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.
Plan and verification
- Identity verification: The query targets Escherichia coli O157:H7 NleB1 (UniProt Q8XBX8), a non-LEE-encoded type III secretion (T3SS) effector belonging to the NleB/SseK family of arginine glycosyltransferases. Multiple structural and functional studies establish NleB1 as an arginine N-acetylglucosaminyltransferase that modifies host death-domain proteins to disrupt immune signaling (GT-A-like fold with family-defining SseK_NleB domain) (giogha2021nleb2fromenteropathogenic pages 2-4, park2018structuralbasisfor pages 1-2). The organism (E. coli A/E pathogens) and family/domain assignment are consistent across primary literature (ding2019structuralandfunctional pages 1-3, park2018structuralbasisfor pages 1-2, giogha2021nleb2fromenteropathogenic pages 2-4).
| Aspect | Summary | Key details (residues, motifs, donors, mechanism) | References |
|---|---|---|---|
| Identity verification | NleB1 is an NleB-family type III-secreted glycosyltransferase from Escherichia coli O157:H7 (UniProt Q8XBX8). | Member of NleB/SseK family (SseK_NleB domain); non-LEE-encoded T3SS effector. | (giogha2021nleb2fromenteropathogenic pages 2-4, park2018structuralbasisfor pages 1-2, giogha2021nleb2fromenteropathogenic pages 26-27) |
| Enzymatic reaction & mechanism | Catalyses transfer of a sugar to arginine side chains (Arg-GlcNAc in vivo for NleB1) using nucleotide-sugar donors. | Donor: UDP-GlcNAc (primary for NleB1); linkage: Arg–GlcNAc. Structural/ mechanistic notes: GT‑A–like fold with HLH/lid elements; active-site features reported include a HEN motif and requirement for a DXD region / critical Glu (e.g., Glu253); structural studies report both retaining (front-face SNi-like) and inverting mechanisms in different analyses. Mn2+ observed in crystal complexes. | (park2018structuralbasisfor pages 1-2, ding2019structuralandfunctional pages 1-3, giogha2021nleb2fromenteropathogenic pages 2-4) |
| Substrate specificity & preferences | Preferentially modifies death-domain (DD) proteins and a limited set of other host proteins; substrate scope can vary across paralogues. | Reported modified residues: TRADD Arg235 (reported target), FADD Arg117 (preferred), RIPK1 Arg603 (validated), GAPDH Arg197/Arg200 (reported). Paralogues (NleB2, SseKs) show altered donor preference or narrower substrate selectivity. | (ding2019structuralandfunctional pages 1-3, giogha2021nleb2fromenteropathogenic pages 11-13, araujogarrido2020typeiiisecretion pages 12-13) |
| Auto-GlcNAcylation | NleB-family enzymes can self-modify and auto-modification promotes enzymatic activity during infection. | Auto-GlcNAc/hexose on internal Arg residues; loss of auto-modification reduces activity toward host DD substrates. | (pan2020bacteriacatalyzedarginineglycosylation pages 1-2, giogha2021nleb2fromenteropathogenic pages 11-13, giogha2021nleb2fromenteropathogenic pages 13-14) |
| Localization / delivery | Delivered into host-cell cytosol by the bacterial type III secretion system (T3SS) where it encounters DD-containing proteins. | Non-LEE-encoded T3SS effector translocated into host; acts in host cytosol at death-receptor signalling complexes. | (park2018structuralbasisfor pages 1-2, giogha2021nleb2fromenteropathogenic pages 2-4, ding2019structuralandfunctional pages 1-3) |
| Pathway context & outcomes | Directly antagonizes death-receptor signalling and NF-κB–linked inflammatory responses, thereby inhibiting apoptosis and necroptosis in infected cells. | Targets interrupt TNFR/FAS/TRAIL DD interactions, block caspase‑8 cleavage and NF‑κB activation, and thereby promote bacterial survival/colonization. | (ding2019structuralandfunctional pages 1-3, giogha2021nleb2fromenteropathogenic pages 11-13, araujogarrido2020typeiiisecretion pages 12-13) |
| Quantitative / experimental highlights | Site-specific and stable Arg-GlcNAc modifications detected by MS; structural complexes solved; in vivo virulence relevance demonstrated in animal models. | Example residue: RIPK1 Arg603 mapped by MS; Arg‑GlcNAc modification is chemically stable (resistant to host glycosidases); crystal complexes include UDP and Mn2+; catalytic DXD mutants abolish activity; NleB activity promotes colonization in mouse models. | (giogha2021nleb2fromenteropathogenic pages 11-13, ding2019structuralandfunctional pages 1-3, giogha2021nleb2fromenteropathogenic pages 4-6) |
| Applications / inhibitors | Anti-virulence rationale: inhibit NleB1/SseK arginine glycosyltransferase activity to restore host signalling; HTS and small-molecule leads reported. | High-throughput screening identified inhibitory compounds (example HTS hits reported) and follow-up small-molecule inhibitors (proof-of-concept compounds) that block Arg‑GlcNAcylation in cells; potential for anti-virulence therapeutics. | (giogha2021nleb2fromenteropathogenic pages 27-28, giogha2021nleb2fromenteropathogenic pages 4-6) |
Table: Concise, evidence-linked summary of NleB1 (E. coli O157:H7, UniProt Q8XBX8): identity, enzymatic chemistry, substrates/residues, localization, pathway effects, experimental highlights, and inhibitor efforts, with source citations for each item.
Comprehensive research report
1) Key concepts and definitions
- Protein and family: NleB1 is a type III–translocated effector glycosyltransferase from E. coli O157:H7 that installs a sugar on arginine side chains of host proteins. It is the prototypic member of the NleB/SseK family, which share a GT-A–like catalytic domain plus auxiliary helix–loop–helix (HLH) and “lid” elements implicated in substrate recognition and active-site gating (park2018structuralbasisfor pages 1-2, giogha2021nleb2fromenteropathogenic pages 2-4).
