GRPEL1 encodes the primary human mitochondrial GrpE-like nucleotide exchange factor (NEF) that functions within the TIM23/PAM import motor complex. It accelerates ADP release from mitochondrial HSP70 (HSPA9/mortalin), enabling the chaperone to rebind ATP and release substrate proteins. GRPEL1 is essential for mitochondrial protein import, matrix protein folding, and Fe-S cluster biogenesis. It binds HSPA9 with high affinity (KD ~39 nM) and forms a stable hetero-oligomer with its paralog GRPEL2. GRPEL1 is the essential basal NEF (pLI ~0.90), while GRPEL2 provides stress-adaptive redox regulation.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
|
GO:0000774
adenyl-nucleotide exchange factor activity
|
IBA
GO_REF:0000033 |
ACCEPT |
Summary: GRPEL1 is a nucleotide exchange factor (NEF) for mitochondrial HSP70 (HSPA9). It accelerates ADP release and ATP rebinding on HSPA9, which is the defining biochemical activity of an adenyl-nucleotide exchange factor. Quantitative binding data show GRPEL1 binds HSPA9 with KD ~39 nM and inhibits single-turnover ATP hydrolysis at saturating concentrations, consistent with NEF activity (Srivastava et al., JBC 2017). The IBA annotation is phylogenetically well-supported, as GrpE family members across bacteria and eukaryotes share this conserved NEF function. This is the core molecular function of GRPEL1.
Reason: Adenyl-nucleotide exchange factor activity is the defining molecular function of GRPEL1. This is strongly supported by in vitro biochemical data (Srivastava et al., JBC 2017) showing direct NEF activity on HSPA9, as well as by conserved domain architecture (GrpE family) and phylogenetic inference.
Supporting Evidence:
PMID:11311562
HMGE expressed in E. coli as a GST fusion protein co-purified with the E. coli Hsp70 protein DnaK in the absence of ATP. DnaK could be released from the GST-HMGE with a Mg-ATP wash.
|
|
GO:0001405
PAM complex, Tim23 associated import motor
|
IBA
GO_REF:0000033 |
ACCEPT |
Summary: GRPEL1 is a component of the PAM (presequence translocase-associated motor) complex. Co-immunoprecipitation experiments in mitochondrial lysates show GRPEL1 associates with HSPA9 and TIMM44 (Srivastava et al., JBC 2017). UniProt lists GRPEL1 as a component of the TIM23 complex (ComplexPortal CPX-6129 and CPX-6130). The IBA annotation is phylogenetically well-supported from the yeast Mge1p ortholog.
Reason: Multiple lines of evidence confirm GRPEL1 as a PAM complex component: co-immunoprecipitation with HSPA9 and TIMM44 (Srivastava et al., JBC 2017), functional conservation with yeast Mge1p in the import motor, and ComplexPortal entries for TIM23 complexes listing GRPEL1.
Supporting Evidence:
PMID:11311562
Subcellular fractionation and immunocytochemistry studies using antisera raized against HMGE show that it is a mitochondrial protein.
|
|
GO:0030150
protein import into mitochondrial matrix
|
IBA
GO_REF:0000033 |
ACCEPT |
Summary: GRPEL1 participates in protein import into the mitochondrial matrix as the NEF for HSPA9 within the PAM/TIM23 import motor. By cycling HSPA9 between ADP- and ATP-bound states, GRPEL1 enables the ratchet mechanism that drives preprotein translocation through the TIM23 channel (Srivastava et al., JBC 2017; Havalova et al., IJMS 2021). The IBA annotation from yeast Mge1p is well-supported.
Reason: GRPEL1 is directly involved in mitochondrial protein import as the NEF component of the PAM import motor. This is the primary biological process in which GRPEL1 functions, supported by its PAM complex membership and essential role in HSPA9 cycling during preprotein translocation.
|
|
GO:0051082
unfolded protein binding
|
IBA
GO_REF:0000033 |
REMOVE |
Summary: This annotation attributes direct unfolded protein binding to GRPEL1. However, GRPEL1 is a nucleotide exchange factor, not a substrate-binding chaperone. The unfolded protein binding activity in the Hsp70 system resides with HSPA9 itself (via its substrate-binding domain) and J-protein co-chaperones that deliver substrates. GRPEL1 acts on the nucleotide-binding domain of HSPA9 to accelerate ADP release, which indirectly causes substrate release. There is no evidence that GRPEL1 directly binds unfolded polypeptide substrates. The IBA annotation propagates from an IDA (PMID:11311562) that conflated the co-chaperone's role in the chaperone cycle with direct substrate binding.
Reason: GRPEL1 is a nucleotide exchange factor that acts on the ATPase domain of HSPA9; it does not directly bind unfolded protein substrates. The chaperone system as a whole handles unfolded proteins, but GRPEL1's specific role is nucleotide exchange. This annotation confuses the system-level function with the molecular-level activity of this specific component. The core MF annotation should be GO:0000774 (adenyl-nucleotide exchange factor activity). The underlying IDA (PMID:11311562) does not demonstrate direct unfolded protein binding by GRPEL1.
