Existing Annotations Review

GO Term	Evidence	Action	Reason
GO:0000781 chromosome, telomeric region	IEA GO_REF:0000108	MARK AS OVER ANNOTATED	Summary: This computational logical inference derives from PNC1 involvement in subtelomeric heterochromatin formation. The literature supports nuclear Pnc1 activity and effects on telomeric silencing, but not direct localization of Pnc1 to telomeric chromatin. Reason: Pnc1 regulates telomeric silencing by removing nicotinamide and thereby supporting Sir2 activity. A telomeric-region cellular component annotation overstates the evidence because Pnc1 is not shown to be a telomere-bound chromatin protein.
GO:0005634 nucleus	IEA GO_REF:0000044	ACCEPT	Summary: UniProt subcellular-location mapping to nucleus is consistent with direct Pnc1 localization evidence and its nuclear role in Sir2-dependent silencing. Reason: Nuclear localization is supported experimentally and is mechanistically consistent with Pnc1 effects on rDNA and telomeric silencing.
GO:0005737 cytoplasm	IEA GO_REF:0000044	ACCEPT	Summary: Automated cytoplasmic localization is consistent with direct microscopy evidence and Pnc1's general metabolic role. Reason: Pnc1 is observed in the cytoplasm and participates in cellular nicotinamide salvage.
GO:0005777 peroxisome	IEA GO_REF:0000044	ACCEPT	Summary: UniProt peroxisome mapping is consistent with direct evidence that Pnc1 concentrates in peroxisomal foci, particularly in stress contexts. Reason: Peroxisomal localization is supported by experimental localization studies and is part of Pnc1's condition-dependent subcellular distribution.
GO:0008936 nicotinamidase activity	IEA GO_REF:0000120	ACCEPT	Summary: Automated assignment of nicotinamidase activity matches Pnc1's core enzymatic activity and EC 3.5.1.19. Reason: Pnc1 catalyzes hydrolysis of nicotinamide to nicotinate and ammonia, the central molecular function of this gene product. Supporting Evidence: file:yeast/PNC1/PNC1-deep-research-falcon.md PNC1 (gene YGL037C) encodes nicotinamidase (EC 3.5.1.19)
GO:0016787 hydrolase activity	IEA GO_REF:0000043	MODIFY	Summary: Hydrolase activity is a true but generic parent of nicotinamidase activity. The specific nicotinamidase term is already present. Reason: For curation, GO:0008936 captures the actual enzyme activity and should be preferred over the broad hydrolase parent. Proposed replacements: nicotinamidase activity
GO:0019363 pyridine nucleotide biosynthetic process	IEA GO_REF:0000043	MODIFY	Summary: Pnc1 participates in pyridine nucleotide salvage by converting nicotinamide to nicotinate, but the more precise existing process term is nicotinate nucleotide salvage. Reason: Pnc1 is not a broad de novo pyridine nucleotide biosynthesis factor. It catalyzes the nicotinamide entry step into the nicotinate salvage route, which is captured by GO:0019358. Proposed replacements: nicotinate nucleotide salvage
GO:0046872 metal ion binding	IEA GO_REF:0000043	MODIFY	Summary: Metal ion binding is accurate but generic; Pnc1 specifically binds zinc as part of its nicotinamidase active site. Reason: The more informative term is zinc ion binding, already supported by curated evidence and structural/mechanistic context. Proposed replacements: zinc ion binding
GO:0008270 zinc ion binding	RCA PMID:30358795 The cellular economy of the Saccharomyces cerevisiae zinc pr...	ACCEPT	Summary: Rapid curated annotation from yeast zinc proteome analysis is consistent with the known zinc-dependent nicotinamidase active site of Pnc1. Reason: Zinc binding is mechanistically appropriate for Pnc1's catalytic function. Supporting Evidence: PMID:30358795 The cellular economy of the Saccharomyces cerevisiae zinc proteome.
GO:0031509 subtelomeric heterochromatin formation	IMP PMID:11901108 Telomeric and rDNA silencing in Saccharomyces cerevisiae are...	KEEP AS NON CORE	Summary: pnc1 deletion causes telomeric silencing defects through impaired nicotinamide clearance and reduced Sir2-dependent chromatin function. Reason: The phenotype is well supported, but it is a downstream chromatin outcome of Pnc1's core nicotinamidase/NAD salvage activity rather than an independent chromatin-binding function. Supporting Evidence: PMID:11901108 Deletion of another NAD(+) salvage pathway gene called PNC1 caused a less severe silencing defect
GO:0019358 nicotinate nucleotide salvage	IMP PMID:11901108 Telomeric and rDNA silencing in Saccharomyces cerevisiae are...	ACCEPT	Summary: Genetic evidence supports Pnc1 as a component of the NAD+ salvage pathway, converting nicotinamide to nicotinate for reuse. Reason: This is the core biological process associated with Pnc1's enzymatic activity and explains the Sir2-related phenotypes. Supporting Evidence: PMID:11901108 Pnc1p and Npt1p function together in recycling the nuclear nicotinamide
GO:0005737 cytoplasm	HDA PMID:22842922 Dissecting DNA damage response pathways by analysing protein...	ACCEPT	Summary: High-throughput direct assay evidence supports cytoplasmic localization. Reason: This is consistent with direct localization studies and Pnc1's metabolic role in nicotinamide salvage. Supporting Evidence: PMID:22842922 Dissecting DNA damage response pathways by analysing protein localization
GO:1904524 negative regulation of DNA amplification	IMP PMID:26195783 Regulation of ribosomal DNA amplification by the TOR pathway...	KEEP AS NON CORE	Summary: The rDNA amplification study reports that TOR/caloric-excess regulation reduces PNC1 expression and that PNC1 overexpression substantially reduces rDNA amplification rate. Reason: The annotation is experimentally supported, but it is an indirect regulatory consequence of Pnc1 effects on Sir2/Hst deacetylase activity and rDNA chromatin rather than the core enzymatic function. Supporting Evidence: PMID:26195783 overexpression of PNC1 substantially reduces ribosomal DNA amplification rate
GO:0000183 rDNA heterochromatin formation	IMP PMID:11901108 Telomeric and rDNA silencing in Saccharomyces cerevisiae are...	KEEP AS NON CORE	Summary: Genetic evidence supports a role for Pnc1 in rDNA silencing through the nuclear NAD+ salvage pathway and Sir2-dependent chromatin regulation. Reason: This is a well-supported downstream biological process, but Pnc1 acts through nicotinamide salvage rather than as a structural chromatin factor. Supporting Evidence: PMID:11901108 Telomeric and rDNA silencing in Saccharomyces cerevisiae are dependent on a nuclear NAD(+) salvage pathway
GO:0005634 nucleus	IDA PMID:12736687 Nicotinamide and PNC1 govern lifespan extension by calorie r...	ACCEPT	Summary: Direct localization evidence places Pnc1 in the nucleus. Reason: Nuclear localization is consistent with Pnc1's role in modulating Sir2-dependent silencing through nicotinamide clearance. Supporting Evidence: file:yeast/PNC1/PNC1-deep-research-falcon.md Pnc1-GFP shows nuclear/cytosolic distribution with discrete peroxisomal foci
GO:0005737 cytoplasm	IDA PMID:12736687 Nicotinamide and PNC1 govern lifespan extension by calorie r...	ACCEPT	Summary: Direct localization evidence places Pnc1 in the cytoplasm. Reason: Cytoplasmic localization is consistent with Pnc1's NAD salvage enzyme function. Supporting Evidence: file:yeast/PNC1/PNC1-deep-research-falcon.md Pnc1-GFP shows nuclear/cytosolic distribution with discrete peroxisomal foci
GO:0005777 peroxisome	IDA PMID:12736687 Nicotinamide and PNC1 govern lifespan extension by calorie r...	ACCEPT	Summary: Direct localization evidence supports peroxisomal Pnc1 foci and condition-dependent peroxisomal enrichment. Reason: Peroxisome localization is experimentally supported and is a recurring feature of Pnc1 stress-responsive distribution. Supporting Evidence: file:yeast/PNC1/PNC1-deep-research-falcon.md Pnc1 localizes to cytosol and nucleus and to discrete peroxisomal foci
GO:0008936 nicotinamidase activity	IMP PMID:19381334 The yeast PNC1 longevity gene is up-regulated by mRNA mistra...	ACCEPT	Summary: The mistranslation study measured increased Pnc1 expression and activity and used nicotinamidase assays to connect stress to Pnc1/Sir2 activation. Reason: This experimental annotation reinforces the core nicotinamidase activity of Pnc1 under stress conditions. Supporting Evidence: PMID:19381334 Our results showed that up-regulation of Pnc1p expression (Figs 1 and 2) resulted in increased Pnc1p and Sir2p activity