- Enzymatic activity: NleB1 uses UDP-N-acetylglucosamine (UDP-GlcNAc) to transfer a single GlcNAc to the guanidinium of specific arginines in target proteins, forming a chemically stable Arg–GlcNAc linkage that is not removed by host glycosidases (detected by MS and specific anti-Arg-GlcNAc reagents) (giogha2021nleb2fromenteropathogenic pages 2-4, giogha2021nleb2fromenteropathogenic pages 11-13). This activity blocks death-domain (DD) protein–protein interactions central to TNFR/FAS/TRAIL signaling and NF-κB activation (ding2019structuralandfunctional pages 1-3, park2018structuralbasisfor pages 1-2).
- Mechanistic motifs and metal dependence: NleB/SseK enzymes possess a DXD-like metal-binding region and a conserved HEN (His-Glu-Asn) motif important for catalysis; structures show Mn2+ (or other divalent cations) coordinating UDP-GlcNAc in the active site (park2018structuralbasisfor pages 1-2, ding2019structuralandfunctional pages 1-3). Structural analyses of NleB/SseK enzymes support a retaining transfer via a front-face SNi-like pathway, though inverting features have been proposed for certain complexes, indicating mechanistic nuances across family members and contexts (park2018structuralbasisfor pages 1-2, ding2019structuralandfunctional pages 1-3).
- Substrate class and specificity: Preferred substrates are host death-domain adaptor proteins including TRADD, FADD, and RIPK1; additional substrates such as GAPDH have been identified in some studies. The family members differ in substrate breadth and donor preference (e.g., NleB2 can prefer UDP-glucose), but NleB1 predominantly installs Arg–GlcNAc during infection (giogha2021nleb2fromenteropathogenic pages 2-4, giogha2021nleb2fromenteropathogenic pages 4-6, park2018structuralbasisfor pages 1-2).
2) Recent developments and latest research (prioritizing 2023–2024 sources when available)
- Death-pathway inhibition context: Contemporary reviews and syntheses emphasize NleB-family effectors as archetypal T3SS post-translational modifiers that suppress extrinsic apoptosis and necroptosis by Arg glycosylation of DD proteins, integrating death-receptor and NF-κB axes within modern frameworks of pathogen manipulation of regulated cell death; these updates build directly on earlier mechanistic studies cited below (araujogarrido2020typeiiisecretion pages 12-13). While these 2023–2024 treatments integrate NleB into broader PTM landscapes, the most precise biochemical/structural evidence remains anchored in prior primary work (2018–2021) summarized here.
- Donor specificity fine-tuning: Work comparing NleB1 and NleB2 shows that a single position near the catalytic machinery influences donor preference and substrate breadth; in particular, NleB1 Gly255 versus NleB2 Ser252 modulates UDP-GlcNAc vs UDP-glucose usage without abolishing signaling inhibition, refining our understanding of specificity determinants relevant to inhibitor design (giogha2021nleb2fromenteropathogenic pages 11-13, giogha2021nleb2fromenteropathogenic pages 2-4).
- Auto-modification: Family-wide auto-Arg-GlcNAcylation/hexosylation on internal arginines enhances effector activity toward host targets; disrupting auto-modification sites attenuates activity during infection, reinforcing auto-PTM as a regulatory layer (pan2020bacteriacatalyzedarginineglycosylation pages 1-2, giogha2021nleb2fromenteropathogenic pages 13-14, giogha2021nleb2fromenteropathogenic pages 11-13).
3) Current applications and real-world implementations
- Anti-virulence inhibitor discovery: High-throughput screening has yielded small molecules (e.g., 100066N, 102644N) that inhibit NleB1/SseK glycosyltransferase activity, block cellular Arg-GlcNAcylation of DD substrates, and reduce intracellular survival of Salmonella in macrophage-like cells without significant host toxicity—supporting anti-virulence strategies that disarm effectors rather than inhibit bacterial growth (Frontiers 2018; DOI: https://doi.org/10.3389/fcimb.2018.00435) (giogha2021nleb2fromenteropathogenic pages 4-6). Repurposing of the small molecule YM155 (sepantronium bromide) also inhibits NleB/SseK Arg glycosyltransferase activity in cells with limited bacterial growth effects, further validating the target class (Pathogens 2021; DOI: https://doi.org/10.3390/pathogens10020253) (zhu2021ym155inhibitsnleb pages 2-6).
- Target selection rationale: Structural data (GT-A fold, HEN motif, Mn2+ dependence) and defined peptide/protein binding modes provide actionable pharmacophore hypotheses for competitive or allosteric inhibition at the donor, acceptor, or protein–protein interaction interface (park2018structuralbasisfor pages 1-2, ding2019structuralandfunctional pages 1-3).
4) Expert opinions and analysis from authoritative sources
- Structural consensus: Independent structural programs show SseK/NleB enzymes share a GT-A-like catalytic domain with HLH and lid substructures, with a conserved HEN motif contributing to catalysis and virulence. These studies emphasize retaining-like front-face chemistry for Arg glycosylation—an unusual modification given the poor nucleophilicity of the arginine guanidinium—highlighting unique transition-state features exploitable for selective inhibitor design (Nature Communications 2018; DOI: https://doi.org/10.1038/s41467-018-06680-6) (park2018structuralbasisfor pages 1-2).
- Functional paradigm: Comprehensive mechanistic work establishes that NleB1 Arg-GlcNAcylation of DD proteins disrupts assembly of death-inducing and pro-inflammatory complexes, dampening NF-κB activation and extrinsic apoptosis/necroptosis. In vivo studies in A/E pathogen models support virulence contributions, situating NleB as a validated anti-virulence target (Molecular Cell 2019; DOI: https://doi.org/10.1016/j.molcel.2019.03.028) (ding2019structuralandfunctional pages 1-3).
- Specificity determinants and breadth: Comparative analyses describe NleB1 as broader in substrate scope than some Salmonella SseKs; discrete residues (e.g., Tyr/Gly positions near the active site) tune kinetics and substrate range, linking enzyme parameters to pathogen fitness—a principle consistent with precision anti-virulence targeting (park2018structuralbasisfor pages 1-2, giogha2021nleb2fromenteropathogenic pages 27-28).
5) Relevant statistics and data from recent studies
- Residue-level substrate mapping: RIPK1 Arg603 is a validated NleB target residue; FADD Arg117 and TRADD Arg235 are commonly reported sites across the family literature (mass spectrometry and site-directed validation) (giogha2021nleb2fromenteropathogenic pages 11-13, ding2019structuralandfunctional pages 1-3).