Supporting Evidence:
PMID:11311562
HMGE expressed in E. coli as a GST fusion protein co-purified with the E. coli Hsp70 protein DnaK in the absence of ATP. DnaK could be released from the GST-HMGE with a Mg-ATP wash.
|
|
GO:0000774
adenyl-nucleotide exchange factor activity
|
IEA
GO_REF:0000002 |
ACCEPT |
Summary: IEA annotation from InterPro domain mapping (IPR000740, GrpE domain). The GrpE domain is the defining structural feature of nucleotide exchange factors for DnaK/Hsp70 chaperones. This electronic annotation is fully consistent with the IBA annotation and experimental evidence.
Reason: Correct IEA mapping. The GrpE domain (IPR000740) is a reliable predictor of adenyl-nucleotide exchange factor activity, and this is confirmed by both phylogenetic (IBA) and experimental evidence for GRPEL1.
|
|
GO:0005759
mitochondrial matrix
|
IEA
GO_REF:0000044 |
ACCEPT |
Summary: IEA annotation from UniProtKB subcellular location vocabulary mapping. GRPEL1 is annotated in UniProt as localizing to the mitochondrial matrix based on PMID:11311562. This electronic annotation is consistent with the IDA annotation from the same publication.
Reason: Correct IEA mapping consistent with experimental IDA evidence. Mitochondrial matrix localization is well established for GRPEL1 by subcellular fractionation and immunocytochemistry (PMID:11311562) and by the Srivastava et al. (JBC 2017) study.
|
|
GO:0006457
protein folding
|
IEA
GO_REF:0000002 |
KEEP AS NON CORE |
Summary: IEA annotation from InterPro domain mapping. GrpE family proteins participate in the Hsp70 chaperone cycle, which assists protein folding. GRPEL1 contributes to protein folding indirectly by enabling HSPA9 to cycle through substrate binding and release, supporting folding of newly imported and misfolded matrix proteins. However, GRPEL1 is not itself a folding chaperone; it is a co-chaperone (NEF) that regulates the chaperone cycle.
Reason: While GRPEL1 participates in the protein folding process through its NEF function in the HSPA9 chaperone cycle, protein folding is not its core evolved function. Its core function is nucleotide exchange factor activity (GO:0000774) within the mitochondrial protein import system. Protein folding is a downstream consequence of HSPA9 cycling that GRPEL1 facilitates, making it a non-core annotation.
|
|
GO:0042802
identical protein binding
|
IEA
GO_REF:0000117 |
ACCEPT |
Summary: IEA annotation from ARBA machine learning. GRPEL1 does form homo-oligomers as shown by size exclusion chromatography and native gel experiments (Srivastava et al., JBC 2017), though the physiologically relevant form appears to be the GRPEL1-GRPEL2 hetero-oligomer (~150-160 kDa). The IPI annotation from PMID:32296183 provides experimental support for self-association.
Reason: GRPEL1 self-association is experimentally supported by IPI data (PMID:32296183) and by biochemical studies showing GRPEL1 homo-oligomerization (Srivastava et al., JBC 2017), though the heteromeric complex with GRPEL2 is the predominant physiological form.
|
|
GO:0042803
protein homodimerization activity
|
IEA
GO_REF:0000002 |
ACCEPT |
Summary: IEA annotation from InterPro domain mapping. GrpE family members are known to dimerize. Bacterial GrpE forms a homodimer. GRPEL1 can self-associate as shown by co-IP and Y2H data (PMID:32296183), and purified GRPEL1 forms oligomers (Srivastava et al., JBC 2017), though the predominant physiological form is the GRPEL1-GRPEL2 hetero-oligomer.
Reason: Homodimerization is a conserved property of GrpE family proteins, and there is experimental evidence that GRPEL1 can self-associate. However, note that in vivo the GRPEL1-GRPEL2 hetero-oligomer may be the predominant species.
|
|
GO:0051087
protein-folding chaperone binding
|
IEA
GO_REF:0000002 |
ACCEPT |
Summary: IEA annotation from InterPro domain mapping. GRPEL1 directly binds the protein-folding chaperone HSPA9/mortalin with high affinity (KD ~39 nM; Srivastava et al., JBC 2017). The original characterization paper (PMID:11311562) also showed GRPEL1 binding to HSP70, HSC70, and HSJ1b. This annotation accurately captures the binding interaction between GRPEL1 and its chaperone partner HSPA9.
Reason: GRPEL1 is a co-chaperone that directly binds the protein-folding chaperone HSPA9 with high affinity. This binding is central to its nucleotide exchange factor function. Supported by multiple lines of evidence including co-IP, biolayer interferometry, and functional assays.
