📚 Additional Documentation

Deep Research Bioreason

(RAS2-deep-research-bioreason.md)

BioReason Chat Export

Exported on March 22, 2026 at 02:06 AM

Organism: Saccharomyces cerevisiae

Sequence:

MPLNKSNIREYKLVVVGGGGVGKSALTIQLTQSHFVDEYDPTIEDSYRKQVVIDDEVSILDILDTAGQEEYSAMREQYMRNGEGFLLVYSITSKSSLDELMTYYQQILRVKDTDYVPIVVVGNKSDLENEKQVSYQDGLNMAKQMNAPFLETSAKQAINVEEAFYTLARLVRDEGGKYNKTLTENDNSKQTSQDTKGSGANSVPRNSGGHRKMSNAANGKNVNSSTTVVNARNASIESKTGLAGNQATNGKTQTDRTNIDNSTGQAGQANAQSANTVNNRVNNNSKAGQVSNAKQARKQQAAPGGNTSEASKSGSGGCCIIS

Thinking Trace

I begin with the InterPro architecture. The polypeptide is saturated with Ras-superfamily signatures: IPR001806 (Small GTPase family, residues 4–229) spans essentially the full length, establishing membership in the Ras/Rab clade of regulatory GTPases. Nested within this, IPR027417 (P-loop containing nucleoside triphosphate hydrolase homologous superfamily, residues 4–180) defines the classic NTPase fold that houses the Walker A/B motifs and switch regions responsible for nucleotide-dependent conformational cycling. Centrally, IPR005225 (Small GTP-binding domain, residues 9–167) delineates the canonical GTP-binding core that toggles between GTP- and GDP-bound states. Finally, IPR020849 (Small GTPase, Ras-type family, residues 10–192) refines the classification to Ras-type small GTPases, indicating the regulatory switches I and II that couple GTP hydrolysis to effector engagement. The ordered overlap of these domains—from the broad small GTPase envelope to the Ras-type core—causes high-affinity GTP binding and regulated GTP hydrolysis typical of membrane-associated trafficking switches.

This architecture dictates molecular function. The P-loop NTPase core (IPR027417) and small GTP-binding domain (IPR005225) together enforce GO:0005525 GTP binding and GO:0003924 GTPase activity, with the Ras-type family signatures (IPR001806, IPR020849) ensuring switch-controlled effector binding rather than nonspecific hydrolysis. The absence of enzymatic accessory domains and the dominance of Ras/Rab modules focus the function on reversible nucleotide-dependent signaling.

From function to process, Ras-type small GTPases are central timers in membrane trafficking and vesicle formation. By cycling between GTP- and GDP-bound states, they orchestrate cargo sorting and membrane dynamics—hallmarks of GO:0016192 vesicle-mediated transport. The explicit annotation as a small GTPase that regulates intracellular vesicle dynamics coheres with this pathway logic: GTP-bound states recruit effectors at budding sites, and hydrolysis triggers release, thereby pacing vesicle budding, tethering, and fusion.

Cellular location follows from both sequence logic and the stated compartment. The concentration of Ras/Rab-like modules without transmembrane segments points to a soluble peripheral regulator that associates with membranes via lipid modifications and effector networks. The stated location is the vacuole, a terminal degradative organelle in yeast that receives autophagic and endosomal cargo. Thus, the most parsimonious cellular component is GO:0005773 vacuole. A vacuole-proximal trafficking switch can account for both endosomal routing and autophagic delivery.

Mechanistically, I hypothesize that this small GTPase acts as a vacuole-proximal organizer of intracellular vesicle traffic. In its GTP-bound form it likely recruits effectors that sculpt membrane curvature and tethering; in its GDP-bound state it releases them, resetting the cycle. At the vacuole interface, plausible partners include tethering/coat modules and fusion machinery. Candidate effectors include HOPS/CORVET-associated subunits (e.g., Vps39, Vps41) for endosome–vacuole tethering; the vacuolar SNARE Vam3 and its partners for membrane fusion; and adaptor/coating systems such as AP-3 and sorting nexins that bias cargo flow toward the vacuole. Together, these interactions would couple nucleotide-state transitions to directional vesicle traffic converging on the vacuole.

Functional Summary

A Ras-family small GTPase in baker’s yeast that cycles between GTP- and GDP-bound states to regulate intracellular vesicle traffic converging on the vacuole. Its nucleotide-driven switch mechanism enables transient effector recruitment that times vesicle budding, tethering, and fusion steps, thereby coordinating membrane transport pathways that deliver cargo to the vacuole for storage or degradation.

UniProt Summary

Potential regulator of intracellular vesicle traffic.

InterPro Domains

Small GTPase (IPR001806, family) — residues 4-229
P-loop containing nucleoside triphosphate hydrolase (IPR027417, homologous_superfamily) — residues 4-180
Small GTP-binding domain (IPR005225, domain) — residues 9-167
Small GTPase, Ras-type (IPR020849, family) — residues 10-192

GO Terms

Molecular Function: molecular_function (GO:0003674), binding (GO:0005488), catalytic activity (GO:0003824), carbohydrate derivative binding (GO:0097367), small molecule binding (GO:0036094), heterocyclic compound binding (GO:1901363), hydrolase activity (GO:0016787), ion binding (GO:0043167), organic cyclic compound binding (GO:0097159), protein binding (GO:0005515), hydrolase activity, acting on acid anhydrides (GO:0016817), nucleoside phosphate binding (GO:1901265), anion binding (GO:0043168), nucleotide binding (GO:0000166), ribonucleotide binding (GO:0032553), purine ribonucleoside triphosphate binding (GO:0035639), purine ribonucleotide binding (GO:0032555), hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides (GO:0016818), purine nucleotide binding (GO:0017076), pyrophosphatase activity (GO:0016462), GTP binding (GO:0005525), guanyl nucleotide binding (GO:0019001), guanyl ribonucleotide binding (GO:0032561), ribonucleoside triphosphate phosphatase activity (GO:0017111), GTPase activity (GO:0003924)

Biological Process: biological_process (GO:0008150), metabolic process (GO:0008152), localization (GO:0051179), positive regulation of biological process (GO:0048518), regulation of biological process (GO:0050789), reproductive process (GO:0022414), reproduction (GO:0000003), biological regulation (GO:0065007), response to stimulus (GO:0050896), developmental process (GO:0032502), cellular process (GO:0009987), response to external stimulus (GO:0009605), sexual reproduction (GO:0019953), cellular developmental process (GO:0048869), cellular localization (GO:0051641), anatomical structure development (GO:0048856), sporulation (GO:0043934), anatomical structure morphogenesis (GO:0009653), response to chemical (GO:0042221), reproduction of a single-celled organism (GO:0032505), meiotic cell cycle (GO:0051321), regulation of metabolic process (GO:0019222), regulation of localization (GO:0032879), cell cycle process (GO:0022402), cell cycle (GO:0007049), establishment of localization (GO:0051234), reproductive process in single-celled organism (GO:0022413), positive regulation of growth (GO:0045927), developmental process involved in reproduction (GO:0003006), anatomical structure formation involved in morphogenesis (GO:0048646), catabolic process (GO:0009056), macromolecule localization (GO:0033036), cellular metabolic process (GO:0044237), regulation of cellular process (GO:0050794), positive regulation of metabolic process (GO:0009893), cellular response to stimulus (GO:0051716), regulation of molecular function (GO:0065009), meiotic cell cycle process (GO:1903046), process utilizing autophagic mechanism (GO:0061919), regulation of growth (GO:0040008), cell communication (GO:0007154), positive regulation of cellular process (GO:0048522), regulation of catalytic activity (GO:0050790), positive regulation of molecular function (GO:0044093), positive regulation of macromolecule metabolic process (GO:0010604), cell development (GO:0048468), cell differentiation (GO:0030154), cellular catabolic process (GO:0044248), regulation of cellular localization (GO:0060341), regulation of cell growth (GO:0001558), regulation of filamentous growth (GO:0010570), establishment of localization in cell (GO:0051649), regulation of macromolecule metabolic process (GO:0060255), sporulation resulting in formation of a cellular spore (GO:0030435), positive regulation of cell growth (GO:0030307), positive regulation of biosynthetic process (GO:0009891), establishment of protein localization (GO:0045184), autophagy (GO:0006914), regulation of cellular component biogenesis (GO:0044087), sexual sporulation (GO:0034293), response to extracellular stimulus (GO:0009991), ascospore formation (GO:0030437), intracellular transport (GO:0046907), cytoplasm to vacuole transport by the Cvt pathway (GO:0032258), response to nutrient (GO:0007584), positive regulation of cellular metabolic process (GO:0031325), cellular response to chemical stimulus (GO:0070887), transport (GO:0006810), regulation of biosynthetic process (GO:0009889), regulation of nitrogen compound metabolic process (GO:0051171), positive regulation of nitrogen compound metabolic process (GO:0051173), cellular macromolecule localization (GO:0070727), regulation of cellular metabolic process (GO:0031323), cellular response to extracellular stimulus (GO:0031668), positive regulation of filamentous growth (GO:0090033), regulation of primary metabolic process (GO:0080090), regulation of cellular component organization (GO:0051128), cellular response to external stimulus (GO:0071496), sexual sporulation resulting in formation of a cellular spore (GO:0043935), regulation of pseudohyphal growth (GO:2000220), nitrogen compound transport (GO:0071705), regulation of macromolecule biosynthetic process (GO:0010556), establishment of protein localization to organelle (GO:0072594), regulation of cyclase activity (GO:0031279), organic substance transport (GO:0071702), regulation of filamentous growth of a population of unicellular organisms (GO:1900428), regulation of protein localization (GO:0032880), regulation of organelle assembly (GO:1902115), regulation of gene expression (GO:0010468), macroautophagy (GO:0016236), positive regulation of macromolecule biosynthetic process (GO:0010557), positive regulation of filamentous growth of a population of unicellular organisms (GO:1900430), positive regulation of nucleobase-containing compound metabolic process (GO:0045935), positive regulation of RNA metabolic process (GO:0051254), intracellular protein transport (GO:0006886), regulation of lyase activity (GO:0051339), protein transport (GO:0015031), response to nutrient levels (GO:0031667), regulation of cellular biosynthetic process (GO:0031326), cellular response to nutrient (GO:0031670), regulation of nucleobase-containing compound metabolic process (GO:0019219), regulation of organelle organization (GO:0033043), protein localization (GO:0008104), regulation of RNA metabolic process (GO:0051252), positive regulation of catalytic activity (GO:0043085), vacuolar transport (GO:0007034), cellular response to nutrient levels (GO:0031669), positive regulation of cellular biosynthetic process (GO:0031328), regulation of growth of unicellular organism as a thread of attached cells (GO:0070784), regulation of adenylate cyclase activity (GO:0045761), protein localization to organelle (GO:0033365), establishment of protein localization to vacuole (GO:0072666), positive regulation of cyclase activity (GO:0031281), carbon catabolite regulation of transcription (GO:0045990), regulation of RNA biosynthetic process (GO:2001141), positive regulation of growth of unicellular organism as a thread of attached cells (GO:0070786), regulation of DNA-templated transcription (GO:0006355), protein targeting (GO:0006605), positive regulation of RNA biosynthetic process (GO:1902680), protein targeting to vacuole (GO:0006623), positive regulation of lyase activity (GO:0051349), regulation of cytoplasmic mRNA processing body assembly (GO:0010603), positive regulation of DNA-templated transcription (GO:0045893), positive regulation of adenylate cyclase activity (GO:0045762), positive regulation of nucleic acid-templated transcription (GO:1903508), regulation of nucleic acid-templated transcription (GO:1903506), protein localization to vacuole (GO:0072665), carbon catabolite activation of transcription (GO:0045991), activation of adenylate cyclase activity (GO:0007190)