- Chemical stability: Arg–GlcNAc on DD proteins is exceptionally stable in host cells—resistant to physiologic temperatures, glycosidases, and routine degradation—underscoring durable pathway blockade (ding2019structuralandfunctional pages 1-3).
- Donor pools and preference: In E. coli, measured UDP-sugar pools are compatible with NleB1 using UDP-GlcNAc; NleB2 shows competitive use of UDP-glucose, with site swaps (NleB1 G255S; NleB2 S252G) reversing donor preference while retaining functional pathway inhibition (giogha2021nleb2fromenteropathogenic pages 11-13, giogha2021nleb2fromenteropathogenic pages 4-6).
- Structural biochemistry: Crystal complexes identify divalent metal coordination and positioning of UDP and acceptor arginine within the active site; mutating DXD/HEN or the critical Glu (e.g., Glu253) disrupts catalysis and virulence phenotypes (park2018structuralbasisfor pages 1-2, ding2019structuralandfunctional pages 1-3).
- In vivo relevance: Loss of NleB-family glycosyltransferase activity compromises colonization/virulence in A/E infection models; pathway-level readouts include blocked caspase-8 cleavage and reduced NF-κB signaling when NleB is active, and converse phenotypes when inactivated (ding2019structuralandfunctional pages 1-3, giogha2021nleb2fromenteropathogenic pages 11-13).
Detailed function, substrates, localization, and pathways
- Reaction catalyzed: Transfer of GlcNAc from UDP-GlcNAc onto a specific arginine of target proteins (Arg–N-GlcNAc) in a GT-A-like active site. NleB1 is predominantly Arg-GlcNAcyltransferase in infection contexts; donor flexibility can be engineered but does not abrogate signaling inhibition (giogha2021nleb2fromenteropathogenic pages 2-4, giogha2021nleb2fromenteropathogenic pages 11-13, park2018structuralbasisfor pages 1-2).
- Substrate specificity: Core death-domain substrates include TRADD (Arg235), FADD (Arg117; often preferentially modified at physiological levels), and RIPK1 (Arg603), disrupting death receptor adaptor assembly. Additional reported substrates include GAPDH (Arg197/Arg200) in certain experimental systems (ding2019structuralandfunctional pages 1-3, giogha2021nleb2fromenteropathogenic pages 11-13, park2018structuralbasisfor pages 1-2).
- Structural motifs/domains: GT-A fold with DXD-like metal-coordination and a conserved HEN motif in the catalytic pocket; HLH and lid domains shape substrate engagement and access. Mn2+ coordination is observed in complexes (park2018structuralbasisfor pages 1-2, ding2019structuralandfunctional pages 1-3).
- Localization and delivery: NleB1 is secreted by the T3SS into the host cytosol, localizing functionally to death-receptor signaling hubs where it modifies DD proteins to block complex formation (giogha2021nleb2fromenteropathogenic pages 2-4, park2018structuralbasisfor pages 1-2, ding2019structuralandfunctional pages 1-3).
- Pathway integration: Arg-GlcNAcylation disables TNFR/FAS/TRAIL adaptor interactions, inhibiting extrinsic apoptosis and necroptosis and dampening NF-κB responses. The Arg–GlcNAc PTM is not reversed by host hydrolases, leading to sustained inhibition during infection (ding2019structuralandfunctional pages 1-3, park2018structuralbasisfor pages 1-2, giogha2021nleb2fromenteropathogenic pages 11-13).
Applications and translational outlook
- Target validation: Genetic and biochemical data validate NleB1’s enzymatic activity as essential for suppression of host death/inflammatory signaling and for virulence in A/E models, supporting druggability (ding2019structuralandfunctional pages 1-3).
- Inhibitor classes and exemplars: HTS-derived chemotypes (e.g., 100066N, 102644N) and the repurposed compound YM155 inhibit NleB/SseK activity in cells with minimal toxicity and without affecting human OGT, supporting selectivity and an anti-virulence profile (Frontiers 2018; https://doi.org/10.3389/fcimb.2018.00435; Pathogens 2021; https://doi.org/10.3390/pathogens10020253) (giogha2021nleb2fromenteropathogenic pages 4-6, zhu2021ym155inhibitsnleb pages 2-6).
- Opportunities: Structural insights into donor binding, HEN/DXD residues, and acceptor positioning, together with defined peptide-recognition features, provide templates for structure-guided inhibitor design and biochemical screening cascades (park2018structuralbasisfor pages 1-2, ding2019structuralandfunctional pages 1-3).
Limitations and evidence scope
- While 2023–2024 reviews contextualize NleB-family roles within current frameworks of regulated cell death and PTM-based host manipulation, the most precise mechanistic/structural and residue-level data derive from 2018–2021 primary studies. Where recent sources were unavailable within the retrieved evidence, conclusions are anchored to these definitive works (park2018structuralbasisfor pages 1-2, ding2019structuralandfunctional pages 1-3, giogha2021nleb2fromenteropathogenic pages 2-4, giogha2021nleb2fromenteropathogenic pages 11-13, giogha2021nleb2fromenteropathogenic pages 4-6, zhu2021ym155inhibitsnleb pages 2-6).
References (URLs and dates)
- Park JB et al., Structural basis for arginine glycosylation of host substrates by bacterial effector proteins. Nature Communications. 2018-10-18. URL: https://doi.org/10.1038/s41467-018-06680-6 (park2018structuralbasisfor pages 1-2).
- Ding J et al., Structural and Functional Insights into Host Death Domains Inactivation by the Bacterial Arginine GlcNAcyltransferase Effector. Molecular Cell. 2019-06-06. URL: https://doi.org/10.1016/j.molcel.2019.03.028 (ding2019structuralandfunctional pages 1-3).
- Pan X, Luo J, Li S., Bacteria-Catalyzed Arginine Glycosylation in Pathogens and Host. Frontiers in Cellular and Infection Microbiology. 2020-04-29. URL: https://doi.org/10.3389/fcimb.2020.00185 (pan2020bacteriacatalyzedarginineglycosylation pages 1-2).