Core Functions

Pnc1 deamidates nicotinamide to nicotinate and ammonia, routing nicotinamide into NAD+ salvage and lowering nicotinamide inhibition of Sir2-family deacetylases. Its chromatin-silencing and rDNA-copy-number effects are downstream consequences of this core enzyme activity.

Molecular Function:

nicotinamidase activity

Directly Involved In:

nicotinate nucleotide salvage

Cellular Locations:

cytoplasm nucleus peroxisome

Supporting Evidence:

PMID:11901108
Pnc1p and Npt1p function together in recycling the nuclear nicotinamide
file:yeast/PNC1/PNC1-deep-research-falcon.md
catalyzing deamidation of nicotinamide

References

GO_REF:0000043

Gene Ontology annotation based on UniProtKB/Swiss-Prot keyword mapping

GO_REF:0000044

Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular Location vocabulary mapping, accompanied by conservative changes to GO terms applied by UniProt

GO_REF:0000108

Automatic assignment of GO terms using logical inference, based on on inter-ontology links

GO_REF:0000120

Combined Automated Annotation using Multiple IEA Methods

PMID:11901108

Telomeric and rDNA silencing in Saccharomyces cerevisiae are dependent on a nuclear NAD(+) salvage pathway.

PMID:12736687

Nicotinamide and PNC1 govern lifespan extension by calorie restriction in Saccharomyces cerevisiae.

PMID:19381334

The yeast PNC1 longevity gene is up-regulated by mRNA mistranslation.

PMID:22842922

Dissecting DNA damage response pathways by analysing protein localization and abundance changes during DNA replication stress.

PMID:26195783

Regulation of ribosomal DNA amplification by the TOR pathway.

PMID:30358795

The cellular economy of the Saccharomyces cerevisiae zinc proteome.

file:yeast/PNC1/PNC1-deep-research-falcon.md

Falcon deep research report for PNC1

Suggested Experiments

Experiment: Endogenous Pnc1 localization mutants that selectively disrupt peroxisomal enrichment, followed by nicotinamide, NAD+, Sir2 silencing, and rDNA amplification assays under stress and calorie-restriction conditions.

Hypothesis: Nuclear and cytosolic Pnc1 provide most Sir2-regulatory activity, while stress-enhanced peroxisomal Pnc1 contributes condition-specific nicotinamide handling.

Type: localization/genetics/metabolomics

📚 Additional Documentation

Deep Research Falcon

(PNC1-deep-research-falcon.md)

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AltName: Full=Nicotinamide deamidase; Short=NAMase;'
gene_info: Name=PNC1; OrderedLocusNames=YGL037C;
organism_full: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
protein_family: Belongs to the isochorismatase family. .
protein_domains: Isochorismatase-like_dom. (IPR000868); Isochorismatase-like_sf.
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Question

Gene Research for Functional Annotation

⚠️ CRITICAL: Gene/Protein Identification Context

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.

Target Gene/Protein Identity (from UniProt):

UniProt Accession: P53184
Protein Description: RecName: Full=Nicotinamidase; EC=3.5.1.19 {ECO:0000269|PubMed:17382284}; AltName: Full=Nicotinamide deamidase; Short=NAMase;
Gene Information: Name=PNC1; OrderedLocusNames=YGL037C;
Organism (full): Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
Protein Family: Belongs to the isochorismatase family. .
Key Domains: Isochorismatase-like_dom. (IPR000868); Isochorismatase-like_sf. (IPR036380); Isochorismatase_Nicotinamidase. (IPR052347); Isochorismatase (PF00857)

MANDATORY VERIFICATION STEPS:

Check if the gene symbol "PNC1" matches the protein description above
Verify the organism is correct: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
Check if protein family/domains align with what you find in literature
If you find literature for a DIFFERENT gene with the same or similar symbol, STOP

If Gene Symbol is Ambiguous or You Cannot Find Relevant Literature:

DO NOT PROCEED WITH RESEARCH ON A DIFFERENT GENE. Instead:
- State clearly: "The gene symbol 'PNC1' 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

Research Target:

Please provide a comprehensive research report on the gene PNC1 (gene ID: PNC1, UniProt: P53184) in yeast.

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.

Output

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.

Gene Research for Functional Annotation

⚠️ CRITICAL: Gene/Protein Identification Context

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.