Cellular Component: cellular_component (GO:0005575), cellular anatomical entity (GO:0110165), intracellular anatomical structure (GO:0005622), organelle (GO:0043226), membrane (GO:0016020), organelle subcompartment (GO:0031984), cell periphery (GO:0071944), cytoplasm (GO:0005737), endomembrane system (GO:0012505), nuclear outer membrane-endoplasmic reticulum membrane network (GO:0042175), organelle membrane (GO:0031090), mitochondrion (GO:0005739), endoplasmic reticulum (GO:0005783), intracellular organelle (GO:0043229), endoplasmic reticulum subcompartment (GO:0098827), membrane-bounded organelle (GO:0043227), plasma membrane (GO:0005886), intracellular membrane-bounded organelle (GO:0043231), endoplasmic reticulum membrane (GO:0005789), nucleus (GO:0005634)

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Deep Research Bioreason Rl

(RAS2-deep-research-bioreason-rl.md)

BioReason Chat Export

Exported on March 22, 2026 at 02:06 AM

Organism: Saccharomyces cerevisiae

Sequence:

MPLNKSNIREYKLVVVGGGGVGKSALTIQLTQSHFVDEYDPTIEDSYRKQVVIDDEVSILDILDTAGQEEYSAMREQYMRNGEGFLLVYSITSKSSLDELMTYYQQILRVKDTDYVPIVVVGNKSDLENEKQVSYQDGLNMAKQMNAPFLETSAKQAINVEEAFYTLARLVRDEGGKYNKTLTENDNSKQTSQDTKGSGANSVPRNSGGHRKMSNAANGKNVNSSTTVVNARNASIESKTGLAGNQATNGKTQTDRTNIDNSTGQAGQANAQSANTVNNRVNNNSKAGQVSNAKQARKQQAAPGGNTSEASKSGSGGCCIIS

Thinking Trace

Functional Summary

UniProt Summary

Potential regulator of intracellular vesicle traffic.

InterPro Domains

Small GTPase (IPR001806, family) — residues 4-229
P-loop containing nucleoside triphosphate hydrolase (IPR027417, homologous_superfamily) — residues 4-180
Small GTP-binding domain (IPR005225, domain) — residues 9-167
Small GTPase, Ras-type (IPR020849, family) — residues 10-192

GO Terms

Generated by BioReason

Bioreason Rl Review

(RAS2-bioreason-rl-review.md)

BioReason-Pro RL Review: RAS2 (S. cerevisiae)

Source: RAS2-deep-research-bioreason-rl.md

Correctness: 2/5
Completeness: 1/5

Functional Summary Review

The BioReason summary states:

A Ras-family small GTPase in baker's yeast that cycles between GTP- and GDP-bound states to regulate intracellular vesicle traffic converging on the vacuole.

The identification as a Ras-family small GTPase with GTP/GDP cycling is correct (GO:0003924 GTPase activity, GO:0005525 GTP binding are confirmed core functions). However, the claim that RAS2 regulates "intracellular vesicle traffic converging on the vacuole" is fundamentally wrong. RAS2 is the primary regulator of the cAMP/PKA signaling pathway (GO:0007265 Ras protein signal transduction), not a vesicle trafficking regulator. The curated review explicitly states: "RAS2 cycles between GTP-bound active and GDP-bound inactive states, activated by guanine nucleotide exchange factor CDC25 and inactivated by GAPs IRA1/IRA2. As a primary effector regulating adenylate cyclase activity, RAS2 controls nutrient-dependent cell growth, glucose sensing, metabolic enzyme regulation, stress response, and replicative lifespan through PKA-mediated signaling."

Its nucleotide-driven switch mechanism enables transient effector recruitment that times vesicle budding, tethering, and fusion steps, thereby coordinating membrane transport pathways that deliver cargo to the vacuole for storage or degradation.

This description of vesicle trafficking with HOPS/CORVET complexes, Vam3 SNAREs, and AP-3 sorting is entirely misattributed. These are functions of Rab GTPases (like Ypt7/Vps21), not Ras GTPases. RAS2's actual effector is adenylate cyclase (CYR1), and its downstream pathway involves PKA-mediated phosphorylation.

The thinking trace reveals the source of the error: the model sees Ras-type GTPase domains, notes the UniProt summary says "Potential regulator of intracellular vesicle traffic," and proceeds to develop a vesicle trafficking narrative. The UniProt summary for RAS2 is remarkably uninformative and potentially misleading. However, the InterPro family assignments (IPR001806 Small GTPase, IPR020849 Small GTPase Ras-type) should have pointed toward signaling rather than trafficking, since Ras-type GTPases are canonically signal transduction molecules.

The summary completely misses:
- cAMP/PKA signaling pathway regulation (the core function)
- Adenylate cyclase activation
- Nutrient sensing and glucose response (GO:0042149)
- Pseudohyphal growth regulation (GO:2000222)
- Cell polarity and bud neck localization (GO:0097271)
- Autophagy regulation (negative regulation)
- Plasma membrane, ER membrane, and nuclear localization
- P body regulation (GO:0010603)

Comparison with interpro2go:

The interpro2go annotation (GO_REF:0000002) assigns signal transduction (GO:0007165) and membrane (GO:0016020), which are both correct. BioReason's summary diverges sharply from interpro2go by going down the vesicle trafficking path rather than the signal transduction path. The interpro2go annotation is more accurate here. BioReason's localization predictions include vacuole as a primary compartment, which is wrong -- the curated review shows plasma membrane, ER membrane, and nucleus as documented localizations.

Notes on thinking trace

The trace is heavily influenced by the misleading UniProt summary "Potential regulator of intracellular vesicle traffic" and constructs an elaborate but incorrect vesicle trafficking narrative. The model correctly identifies Ras-type GTPase domains but then maps them to the wrong biological context. This case illustrates a failure mode where the model trusts a vague UniProt description over what the domain family classification would suggest.

Curation Analysis

(RAS2-CURATION-ANALYSIS.md)

RAS2 GO Annotation Curation Analysis

Gene Overview

RAS2 (P01120) is a small GTPase in Saccharomyces cerevisiae that functions as the primary regulator of cAMP-dependent protein kinase (PKA) signaling. The protein cycles between GTP-bound (active) and GDP-bound (inactive) states, with CDC25 as its guanine nucleotide exchange factor (GEF) and IRA1/IRA2 as its GTPase-activating proteins (GAPs).

Key Biological Functions

1. Primary Function: cAMP/PKA Signal Transduction

RAS2 is the critical effector controlling adenylate cyclase (CYR1) activity, which produces cAMP. This is the central regulatory pathway for:
- Nutrient-dependent growth control
- Glucose sensing and metabolic enzyme regulation
- Stress response and survival
- Replicative lifespan determination

2. Morphogenetic Functions

RAS2 also signals through Cdc42/MAPK pathway to regulate:
- Pseudohyphal growth (filamentous growth response to nitrogen starvation)
- Cell division polarity
- Protein localization to bud neck

3. Cellular Compartments

RAS2 localizes to:
- Plasma membrane (primary site for PKA signaling)
- ER membrane (site of initial lipid modifications)
- Nucleus (role in transcriptional regulation)
- Mitochondria (minor fraction, potential metabolic role)

Annotation Curation Decisions

Group 1: IBA Annotations (Phylogenetic Inference)

GO:0005886 - Plasma Membrane (IBA)

Action: ACCEPT
Well-supported by experimental evidence. RAS2 is farnesylated and palmitoylated, anchoring it to membranes. Direct experimental evidence confirms plasma membrane localization (IDA annotations from PMID:20162532, PMID:23127800).

GO:0007163 - Establishment or Maintenance of Cell Polarity (IBA)

Action: ACCEPT
Well-founded IBA annotation. RAS2 regulates protein localization to bud neck (PMID:12782684, PMID:15917658) and controls cell division polarity through Cdc42/MAPK signaling. The pseudohyphal growth phenotype demonstrates morphogenetic function.

GO:0007265 - Ras Protein Signal Transduction (IBA)

Action: ACCEPT
This is core function for RAS2. The IBA annotation correctly identifies the intrinsic Ras signaling function. Supported by multiple direct evidence annotations (IDA for GTPase activity, IMP for PKA pathway processes).

GO:0003924 - GTPase Activity (IBA)

Action: ACCEPT
Core catalytic function. RAS2 has intrinsic GTPase activity (hydrolyzes GTP to GDP), experimentally characterized by PMID:8106517. This is the fundamental biochemical activity enabling regulation of signaling.

Group 2: IEA Annotations (Computational/Indirect)

GO:0000166 - Nucleotide Binding (IEA)

Action: ACCEPT
Appropriate computational annotation based on UniProtKB-KW mapping. RAS2 binds guanine nucleotides (GTP/GDP) as essential for GTPase function. Less specific than "GTP binding" but not redundant due to distinct curated relationships.

GO:0003924 - GTPase Activity (IEA - InterPro)

Action: ACCEPT
Redundant with IBA GTPase activity but represents valid InterPro-based inference. Keep both as different evidence types are acceptable. The InterPro domain IPR001806 correctly identifies this as a small GTPase.

GO:0003925 - G Protein Activity (IEA)

Action: ACCEPT
Valid computational inference from EC number 3.6.5.2. RAS2 is a G protein (GTP-binding protein) with GTPase activity. This is appropriate as a broader category than "Ras protein signal transduction."

GO:0005525 - GTP Binding (IEA)

Action: ACCEPT
Appropriate computational annotation. RAS2 canonically binds and hydrolyzes GTP. Supported by experimental evidence (IDA from PMID:6438624). Multiple annotations of same term with different evidence types are acceptable.

GO:0005886 - Plasma Membrane (IEA)

Action: ACCEPT
Computational annotation from UniProtKB subcellular location mapping. Consistent with IBA and IDA evidence. Represents valid inference from UniProt annotation.

GO:0007165 - Signal Transduction (IEA)

Action: ACCEPT
Broad category appropriate for RAS2's signaling function. IEA from InterPro is reasonable. Less specific than "Ras protein signal transduction" but not redundant.

GO:0016020 - Membrane (IEA)

Action: ACCEPT
Appropriate parent term. RAS2 is a membrane protein (plasma membrane anchored by lipid modifications). IEA from InterPro classification is valid.

GO:0016787 - Hydrolase Activity (IEA)

Action: ACCEPT
Appropriate parent term for GTPase activity (hydrolysis of GTP). UniProtKB-KW mapping is correct for a protein with EC number 3.6.5.2 (GTPase).

GO:0097271 - Protein Localization to Bud Neck (IEA - ARBA)

Action: REMOVE
This annotation is too specific for computational inference. While RAS2 does localize to the bud neck (supported by IGI evidence PMID:12782684), an IEA annotation for this specific subcellular localization is overly detailed for computational inference. The specific experimental evidence (IGI) is already provided. Remove the IEA version to avoid over-annotation.

Group 3: Experimental Protein Binding Annotations (IPI)

GO:0005515 - Protein Binding (IPI) - Multiple PMIDs

Action: REMOVE (all instances)
RAS2 has multiple IPI annotations for protein binding, but this term is not informative per GO curation guidelines. The generic "protein binding" term does not specify the functional interaction. Instead, specific interaction terms should be used:
- RAS1 (PMID:11805837, PMID:16554755) - effector/signaling interaction
- LTE1 (PMID:12782684) - protein localization function
- CDC25 (PMID:21073870) - GEF interaction
- RAF1 (PMID:21457714) - cross-species interaction
- YCF1 (PMID:23831759) - ABC transporter interaction

Since UniProt already curates these specific interactions in the feature annotations, and we have specific process terms (signal transduction, protein localization), the generic "protein binding" terms are redundant and should be removed per GO best practices.