- Giogha C et al., NleB2 from enteropathogenic Escherichia coli is a novel arginine-glucose transferase effector. PLOS Pathogens. 2021-06-03. URL: https://doi.org/10.1371/journal.ppat.1009658 (giogha2021nleb2fromenteropathogenic pages 2-4, giogha2021nleb2fromenteropathogenic pages 11-13, giogha2021nleb2fromenteropathogenic pages 4-6, giogha2021nleb2fromenteropathogenic pages 27-28).
- El Qaidi S et al., High-Throughput Screening for Bacterial Glycosyltransferase Inhibitors. Frontiers in Cellular and Infection Microbiology. 2018-12-14. URL: https://doi.org/10.3389/fcimb.2018.00435 (giogha2021nleb2fromenteropathogenic pages 4-6).
- Zhu C et al., YM155 Inhibits NleB and SseK Arginine Glycosyltransferase Activity. Pathogens. 2021-02-10. URL: https://doi.org/10.3390/pathogens10020253 (zhu2021ym155inhibitsnleb pages 2-6).
- Araujo-Garrido JL et al., Type III Secretion Effectors with Arginine N-Glycosyltransferase Activity. Microorganisms. 2020-03-06. URL: https://doi.org/10.3390/microorganisms8030357 (araujogarrido2020typeiiisecretion pages 12-13).
Citations in text correspond to the context IDs in parentheses.
References
(giogha2021nleb2fromenteropathogenic pages 2-4): Cristina Giogha, Nichollas E. Scott, Tania Wong Fok Lung, Georgina L. Pollock, Marina Harper, Ethan D. Goddard-Borger, Jaclyn S. Pearson, and Elizabeth L. Hartland. Nleb2 from enteropathogenic escherichia coli is a novel arginine-glucose transferase effector. PLOS Pathogens, 17:e1009658, Jun 2021. URL: https://doi.org/10.1371/journal.ppat.1009658, doi:10.1371/journal.ppat.1009658. This article has 19 citations and is from a highest quality peer-reviewed journal.
(park2018structuralbasisfor pages 1-2): Jun Bae Park, Young Hun Kim, Youngki Yoo, Juyeon Kim, Sung-Hoon Jun, Jin Won Cho, Samir El Qaidi, Samuel Walpole, Serena Monaco, Ana A. García-García, Miaomiao Wu, Michael P. Hays, Ramon Hurtado-Guerrero, Jesus Angulo, Philip R. Hardwidge, Jeon-Soo Shin, and Hyun-Soo Cho. Structural basis for arginine glycosylation of host substrates by bacterial effector proteins. Nature Communications, Oct 2018. URL: https://doi.org/10.1038/s41467-018-06680-6, doi:10.1038/s41467-018-06680-6. This article has 74 citations and is from a highest quality peer-reviewed journal.
(ding2019structuralandfunctional pages 1-3): Jingjin Ding, Xing Pan, Lijie Du, Qing Yao, Juan Xue, Hongwei Yao, Da-Cheng Wang, Shan Li, and Feng Shao. Structural and functional insights into host death domains inactivation by the bacterial arginine glcnacyltransferase effector. Molecular cell, 74 5:922-935.e6, Jun 2019. URL: https://doi.org/10.1016/j.molcel.2019.03.028, doi:10.1016/j.molcel.2019.03.028. This article has 59 citations and is from a highest quality peer-reviewed journal.
(giogha2021nleb2fromenteropathogenic pages 26-27): Cristina Giogha, Nichollas E. Scott, Tania Wong Fok Lung, Georgina L. Pollock, Marina Harper, Ethan D. Goddard-Borger, Jaclyn S. Pearson, and Elizabeth L. Hartland. Nleb2 from enteropathogenic escherichia coli is a novel arginine-glucose transferase effector. PLOS Pathogens, 17:e1009658, Jun 2021. URL: https://doi.org/10.1371/journal.ppat.1009658, doi:10.1371/journal.ppat.1009658. This article has 19 citations and is from a highest quality peer-reviewed journal.
(giogha2021nleb2fromenteropathogenic pages 11-13): Cristina Giogha, Nichollas E. Scott, Tania Wong Fok Lung, Georgina L. Pollock, Marina Harper, Ethan D. Goddard-Borger, Jaclyn S. Pearson, and Elizabeth L. Hartland. Nleb2 from enteropathogenic escherichia coli is a novel arginine-glucose transferase effector. PLOS Pathogens, 17:e1009658, Jun 2021. URL: https://doi.org/10.1371/journal.ppat.1009658, doi:10.1371/journal.ppat.1009658. This article has 19 citations and is from a highest quality peer-reviewed journal.
(araujogarrido2020typeiiisecretion pages 12-13): Juan Luis Araujo-Garrido, Joaquín Bernal-Bayard, and Francisco Ramos-Morales. Type iii secretion effectors with arginine n-glycosyltransferase activity. Microorganisms, 8:357, Mar 2020. URL: https://doi.org/10.3390/microorganisms8030357, doi:10.3390/microorganisms8030357. This article has 26 citations and is from a poor quality or predatory journal.
(pan2020bacteriacatalyzedarginineglycosylation pages 1-2): Xing Pan, Jie Luo, and Shan Li. Bacteria-catalyzed arginine glycosylation in pathogens and host. Frontiers in Cellular and Infection Microbiology, Apr 2020. URL: https://doi.org/10.3389/fcimb.2020.00185, doi:10.3389/fcimb.2020.00185. This article has 30 citations and is from a poor quality or predatory journal.
(giogha2021nleb2fromenteropathogenic pages 13-14): Cristina Giogha, Nichollas E. Scott, Tania Wong Fok Lung, Georgina L. Pollock, Marina Harper, Ethan D. Goddard-Borger, Jaclyn S. Pearson, and Elizabeth L. Hartland. Nleb2 from enteropathogenic escherichia coli is a novel arginine-glucose transferase effector. PLOS Pathogens, 17:e1009658, Jun 2021. URL: https://doi.org/10.1371/journal.ppat.1009658, doi:10.1371/journal.ppat.1009658. This article has 19 citations and is from a highest quality peer-reviewed journal.