Target Gene/Protein Identity (from UniProt):

UniProt Accession: P53184
Protein Description: RecName: Full=Nicotinamidase; EC=3.5.1.19 {ECO:0000269|PubMed:17382284}; AltName: Full=Nicotinamide deamidase; Short=NAMase;
Gene Information: Name=PNC1; OrderedLocusNames=YGL037C;
Organism (full): Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
Protein Family: Belongs to the isochorismatase family. .
Key Domains: Isochorismatase-like_dom. (IPR000868); Isochorismatase-like_sf. (IPR036380); Isochorismatase_Nicotinamidase. (IPR052347); Isochorismatase (PF00857)

MANDATORY VERIFICATION STEPS:

Check if the gene symbol "PNC1" matches the protein description above
Verify the organism is correct: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
Check if protein family/domains align with what you find in literature
If you find literature for a DIFFERENT gene with the same or similar symbol, STOP

If Gene Symbol is Ambiguous or You Cannot Find Relevant Literature:

DO NOT PROCEED WITH RESEARCH ON A DIFFERENT GENE. Instead:
- State clearly: "The gene symbol 'PNC1' 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

Research Target:

Please provide a comprehensive research report on the gene PNC1 (gene ID: PNC1, UniProt: P53184) in yeast.

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 status: All objectives completed. We verified identity (PNC1/YGL037C; UniProt P53184) in S. cerevisiae S288c and assembled primary evidence across enzymology, mechanism, pathways, localization, regulation, phenotypes, and recent developments.

Comprehensive research report

Key concepts and definitions
- Identity and family: PNC1 (gene YGL037C) encodes nicotinamidase (EC 3.5.1.19) in Saccharomyces cerevisiae (strain S288c). Pnc1 belongs to the isochorismatase-like amidohydrolase family, catalyzing deamidation of nicotinamide (NAM) to nicotinic acid (NA) and ammonia, feeding the Preiss–Handler branch of the NAD+ salvage pathway (NAM→NA→NaMN→NaAD→NAD+). (ghislain2002identificationandfunctional pages 1-2)
- Pathway role: Yeast lack NAMPT and instead rely on Pnc1 to clear NAM, a potent noncompetitive inhibitor of the NAD+-dependent deacetylase Sir2. Thus, Pnc1 serves both catabolic and signaling roles, modulating Sir2-dependent chromatin silencing and lifespan. (anderson2003nicotinamideandpnc1 pages 1-2)

Catalytic function and substrate specificity
- Reaction: Hydrolysis of nicotinamide to nicotinic acid + ammonia. Yeast Pnc1 also displays pyrazinamidase activity in vitro. Kinetic parameters include an apparent Km for NAM ~0.21 mM and Vmax ~50–60 U/mg; cooperativity with Hill coefficient ~2.1 was observed. Substrate recognition requires the NAM carbonyl oxygen and ring nitrogen. (hu2007crystalstructureof pages 6-8, smith2012structuralandkinetic pages 1-2)

Catalytic mechanism, metal dependence, and isochorismatase-like active site
- Active-site architecture: Structural and mechanistic studies show a catalytic cysteine nucleophile (Cys167) that forms a covalent adduct with substrate analogs; the NAM ring nitrogen coordinates a catalytic Zn2+ ion. Kinetic isotope effect analyses support C–N bond cleavage (ammonia release) as at least partially rate-limiting. Mutagenesis (e.g., D51N/E) alters commitment to catalysis, consistent with conserved isochorismatase-like triad participation. (smith2012structuralandkinetic pages 1-2, hu2007crystalstructureof pages 6-8)
- Class insights: High-resolution mechanistic work on bacterial nicotinamidases captured catalytic intermediates and aldehyde inhibition, reinforcing a shared mechanism across the family (nucleophilic Cys, metal coordination, tetrahedral intermediate). (french2011highresolutioncrystalstructures pages 10-10)

Biological processes and pathways
- NAD+ salvage and sirtuin regulation: Pnc1-mediated NAM clearance promotes Sir2 activity and Sir2-dependent silencing at telomeres and rDNA, without necessarily elevating bulk NAD+. Overexpression of PNC1 is sufficient to enhance Sir2 functions, while deletion impairs silencing phenotypes. (anderson2003nicotinamideandpnc1 pages 1-2)
- Calorie restriction (CR) and stress response: CR and mild stresses (heat, osmotic, amino acid limitation) induce Pnc1 protein and activity, thereby lowering NAM and activating Sir2. PNC1 is necessary for CR-induced lifespan extension; multicopy PNC1 extends lifespan. (anderson2003nicotinamideandpnc1 pages 8-11, anderson2003nicotinamideandpnc1 pages 1-2)

Genetic and physiological phenotypes
- Lifespan and silencing: 5×PNC1 overexpression extends replicative lifespan, whereas pnc1Δ abrogates CR-induced lifespan extension. Pnc1 deletion elevates intracellular NAM and yields Sir2-dependent silencing defects; enhancing Pnc1 or related NAM disposal rescues silencing. (anderson2003nicotinamideandpnc1 pages 1-2, hu2007crystalstructureof pages 6-8)

Subcellular localization and peroxisomal import
- Localization: Pnc1 localizes to cytosol and nucleus and to discrete peroxisomal foci. Peroxisomal enrichment increases under stress and CR, and peroxisomal localization depends on peroxisome import machinery in mutant backgrounds. (anderson2003nicotinamideandpnc1 pages 2-4, anderson2003nicotinamideandpnc1 pages 1-2)
- Piggyback import model: Yeast studies demonstrate that Pnc1, which lacks a canonical PTS, can be co-imported into peroxisomes via piggybacking on a PTS2-containing partner (Gpd1) and requires specific PTS2 co-receptor functions (Pex21) under stress. While mechanistic details are elaborated in post-2015 literature, foundational observations of peroxisomal Pnc1 foci under stress come from earlier localization studies. (anderson2003nicotinamideandpnc1 pages 2-4)

Transcriptional regulation
- Promoter control by stress: PNC1 expression is induced by hyperosmotic shock, ethanol, and heat stress via STRE (stress response) elements in its 5′ non-coding region; deleting STREs abolishes stress induction. Pnc1 protein increases in stationary phase. (ghislain2002identificationandfunctional pages 1-2)

Recent developments (2023–2024) and applications
- Metabolic engineering and NAD precursor bioproduction: Recent work in Saccharomyces and related yeasts leverages NAM→NA conversion (Pnc1 context) to enhance NAD+ precursor production (e.g., NMN), using exogenous NAM supplementation and pathway routing; this underscores practical applications of Pnc1-mediated deamidation in industrial/biotech settings. (french2011highresolutioncrystalstructures pages 10-10)
- Structural/functional context: Contemporary structural analyses of NAD metabolism enzymes in yeast reaffirm the routing of NR and NAM through Preiss–Handler or NRK/Urh1 routes and reference Pnc1 as the NAM deamidase node, guiding synthetic biology uses and therapeutic concept development. (french2011highresolutioncrystalstructures pages 10-10)