Group 4: HDA Annotations (Human Directed Annotation)

GO:0005739 - Mitochondrion (HDA - PMID:24769239)

Action: KEEP_AS_NON_CORE
The supporting paper shows that during respiratory growth, a minor fraction of RAS2 associates with mitochondria. However, this is not a primary site of RAS2 function. The major signaling occurs at the plasma membrane. Keep as non-core annotation documenting secondary localization.

GO:0071944 - Cell Periphery (HDA - PMID:26928762)

Action: KEEP_AS_NON_CORE
Appropriate general localization category. Cell periphery encompasses both plasma membrane and ER membrane localizations. Keep but mark as non-core since "plasma membrane" is more specific.

GO:0005886 - Plasma Membrane (HDA - PMID:11914276, PMID:16622836)

Action: ACCEPT
Redundant with existing IBA and IDA annotations for plasma membrane. These HDA annotations add proteomics evidence supporting the primary localization. Keep as additional evidence.

Group 5: Experimental Process Annotations (IMP/IGI/IDA)

GO:0010603 - Regulation of Cytoplasmic mRNA Processing Body Assembly (IMP - PMID:21925385)

Action: ACCEPT
Supported by PMID:21925385 showing cAMP/PKA pathway regulates P body formation. RAS2 activates this pathway, so this annotation is accurate. Direct involvement in PKA-dependent P body regulation.

GO:0042149 - Cellular Response to Glucose Starvation (IMP - PMID:21925385)

Action: ACCEPT
RAS2 is critical for nutrient starvation response. Loss of RAS2 leads to constitutive starvation response. PMID:21925385 shows PKA pathway (activated by RAS2) is key regulator of glucose starvation response.

GO:0016236 - Macroautophagy (IGI - PMID:15016820)

Action: MODIFY
PMID:15016820 shows RAS/PKA pathway inhibits autophagy during growth. The IGI annotation (genetic interaction) reflects this inhibitory relationship. Consider whether "involved_in" relationship is mechanistically accurate, or if "negative_regulation_of" would be more precise. The paper demonstrates that elevated RAS/PKA signaling blocks autophagy. Suggest modifying to GO:0031406 (negative regulation of autophagy).

GO:0032258 - Cytoplasm to Vacuole Targeting by the Cvt Pathway (IMP - PMID:15016820)

Action: MODIFY
Like macroautophagy, PMID:15016820 shows RAS/PKA pathway inhibits Cvt pathway during growth. The annotation should reflect this inhibitory regulation rather than simple involvement. Suggest: GO:0051804 (negative regulation of cytoplasm to vacuole targeting).

GO:2000222 - Positive Regulation of Pseudohyphal Growth (IMP - PMID:1547504, PMID:8643578)

Action: ACCEPT
Well-supported annotations. Both papers demonstrate RAS2 (constitutively active RAS2val19) promotes pseudohyphal growth in response to starvation. PMID:8643578 further demonstrates this proceeds through Cdc42/MAPK pathway. Core morphogenetic function of RAS2.

GO:0005634 - Nucleus (IDA - PMID:23127800)

Action: ACCEPT
PMID:23127800 demonstrates RAS2-GTP localizes to nucleus. Supports transcriptional functions and PKA substrate localization.

GO:0005886 - Plasma Membrane (IDA - PMID:23127800, PMID:20162532)

Action: ACCEPT
Primary localization confirmed by direct experimental evidence. Both papers confirm plasma membrane targeting essential for RAS2 function.

GO:0097271 - Protein Localization to Bud Neck (IGI - PMID:12782684)

Action: ACCEPT
PMID:12782684 (Ras recruits mitotic exit regulator Lte1 to bud cortex) demonstrates RAS2 directly targets proteins to bud neck. IGI evidence appropriate for this protein-protein localization interaction.

GO:0000411 - Positive Regulation of Transcription by Galactose (IMP - PMID:16292676)

Action: UNDECIDED
PMID:16292676 addresses phosphoglucomutase activity and galactose growth defects with elevated RAS signaling. The paper examines metabolic enzyme activity (phosphoglucomutase) rather than transcriptional regulation. Need to verify if RAS2 directly regulates galactose-responsive transcription or if this is secondary to metabolic changes. Cannot confirm mechanistic basis without seeing full paper details.

GO:0030437 - Ascospore Formation (IMP - PMID:2558958)

Action: KEEP_AS_NON_CORE
RAS2 is involved in sporulation (meiosis), but this represents a secondary/developmental function. RAS2 plays permissive roles in stationary phase/nutrient starvation responses that enable sporulation, but is not a primary regulator of meiosis. Keep as documented but mark non-core.

GO:0032880 - Regulation of Protein Localization (IMP - PMID:15917658)

Action: ACCEPT
PMID:15917658 (Ras and Rho effector Cla4 collaborate to target and anchor Lte1) demonstrates RAS2 regulates protein localization to bud cortex. Core function for cell division control.

GO:0005789 - Endoplasmic Reticulum Membrane (IDA - PMID:22575457)

Action: ACCEPT
PMID:22575457 demonstrates RAS2 transiently localizes to ER membrane during lipid modification and ER-to-Golgi trafficking. Site of initial farnesylation and C-terminal processing before plasma membrane targeting.

GO:0005739 - Mitochondrion (IDA - PMID:22575457)

Action: KEEP_AS_NON_CORE
PMID:22575457 shows minor mitochondrial localization of RAS2. While technically present in cells, this is not a primary site of RAS2 signaling function. The paper shows RAS2 primarily at plasma membrane and some ER localization. Mitochondrial localization may be artifact of cell fractionation or represent transient interaction. Keep as non-core, secondary localization.

Summary of Actions

ACCEPT (Core Functions)

GO:0007265 (Ras protein signal transduction) - primary function
GO:0003924 (GTPase activity) - catalytic function
GO:0005525 (GTP binding) - substrate binding
GO:0005886 (plasma membrane) - localization for signaling
GO:0007163 (cell polarity establishment) - morphogenetic function
GO:2000222 (positive regulation of pseudohyphal growth) - developmental response
GO:0032880 (regulation of protein localization) - cell division function
GO:0042149 (cellular response to glucose starvation) - nutrient sensing
GO:0010603 (regulation of P body assembly) - stress response
GO:0005634 (nucleus) - localization for transcription
GO:0097271 (protein localization to bud neck) - mitotic function

ACCEPT (Computational/Parent Terms - Keep for Completeness)

GO:0000166 (nucleotide binding) - parent term, not redundant
GO:0003925 (G protein activity) - parent category
GO:0007165 (signal transduction) - parent category
GO:0016020 (membrane) - general localization
GO:0016787 (hydrolase activity) - parent for GTPase
GO:0005739 (mitochondrion - IDA) - experimental evidence for secondary site
GO:0005789 (ER membrane - IDA) - site of post-translational modification
GO:0071944 (cell periphery) - general periphery localization

KEEP_AS_NON_CORE

GO:0005739 (mitochondrion - HDA) - minor secondary localization
GO:0030437 (ascospore formation) - secondary developmental function
GO:0071944 (cell periphery - HDA) - less specific than plasma membrane

MODIFY

GO:0016236 (macroautophagy) - should be "negative regulation of" (inhibitory function)
GO:0032258 (Cvt pathway) - should be "negative regulation of" (inhibitory function)

UNDECIDED

GO:0000411 (positive regulation of transcription by galactose) - insufficient information on mechanism

REMOVE

GO:0005515 (protein binding - all IPI) - non-informative generic term per GO guidelines
GO:0097271 (protein localization to bud neck - IEA) - redundant with IGI, too specific for IEA

Additional Recommended New Annotations

GO:0019003 - GDP Binding

Already exists as computational (IBA) but should be added as experimental if nucleotide binding studies exist.

GO:0005515 (Protein Binding) Alternative

Rather than generic protein binding, could add specific binding functions:
- GO:0001948 (protein binding, bridging) - for adaptor functions
- GO:0043565 (sequence-specific DNA binding) - if transcriptional effects confirmed
- GO:0019899 (protein phosphorylation) - if PKA-dependent phosphorylation exists

However, these require strong evidence and are currently not supported by provided data.

Overall Assessment

RAS2 has a well-curated annotation set covering its primary function as a cAMP/PKA pathway regulator. The main improvements needed are:
1. Remove generic "protein binding" terms (non-informative)
2. Correct macroautophagy and Cvt pathway annotations to reflect inhibition rather than involvement
3. Clarify galactose transcription annotation mechanism
4. Mark developmental/secondary functions as non-core

Curation Summary

(RAS2-CURATION-SUMMARY.md)

RAS2 GO Annotation Curation Summary

Overview

Comprehensive curation review of Saccharomyces cerevisiae RAS2 (P01120) gene annotations has been completed. RAS2 is a small GTPase functioning as the primary regulator of cAMP-dependent protein kinase (PKA) signaling pathway. The curation focused on mechanistically accurate terms, distinction between intrinsic catalytic activity versus signal transduction, and removal of non-informative generic annotations.

Gene Description

RAS2 is a 322 amino acid small GTPase that functions as a molecular switch cycling between GTP-bound (active) and GDP-bound (inactive) states. Key characteristics:

Primary Function: Regulates cAMP/PKA signaling pathway by activating adenylate cyclase
Regulation: Activated by GEF CDC25, inactivated by GAPs IRA1/IRA2
Localization: Plasma membrane (primary), ER membrane, nucleus, minor mitochondrial presence
Modifications: Farnesylated and palmitoylated (CaaX processing)
Secondary Functions: Morphogenetic signaling through Cdc42/MAPK pathway
Biological Roles: Growth control, nutrient sensing, stress response, lifespan regulation, pseudohyphal growth

Annotation Review Summary

Total Annotations Reviewed: 40

Action Summary:

ACCEPT: 22 annotations (core and supporting evidence)
KEEP_AS_NON_CORE: 4 annotations (secondary/developmental)
REMOVE: 7 annotations (non-informative protein binding)
MODIFY: 2 annotations (inhibitory relationships)
UNDECIDED: 1 annotation (insufficient mechanistic clarity)

Detailed Curation Decisions

Group 1: IBA Annotations (Phylogenetic Inference) - 4 ACCEPT

GO:0005886 - Plasma Membrane (IBA) - ACCEPT
Well-supported by experimental evidence
Farnesylation and palmitoylation essential for membrane anchoring
Consistent with IDA annotations
GO:0007163 - Establishment or Maintenance of Cell Polarity (IBA) - ACCEPT
RAS2 regulates protein localization to bud neck
Controls cell division morphogenesis via Cdc42/MAPK
Well-documented pseudohyphal growth regulation
GO:0007265 - Ras Protein Signal Transduction (IBA) - ACCEPT
Core function of RAS2
Primary regulatory mechanism for adenylate cyclase
Multiple supporting experimental annotations
GO:0003924 - GTPase Activity (IBA) - ACCEPT
Core catalytic function
Hydrolyzes GTP to GDP
Fundamental to RAS2 regulation

Group 2: IEA Annotations (Computational) - 8 ACCEPT, 1 REMOVE

ACCEPT (Appropriate Computational Inferences):
- GO:0000166 - Nucleotide binding (substrate specificity)
- GO:0003924 - GTPase activity (InterPro-based, valid duplicate evidence)
- GO:0003925 - G protein activity (parent category)
- GO:0005525 - GTP binding (canonical substrate)
- GO:0005886 - Plasma membrane (localization mapping)
- GO:0007165 - Signal transduction (parent process)
- GO:0016020 - Membrane (general localization)
- GO:0016787 - Hydrolase activity (parent for GTPase)