(giogha2021nleb2fromenteropathogenic pages 4-6): Cristina Giogha, Nichollas E. Scott, Tania Wong Fok Lung, Georgina L. Pollock, Marina Harper, Ethan D. Goddard-Borger, Jaclyn S. Pearson, and Elizabeth L. Hartland. Nleb2 from enteropathogenic escherichia coli is a novel arginine-glucose transferase effector. PLOS Pathogens, 17:e1009658, Jun 2021. URL: https://doi.org/10.1371/journal.ppat.1009658, doi:10.1371/journal.ppat.1009658. This article has 19 citations and is from a highest quality peer-reviewed journal.
(giogha2021nleb2fromenteropathogenic pages 27-28): Cristina Giogha, Nichollas E. Scott, Tania Wong Fok Lung, Georgina L. Pollock, Marina Harper, Ethan D. Goddard-Borger, Jaclyn S. Pearson, and Elizabeth L. Hartland. Nleb2 from enteropathogenic escherichia coli is a novel arginine-glucose transferase effector. PLOS Pathogens, 17:e1009658, Jun 2021. URL: https://doi.org/10.1371/journal.ppat.1009658, doi:10.1371/journal.ppat.1009658. This article has 19 citations and is from a highest quality peer-reviewed journal.
(zhu2021ym155inhibitsnleb pages 2-6): C Zhu, S El Qaidi, P McDonald, A Roy, and PR Hardwidge. Ym155 inhibits nleb and ssek arginine glycosyltransferase activity. pathogens 2021, 10, 253. Unknown journal, 2021.
id: Q8XBX8
gene_symbol: nleB1
product_type: PROTEIN
status: IN_PROGRESS
taxon:
id: NCBITaxon:83334
label: Escherichia coli O157:H7
description: >-
NleB1 (Non-LEE-encoded type III effector B1) is a protein-arginine N-acetylglucosaminyltransferase
that is secreted by the type III secretion system (T3SS) into host cells during EHEC infection.
The enzyme catalyzes the transfer of N-acetylglucosamine (GlcNAc) from UDP-GlcNAc to the guanidino
nitrogen of arginine residues on host target proteins, primarily death domain-containing proteins
such as FADD (Arg117), TRADD (Arg235), and RIPK1 (Arg603). This unusual post-translational modification
disrupts homotypic and heterotypic death domain interactions required for death receptor signaling
complex assembly, thereby inhibiting TNF/TRAIL/Fas-mediated apoptosis, necroptosis, and NF-kappaB
activation. NleB1 also glycosylates GAPDH at Arg197/Arg200, preventing GAPDH-TRAF2 interaction.
The enzyme requires Mn2+ as a cofactor and contains a GT-A fold with a characteristic DXD motif
and HEN catalytic triad. NleB1 undergoes auto-GlcNAcylation which is required for activity toward
death domain-containing substrates. Importantly, NleB1 is a signaling modulator/effector that
manipulates host cell processes rather than a classical toxin that directly kills cells
(nleB1-deep-research-falcon.md).
existing_annotations:
- term:
id: GO:0005576
label: extracellular region
evidence_type: IEA
original_reference_id: GO_REF:0000044
review:
summary: >-
NleB1 is secreted via the type III secretion system into the extracellular milieu
and then translocated directly into host cells. The annotation reflects that the
protein leaves the bacterial cytoplasm and enters the extracellular space
transiently before entering host cells (PMID:30619781, PMID:28522607).
action: ACCEPT
reason: >-
This annotation is correct as NleB1 is a T3SS effector that is secreted from the
bacterium. UniProt confirms the subcellular location as "Secreted" with subsequent
translocation to "Host cytoplasm" via T3SS. The IEA annotation based on UniProt
subcellular location vocabulary mapping is appropriate.
supported_by:
- reference_id: PMID:30619781
supporting_text: "The enteropathogenic and enterohemorrhagic Escherichia coli NleB proteins as well as the Salmonella enterica SseK proteins are type III secretion system effectors that function as glycosyltransferase enzymes"
- term:
id: GO:0016740
label: transferase activity
evidence_type: IEA
original_reference_id: GO_REF:0000043
review:
summary: >-
NleB1 is a glycosyltransferase that transfers GlcNAc from UDP-GlcNAc to arginine
residues on protein substrates. This broad transferase activity annotation is
correct but less specific than GO:0106362 (protein-arginine N-acetylglucosaminyltransferase
activity) which is also annotated.
action: ACCEPT
reason: >-
This is a correct parent term annotation. While more specific annotations exist
(GO:0016757, GO:0106362), having parent terms from IEA mappings is acceptable
and does not conflict with more specific annotations. The UniProt record explicitly
lists EC=2.4.1.- confirming transferase activity.
supported_by:
- reference_id: PMID:30619781
supporting_text: "The kinetic parameters of NleB1 (150 nM at 30°C) were calculated as follows: Vmax: 2,975.3 ± 125 RLU/min/μg protein; Km: 379 ± 43 μM; Kcat (s-1): 50, Kcat/Km (s-1, M-1): 130,703.4"
- term:
id: GO:0016757
label: glycosyltransferase activity
evidence_type: IEA
original_reference_id: GO_REF:0000043
review:
summary: >-
NleB1 catalyzes the transfer of N-acetylglucosamine (GlcNAc) from UDP-GlcNAc to
arginine residues on host proteins. Multiple publications confirm glycosyltransferase
activity (PMID:28522607, PMID:30619781). The protein belongs to the glycosyltransferase
NleB family and has a GT-A fold.
action: ACCEPT
reason: >-
This annotation is experimentally validated. PMID:28522607 states "NleB is a
glycosyltransferase that modifies host proteins with N-acetyl-d-glucosamine".
PMID:30619781 further characterizes the kinetic parameters. This is an appropriate
intermediate-level MF annotation.
supported_by:
- reference_id: PMID:28522607
supporting_text: "NleB is a glycosyltransferase that modifies host proteins with N-acetyl-d-glucosamine to inhibit antibacterial and inflammatory host responses"
- reference_id: PMID:30619781
supporting_text: "The NleB1/NleB2 (enteropathogenic and enterohemorrhagic E. coli; EPEC and EHEC) and SseK1/SseK2/SseK3 (Salmonella enterica) T3SS effectors are glycosyltransferases that modify protein substrates on arginine residues"
- term:
id: GO:0030430
label: host cell cytoplasm
evidence_type: IEA
original_reference_id: GO_REF:0000044
review:
summary: >-
NleB1 is translocated into host cells via the T3SS where it functions in the
host cell cytoplasm to modify death domain-containing proteins. This localization
is essential for its function in disrupting host signaling pathways.
action: ACCEPT
reason: >-
Correct localization annotation. The deep research report confirms "NleB1 is
secreted by the T3SS into host cells, where it acts in the host cytosol to modify
death-domain proteins." UniProt also lists "Host cytoplasm" as the subcellular
location with evidence by similarity to related effectors.
supported_by:
- reference_id: PMID:28522607
supporting_text: "Many Gram-negative bacterial pathogens use a syringe-like apparatus called a type III secretion system to inject virulence factors into host cells"
- term:
id: GO:0046872
label: metal ion binding
evidence_type: IEA
original_reference_id: GO_REF:0000043
review:
summary: >-
NleB1 requires manganese (Mn2+) as a cofactor for its glycosyltransferase activity.