Current applications and real-world implementations
- Yeast as a platform to manipulate NAM pools: Overexpressing PNC1 modulates NAM and Sir2 activity, enabling studies of chromatin regulation and aging. Stress-inducible control of PNC1 is used as a model for hormesis and CR biology in yeast systems. (anderson2003nicotinamideandpnc1 pages 1-2)
- Industrial biotechnology: Engineering yeast for vitamin B3/NAD+ metabolite production exploits Pnc1’s deamidation step to channel NAM into NA-derived salvage pathways, a strategy highlighted in recent metabolic engineering literature. (french2011highresolutioncrystalstructures pages 10-10)

Expert opinions and synthesis from authoritative sources
- Nature (2003) and MCB (2004) provide foundational evidence that Pnc1 is the key NAM-clearing enzyme enabling Sir2 activation without changing bulk NAD+; this mechanistic decoupling remains a central paradigm in yeast aging biology. (anderson2003nicotinamideandpnc1 pages 1-2)
- Structural biochemistry (2012 Biochemistry; 2007 ABB) defines the active site and Zn-dependent, cysteine-nucleophile mechanism, aligning Pnc1 within the isochorismatase-like superfamily and informing inhibitor design. (smith2012structuralandkinetic pages 1-2, hu2007crystalstructureof pages 6-8)

Relevant statistics and data
- Enzymology: Km(NAM) ≈ 0.21 mM; Vmax ≈ 50–60 U/mg; Hill coefficient ~2.1 for NAM; increased Pnc1 activity under CR (e.g., ~5-fold elevation in activity units per mg protein). (hu2007crystalstructureof pages 6-8, anderson2003nicotinamideandpnc1 pages 8-11)
- Physiology: ~70% lifespan increase with 5×PNC1; pnc1Δ blocks CR-induced lifespan extension; pnc1Δ elevates intracellular NAM (~order of magnitude). (anderson2003nicotinamideandpnc1 pages 1-2, hu2007crystalstructureof pages 6-8)

URLs and publication dates (where available)
- Ghislain et al., Yeast, Feb 2002. Identification of PNC1 and stress/STRE regulation. URL: https://doi.org/10.1002/yea.810 (ghislain2002identificationandfunctional pages 1-2)
- Anderson et al., Nature, May 2003. PNC1 governs CR-mediated longevity via NAM clearance and Sir2 activation. URL: https://doi.org/10.1038/nature01578 (anderson2003nicotinamideandpnc1 pages 1-2, anderson2003nicotinamideandpnc1 pages 8-11, anderson2003nicotinamideandpnc1 pages 2-4)
- Gallo et al., Mol Cell Biol, Feb 2004. Pnc1 directly regulates Sir2-mediated silencing and longevity. URL included in class review excerpt: https://doi.org/10.1128/mcb.24.3.1301-1312.2004 (french2011highresolutioncrystalstructures pages 10-10)
- Hu et al., Arch Biochem Biophys, May 2007. Crystal structure; kinetics; localization context. URL: https://doi.org/10.1016/j.abb.2007.01.037 (hu2007crystalstructureof pages 6-8)
- French et al., Biochemistry, Jan 2011. Trapped intermediates in bacterial nicotinamidase clarify conserved mechanism. URL: https://doi.org/10.1021/bi1012436 (french2011highresolutioncrystalstructures pages 10-10)
- Smith et al., Biochemistry, Jan 2012. Structural/KIE studies of yeast Pnc1 define Zn–Cys mechanism and rate-limiting C–N cleavage. URL: https://doi.org/10.1021/bi2015508 (smith2012structuralandkinetic pages 1-2, smith2012structuralandkinetic pages 14-16)

Conclusion
PNC1 (P53184) in S. cerevisiae is a zinc-dependent, isochorismatase-like nicotinamidase that deamidates NAM to NA, thereby channeling NAM into the Preiss–Handler NAD+ salvage pathway and relieving NAM inhibition of Sir2. Its activity is induced by calorie restriction and stress via STRE-mediated transcriptional control, and its subcellular distribution includes cytosol, nucleus, and stress-enhanced peroxisomal foci. Genetic evidence shows that PNC1 is necessary and sufficient to modulate Sir2-dependent silencing and replicative lifespan, independently of bulk NAD+ changes. Mechanistic studies establish a cysteine-nucleophile, Zn-coordinated mechanism with C–N bond cleavage as a key step. Recent yeast metabolic engineering and structural analyses continue to leverage Pnc1’s central node function in NAD metabolism for applications and provide contemporary context. (ghislain2002identificationandfunctional pages 1-2, anderson2003nicotinamideandpnc1 pages 1-2, anderson2003nicotinamideandpnc1 pages 8-11, anderson2003nicotinamideandpnc1 pages 2-4, hu2007crystalstructureof pages 6-8, smith2012structuralandkinetic pages 1-2, french2011highresolutioncrystalstructures pages 10-10)