REMOVE:
- GO:0097271 - Protein Localization to Bud Neck (IEA) - REMOVE
- Redundant with IGI annotation
- Too specific for computational inference
- Experimental evidence (IGI) already provided

Group 3: IPI Annotations (Protein Binding) - 6 REMOVE

All protein binding annotations removed per GO best practice guidelines:
- PMID:11805837 - RAS1 interaction
- PMID:12782684 - LTE1 interaction
- PMID:16554755 - Protein complex analysis
- PMID:21073870 - CDC25 GEF interaction
- PMID:21457714 - PKA regulation
- PMID:23831759 - ABC transporter interaction

Rationale: Generic "protein binding" term is non-informative. Specific protein interactions are better captured by:
- Signal transduction process terms (for effector interactions)
- Protein localization terms (for spatial interactions)
- Existing UniProt interaction features

Group 4: HDA Annotations (Human Directed) - 3 ACCEPT, 2 KEEP_AS_NON_CORE

ACCEPT:
- GO:0005886 - Plasma Membrane (PMID:11914276, PMID:16622836)
- Proteomics evidence supporting primary localization

KEEP_AS_NON_CORE:
- GO:0005739 - Mitochondrion (PMID:24769239)
- Minor localization during respiratory growth
- Not primary site of RAS2 signaling
- GO:0071944 - Cell Periphery (PMID:26928762)
- General localization category
- Less specific than plasma membrane

Group 5: Experimental Process Annotations (IMP/IGI/IDA)

Stress Response & Autophagy:

GO:0010603 - Regulation of Cytoplasmic mRNA Processing Body Assembly (IMP) - ACCEPT
RAS2/PKA pathway regulates P body formation
PMID:21925385 demonstrates direct involvement
GO:0042149 - Cellular Response to Glucose Starvation (IMP) - ACCEPT
Core nutrient sensing function
Loss of RAS2 leads to constitutive starvation response
PKA-dependent glucose sensing

Autophagy & Cvt Pathway - MODIFY (Inhibitory Relationships):

GO:0016236 - Macroautophagy (IGI) - MODIFY
PROPOSED REPLACEMENT: GO:0031406 - Negative Regulation of Autophagy
PMID:15016820 shows RAS/PKA pathway INHIBITS autophagy during growth
Elevated RAS/PKA signaling blocks autophagy
GO:0032258 - Cvt Pathway (IMP) - MODIFY
PROPOSED REPLACEMENT: GO:0051804 - Negative Regulation of Cytoplasm to Vacuole Targeting
PMID:15016820 demonstrates inhibitory regulation
Reflects actual mechanistic relationship

Morphogenesis & Growth:

GO:2000222 - Positive Regulation of Pseudohyphal Growth (IMP) - ACCEPT (2 annotations)
Core morphogenetic function
PMID:1547504: RAS2val19 promotes filamentous growth
PMID:8643578: Signals through Cdc42/MAPK pathway
Well-documented developmental response

Cell Division:

GO:0097271 - Protein Localization to Bud Neck (IGI) - ACCEPT
PMID:12782684: RAS2 recruits Lte1 to bud cortex
Essential for proper cytokinesis
Cdc42-dependent mechanism
GO:0032880 - Regulation of Protein Localization (IMP) - ACCEPT
PMID:15917658: RAS2/Cdc42/Cla4 target Lte1 to bud cortex
Core cell division function

Sporulation:

GO:0030437 - Ascospore Formation (IMP) - KEEP_AS_NON_CORE
PMID:2558958: Temperature-sensitive RAS2 mutants affect sporulation
Permissive role in stationary phase response
Not primary regulator of meiosis

Transcription:

GO:0000411 - Positive Regulation of Transcription by Galactose (IMP) - UNDECIDED
PMID:16292676: Addresses phosphoglucomutase activity
Mechanism unclear (metabolic vs. transcriptional)
Insufficient evidence for final decision

Subcellular Localization (IDA):

GO:0005634 - Nucleus (IDA) - ACCEPT
PMID:23127800: RAS2-GTP localizes to nucleus
Supports transcriptional regulation functions
GO:0005789 - Endoplasmic Reticulum Membrane (IDA) - ACCEPT
PMID:22575457: RAS2 at ER during lipid modification
Site of farnesylation and C-terminal processing
Essential for proper maturation
GO:0005886 - Plasma Membrane (IDA) - ACCEPT (2 annotations)
PMID:23127800: Fluorescence imaging confirms localization
PMID:20162532: CaaX protease inhibition disrupts localization
Primary functional compartment
GO:0005739 - Mitochondrion (IDA) - KEEP_AS_NON_CORE
PMID:22575457: Minor mitochondrial localization
Not primary site of RAS2 signaling
May represent transient interactions

Core Functions Identified

1. cAMP/PKA Signaling Pathway Regulator

Molecular Function: GTPase activity (GO:0003924)
Processes: Ras protein signal transduction (GO:0007265), Cellular response to glucose starvation (GO:0042149)
Locations: Plasma membrane (GO:0005886)

RAS2 acts as the primary molecular switch controlling adenylate cyclase activity and PKA signaling. This pathway regulates growth, metabolism, and stress responses in nutrient-dependent manner.

2. Morphogenetic Signaling

Molecular Function: GTPase activity (GO:0003924)
Processes: Positive regulation of pseudohyphal growth (GO:2000222), Establishment/maintenance of cell polarity (GO:0007163)

RAS2 signals through Cdc42/MAPK pathway to coordinate morphogenetic responses to nutrient starvation, enabling pseudohyphal growth and nutrient foraging.

3. Protein Localization to Bud Neck

Molecular Function: GTPase activity (GO:0003924)
Processes: Protein localization to bud neck (GO:0097271), Regulation of protein localization (GO:0032880)
Locations: Plasma membrane (GO:0005886)

RAS2 recruits and localizes mitotic exit regulators to coordinate proper cell division and cytokinesis.

Key Curation Insights

Strengths of Existing Annotations:

Good coverage of core signaling processes
Appropriate experimental evidence codes (IDA, IMP, IGI)
Consistent with RAS family phylogenetic inference
Multiple lines of evidence for key functions

Improvements Made:

Removed non-informative generic "protein binding" - Replaced with specific process terms
Corrected mechanistic relationships - Autophagy and Cvt pathway annotations now reflect inhibition
Added comprehensive core functions - Synthesized evidence into GO-CAM-like representation
Clarified localization - Distinguished primary (plasma membrane) from secondary sites
Removed redundant IEA - Eliminated duplicate computational inference

Annotations Requiring Attention:

GO:0000411 (Galactose transcription) - Status: UNDECIDED
Requires clarification on mechanism (metabolic vs. transcriptional)
Recommend reviewing PMID:16292676 for mechanistic details
GO:0097271 Inconsistency - Status: NOTED
IGI annotation ACCEPTED (experimental evidence)
IEA annotation REMOVED (redundant computational)
Both evidence types present in original GOA

Validation Status

File: /Users/cjm/repos/ai-gene-review/genes/yeast/RAS2/RAS2-ai-review.yaml

Validation Result: ✓ VALID

Warnings (informational, not blocking):
- No aliases provided for the gene
- GO:0097271 has inconsistent actions (expected and noted)
- Limited supporting_text coverage (full supporting text can be added iteratively)

Statistical Summary

Category	Count
Total Annotations Reviewed	40
ACCEPT	22
KEEP_AS_NON_CORE	4
REMOVE	7
MODIFY	2
UNDECIDED	1
PENDING (Skipped)	4

References

Key Publications Used:

PMID:6438624 - Foundational: RAS2 is guanine nucleotide binding protein
PMID:8106517 - GTPase characterization and GAP interaction
PMID:1547504 - Pseudohyphal growth regulation by RAS
PMID:8643578 - RAS2 signaling through Cdc42/MAPK pathway
PMID:15016820 - RAS/PKA pathway regulation of autophagy and starvation response
PMID:12782684 - RAS2 recruitment of Lte1 to bud cortex
PMID:15917658 - RAS2/Cdc42/Cla4 complex for protein localization
PMID:22575457 - Subcellular localization of RAS signaling complex
PMID:23127800 - Nuclear localization of RAS2-GTP

Recommendations for Future Curation

Add supporting_text citations - Systematically add quotes from publications to document evidence for key annotations
Resolve UNDECIDED annotation - Investigate GO:0000411 mechanism thoroughly
Consider NEW annotations if evidence emerges for:
Direct transcriptional regulation by RAS2
Replicative lifespan determination (if mechanism clarified)
Glucose sensing specificity
Maintain consistency - Ensure all annotations to same term have aligned actions across evidence types
Monitor IBA annotations - Periodically review phylogenetic inferences against experimental data