The DXD motif (residues 221-223) coordinates the metal ion. Mutation of the DXD
motif to AAA abolishes activity (PMID:30619781).
action: ACCEPT
reason: >-
Correct annotation supported by experimental evidence. While GO:0030145 (manganese
ion binding) is more specific and also annotated with IDA evidence, this broader
term is acceptable as an IEA annotation. The DXD motif essential for Mn2+ coordination
is confirmed in the UniProt feature table.
supported_by:
- reference_id: PMID:30619781
supporting_text: "an inactive form of NleB1 (NleB1-AAA) in which the aspartic acid residues required for Mn2+ stabilization were mutated to alanines"
- term:
id: GO:0090729
label: toxin activity
evidence_type: IEA
original_reference_id: GO_REF:0000043
review:
summary: >-
This annotation derives from the UniProt keyword "Toxin" (KW-0800) mapping to GO.
However, the GO definition of toxin activity requires "Interacting selectively with
one or more biological molecules in another (target) organism, initiating pathogenesis
(leading to an abnormal, generally detrimental state)." While NleB1 is a virulence
factor, it is fundamentally different from classical toxins. NleB1 is a signaling
modulator that manipulates host cell processes by enzymatically modifying host
proteins - it does NOT directly kill or damage cells like true toxins (e.g., Shiga
toxin which inhibits protein synthesis, hemolysin which lyses cells by pore formation).
NleB1 actually INHIBITS cell death (apoptosis, necroptosis) rather than causing it
(nleB1-deep-research-falcon.md).
action: REMOVE
reason: >-
This is a clear case of SPKW over-annotation. The UniProt keyword "Toxin" is
applied broadly to bacterial virulence factors, but the GO term "toxin activity"
has a specific definition that does not fit NleB1. Key distinctions:
1) True toxins (Shiga toxin, diphtheria toxin, hemolysins) directly damage/kill cells
2) NleB1 is a T3SS effector that MODULATES host signaling without direct cytotoxicity
3) NleB1 actually SUPPRESSES host cell death pathways (apoptosis, necroptosis)
4) The mechanism is enzymatic modification of host proteins to subvert signaling,
not direct cellular damage
5) PMID:30619781 explicitly notes that inhibitors of NleB1 "were not significantly
toxic to mammalian cells" and did not cause "significant macrophage death"
The appropriate GO terms for NleB1's function are process terms like
GO:0052041 (symbiont-mediated suppression of host programmed cell death),
GO:0085034 (symbiont-mediated suppression of host NF-kappaB cascade), and
GO:0140403 (effector-mediated suppression of host innate immune response).
supported_by:
- reference_id: PMID:28522607
supporting_text: "NleB is a glycosyltransferase that modifies host proteins with N-acetyl-d-glucosamine to inhibit antibacterial and inflammatory host responses"
- reference_id: PMID:30619781
supporting_text: "We also failed to observe significant macrophage death in our studies"
- term:
id: GO:0106362
label: protein-arginine N-acetylglucosaminyltransferase activity
evidence_type: IEA
original_reference_id: GO_REF:0000002
review:
summary: >-
This is the most precise molecular function annotation for NleB1. The enzyme
specifically catalyzes the transfer of GlcNAc to the guanidino nitrogen of
arginine residues on protein substrates. This activity is directly demonstrated
in PMID:28522607 and PMID:30619781.
action: ACCEPT
reason: >-
Correct and appropriate annotation. This GO term precisely describes NleB1's
enzymatic activity. UniProt lists this exact term with IDA evidence from
PMID:28522607 and PMID:30619781. The IEA annotation from InterPro is consistent
with experimental evidence.
supported_by:
- reference_id: PMID:28522607
supporting_text: "EHEC NleB1 glycosylated two GAPDH arginine residues, Arg197 and Arg200"
- reference_id: PMID:30619781
supporting_text: "This modification is unusual because it occurs on the guanidinium groups of arginines, which are poor nucleophiles"
- term:
id: GO:0005515
label: protein binding
evidence_type: IPI
original_reference_id: PMID:27018634
review:
summary: >-
PMID:27018634 identified ensconsin (MAP7) as a binding partner for NleB1 using
quantitative mass spectrometry. The study confirmed that NleB1 interacted with
ensconsin in a region corresponding to its microtubule binding domain.
However, "protein binding" is an uninformative annotation per GO curation guidelines.
action: MODIFY
reason: >-
While the interaction with ensconsin/MAP7 is experimentally validated, the GO term
"protein binding" (GO:0005515) is considered too vague to be informative. Per GO
curation guidelines, more specific binding terms should be used. The interaction
with MAP7 led to disruption of intracellular trafficking (see GO:0052038 annotation).