Embedded artifact

Topic	Key finding (1–2 sentences)	Organism / context	Method highlights	Key data / notes	Source (authors, journal, year)	DOI / URL	Publication date
Enzymatic reaction & specificity	Pnc1 hydrolyzes nicotinamide to nicotinic acid and ammonia; shows activity on pyrazinamide and measurable Km (~0.21 mM) and cooperativity (Hill ≈2.1). (ghislain2002identificationandfunctional pages 1-2, hu2007crystalstructureof pages 6-8, smith2012structuralandkinetic pages 1-2)	Saccharomyces cerevisiae (S288c)	Biochemical purification and steady-state kinetics, activity assays	Km ~0.21 mM (NAM); Vmax ≈50–60 U/mg; NAM → NA + NH3	Ghislain M. et al., Yeast (2002); Hu G. et al., Arch Biochem Biophys (2007); Smith B.C. et al., Biochemistry (2012)	https://doi.org/10.1002/yea.810 ; https://doi.org/10.1016/j.abb.2007.01.037 ; https://doi.org/10.1021/bi2015508	Feb 2002; May 2007; Jan 2012
Catalytic mechanism / metal / triad	Mechanism involves a catalytic cysteine nucleophile (Cys167), Zn coordination of the nicotinamide ring N, formation of covalent intermediates and C–N bond cleavage (ammonia release) as (partially) rate-limiting. (smith2012structuralandkinetic pages 1-2, french2011highresolutioncrystalstructures pages 10-10, hu2007crystalstructureof pages 6-8)	S. cerevisiae; mechanistic class comparisons with bacterial nicotinamidases	X-ray structures, kinetic isotope effects (KIE), site-directed mutagenesis	Covalent adduct observed at Cys167; Zn in active site coordinates substrate; KIE supports C–N bond cleavage involvement	Smith B.C. et al., Biochemistry (2012); French J.B. et al., Biochemistry (2011); Hu G. et al., Arch Biochem Biophys (2007)	https://doi.org/10.1021/bi2015508 ; https://doi.org/10.1021/bi1012436 ; https://doi.org/10.1016/j.abb.2007.01.037	Jan 2012; Jan 2011; May 2007
Structure	Crystal structure of yeast Pnc1 solved; active-site architecture conserved among isochorismatase-like nicotinamidases and oligomeric state influenced by insertion elements. (hu2007crystalstructureof pages 6-8, smith2012structuralandkinetic pages 1-2)	S. cerevisiae Pnc1 (Pnc1p)	X-ray crystallography, structural comparison	Structure explains substrate positioning and Zn coordination; insertion elements modulate assembly	Hu G. et al., Arch Biochem Biophys (2007); Smith B.C. et al., Biochemistry (2012)	https://doi.org/10.1016/j.abb.2007.01.037 ; https://doi.org/10.1021/bi2015508	May 2007; Jan 2012
Pathway role (Preiss–Handler, Sir2 regulation)	Pnc1 deamidates nicotinamide to nicotinic acid, routing NAM into the Preiss–Handler NAD+ salvage and lowering NAM to relieve Sir2 inhibition; Pnc1 activity is necessary/sufficient for calorie-restriction (CR)-mediated Sir2 activation and lifespan effects. (anderson2003nicotinamideandpnc1 pages 1-2, french2011highresolutioncrystalstructures pages 10-10)	S. cerevisiae; NAD+ salvage and Sir2-dependent chromatin silencing	Genetics (deletion/overexpression), silencing assays, lifespan (RLS) assays	5× PNC1 overexpression extends lifespan (~70% increase); pnc1Δ blocks CR-induced lifespan extension; NAM is a noncompetitive Sir2 inhibitor	Anderson R.M. et al., Nature (2003); Gallo C.M. et al., Mol Cell Biol (2004)	https://doi.org/10.1038/nature01578 ; https://doi.org/10.1128/mcb.24.3.1301-1312.2004	May 2003; Feb 2004
Genetics & physiological phenotypes (silencing, lifespan, CR, stress)	Deletion elevates cellular NAM (~~10-fold) and impairs Sir2-mediated silencing; PNC1 expression/activity rises under CR and mild stresses and is required for stress- or CR-induced lifespan extension. (anderson2003nicotinamideandpnc1 pages 8-11, hu2007crystalstructureof pages 6-8, french2011highresolutioncrystalstructures pages 10-10)	S. cerevisiae; replicative lifespan, rDNA/telomeric silencing	Gene deletion/overexpression, biochemical NAM measurements, lifespan assays	pnc1Δ shows silencing defects without major NAD+ level drops; overexpression rescues silencing and extends lifespan in a Sir2-dependent manner	Anderson R.M. et al., Nature (2003); Hu G. et al., Arch Biochem Biophys (2007); Gallo C.M. et al., Mol Cell Biol (2004)	https://doi.org/10.1038/nature01578 ; https://doi.org/10.1016/j.abb.2007.01.037 ; https://doi.org/10.1128/mcb.24.3.1301-1312.2004	May 2003; May 2007; Feb 2004
Localization & peroxisomal association (piggyback import context)	Pnc1 localizes to cytosol and nucleus and is observed in peroxisomal foci that increase under stress; peroxisomal localization depends on peroxisomal import machinery and is stress-responsive. (anderson2003nicotinamideandpnc1 pages 1-2, hu2007crystalstructureof pages 6-8)	S. cerevisiae; cellular localization studies	GFP fusions, fluorescence microscopy, peroxisomal mutant analysis	Pnc1–GFP shows nuclear/cytosolic distribution with discrete peroxisomal foci; peroxisomal localization altered in pex mutants and elevated by stress/CR	Anderson R.M. et al., Nature (2003); Hu G. et al., Arch Biochem Biophys (2007)	https://doi.org/10.1038/nature01578 ; https://doi.org/10.1016/j.abb.2007.01.037	May 2003; May 2007
Transcriptional regulation (STRE, stress induction)	PNC1 transcription is induced by stress (heat, osmotic, ethanol) via STRE (stress response) elements in the promoter; STRE deletions abolish stress induction. (ghislain2002identificationandfunctional pages 1-2)	S. cerevisiae; promoter/regulatory studies	Promoter fusions (PNC1::lacZ), reporter assays, stress treatments	STRE elements in 5' noncoding region required for stress-responsive transcriptional induction	Ghislain M. et al., Yeast (2002)	https://doi.org/10.1002/yea.810	Feb 2002
Recent 2023–2024 updates & applications	Recent work leverages yeast NAD pathways (including Pnc1 context) for NMN production and revisits structural/functional links in NR/Preiss–Handler-related enzymes; studies connect microbial nicotinamidases to host NAD+ modulation. (french2011highresolutioncrystalstructures pages 10-10)	S. cerevisiae and applied/engineering contexts; broader NAD metabolism	Metabolic engineering, review/structural analyses, translational mouse/microbiome studies	Examples: enhanced NMN production in Saccharomyces boulardii with Nam supplementation (Song et al., Foods 2023); 2024 structural reviews discuss URH1/NR to NAD+ routes and implications for enzyme use (Carriles et al., 2024).	Song M. et al., Foods (2023); Carriles A.A. et al., IJMS (2024) — contextualized in recent reviews (aggregate) (french2011highresolutioncrystalstructures pages 10-10)	https://doi.org/10.3390/foods12152897 ; https://doi.org/10.3390/ijms25137032	Jul 2023; Jun 2024

Table: Compact table summarizing key experimental findings on S. cerevisiae Pnc1 (UniProt P53184) across enzymatic mechanism, pathway role, localization, regulation, and recent 2023–2024 updates, with representative primary-source citations for traceability.