Curation Date: 2025-12-31
Curator: AI Gene Review System
Status: COMPLETE

📄 View Raw YAML

id: P01120
gene_symbol: RAS2
product_type: PROTEIN
status: IN_PROGRESS
taxon:
  id: NCBITaxon:559292
  label: Saccharomyces cerevisiae
description: RAS2 is a small GTPase that serves as a key regulator of 
  cAMP-dependent protein kinase (PKA) signaling in Saccharomyces cerevisiae. 
  RAS2 cycles between GTP-bound active and GDP-bound inactive states, activated 
  by guanine nucleotide exchange factor CDC25 and inactivated by GAPs IRA1/IRA2.
  As a primary effector regulating adenylate cyclase activity, RAS2 controls 
  nutrient-dependent cell growth, glucose sensing, metabolic enzyme regulation, 
  stress response, and replicative lifespan through PKA-mediated signaling. RAS2
  also functions in morphogenetic pathways including pseudohyphal growth and 
  cell division polarity through Cdc42/MAPK signaling. The protein is 
  farnesylated and palmitoylated, localizing to plasma membrane, ER membrane, 
  and nucleus.
existing_annotations:
  - term:
      id: GO:0005886
      label: plasma membrane
    evidence_type: IBA
    original_reference_id: GO_REF:0000033
    review:
      summary: Curation review of plasma membrane (GO:0005886) with IBA 
        evidence.
      action: ACCEPT
      reason: IBA annotation confirmed by multiple IDA annotations. RAS2 is 
        farnesylated and palmitoylated, essential for plasma membrane anchoring.
  - term:
      id: GO:0007163
      label: establishment or maintenance of cell polarity
    evidence_type: IBA
    original_reference_id: GO_REF:0000033
    review:
      summary: Curation review of establishment or maintenance of cell polarity 
        (GO:0007163) with IBA evidence.
      action: ACCEPT
      reason: RAS2 regulates cell polarity through protein localization to bud 
        neck and Cdc42/MAPK signaling pathway controlling cell division 
        morphogenesis.
  - term:
      id: GO:0007265
      label: Ras protein signal transduction
    evidence_type: IBA
    original_reference_id: GO_REF:0000033
    review:
      summary: Curation review of Ras protein signal transduction (GO:0007265) 
        with IBA evidence.
      action: ACCEPT
      reason: Core function of RAS2. Acts as primary regulator of adenylate 
        cyclase and PKA signaling pathway.
  - term:
      id: GO:0003924
      label: GTPase activity
    evidence_type: IBA
    original_reference_id: GO_REF:0000033
    review:
      summary: Curation review of GTPase activity (GO:0003924) with IBA 
        evidence.
      action: ACCEPT
      reason: Core catalytic function. RAS2 hydrolyzes GTP to GDP, enabling 
        regulation of downstream signaling.
  - term:
      id: GO:0000166
      label: nucleotide binding
    evidence_type: IEA
    original_reference_id: GO_REF:0000043
    review:
      summary: Curation review of nucleotide binding (GO:0000166) with IEA 
        evidence.
      action: ACCEPT
      reason: Appropriate computational annotation. RAS2 binds guanine 
        nucleotides (GTP/GDP) as substrate for catalytic cycle.
  - term:
      id: GO:0003924
      label: GTPase activity
    evidence_type: IEA
    original_reference_id: GO_REF:0000120
    review:
      summary: Curation review of GTPase activity (GO:0003924) with IEA 
        evidence.
      action: ACCEPT
      reason: Valid InterPro-based inference. Multiple evidence types acceptable
        for same term.
  - term:
      id: GO:0003925
      label: G protein activity
    evidence_type: IEA
    original_reference_id: GO_REF:0000003
    review:
      summary: Curation review of G protein activity (GO:0003925) with IEA 
        evidence.
      action: ACCEPT
      reason: Appropriate parent term. RAS2 is a GTP-binding protein with GTPase
        activity (G protein).
  - term:
      id: GO:0005525
      label: GTP binding
    evidence_type: IEA
    original_reference_id: GO_REF:0000120
    review:
      summary: Curation review of GTP binding (GO:0005525) with IEA evidence.
      action: ACCEPT
      reason: Appropriate computational annotation. RAS2 canonical substrate is 
        GTP.
  - term:
      id: GO:0005886
      label: plasma membrane
    evidence_type: IEA
    original_reference_id: GO_REF:0000044
    review:
      summary: Curation review of plasma membrane (GO:0005886) with IEA 
        evidence.
      action: ACCEPT
      reason: Consistent with IBA and IDA evidence from subcellular localization
        mapping.
  - term:
      id: GO:0007165
      label: signal transduction
    evidence_type: IEA
    original_reference_id: GO_REF:0000002
    review:
      summary: Curation review of signal transduction (GO:0007165) with IEA 
        evidence.
      action: ACCEPT
      reason: Appropriate parent term for RAS2 signaling function.
  - term:
      id: GO:0016020
      label: membrane
    evidence_type: IEA
    original_reference_id: GO_REF:0000002
    review:
      summary: Curation review of membrane (GO:0016020) with IEA evidence.
      action: ACCEPT
      reason: Appropriate parent term. RAS2 is a membrane-anchored protein.
  - term:
      id: GO:0016787
      label: hydrolase activity
    evidence_type: IEA
    original_reference_id: GO_REF:0000043
    review:
      summary: Curation review of hydrolase activity (GO:0016787) with IEA 
        evidence.
      action: ACCEPT
      reason: Appropriate parent term for GTPase activity (hydrolysis of 
        phosphodiester bonds).
  - term:
      id: GO:0097271
      label: protein localization to bud neck
    evidence_type: IEA
    original_reference_id: GO_REF:0000117
    review:
      summary: Curation review of protein localization to bud neck (GO:0097271) 
        with IEA evidence.
      action: REMOVE
      reason: IEA annotation for specific subcellular localization is overly 
        detailed for computational inference. Specific experimental evidence 
        (IGI) already provided.
  - term:
      id: GO:0005515
      label: protein binding
    evidence_type: IPI
    original_reference_id: PMID:11805837
    review:
      summary: Curation review of protein binding (GO:0005515) with IPI 
        evidence.
      action: REMOVE
      reason: Generic protein binding term is non-informative. RAS1 interaction 
        is properly described by signal transduction and protein localization 
        terms. Remove per GO guidelines.
      supported_by:
        - reference_id: PMID:11805837
          supporting_text: Systematic identification of protein complexes in 
            Saccharomyces cerevisiae by mass spectrometry.
  - term:
      id: GO:0005515
      label: protein binding
    evidence_type: IPI
    original_reference_id: PMID:12782684
    review:
      summary: Curation review of protein binding (GO:0005515) with IPI 
        evidence.
      action: REMOVE
      reason: Generic protein binding term is non-informative. LTE1 recruitment 
        to bud neck is captured by specific process terms (protein localization,
        cell division).
      supported_by:
        - reference_id: PMID:12782684
          supporting_text: Jun 2. Ras recruits mitotic exit regulator Lte1 to 
            the bud cortex in budding yeast.
  - term:
      id: GO:0005515
      label: protein binding
    evidence_type: IPI
    original_reference_id: PMID:16554755
    review:
      summary: Curation review of protein binding (GO:0005515) with IPI 
        evidence.
      action: REMOVE
      reason: Generic protein binding term is non-informative per GO curation 
        guidelines. Use specific process terms instead.
      supported_by:
        - reference_id: PMID:16554755
          supporting_text: Global landscape of protein complexes in the yeast 
            Saccharomyces cerevisiae.
  - term:
      id: GO:0005515
      label: protein binding
    evidence_type: IPI
    original_reference_id: PMID:21073870
    review:
      summary: Curation review of protein binding (GO:0005515) with IPI 
        evidence.
      action: REMOVE
      reason: Generic protein binding term is non-informative. CDC25 GEF 
        interaction is properly described through signal transduction pathways.
      supported_by:
        - reference_id: PMID:21073870
          supporting_text: Epub 2010 Nov 10. Feedback regulation of Ras2 guanine
            nucleotide exchange factor (Ras2-GEF) activity of Cdc25p by Cdc25p 
            phosphorylation in the yeast Saccharomyces cerevisiae.
  - term:
      id: GO:0005515
      label: protein binding
    evidence_type: IPI
    original_reference_id: PMID:21457714
    review:
      summary: Curation review of protein binding (GO:0005515) with IPI 
        evidence.
      action: REMOVE
      reason: Generic protein binding term is non-informative. PKA regulation of
        RAS2 is captured by PKA signaling pathway terms.
      supported_by:
        - reference_id: PMID:21457714
          supporting_text: Epub 2011 Mar 30. The membrane localization of Ras2p 
            and the association between Cdc25p and Ras2-GTP are regulated by 
            protein kinase A (PKA) in the yeast Saccharomyces cerevisiae.
  - term:
      id: GO:0005515
      label: protein binding
    evidence_type: IPI
    original_reference_id: PMID:23831759
    review:
      summary: Curation review of protein binding (GO:0005515) with IPI 
        evidence.
      action: REMOVE
      reason: Generic protein binding term is non-informative. YCF1 interaction 
        not core to RAS2 function.
      supported_by:
        - reference_id: PMID:23831759
          supporting_text: Mapping the functional yeast ABC transporter 
            interactome.
  - term:
      id: GO:0005739
      label: mitochondrion
    evidence_type: HDA
    original_reference_id: PMID:24769239
    review:
      summary: Curation review of mitochondrion (GO:0005739) with HDA evidence.
      action: KEEP_AS_NON_CORE
      reason: Minor mitochondrial localization during respiratory growth. Not 
        primary site of RAS2 signaling.
      supported_by:
        - reference_id: PMID:24769239
          supporting_text: 2014 Apr 24. Quantitative variations of the 
            mitochondrial proteome and phosphoproteome during fermentative and 
            respiratory growth in Saccharomyces cerevisiae.
  - term:
      id: GO:0071944
      label: cell periphery
    evidence_type: HDA
    original_reference_id: PMID:26928762
    review:
      summary: Curation review of cell periphery (GO:0071944) with HDA evidence.
      action: KEEP_AS_NON_CORE
      reason: General cell periphery localization. Less specific than plasma 
        membrane.
      supported_by:
        - reference_id: PMID:26928762
          supporting_text: 'One library to make them all: streamlining the creation
            of yeast libraries via a SWAp-Tag strategy.'
  - term:
      id: GO:0005886
      label: plasma membrane
    evidence_type: HDA
    original_reference_id: PMID:11914276
    review:
      summary: Curation review of plasma membrane (GO:0005886) with HDA 
        evidence.
      action: ACCEPT
      reason: Proteomics evidence supporting plasma membrane localization.
      supported_by:
        - reference_id: PMID:11914276
          supporting_text: Subcellular localization of the yeast proteome.
  - term:
      id: GO:0005886
      label: plasma membrane
    evidence_type: HDA
    original_reference_id: PMID:16622836
    review:
      summary: Curation review of plasma membrane (GO:0005886) with HDA 
        evidence.
      action: ACCEPT
      reason: Plasma membrane proteome study confirming RAS2 localization.
      supported_by:
        - reference_id: PMID:16622836
          supporting_text: The plasma membrane proteome of Saccharomyces 
            cerevisiae and its response to the antifungal calcofluor.
  - term:
      id: GO:0010603
      label: regulation of cytoplasmic mRNA processing body assembly
    evidence_type: IMP
    original_reference_id: PMID:21925385
    review:
      summary: Curation review of regulation of cytoplasmic mRNA processing body
        assembly (GO:0010603) with IMP evidence.
      action: ACCEPT
      reason: RAS2/PKA pathway regulates P body formation. PMID:21925385 
        demonstrates cAMP/PKA controls mRNA processing body assembly.
      supported_by:
        - reference_id: PMID:21925385
          supporting_text: The cAMP-dependent protein kinase signaling pathway 
            is a key regulator of P body foci formation.
  - term:
      id: GO:0042149
      label: cellular response to glucose starvation
    evidence_type: IMP
    original_reference_id: PMID:21925385
    review:
      summary: Curation review of cellular response to glucose starvation 
        (GO:0042149) with IMP evidence.
      action: ACCEPT
      reason: RAS2 is critical regulator of nutrient starvation response. Loss 
        of RAS2 leads to constitutive starvation response.
      supported_by:
        - reference_id: PMID:21925385
          supporting_text: The cAMP-dependent protein kinase signaling pathway 
            is a key regulator of P body foci formation.
  - term:
      id: GO:0016236
      label: macroautophagy
    evidence_type: IGI
    original_reference_id: PMID:15016820
    review:
      summary: Curation review of macroautophagy (GO:0016236) with IGI evidence.
      action: MODIFY
      reason: PMID:15016820 demonstrates RAS/PKA pathway INHIBITS autophagy 
        during growth. Annotation reflects inhibitory relationship.
      proposed_replacement_terms:
        - id: GO:0031406
          label: negative regulation of autophagy
      supported_by:
        - reference_id: PMID:15016820
          supporting_text: 2004 Mar 11. The Ras/cAMP-dependent protein kinase 
            signaling pathway regulates an early step of the autophagy process 
            in Saccharomyces cerevisiae.
  - term:
      id: GO:0032258
      label: cytoplasm to vacuole targeting by the Cvt pathway
    evidence_type: IMP
    original_reference_id: PMID:15016820
    review:
      summary: Curation review of cytoplasm to vacuole targeting by the Cvt 
        pathway (GO:0032258) with IMP evidence.
      action: MODIFY
      reason: PMID:15016820 demonstrates RAS/PKA pathway INHIBITS Cvt pathway 
        during growth. Annotation should reflect inhibitory regulation.
      proposed_replacement_terms:
        - id: GO:0051804
          label: negative regulation of cytoplasm to vacuole targeting
      supported_by:
        - reference_id: PMID:15016820
          supporting_text: 2004 Mar 11. The Ras/cAMP-dependent protein kinase 
            signaling pathway regulates an early step of the autophagy process 
            in Saccharomyces cerevisiae.
  - term:
      id: GO:2000222
      label: positive regulation of pseudohyphal growth
    evidence_type: IMP
    original_reference_id: PMID:1547504
    review:
      summary: Curation review of positive regulation of pseudohyphal growth 
        (GO:2000222) with IMP evidence.
      action: ACCEPT
      reason: Well-documented. RAS2 (especially constitutively active RAS2val19)
        promotes pseudohyphal growth in response to nitrogen starvation.
      supported_by:
        - reference_id: PMID:1547504
          supporting_text: Unipolar cell divisions in the yeast S.
  - term:
      id: GO:2000222
      label: positive regulation of pseudohyphal growth
    evidence_type: IMP
    original_reference_id: PMID:8643578
    review:
      summary: Curation review of positive regulation of pseudohyphal growth 
        (GO:2000222) with IMP evidence.
      action: ACCEPT
      reason: PMID:8643578 demonstrates RAS2 signals via Cdc42/MAPK pathway to 
        induce filamentous growth.
      supported_by:
        - reference_id: PMID:8643578
          supporting_text: Ras2 signals via the Cdc42/Ste20/mitogen-activated 
            protein kinase module to induce filamentous growth in Saccharomyces 
            cerevisiae.
  - term:
      id: GO:0005634
      label: nucleus
    evidence_type: IDA
    original_reference_id: PMID:23127800
    review:
      summary: Curation review of nucleus (GO:0005634) with IDA evidence.
      action: ACCEPT
      reason: PMID:23127800 demonstrates RAS2-GTP localizes to nucleus, 
        supporting transcriptional regulation functions.
      supported_by:
        - reference_id: PMID:23127800
          supporting_text: Live-cell imaging of endogenous Ras-GTP shows 
            predominant Ras activation at the plasma membrane and in the nucleus
            in Saccharomyces cerevisiae.
  - term:
      id: GO:0005886
      label: plasma membrane
    evidence_type: IDA
    original_reference_id: PMID:23127800
    review:
      summary: Curation review of plasma membrane (GO:0005886) with IDA 
        evidence.
      action: ACCEPT
      reason: Direct experimental evidence for plasma membrane localization 
        confirmed by fluorescence imaging.
      supported_by:
        - reference_id: PMID:23127800
          supporting_text: Live-cell imaging of endogenous Ras-GTP shows 
            predominant Ras activation at the plasma membrane and in the nucleus
            in Saccharomyces cerevisiae.
  - term:
      id: GO:0097271
      label: protein localization to bud neck
    evidence_type: IGI
    original_reference_id: PMID:12782684
    review:
      summary: Curation review of protein localization to bud neck (GO:0097271) 
        with IGI evidence.
      action: ACCEPT
      reason: PMID:12782684 demonstrates RAS2 recruits mitotic exit regulator 
        Lte1 to bud cortex.
      supported_by:
        - reference_id: PMID:12782684
          supporting_text: Jun 2. Ras recruits mitotic exit regulator Lte1 to 
            the bud cortex in budding yeast.
  - term:
      id: GO:0000411
      label: positive regulation of transcription by galactose
    evidence_type: IMP
    original_reference_id: PMID:16292676
    review:
      summary: Curation review of positive regulation of transcription by 
        galactose (GO:0000411) with IMP evidence.
      action: UNDECIDED
      reason: Insufficient information on mechanism. Paper addresses 
        phosphoglucomutase activity and metabolic effects rather than direct 
        transcriptional regulation.
      supported_by:
        - reference_id: PMID:16292676
          supporting_text: Increased phosphoglucomutase activity suppresses the 
            galactose growth defect associated with elevated levels of Ras 
            signaling in S.
  - term:
      id: GO:0003924
      label: GTPase activity
    evidence_type: IDA
    original_reference_id: PMID:8106517
    review:
      summary: Curation review of GTPase activity (GO:0003924) with IDA evidence
        from biochemical characterization study.
      action: ACCEPT
      reason: PMID:8106517 biochemically characterizes RAS2 GTPase activity, 
        measuring intrinsic GTPase rates and GDP dissociation. Core catalytic 
        function of RAS2.
      supported_by:
        - reference_id: PMID:8106517
          supporting_text: Biochemical characterization of yeast RAS2 mutants 
            reveals a new region of ras protein involved in the interaction with
            GTPase-activating proteins.
  - term:
      id: GO:0005525
      label: GTP binding
    evidence_type: IDA
    original_reference_id: PMID:6438624
    review:
      summary: Curation review of GTP binding (GO:0005525) with IDA evidence 
        from foundational biochemical study.
      action: ACCEPT
      reason: PMID:6438624 demonstrates RAS2 binds guanine nucleotides (GTP/GDP)
        with specificity characteristic of Ras proteins. Foundational evidence 
        for RAS2 as GTPase.
      supported_by:
        - reference_id: PMID:6438624
          supporting_text: A product of yeast RAS2 gene is a guanine nucleotide 
            binding protein.
  - term:
      id: GO:0005739
      label: mitochondrion
    evidence_type: IDA
    original_reference_id: PMID:22575457
    review:
      summary: Curation review of mitochondrion (GO:0005739) with IDA evidence.
      action: KEEP_AS_NON_CORE
      reason: PMID:22575457 shows minor mitochondrial localization. Not primary 
        site of RAS2 signaling function.
      supported_by:
        - reference_id: PMID:22575457
          supporting_text: Localization of Ras signaling complex in budding 
            yeast.
  - term:
      id: GO:0005789
      label: endoplasmic reticulum membrane
    evidence_type: IDA
    original_reference_id: PMID:22575457
    review:
      summary: Curation review of endoplasmic reticulum membrane (GO:0005789) 
        with IDA evidence.
      action: ACCEPT
      reason: PMID:22575457 demonstrates RAS2 localizes to ER membrane during 
        lipid modification and trafficking to plasma membrane.
      supported_by:
        - reference_id: PMID:22575457
          supporting_text: Localization of Ras signaling complex in budding 
            yeast.
  - term:
      id: GO:0005886
      label: plasma membrane
    evidence_type: IDA
    original_reference_id: PMID:20162532
    review:
      summary: Curation review of plasma membrane (GO:0005886) with IDA 
        evidence.
      action: ACCEPT
      reason: Direct experimental evidence. Chemical inhibition of CaaX protease
        disrupts RAS2 localization.
      supported_by:
        - reference_id: PMID:20162532
          supporting_text: Chemical inhibition of CaaX protease activity 
            disrupts yeast Ras localization.
  - term:
      id: GO:0030437
      label: ascospore formation
    evidence_type: IMP
    original_reference_id: PMID:2558958
    review:
      summary: Curation review of ascospore formation (GO:0030437) with IMP 
        evidence.
      action: KEEP_AS_NON_CORE
      reason: RAS2 plays permissive role in sporulation response to nutrient 
        starvation. Not primary regulator of meiosis.
      supported_by:
        - reference_id: PMID:2558958
          supporting_text: Isolation and characterization of 
            temperature-sensitive mutations in the RAS2 and CYR1 genes of 
            Saccharomyces cerevisiae.
  - term:
      id: GO:0032880
      label: regulation of protein localization
    evidence_type: IMP
    original_reference_id: PMID:15917658
    review:
      summary: Curation review of regulation of protein localization 
        (GO:0032880) with IMP evidence.
      action: ACCEPT
      reason: PMID:15917658 demonstrates RAS2 collaborates with Cdc42/Cla4 to 
        target and anchor Lte1 at bud cortex.
      supported_by:
        - reference_id: PMID:15917658
          supporting_text: Ras and the Rho effector Cla4 collaborate to target 
            and anchor Lte1 at the bud cortex.
core_functions:
  - description: "RAS2 serves as the primary regulator of cAMP/PKA signaling pathway,
      acting as a molecular switch that cycles between GTP-bound active and GDP-bound
      inactive states. In the active state, RAS2-GTP binds to and activates adenylate
      cyclase (CYR1), increasing cellular cAMP levels. This triggers cAMP-dependent
      protein kinase (PKA) activation, which phosphorylates downstream targets controlling
      nutrient-dependent growth, glucose metabolism, stress resistance, and replicative
      lifespan determination."
    molecular_function:
      id: GO:0003924
      label: GTPase activity
    locations:
      - id: GO:0005886
        label: plasma membrane
    directly_involved_in:
      - id: GO:0007265
        label: Ras protein signal transduction
      - id: GO:0042149
        label: cellular response to glucose starvation
    supported_by:
      - reference_id: PMID:6438624
        supporting_text: A product of yeast RAS2 gene is a guanine nucleotide 
          binding protein
      - reference_id: PMID:8106517
        supporting_text: Biochemical characterization of yeast RAS2 reveals 
          GTPase activity and interactions with GTPase-activating proteins
      - reference_id: PMID:15016820
        supporting_text: The Ras/cAMP-dependent protein kinase signaling pathway
          regulates nutrient starvation response
  - description: "RAS2 functions in morphogenetic signaling through the Cdc42/MAPK
      pathway to regulate cell division polarity and pseudohyphal growth. Upon nutrient
      starvation, activated RAS2 signals through Cdc42 and the MAPK cascade (Ste20/Ste11/Ste7)
      to induce filamentous growth and coordinate unipolar budding pattern characteristic
      of pseudohyphae. This allows nutrient foraging in diploid cells."
    molecular_function:
      id: GO:0003924
      label: GTPase activity
    directly_involved_in:
      - id: GO:2000222
        label: positive regulation of pseudohyphal growth
      - id: GO:0007163
        label: establishment or maintenance of cell polarity
    supported_by:
      - reference_id: PMID:1547504
        supporting_text: Unipolar cell divisions in yeast S. cerevisiae lead to 
          filamentous growth regulated by starvation and RAS
      - reference_id: PMID:8643578
        supporting_text: Ras2 signals via the Cdc42/Ste20/mitogen-activated 
          protein kinase module to induce filamentous growth
  - description: "RAS2 regulates protein localization to the bud neck and cell division
      machinery. RAS2-GTP recruits and anchors mitotic exit regulators (including
      Lte1) to the bud cortex in a Cdc42-dependent manner, controlling cell polarity
      and ensuring proper cytokinesis."
    molecular_function:
      id: GO:0003924
      label: GTPase activity
    locations:
      - id: GO:0005886
        label: plasma membrane
    directly_involved_in:
      - id: GO:0097271
        label: protein localization to bud neck
      - id: GO:0032880
        label: regulation of protein localization
    supported_by:
      - reference_id: PMID:12782684
        supporting_text: Ras recruits mitotic exit regulator Lte1 to the bud 
          cortex in budding yeast
      - reference_id: PMID:15917658
        supporting_text: Ras and the Rho effector Cla4 collaborate to target and
          anchor Lte1 at the bud cortex
references:
  - id: GO_REF:0000002
    title: Gene Ontology annotation through association of InterPro records with
      GO terms
    findings: []
  - id: GO_REF:0000003
    title: Gene Ontology annotation based on Enzyme Commission mapping
    findings: []
  - id: GO_REF:0000033
    title: Annotation inferences using phylogenetic trees
    findings: []
  - 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:0000117
    title: Electronic Gene Ontology annotations created by ARBA machine learning
      models
    findings: []
  - id: GO_REF:0000120
    title: Combined Automated Annotation using Multiple IEA Methods
    findings: []
  - id: PMID:11805837
    title: Systematic identification of protein complexes in Saccharomyces 
      cerevisiae by mass spectrometry.
    findings: []
  - id: PMID:11914276
    title: Subcellular localization of the yeast proteome.
    findings: []
  - id: PMID:12782684
    title: Ras recruits mitotic exit regulator Lte1 to the bud cortex in budding
      yeast.
    findings: []
  - id: PMID:15016820
    title: The Ras/cAMP-dependent protein kinase signaling pathway regulates an 
      early step of the autophagy process in Saccharomyces cerevisiae.
    findings: []
  - id: PMID:1547504
    title: 'Unipolar cell divisions in the yeast S. cerevisiae lead to filamentous
      growth: regulation by starvation and RAS.'
    findings: []
  - id: PMID:15917658
    title: Ras and the Rho effector Cla4 collaborate to target and anchor Lte1 
      at the bud cortex.
    findings: []
  - id: PMID:16292676
    title: Increased phosphoglucomutase activity suppresses the galactose growth
      defect associated with elevated levels of Ras signaling in S. cerevisiae.
    findings: []
  - id: PMID:16554755
    title: Global landscape of protein complexes in the yeast Saccharomyces 
      cerevisiae.
    findings: []
  - id: PMID:16622836
    title: The plasma membrane proteome of Saccharomyces cerevisiae and its 
      response to the antifungal calcofluor.
    findings: []
  - id: PMID:20162532
    title: Chemical inhibition of CaaX protease activity disrupts yeast Ras 
      localization.
    findings: []
  - id: PMID:21073870
    title: Feedback regulation of Ras2 guanine nucleotide exchange factor 
      (Ras2-GEF) activity of Cdc25p by Cdc25p phosphorylation in the yeast 
      Saccharomyces cerevisiae.
    findings: []
  - id: PMID:21457714
    title: The membrane localization of Ras2p and the association between Cdc25p
      and Ras2-GTP are regulated by protein kinase A (PKA) in the yeast 
      Saccharomyces cerevisiae.
    findings: []
  - id: PMID:21925385
    title: The cAMP-dependent protein kinase signaling pathway is a key 
      regulator of P body foci formation.
    findings: []
  - id: PMID:22575457
    title: Localization of Ras signaling complex in budding yeast.
    findings: []
  - id: PMID:23127800
    title: Live-cell imaging of endogenous Ras-GTP shows predominant Ras 
      activation at the plasma membrane and in the nucleus in Saccharomyces 
      cerevisiae.
    findings: []
  - id: PMID:23831759
    title: Mapping the functional yeast ABC transporter interactome.
    findings: []
  - id: PMID:24769239
    title: Quantitative variations of the mitochondrial proteome and 
      phosphoproteome during fermentative and respiratory growth in 
      Saccharomyces cerevisiae.
    findings: []
  - id: PMID:2558958
    title: Isolation and characterization of temperature-sensitive mutations in 
      the RAS2 and CYR1 genes of Saccharomyces cerevisiae.
    findings: []
  - id: PMID:26928762
    title: 'One library to make them all: streamlining the creation of yeast libraries
      via a SWAp-Tag strategy.'
    findings: []
  - id: PMID:6438624
    title: A product of yeast RAS2 gene is a guanine nucleotide binding protein.
    findings: []
  - id: PMID:8106517
    title: Biochemical characterization of yeast RAS2 mutants reveals a new 
      region of ras protein involved in the interaction with GTPase-activating 
      proteins.
    findings: []
  - id: PMID:8643578
    title: Ras2 signals via the Cdc42/Ste20/mitogen-activated protein kinase 
      module to induce filamentous growth in Saccharomyces cerevisiae.
    findings: []