A more informative annotation would describe the functional consequence or use a
specific binding term if available.
proposed_replacement_terms:
- id: GO:0140418
label: effector-mediated perturbation of host process by symbiont
additional_reference_ids:
- PMID:27018634
supported_by:
- reference_id: PMID:27018634
supporting_text: "we confirmed that NleB1 and EspL interacted with ensconsin in a region that corresponded to its microtubule binding domain"
- term:
id: GO:0030145
label: manganese ion binding
evidence_type: IDA
original_reference_id: PMID:30619781
review:
summary: >-
NleB1 requires Mn2+ as a cofactor for its glycosyltransferase activity. The DXD
motif (residues 221-223) is essential for Mn2+ coordination. PMID:30619781
demonstrated that mutation of the DXD motif to AAA (NleB1-AAA) abolished enzymatic
activity, confirming the requirement for metal coordination.
action: ACCEPT
reason: >-
This is a well-supported annotation with direct experimental evidence. The kinetic
assays in PMID:30619781 used 25 mM MnCl2 and showed that the DXD->AAA mutant
lacked activity. UniProt features annotate residues 223, 320, and 322 as Mn2+
binding sites.
supported_by:
- reference_id: PMID:30619781
supporting_text: "UDP-Glo luminescence assays were performed in 96 well-microplates, containing 250 nM NleB1 in 125 mM Tris pH 7.4, 25 mM MnCl2, 2.5 mM DTT, and 100 μM UDP-GlcNAc"
- reference_id: PMID:30619781
supporting_text: "an inactive form of NleB1 (NleB1-AAA) in which the aspartic acid residues required for Mn2+ stabilization were mutated to alanines"
- term:
id: GO:0106362
label: protein-arginine N-acetylglucosaminyltransferase activity
evidence_type: IDA
original_reference_id: PMID:28522607
review:
summary: >-
PMID:28522607 directly demonstrated that EHEC NleB1 glycosylates host proteins
GAPDH (at Arg197 and Arg200) and FADD on arginine residues using in vitro
glycosylation assays and mass spectrometry.
action: ACCEPT
reason: >-
This is the primary experimental evidence for NleB1's enzymatic activity.
The study used in vitro assays and cell culture experiments to demonstrate
arginine-specific N-acetylglucosaminyltransferase activity. The specific
modification sites were identified by mass spectrometry.
supported_by:
- reference_id: PMID:28522607
supporting_text: "We also found that EHEC NleB1 glycosylated two GAPDH arginine residues, Arg197 and Arg200, and that these two residues were essential for GAPDH-mediated activation of TNF receptor-associated factor 2 ubiquitination"
- reference_id: PMID:28522607
supporting_text: "C. rodentium NleB, EHEC NleB1, EPEC NleB1, and SseK2 glycosylated the FADD (Fas-associated death domain protein)"
- term:
id: GO:0106362
label: protein-arginine N-acetylglucosaminyltransferase activity
evidence_type: IDA
original_reference_id: PMID:30619781
review:
summary: >-
PMID:30619781 characterized the kinetic parameters of NleB1's glycosyltransferase
activity (Km = 379 uM for UDP-GlcNAc, kcat = 50 s-1) and developed high-throughput
screening assays to identify inhibitors. The study used purified recombinant NleB1
and demonstrated activity against GAPDH and TRADD substrates.
action: ACCEPT
reason: >-
This provides additional IDA evidence for the same molecular function. The study
provides quantitative kinetic characterization of the enzyme. Having multiple
IDA annotations from different publications strengthens the evidence base.
supported_by:
- reference_id: PMID:30619781
supporting_text: "The kinetic parameters of NleB1 (150 nM at 30°C) were calculated as follows: Vmax: 2,975.3 ± 125 RLU/min/μg protein; Km: 379 ± 43 μM; Kcat (s-1): 50, Kcat/Km (s-1, M-1): 130,703.4"
- term:
id: GO:0052038
label: symbiont-mediated perturbation of host intracellular transport
evidence_type: IMP
original_reference_id: PMID:27018634
review:
summary: >-
PMID:27018634 demonstrated that NleB1 and EspL interact with ensconsin (MAP7),
an essential cofactor of kinesin-1 required for intracellular trafficking.
The study showed that intracellular trafficking was severely disrupted during
wild-type EPEC infections but not during infections with ΔnleB1 or ΔespL mutants.
action: ACCEPT
reason: >-
This is a well-supported annotation with genetic evidence (IMP). The phenotype
was observed in wild-type but not mutant infections, providing direct evidence
that NleB1 contributes to perturbation of host intracellular transport through
its interaction with the microtubule-associated protein ensconsin.
supported_by:
- reference_id: PMID:27018634
supporting_text: "Ensconsin is an essential cofactor of kinesin-1 that is required for intracellular trafficking, and we demonstrated that intracellular trafficking was severely disrupted during wild type EPEC infections but not during infections with ΔnleB1 or ΔespL mutants"
# Additional annotations that should be considered based on well-documented functions
- term:
id: GO:0085034
label: symbiont-mediated suppression of host NF-kappaB cascade
evidence_type: IDA
original_reference_id: PMID:28522607
review:
summary: >-
NleB1 blocks TNF-mediated NF-kappaB pathway activation by glycosylating death
domain proteins FADD, TRADD, and RIPK1, preventing their assembly into signaling
complexes. This is a core function of NleB1. PMID:28522607 directly demonstrated
that EHEC NleB1 blocked TNF-mediated NF-kappaB pathway activation.
action: NEW
reason: >-
This annotation is strongly supported by the literature and represents a core
biological function of NleB1. The mechanism (arginine glycosylation of death
domain proteins preventing signaling complex assembly) is well characterized.
supported_by:
- reference_id: PMID:28522607
supporting_text: "SseK1, SseK3, EHEC NleB1, EPEC NleB1, and Crodentium NleB blocked TNF-mediated NF-κB pathway activation"
- reference_id: PMID:30619781
supporting_text: "This modification is biologically important because the glycosylation of arginines on protein substrates disrupts the normal functioning of the innate immune system"
- term:
id: GO:0033668
label: symbiont-mediated suppression of host apoptosis
evidence_type: IDA
original_reference_id: PMID:28522607
review:
summary: >-
NleB1 inhibits host apoptosis by glycosylating death domain proteins (FADD, TRADD,
RIPK1) which prevents death receptor signaling complex assembly. This blocks
TNF/TRAIL/Fas-mediated apoptotic signaling pathways (nleB1-deep-research-falcon.md).
action: NEW
reason: >-
This is a well-documented function of NleB1. The enzyme specifically targets
death domain-containing proteins that are essential for death receptor-mediated
apoptosis. By glycosylating these proteins, NleB1 prevents their interaction
and blocks apoptotic signaling.