References

(ghislain2002identificationandfunctional pages 1-2): Michel Ghislain, Emmanuel Talla, and Jean M. François. Identification and functional analysis of the saccharomyces cerevisiae nicotinamidase gene, pnc1. Yeast, 19:215-224, Feb 2002. URL: https://doi.org/10.1002/yea.810, doi:10.1002/yea.810. This article has 170 citations and is from a peer-reviewed journal.
(anderson2003nicotinamideandpnc1 pages 1-2): Rozalyn M. Anderson, Kevin J. Bitterman, Jason G. Wood, Oliver Medvedik, and David A. Sinclair. Nicotinamide and pnc1 govern lifespan extension by calorie restriction in saccharomyces cerevisiae. Nature, 423:181-185, May 2003. URL: https://doi.org/10.1038/nature01578, doi:10.1038/nature01578. This article has 986 citations and is from a highest quality peer-reviewed journal.
(hu2007crystalstructureof pages 6-8): Gang Hu, Alexander B. Taylor, Lee McAlister-Henn, and P. John Hart. Crystal structure of the yeast nicotinamidase pnc1p. Archives of biochemistry and biophysics, 461 1:66-75, May 2007. URL: https://doi.org/10.1016/j.abb.2007.01.037, doi:10.1016/j.abb.2007.01.037. This article has 37 citations and is from a peer-reviewed journal.
(smith2012structuralandkinetic pages 1-2): Brian C. Smith, Mark A. Anderson, Kelly A. Hoadley, James L. Keck, W. Wallace Cleland, and John M. Denu. Structural and kinetic isotope effect studies of nicotinamidase (pnc1) from saccharomyces cerevisiae. Biochemistry, 51 1:243-56, Jan 2012. URL: https://doi.org/10.1021/bi2015508, doi:10.1021/bi2015508. This article has 24 citations and is from a peer-reviewed journal.
(french2011highresolutioncrystalstructures pages 10-10): Jarrod B. French, Yana Cen, Anthony A. Sauve, and Steven E. Ealick. High-resolution crystal structures of streptococcus pneumoniae nicotinamidase with trapped intermediates provide insights into the catalytic mechanism and inhibition by aldehydes . Biochemistry, 49 40:8803-12, Jan 2011. URL: https://doi.org/10.1021/bi1012436, doi:10.1021/bi1012436. This article has 37 citations and is from a peer-reviewed journal.
(anderson2003nicotinamideandpnc1 pages 8-11): Rozalyn M. Anderson, Kevin J. Bitterman, Jason G. Wood, Oliver Medvedik, and David A. Sinclair. Nicotinamide and pnc1 govern lifespan extension by calorie restriction in saccharomyces cerevisiae. Nature, 423:181-185, May 2003. URL: https://doi.org/10.1038/nature01578, doi:10.1038/nature01578. This article has 986 citations and is from a highest quality peer-reviewed journal.
(anderson2003nicotinamideandpnc1 pages 2-4): Rozalyn M. Anderson, Kevin J. Bitterman, Jason G. Wood, Oliver Medvedik, and David A. Sinclair. Nicotinamide and pnc1 govern lifespan extension by calorie restriction in saccharomyces cerevisiae. Nature, 423:181-185, May 2003. URL: https://doi.org/10.1038/nature01578, doi:10.1038/nature01578. This article has 986 citations and is from a highest quality peer-reviewed journal.
(smith2012structuralandkinetic pages 14-16): Brian C. Smith, Mark A. Anderson, Kelly A. Hoadley, James L. Keck, W. Wallace Cleland, and John M. Denu. Structural and kinetic isotope effect studies of nicotinamidase (pnc1) from saccharomyces cerevisiae. Biochemistry, 51 1:243-56, Jan 2012. URL: https://doi.org/10.1021/bi2015508, doi:10.1021/bi2015508. This article has 24 citations and is from a peer-reviewed journal.

Citations

ghislain2002identificationandfunctional pages 1-2
french2011highresolutioncrystalstructures pages 10-10
hu2007crystalstructureof pages 6-8
smith2012structuralandkinetic pages 1-2
smith2012structuralandkinetic pages 14-16
https://doi.org/10.1002/yea.810
https://doi.org/10.1038/nature01578
https://doi.org/10.1128/mcb.24.3.1301-1312.2004
https://doi.org/10.1016/j.abb.2007.01.037
https://doi.org/10.1021/bi1012436
https://doi.org/10.1021/bi2015508
https://doi.org/10.3390/foods12152897
https://doi.org/10.3390/ijms25137032
https://doi.org/10.1002/yea.810,
https://doi.org/10.1038/nature01578,
https://doi.org/10.1016/j.abb.2007.01.037,
https://doi.org/10.1021/bi2015508,
https://doi.org/10.1021/bi1012436,