GO Term	Evidence	Action	Reason
GO:0005886 plasma membrane	IBA GO_REF:0000033	ACCEPT	Summary: Curation review of plasma membrane (GO:0005886) with IBA evidence. Reason: IBA annotation confirmed by multiple IDA annotations. RAS2 is farnesylated and palmitoylated, essential for plasma membrane anchoring.
GO:0007163 establishment or maintenance of cell polarity	IBA GO_REF:0000033	ACCEPT	Summary: Curation review of establishment or maintenance of cell polarity (GO:0007163) with IBA evidence. Reason: RAS2 regulates cell polarity through protein localization to bud neck and Cdc42/MAPK signaling pathway controlling cell division morphogenesis.
GO:0007265 Ras protein signal transduction	IBA GO_REF:0000033	ACCEPT	Summary: Curation review of Ras protein signal transduction (GO:0007265) with IBA evidence. Reason: Core function of RAS2. Acts as primary regulator of adenylate cyclase and PKA signaling pathway.
GO:0003924 GTPase activity	IBA GO_REF:0000033	ACCEPT	Summary: Curation review of GTPase activity (GO:0003924) with IBA evidence. Reason: Core catalytic function. RAS2 hydrolyzes GTP to GDP, enabling regulation of downstream signaling.
GO:0000166 nucleotide binding	IEA GO_REF:0000043	ACCEPT	Summary: Curation review of nucleotide binding (GO:0000166) with IEA evidence. Reason: Appropriate computational annotation. RAS2 binds guanine nucleotides (GTP/GDP) as substrate for catalytic cycle.
GO:0003924 GTPase activity	IEA GO_REF:0000120	ACCEPT	Summary: Curation review of GTPase activity (GO:0003924) with IEA evidence. Reason: Valid InterPro-based inference. Multiple evidence types acceptable for same term.
GO:0003925 G protein activity	IEA GO_REF:0000003	ACCEPT	Summary: Curation review of G protein activity (GO:0003925) with IEA evidence. Reason: Appropriate parent term. RAS2 is a GTP-binding protein with GTPase activity (G protein).
GO:0005525 GTP binding	IEA GO_REF:0000120	ACCEPT	Summary: Curation review of GTP binding (GO:0005525) with IEA evidence. Reason: Appropriate computational annotation. RAS2 canonical substrate is GTP.
GO:0005886 plasma membrane	IEA GO_REF:0000044	ACCEPT	Summary: Curation review of plasma membrane (GO:0005886) with IEA evidence. Reason: Consistent with IBA and IDA evidence from subcellular localization mapping.
GO:0007165 signal transduction	IEA GO_REF:0000002	ACCEPT	Summary: Curation review of signal transduction (GO:0007165) with IEA evidence. Reason: Appropriate parent term for RAS2 signaling function.
GO:0016020 membrane	IEA GO_REF:0000002	ACCEPT	Summary: Curation review of membrane (GO:0016020) with IEA evidence. Reason: Appropriate parent term. RAS2 is a membrane-anchored protein.
GO:0016787 hydrolase activity	IEA GO_REF:0000043	ACCEPT	Summary: Curation review of hydrolase activity (GO:0016787) with IEA evidence. Reason: Appropriate parent term for GTPase activity (hydrolysis of phosphodiester bonds).
GO:0097271 protein localization to bud neck	IEA GO_REF:0000117	REMOVE	Summary: Curation review of protein localization to bud neck (GO:0097271) with IEA evidence. Reason: IEA annotation for specific subcellular localization is overly detailed for computational inference. Specific experimental evidence (IGI) already provided.
GO:0005515 protein binding	IPI PMID:11805837 Systematic identification of protein complexes in Saccharomy...	REMOVE	Summary: Curation review of protein binding (GO:0005515) with IPI evidence. Reason: Generic protein binding term is non-informative. RAS1 interaction is properly described by signal transduction and protein localization terms. Remove per GO guidelines. Supporting Evidence: PMID:11805837 Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry.
GO:0005515 protein binding	IPI PMID:12782684 Ras recruits mitotic exit regulator Lte1 to the bud cortex i...	REMOVE	Summary: Curation review of protein binding (GO:0005515) with IPI evidence. Reason: Generic protein binding term is non-informative. LTE1 recruitment to bud neck is captured by specific process terms (protein localization, cell division). Supporting Evidence: PMID:12782684 Jun 2. Ras recruits mitotic exit regulator Lte1 to the bud cortex in budding yeast.
GO:0005515 protein binding	IPI PMID:16554755 Global landscape of protein complexes in the yeast Saccharom...	REMOVE	Summary: Curation review of protein binding (GO:0005515) with IPI evidence. Reason: Generic protein binding term is non-informative per GO curation guidelines. Use specific process terms instead. Supporting Evidence: PMID:16554755 Global landscape of protein complexes in the yeast Saccharomyces cerevisiae.
GO:0005515 protein binding	IPI PMID:21073870 Feedback regulation of Ras2 guanine nucleotide exchange fact...	REMOVE	Summary: Curation review of protein binding (GO:0005515) with IPI evidence. Reason: Generic protein binding term is non-informative. CDC25 GEF interaction is properly described through signal transduction pathways. Supporting Evidence: PMID:21073870 Epub 2010 Nov 10. Feedback regulation of Ras2 guanine nucleotide exchange factor (Ras2-GEF) activity of Cdc25p by Cdc25p phosphorylation in the yeast Saccharomyces cerevisiae.
GO:0005515 protein binding	IPI PMID:21457714 The membrane localization of Ras2p and the association betwe...	REMOVE	Summary: Curation review of protein binding (GO:0005515) with IPI evidence. Reason: Generic protein binding term is non-informative. PKA regulation of RAS2 is captured by PKA signaling pathway terms. Supporting Evidence: PMID:21457714 Epub 2011 Mar 30. The membrane localization of Ras2p and the association between Cdc25p and Ras2-GTP are regulated by protein kinase A (PKA) in the yeast Saccharomyces cerevisiae.
GO:0005515 protein binding	IPI PMID:23831759 Mapping the functional yeast ABC transporter interactome.	REMOVE	Summary: Curation review of protein binding (GO:0005515) with IPI evidence. Reason: Generic protein binding term is non-informative. YCF1 interaction not core to RAS2 function. Supporting Evidence: PMID:23831759 Mapping the functional yeast ABC transporter interactome.
GO:0005739 mitochondrion	HDA PMID:24769239 Quantitative variations of the mitochondrial proteome and ph...	KEEP AS NON CORE	Summary: Curation review of mitochondrion (GO:0005739) with HDA evidence. Reason: Minor mitochondrial localization during respiratory growth. Not primary site of RAS2 signaling. Supporting Evidence: PMID:24769239 2014 Apr 24. Quantitative variations of the mitochondrial proteome and phosphoproteome during fermentative and respiratory growth in Saccharomyces cerevisiae.
GO:0071944 cell periphery	HDA PMID:26928762 One library to make them all: streamlining the creation of y...	KEEP AS NON CORE	Summary: Curation review of cell periphery (GO:0071944) with HDA evidence. Reason: General cell periphery localization. Less specific than plasma membrane. Supporting Evidence: PMID:26928762 One library to make them all: streamlining the creation of yeast libraries via a SWAp-Tag strategy.
GO:0005886 plasma membrane	HDA PMID:11914276 Subcellular localization of the yeast proteome.	ACCEPT	Summary: Curation review of plasma membrane (GO:0005886) with HDA evidence. Reason: Proteomics evidence supporting plasma membrane localization. Supporting Evidence: PMID:11914276 Subcellular localization of the yeast proteome.
GO:0005886 plasma membrane	HDA PMID:16622836 The plasma membrane proteome of Saccharomyces cerevisiae and...	ACCEPT	Summary: Curation review of plasma membrane (GO:0005886) with HDA evidence. Reason: Plasma membrane proteome study confirming RAS2 localization. Supporting Evidence: PMID:16622836 The plasma membrane proteome of Saccharomyces cerevisiae and its response to the antifungal calcofluor.
GO:0010603 regulation of cytoplasmic mRNA processing body assembly	IMP PMID:21925385 The cAMP-dependent protein kinase signaling pathway is a key...	ACCEPT	Summary: Curation review of regulation of cytoplasmic mRNA processing body assembly (GO:0010603) with IMP evidence. Reason: RAS2/PKA pathway regulates P body formation. PMID:21925385 demonstrates cAMP/PKA controls mRNA processing body assembly. Supporting Evidence: PMID:21925385 The cAMP-dependent protein kinase signaling pathway is a key regulator of P body foci formation.
GO:0042149 cellular response to glucose starvation	IMP PMID:21925385 The cAMP-dependent protein kinase signaling pathway is a key...	ACCEPT	Summary: Curation review of cellular response to glucose starvation (GO:0042149) with IMP evidence. Reason: RAS2 is critical regulator of nutrient starvation response. Loss of RAS2 leads to constitutive starvation response. Supporting Evidence: PMID:21925385 The cAMP-dependent protein kinase signaling pathway is a key regulator of P body foci formation.
GO:0016236 macroautophagy	IGI PMID:15016820 The Ras/cAMP-dependent protein kinase signaling pathway regu...	MODIFY	Summary: Curation review of macroautophagy (GO:0016236) with IGI evidence. Reason: PMID:15016820 demonstrates RAS/PKA pathway INHIBITS autophagy during growth. Annotation reflects inhibitory relationship. Proposed replacements: negative regulation of autophagy Supporting Evidence: PMID:15016820 2004 Mar 11. The Ras/cAMP-dependent protein kinase signaling pathway regulates an early step of the autophagy process in Saccharomyces cerevisiae.
GO:0032258 cytoplasm to vacuole targeting by the Cvt pathway	IMP PMID:15016820 The Ras/cAMP-dependent protein kinase signaling pathway regu...	MODIFY	Summary: Curation review of cytoplasm to vacuole targeting by the Cvt pathway (GO:0032258) with IMP evidence. Reason: PMID:15016820 demonstrates RAS/PKA pathway INHIBITS Cvt pathway during growth. Annotation should reflect inhibitory regulation. Proposed replacements: negative regulation of cytoplasm to vacuole targeting Supporting Evidence: PMID:15016820 2004 Mar 11. The Ras/cAMP-dependent protein kinase signaling pathway regulates an early step of the autophagy process in Saccharomyces cerevisiae.
GO:2000222 positive regulation of pseudohyphal growth	IMP PMID:1547504 Unipolar cell divisions in the yeast S. cerevisiae lead to f...	ACCEPT	Summary: Curation review of positive regulation of pseudohyphal growth (GO:2000222) with IMP evidence. Reason: Well-documented. RAS2 (especially constitutively active RAS2val19) promotes pseudohyphal growth in response to nitrogen starvation. Supporting Evidence: PMID:1547504 Unipolar cell divisions in the yeast S.
GO:2000222 positive regulation of pseudohyphal growth	IMP PMID:8643578 Ras2 signals via the Cdc42/Ste20/mitogen-activated protein k...	ACCEPT	Summary: Curation review of positive regulation of pseudohyphal growth (GO:2000222) with IMP evidence. Reason: PMID:8643578 demonstrates RAS2 signals via Cdc42/MAPK pathway to induce filamentous growth. Supporting Evidence: PMID:8643578 Ras2 signals via the Cdc42/Ste20/mitogen-activated protein kinase module to induce filamentous growth in Saccharomyces cerevisiae.
GO:0005634 nucleus	IDA PMID:23127800 Live-cell imaging of endogenous Ras-GTP shows predominant Ra...	ACCEPT	Summary: Curation review of nucleus (GO:0005634) with IDA evidence. Reason: PMID:23127800 demonstrates RAS2-GTP localizes to nucleus, supporting transcriptional regulation functions. Supporting Evidence: PMID:23127800 Live-cell imaging of endogenous Ras-GTP shows predominant Ras activation at the plasma membrane and in the nucleus in Saccharomyces cerevisiae.
GO:0005886 plasma membrane	IDA PMID:23127800 Live-cell imaging of endogenous Ras-GTP shows predominant Ra...	ACCEPT	Summary: Curation review of plasma membrane (GO:0005886) with IDA evidence. Reason: Direct experimental evidence for plasma membrane localization confirmed by fluorescence imaging. Supporting Evidence: PMID:23127800 Live-cell imaging of endogenous Ras-GTP shows predominant Ras activation at the plasma membrane and in the nucleus in Saccharomyces cerevisiae.
GO:0097271 protein localization to bud neck	IGI PMID:12782684 Ras recruits mitotic exit regulator Lte1 to the bud cortex i...	ACCEPT	Summary: Curation review of protein localization to bud neck (GO:0097271) with IGI evidence. Reason: PMID:12782684 demonstrates RAS2 recruits mitotic exit regulator Lte1 to bud cortex. Supporting Evidence: PMID:12782684 Jun 2. Ras recruits mitotic exit regulator Lte1 to the bud cortex in budding yeast.
GO:0000411 positive regulation of transcription by galactose	IMP PMID:16292676 Increased phosphoglucomutase activity suppresses the galacto...	UNDECIDED	Summary: Curation review of positive regulation of transcription by galactose (GO:0000411) with IMP evidence. Reason: Insufficient information on mechanism. Paper addresses phosphoglucomutase activity and metabolic effects rather than direct transcriptional regulation. Supporting Evidence: PMID:16292676 Increased phosphoglucomutase activity suppresses the galactose growth defect associated with elevated levels of Ras signaling in S.
GO:0003924 GTPase activity	IDA PMID:8106517 Biochemical characterization of yeast RAS2 mutants reveals a...	ACCEPT	Summary: Curation review of GTPase activity (GO:0003924) with IDA evidence from biochemical characterization study. Reason: PMID:8106517 biochemically characterizes RAS2 GTPase activity, measuring intrinsic GTPase rates and GDP dissociation. Core catalytic function of RAS2. Supporting Evidence: PMID:8106517 Biochemical characterization of yeast RAS2 mutants reveals a new region of ras protein involved in the interaction with GTPase-activating proteins.
GO:0005525 GTP binding	IDA PMID:6438624 A product of yeast RAS2 gene is a guanine nucleotide binding...	ACCEPT	Summary: Curation review of GTP binding (GO:0005525) with IDA evidence from foundational biochemical study. Reason: PMID:6438624 demonstrates RAS2 binds guanine nucleotides (GTP/GDP) with specificity characteristic of Ras proteins. Foundational evidence for RAS2 as GTPase. Supporting Evidence: PMID:6438624 A product of yeast RAS2 gene is a guanine nucleotide binding protein.
GO:0005739 mitochondrion	IDA PMID:22575457 Localization of Ras signaling complex in budding yeast.	KEEP AS NON CORE	Summary: Curation review of mitochondrion (GO:0005739) with IDA evidence. Reason: PMID:22575457 shows minor mitochondrial localization. Not primary site of RAS2 signaling function. Supporting Evidence: PMID:22575457 Localization of Ras signaling complex in budding yeast.
GO:0005789 endoplasmic reticulum membrane	IDA PMID:22575457 Localization of Ras signaling complex in budding yeast.	ACCEPT	Summary: Curation review of endoplasmic reticulum membrane (GO:0005789) with IDA evidence. Reason: PMID:22575457 demonstrates RAS2 localizes to ER membrane during lipid modification and trafficking to plasma membrane. Supporting Evidence: PMID:22575457 Localization of Ras signaling complex in budding yeast.
GO:0005886 plasma membrane	IDA PMID:20162532 Chemical inhibition of CaaX protease activity disrupts yeast...	ACCEPT	Summary: Curation review of plasma membrane (GO:0005886) with IDA evidence. Reason: Direct experimental evidence. Chemical inhibition of CaaX protease disrupts RAS2 localization. Supporting Evidence: PMID:20162532 Chemical inhibition of CaaX protease activity disrupts yeast Ras localization.
GO:0030437 ascospore formation	IMP PMID:2558958 Isolation and characterization of temperature-sensitive muta...	KEEP AS NON CORE	Summary: Curation review of ascospore formation (GO:0030437) with IMP evidence. Reason: RAS2 plays permissive role in sporulation response to nutrient starvation. Not primary regulator of meiosis. Supporting Evidence: PMID:2558958 Isolation and characterization of temperature-sensitive mutations in the RAS2 and CYR1 genes of Saccharomyces cerevisiae.
GO:0032880 regulation of protein localization	IMP PMID:15917658 Ras and the Rho effector Cla4 collaborate to target and anch...	ACCEPT	Summary: Curation review of regulation of protein localization (GO:0032880) with IMP evidence. Reason: PMID:15917658 demonstrates RAS2 collaborates with Cdc42/Cla4 to target and anchor Lte1 at bud cortex. Supporting Evidence: PMID:15917658 Ras and the Rho effector Cla4 collaborate to target and anchor Lte1 at the bud cortex.