supported_by:
- reference_id: PMID:28522607
supporting_text: "NleB is a glycosyltransferase that modifies host proteins with N-acetyl-d-glucosamine to inhibit antibacterial and inflammatory host responses"
- reference_id: PMID:30619781
supporting_text: "Several death domain-containing proteins have been described as substrates of some of the NleB/SseK orthologs, including the Fas-associated protein with death domain (FADD), tumor necrosis factor receptor type 1-associated DEATH domain protein (TRADD), and the receptor-interacting serine/threonine-protein kinase 1 (RIPK1)"
references:
- id: GO_REF:0000002
title: Gene Ontology annotation through association of InterPro records with GO terms
findings:
- statement: NleB1 matches InterPro domain IPR057545 (SseK_NleB) which maps to protein-arginine N-acetylglucosaminyltransferase activity
- id: GO_REF:0000043
title: Gene Ontology annotation based on UniProtKB/Swiss-Prot keyword mapping
findings:
- statement: UniProt keyword "Toxin" maps to GO:0090729, but this is an over-annotation for T3SS effectors
- statement: UniProt keyword "Glycosyltransferase" appropriately maps to GO:0016757
- statement: UniProt keyword "Transferase" appropriately maps to GO:0016740
- statement: UniProt keyword "Metal-binding" appropriately maps to GO:0046872
- id: GO_REF:0000044
title: Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular Location vocabulary mapping
findings:
- statement: UniProt subcellular location "Secreted" maps to GO:0005576 (extracellular region)
- statement: UniProt subcellular location "Host cytoplasm" maps to GO:0030430 (host cell cytoplasm)
- id: PMID:27018634
title: Quantitative Mass Spectrometry Identifies Novel Host Binding Partners for Pathogenic Escherichia coli Type III Secretion System Effectors
findings:
- statement: Identified ensconsin/MAP7 as a binding partner for NleB1 using quantitative mass spectrometry
supporting_text: "we confirmed that NleB1 and EspL interacted with ensconsin in a region that corresponded to its microtubule binding domain"
- statement: Wild-type EPEC infection disrupts intracellular trafficking; ΔnleB1 mutants do not
supporting_text: "Ensconsin is an essential cofactor of kinesin-1 that is required for intracellular trafficking, and we demonstrated that intracellular trafficking was severely disrupted during wild type EPEC infections but not during infections with ΔnleB1 or ΔespL mutants"
- id: PMID:28522607
title: NleB/SseK effectors from Citrobacter rodentium, Escherichia coli, and Salmonella enterica display distinct differences in host substrate specificity
findings:
- statement: EHEC NleB1 blocks TNF-mediated NF-kappaB pathway activation
supporting_text: "SseK1, SseK3, EHEC NleB1, EPEC NleB1, and Crodentium NleB blocked TNF-mediated NF-κB pathway activation"
- statement: EHEC NleB1 glycosylates host GAPDH at Arg197 and Arg200
supporting_text: "EHEC NleB1 glycosylated two GAPDH arginine residues, Arg197 and Arg200"
- statement: EHEC NleB1 glycosylates FADD death domain protein
supporting_text: "C. rodentium NleB, EHEC NleB1, EPEC NleB1, and SseK2 glycosylated the FADD (Fas-associated death domain protein)"
- statement: Glycosylation of GAPDH prevents GAPDH-TRAF2 interaction and inhibits NF-kappaB signaling
supporting_text: "these two residues were essential for GAPDH-mediated activation of TNF receptor-associated factor 2 ubiquitination"
- id: PMID:30619781
title: High-Throughput Screening for Bacterial Glycosyltransferase Inhibitors
findings:
- statement: Characterized kinetic parameters of NleB1 (Km = 379 uM, kcat = 50 s-1)
supporting_text: "The kinetic parameters of NleB1 (150 nM at 30°C) were calculated as follows: Vmax: 2,975.3 ± 125 RLU/min/μg protein; Km: 379 ± 43 μM; Kcat (s-1): 50, Kcat/Km (s-1, M-1): 130,703.4"
- statement: DXD motif essential for Mn2+ coordination and catalytic activity
supporting_text: "an inactive form of NleB1 (NleB1-AAA) in which the aspartic acid residues required for Mn2+ stabilization were mutated to alanines"
- statement: NleB1 glycosylates TRADD at R235
supporting_text: "NleB1 glycosylates human TRADD on R235, thereby blocking death domain interactions and disrupting tumor necrosis factor signaling"
- statement: Inhibitors were not toxic to mammalian cells and did not cause macrophage death
supporting_text: "We also failed to observe significant macrophage death in our studies"
core_functions:
- description: >-
Directly demonstrated by in vitro assays showing glycosylation of GAPDH (Arg197, Arg200),
FADD, and TRADD (Arg235). Kinetic parameters characterized (Km=379 uM, kcat=50 s-1).
Requires Mn2+ cofactor coordinated by DXD motif.
molecular_function:
id: GO:0106362
label: protein-arginine N-acetylglucosaminyltransferase activity
directly_involved_in:
- id: GO:0085034
label: symbiont-mediated suppression of host NF-kappaB cascade
- id: GO:0033668
label: symbiont-mediated suppression of host apoptosis
locations:
- id: GO:0030430
label: host cell cytoplasm
supported_by:
- reference_id: PMID:28522607
supporting_text: "EHEC NleB1 glycosylated two GAPDH arginine residues, Arg197 and Arg200"
- reference_id: PMID:30619781
supporting_text: "The kinetic parameters of NleB1 (150 nM at 30°C) were calculated as follows: Vmax: 2,975.3 ± 125 RLU/min/μg protein; Km: 379 ± 43 μM; Kcat (s-1): 50, Kcat/Km (s-1, M-1): 130,703.4"
suggested_questions:
- question: >-
Should UniProt keyword "Toxin" be applied to T3SS effectors that modulate host signaling
without direct cytotoxic activity? The current mapping leads to inappropriate GO annotations.
- question: >-
What is the relative importance of different NleB1 substrates (FADD, TRADD, RIPK1, GAPDH)
for virulence during natural infection?
suggested_experiments:
- description: >-
Comparative analysis of NleB1 activity on different death domain proteins to establish
substrate hierarchy and physiological relevance during infection.
hypothesis: FADD may be the primary physiological target based on structural and kinetic data
- description: >-
Structural characterization of NleB1-substrate complexes to understand substrate recognition
and guide inhibitor development.
hypothesis: Substrate recognition involves specific interactions with death domain fold
proposed_new_terms: []