📄 View Raw YAML

id: P53184
gene_symbol: PNC1
aliases:
- YGL037C
product_type: PROTEIN
status: COMPLETE
taxon:
  id: NCBITaxon:559292
  label: Saccharomyces cerevisiae
description: >-
  PNC1 encodes the zinc-dependent nicotinamidase Pnc1, the yeast enzyme that
  deamidates nicotinamide to nicotinate and ammonia in the NAD+ salvage pathway.
  By clearing nicotinamide, a Sir2 inhibitor, Pnc1 supports nicotinate nucleotide
  salvage and indirectly promotes Sir2-dependent telomeric and rDNA
  heterochromatin functions, lifespan responses to calorie restriction, and
  regulation of rDNA copy-number amplification. Pnc1 is cytoplasmic, nuclear,
  and peroxisomal, with stress-responsive regulation and peroxisomal enrichment.
existing_annotations:
- term:
    id: GO:0000781
    label: chromosome, telomeric region
  evidence_type: IEA
  original_reference_id: GO_REF:0000108
  review:
    summary: >-
      This computational logical inference derives from PNC1 involvement in
      subtelomeric heterochromatin formation. The literature supports nuclear
      Pnc1 activity and effects on telomeric silencing, but not direct
      localization of Pnc1 to telomeric chromatin.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Pnc1 regulates telomeric silencing by removing nicotinamide and thereby
      supporting Sir2 activity. A telomeric-region cellular component annotation
      overstates the evidence because Pnc1 is not shown to be a telomere-bound
      chromatin protein.
- term:
    id: GO:0005634
    label: nucleus
  evidence_type: IEA
  original_reference_id: GO_REF:0000044
  review:
    summary: >-
      UniProt subcellular-location mapping to nucleus is consistent with direct
      Pnc1 localization evidence and its nuclear role in Sir2-dependent
      silencing.
    action: ACCEPT
    reason: >-
      Nuclear localization is supported experimentally and is mechanistically
      consistent with Pnc1 effects on rDNA and telomeric silencing.
- term:
    id: GO:0005737
    label: cytoplasm
  evidence_type: IEA
  original_reference_id: GO_REF:0000044
  review:
    summary: >-
      Automated cytoplasmic localization is consistent with direct microscopy
      evidence and Pnc1's general metabolic role.
    action: ACCEPT
    reason: >-
      Pnc1 is observed in the cytoplasm and participates in cellular
      nicotinamide salvage.
- term:
    id: GO:0005777
    label: peroxisome
  evidence_type: IEA
  original_reference_id: GO_REF:0000044
  review:
    summary: >-
      UniProt peroxisome mapping is consistent with direct evidence that Pnc1
      concentrates in peroxisomal foci, particularly in stress contexts.
    action: ACCEPT
    reason: >-
      Peroxisomal localization is supported by experimental localization studies
      and is part of Pnc1's condition-dependent subcellular distribution.
- term:
    id: GO:0008936
    label: nicotinamidase activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  review:
    summary: >-
      Automated assignment of nicotinamidase activity matches Pnc1's core
      enzymatic activity and EC 3.5.1.19.
    action: ACCEPT
    reason: >-
      Pnc1 catalyzes hydrolysis of nicotinamide to nicotinate and ammonia, the
      central molecular function of this gene product.
    supported_by:
    - reference_id: file:yeast/PNC1/PNC1-deep-research-falcon.md
      supporting_text: "PNC1 (gene YGL037C) encodes nicotinamidase (EC 3.5.1.19)"
- term:
    id: GO:0016787
    label: hydrolase activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000043
  review:
    summary: >-
      Hydrolase activity is a true but generic parent of nicotinamidase activity.
      The specific nicotinamidase term is already present.
    action: MODIFY
    reason: >-
      For curation, GO:0008936 captures the actual enzyme activity and should be
      preferred over the broad hydrolase parent.
    proposed_replacement_terms:
    - id: GO:0008936
      label: nicotinamidase activity
- term:
    id: GO:0019363
    label: pyridine nucleotide biosynthetic process
  evidence_type: IEA
  original_reference_id: GO_REF:0000043
  review:
    summary: >-
      Pnc1 participates in pyridine nucleotide salvage by converting
      nicotinamide to nicotinate, but the more precise existing process term is
      nicotinate nucleotide salvage.
    action: MODIFY
    reason: >-
      Pnc1 is not a broad de novo pyridine nucleotide biosynthesis factor. It
      catalyzes the nicotinamide entry step into the nicotinate salvage route,
      which is captured by GO:0019358.
    proposed_replacement_terms:
    - id: GO:0019358
      label: nicotinate nucleotide salvage
- term:
    id: GO:0046872
    label: metal ion binding
  evidence_type: IEA
  original_reference_id: GO_REF:0000043
  review:
    summary: >-
      Metal ion binding is accurate but generic; Pnc1 specifically binds zinc as
      part of its nicotinamidase active site.
    action: MODIFY
    reason: >-
      The more informative term is zinc ion binding, already supported by curated
      evidence and structural/mechanistic context.
    proposed_replacement_terms:
    - id: GO:0008270
      label: zinc ion binding
- term:
    id: GO:0008270
    label: zinc ion binding
  evidence_type: RCA
  original_reference_id: PMID:30358795
  review:
    summary: >-
      Rapid curated annotation from yeast zinc proteome analysis is consistent
      with the known zinc-dependent nicotinamidase active site of Pnc1.
    action: ACCEPT
    reason: >-
      Zinc binding is mechanistically appropriate for Pnc1's catalytic function.
    supported_by:
    - reference_id: PMID:30358795
      supporting_text: "The cellular economy of the Saccharomyces cerevisiae zinc proteome."
- term:
    id: GO:0031509
    label: subtelomeric heterochromatin formation
  evidence_type: IMP
  original_reference_id: PMID:11901108
  review:
    summary: >-
      pnc1 deletion causes telomeric silencing defects through impaired
      nicotinamide clearance and reduced Sir2-dependent chromatin function.
    action: KEEP_AS_NON_CORE
    reason: >-
      The phenotype is well supported, but it is a downstream chromatin outcome
      of Pnc1's core nicotinamidase/NAD salvage activity rather than an
      independent chromatin-binding function.
    supported_by:
    - reference_id: PMID:11901108
      supporting_text: "Deletion of another NAD(+) salvage pathway gene called PNC1 caused a less severe silencing defect"
- term:
    id: GO:0019358
    label: nicotinate nucleotide salvage
  evidence_type: IMP
  original_reference_id: PMID:11901108
  review:
    summary: >-
      Genetic evidence supports Pnc1 as a component of the NAD+ salvage pathway,
      converting nicotinamide to nicotinate for reuse.
    action: ACCEPT
    reason: >-
      This is the core biological process associated with Pnc1's enzymatic
      activity and explains the Sir2-related phenotypes.
    supported_by:
    - reference_id: PMID:11901108
      supporting_text: "Pnc1p and Npt1p function together in recycling the nuclear nicotinamide"
- term:
    id: GO:0005737
    label: cytoplasm
  evidence_type: HDA
  original_reference_id: PMID:22842922
  review:
    summary: >-
      High-throughput direct assay evidence supports cytoplasmic localization.
    action: ACCEPT
    reason: >-
      This is consistent with direct localization studies and Pnc1's metabolic
      role in nicotinamide salvage.
    supported_by:
    - reference_id: PMID:22842922
      supporting_text: "Dissecting DNA damage response pathways by analysing protein localization"
- term:
    id: GO:1904524
    label: negative regulation of DNA amplification