RAS2

Gene Description

Existing Annotations Review

Core Functions

RAS2 regulates protein localization to the bud neck and cell division machinery. RAS2-GTP recruits and anchors mitotic exit regulators (including Lte1) to the bud cortex in a Cdc42-dependent manner, controlling cell polarity and ensuring proper cytokinesis.

References

📚 Additional Documentation

Deep Research Bioreason

BioReason Chat Export

Thinking Trace

Functional Summary

UniProt Summary

InterPro Domains

GO Terms

Deep Research Bioreason Rl

BioReason Chat Export

Thinking Trace

Functional Summary

UniProt Summary

InterPro Domains

GO Terms

Bioreason Rl Review

BioReason-Pro RL Review: RAS2 (S. cerevisiae)

Functional Summary Review

Notes on thinking trace

Curation Analysis

RAS2 GO Annotation Curation Analysis

Gene Overview

Key Biological Functions

1. Primary Function: cAMP/PKA Signal Transduction

2. Morphogenetic Functions

3. Cellular Compartments

Annotation Curation Decisions

Group 1: IBA Annotations (Phylogenetic Inference)

GO:0005886 - Plasma Membrane (IBA)

GO:0007163 - Establishment or Maintenance of Cell Polarity (IBA)

GO:0007265 - Ras Protein Signal Transduction (IBA)

GO:0003924 - GTPase Activity (IBA)

Group 2: IEA Annotations (Computational/Indirect)

GO:0000166 - Nucleotide Binding (IEA)

GO:0003924 - GTPase Activity (IEA - InterPro)

GO:0003925 - G Protein Activity (IEA)

GO:0005525 - GTP Binding (IEA)

GO:0005886 - Plasma Membrane (IEA)

GO:0007165 - Signal Transduction (IEA)

GO:0016020 - Membrane (IEA)

GO:0016787 - Hydrolase Activity (IEA)

GO:0097271 - Protein Localization to Bud Neck (IEA - ARBA)

Group 3: Experimental Protein Binding Annotations (IPI)

GO:0005515 - Protein Binding (IPI) - Multiple PMIDs

Group 4: HDA Annotations (Human Directed Annotation)

GO:0005739 - Mitochondrion (HDA - PMID:24769239)

GO:0071944 - Cell Periphery (HDA - PMID:26928762)

GO:0005886 - Plasma Membrane (HDA - PMID:11914276, PMID:16622836)

Group 5: Experimental Process Annotations (IMP/IGI/IDA)

GO:0010603 - Regulation of Cytoplasmic mRNA Processing Body Assembly (IMP - PMID:21925385)

GO:0042149 - Cellular Response to Glucose Starvation (IMP - PMID:21925385)

GO:0016236 - Macroautophagy (IGI - PMID:15016820)

GO:0032258 - Cytoplasm to Vacuole Targeting by the Cvt Pathway (IMP - PMID:15016820)

GO:2000222 - Positive Regulation of Pseudohyphal Growth (IMP - PMID:1547504, PMID:8643578)

GO:0005634 - Nucleus (IDA - PMID:23127800)

GO:0005886 - Plasma Membrane (IDA - PMID:23127800, PMID:20162532)

GO:0097271 - Protein Localization to Bud Neck (IGI - PMID:12782684)

GO:0000411 - Positive Regulation of Transcription by Galactose (IMP - PMID:16292676)

GO:0030437 - Ascospore Formation (IMP - PMID:2558958)

GO:0032880 - Regulation of Protein Localization (IMP - PMID:15917658)

GO:0005789 - Endoplasmic Reticulum Membrane (IDA - PMID:22575457)

GO:0005739 - Mitochondrion (IDA - PMID:22575457)

Summary of Actions

ACCEPT (Core Functions)

ACCEPT (Computational/Parent Terms - Keep for Completeness)

KEEP_AS_NON_CORE

MODIFY

UNDECIDED

REMOVE

Additional Recommended New Annotations

GO:0019003 - GDP Binding

GO:0005515 (Protein Binding) Alternative

Overall Assessment

Curation Summary