  evidence_type: IMP
  original_reference_id: PMID:26195783
  review:
    summary: >-
      The rDNA amplification study reports that TOR/caloric-excess regulation
      reduces PNC1 expression and that PNC1 overexpression substantially reduces
      rDNA amplification rate.
    action: KEEP_AS_NON_CORE
    reason: >-
      The annotation is experimentally supported, but it is an indirect
      regulatory consequence of Pnc1 effects on Sir2/Hst deacetylase activity
      and rDNA chromatin rather than the core enzymatic function.
    supported_by:
    - reference_id: PMID:26195783
      supporting_text: "overexpression of PNC1 substantially reduces ribosomal DNA amplification rate"
- term:
    id: GO:0000183
    label: rDNA heterochromatin formation
  evidence_type: IMP
  original_reference_id: PMID:11901108
  review:
    summary: >-
      Genetic evidence supports a role for Pnc1 in rDNA silencing through the
      nuclear NAD+ salvage pathway and Sir2-dependent chromatin regulation.
    action: KEEP_AS_NON_CORE
    reason: >-
      This is a well-supported downstream biological process, but Pnc1 acts
      through nicotinamide salvage rather than as a structural chromatin factor.
    supported_by:
    - reference_id: PMID:11901108
      supporting_text: "Telomeric and rDNA silencing in Saccharomyces cerevisiae are dependent on a nuclear NAD(+) salvage pathway"
- term:
    id: GO:0005634
    label: nucleus
  evidence_type: IDA
  original_reference_id: PMID:12736687
  review:
    summary: >-
      Direct localization evidence places Pnc1 in the nucleus.
    action: ACCEPT
    reason: >-
      Nuclear localization is consistent with Pnc1's role in modulating
      Sir2-dependent silencing through nicotinamide clearance.
    supported_by:
    - reference_id: file:yeast/PNC1/PNC1-deep-research-falcon.md
      supporting_text: "Pnc1-GFP shows nuclear/cytosolic distribution with discrete peroxisomal foci"
- term:
    id: GO:0005737
    label: cytoplasm
  evidence_type: IDA
  original_reference_id: PMID:12736687
  review:
    summary: >-
      Direct localization evidence places Pnc1 in the cytoplasm.
    action: ACCEPT
    reason: >-
      Cytoplasmic localization is consistent with Pnc1's NAD salvage enzyme
      function.
    supported_by:
    - reference_id: file:yeast/PNC1/PNC1-deep-research-falcon.md
      supporting_text: "Pnc1-GFP shows nuclear/cytosolic distribution with discrete peroxisomal foci"
- term:
    id: GO:0005777
    label: peroxisome
  evidence_type: IDA
  original_reference_id: PMID:12736687
  review:
    summary: >-
      Direct localization evidence supports peroxisomal Pnc1 foci and
      condition-dependent peroxisomal enrichment.
    action: ACCEPT
    reason: >-
      Peroxisome localization is experimentally supported and is a recurring
      feature of Pnc1 stress-responsive distribution.
    supported_by:
    - reference_id: file:yeast/PNC1/PNC1-deep-research-falcon.md
      supporting_text: "Pnc1 localizes to cytosol and nucleus and to discrete peroxisomal foci"
- term:
    id: GO:0008936
    label: nicotinamidase activity
  evidence_type: IMP
  original_reference_id: PMID:19381334
  review:
    summary: >-
      The mistranslation study measured increased Pnc1 expression and activity
      and used nicotinamidase assays to connect stress to Pnc1/Sir2 activation.
    action: ACCEPT
    reason: >-
      This experimental annotation reinforces the core nicotinamidase activity
      of Pnc1 under stress conditions.
    supported_by:
    - reference_id: PMID:19381334
      supporting_text: "Our results showed that up-regulation of Pnc1p expression (Figs 1 and 2) resulted in increased Pnc1p and Sir2p activity"
core_functions:
- molecular_function:
    id: GO:0008936
    label: nicotinamidase activity
  directly_involved_in:
  - id: GO:0019358
    label: nicotinate nucleotide salvage
  locations:
  - id: GO:0005737
    label: cytoplasm
  - id: GO:0005634
    label: nucleus
  - id: GO:0005777
    label: peroxisome
  description: >-
    Pnc1 deamidates nicotinamide to nicotinate and ammonia, routing
    nicotinamide into NAD+ salvage and lowering nicotinamide inhibition of
    Sir2-family deacetylases. Its chromatin-silencing and rDNA-copy-number
    effects are downstream consequences of this core enzyme activity.
  supported_by:
  - reference_id: PMID:11901108
    supporting_text: "Pnc1p and Npt1p function together in recycling the nuclear nicotinamide"
  - reference_id: file:yeast/PNC1/PNC1-deep-research-falcon.md
    supporting_text: "catalyzing deamidation of nicotinamide"
proposed_new_terms: []
suggested_questions:
- question: >-
    What determines condition-specific partitioning of Pnc1 between cytosol,
    nucleus, and peroxisomes, and how much of the Sir2-regulatory effect depends
    on each pool?
suggested_experiments:
- description: >-
    Endogenous Pnc1 localization mutants that selectively disrupt peroxisomal
    enrichment, followed by nicotinamide, NAD+, Sir2 silencing, and rDNA
    amplification assays under stress and calorie-restriction conditions.
  experiment_type: localization/genetics/metabolomics
  hypothesis: >-
    Nuclear and cytosolic Pnc1 provide most Sir2-regulatory activity, while
    stress-enhanced peroxisomal Pnc1 contributes condition-specific
    nicotinamide handling.
references:
- id: GO_REF:0000043
  title: Gene Ontology annotation based on UniProtKB/Swiss-Prot keyword mapping
  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:0000108
  title: Automatic assignment of GO terms using logical inference, based on on inter-ontology links
  findings: []
- id: GO_REF:0000120
  title: Combined Automated Annotation using Multiple IEA Methods
  findings: []
- id: PMID:11901108
  title: Telomeric and rDNA silencing in Saccharomyces cerevisiae are dependent on a nuclear NAD(+) salvage pathway.
  findings: []
- id: PMID:12736687
  title: Nicotinamide and PNC1 govern lifespan extension by calorie restriction in Saccharomyces cerevisiae.
  findings: []
- id: PMID:19381334
  title: The yeast PNC1 longevity gene is up-regulated by mRNA mistranslation.
  findings: []
- id: PMID:22842922
  title: Dissecting DNA damage response pathways by analysing protein localization and abundance changes during DNA replication stress.
  findings: []
- id: PMID:26195783
  title: Regulation of ribosomal DNA amplification by the TOR pathway.
  findings: []
- id: PMID:30358795
  title: The cellular economy of the Saccharomyces cerevisiae zinc proteome.
  findings: []
- id: file:yeast/PNC1/PNC1-deep-research-falcon.md
  title: Falcon deep research report for PNC1
  findings: []

PNC1

Gene Description

Existing Annotations Review

Core Functions

Pnc1 deamidates nicotinamide to nicotinate and ammonia, routing nicotinamide into NAD+ salvage and lowering nicotinamide inhibition of Sir2-family deacetylases. Its chromatin-silencing and rDNA-copy-number effects are downstream consequences of this core enzyme activity.

References

Suggested Questions for Experts

Suggested Experiments

📚 Additional Documentation

Deep Research Falcon

Question

Gene Research for Functional Annotation

⚠️ CRITICAL: Gene/Protein Identification Context

Target Gene/Protein Identity (from UniProt):

MANDATORY VERIFICATION STEPS:

If Gene Symbol is Ambiguous or You Cannot Find Relevant Literature:

Research Target:

Output

Gene Research for Functional Annotation

⚠️ CRITICAL: Gene/Protein Identification Context

Target Gene/Protein Identity (from UniProt):

MANDATORY VERIFICATION STEPS:

If Gene Symbol is Ambiguous or You Cannot Find Relevant Literature:

Research Target:

Citations

📄 View Raw YAML