Supporting Evidence:
PMID:11311562
HMGE expressed in E. coli as a GST fusion protein co-purified with the E. coli Hsp70 protein DnaK in the absence of ATP. DnaK could be released from the GST-HMGE with a Mg-ATP wash. ...HMGE also appears to bind the constitutive cytosolic Hsp70, Hsc70, in addition to mitochondrial Hsp70, Mt-Hsp70.
|
|
GO:0005515
protein binding
|
IPI
PMID:28514442 Architecture of the human interactome defines protein commun... |
MARK AS OVER ANNOTATED |
Summary: High-throughput interactome study. The WITH/FROM field indicates interaction with HSPA9 (P38646), which is the known physiological partner of GRPEL1. However, protein binding is uninformative as a GO term; the specific interaction is better captured by GO:0051087 (protein-folding chaperone binding) and GO:0000774 (adenyl-nucleotide exchange factor activity).
Reason: Protein binding (GO:0005515) is uninformative per GO curation guidelines. The GRPEL1-HSPA9 interaction is better captured by more specific terms already annotated (GO:0051087 and GO:0000774).
|
|
GO:0005515
protein binding
|
IPI
PMID:30021884 Histone Interaction Landscapes Visualized by Crosslinking Ma... |
MARK AS OVER ANNOTATED |
Summary: High-throughput crosslinking mass spectrometry study of histone interactions in cell nuclei. The WITH/FROM field indicates interaction with HSPA9 (P38646). The study context (histone interaction landscapes in nuclei) is not directly relevant to GRPEL1's mitochondrial function. The GRPEL1-HSPA9 interaction is well established but protein binding is uninformative.
Reason: Protein binding (GO:0005515) is uninformative. The GRPEL1-HSPA9 interaction is real but already captured by more specific terms. The study context (nuclear histone interactions) is tangential to GRPEL1's mitochondrial function.
|
|
GO:0005515
protein binding
|
IPI
PMID:32296183 A reference map of the human binary protein interactome. |
MARK AS OVER ANNOTATED |
Summary: Reference map of the human binary protein interactome (HuRI). Multiple interactors detected for GRPEL1 including POLR1C (O15160), GALT (P07902), CCDC57 (Q2TAC2-2), and SPG21 (Q9NZD8). These are high-throughput Y2H interactions. Some may represent artifacts from overexpression; GALT and POLR1C are not established mitochondrial matrix proteins. Protein binding is uninformative.
Reason: Protein binding (GO:0005515) is uninformative per GO curation guidelines. Several of the detected interactors (GALT, POLR1C, CCDC57, SPG21) are from high-throughput Y2H and may not represent physiologically relevant interactions for a mitochondrial matrix protein.
|
|
GO:0005515
protein binding
|
IPI
PMID:33961781 Dual proteome-scale networks reveal cell-specific remodeling... |
MARK AS OVER ANNOTATED |
Summary: Dual proteome-scale network study detecting GRPEL1 interaction with HSPA9 (P38646). This confirms the well-established GRPEL1-HSPA9 interaction, but protein binding is uninformative as a GO term.
Reason: Protein binding (GO:0005515) is uninformative. The GRPEL1-HSPA9 interaction is the core functional interaction already captured by more specific terms (GO:0051087, GO:0000774).
|
|
GO:0042802
identical protein binding
|
IPI
PMID:32296183 A reference map of the human binary protein interactome. |
ACCEPT |
Summary: The HuRI binary interactome study detected GRPEL1 self-interaction (WITH/FROM: Q9HAV7). This is consistent with the known oligomeric behavior of GrpE family proteins. Srivastava et al. (JBC 2017) showed that purified GRPEL1 forms oligomers, though the physiologically predominant form is the GRPEL1-GRPEL2 hetero-oligomer.
Reason: Experimental IPI evidence for GRPEL1 self-interaction from a binary interactome study. This is consistent with known GrpE family homodimerization and biochemical evidence of GRPEL1 oligomerization.
|
|
GO:0005739
mitochondrion
|
IDA
GO_REF:0000052 |
ACCEPT |
Summary: IDA annotation from HPA immunofluorescence data. GRPEL1 mitochondrial localization is well established by multiple methods including subcellular fractionation and immunocytochemistry (PMID:11311562), and microscopy with mitochondrial markers (Srivastava et al., JBC 2017). This is a broader term than GO:0005759 (mitochondrial matrix) but still correct.
Reason: Mitochondrial localization is firmly established for GRPEL1. While GO:0005759 (mitochondrial matrix) is more specific, this broader IDA annotation from HPA immunofluorescence is also correct and independently confirms the localization.
Supporting Evidence:
PMID:11311562
Subcellular fractionation and immunocytochemistry studies using antisera raized against HMGE show that it is a mitochondrial protein.
|
|
GO:0005743
mitochondrial inner membrane
|
NAS
PMID:10339406 Genetic and structural characterization of the human mitocho... |
KEEP AS NON CORE |
Summary: NAS annotation from ComplexPortal based on Bauer et al. (1999) which characterized the human TIM23 translocase. The paper describes hTim44 localization in the matrix and TIM23/TIM17 in the inner membrane. GRPEL1 itself was not characterized in this paper (it was identified later in 2001). GRPEL1 is a soluble matrix protein that associates with the inner membrane via its interaction with the PAM/TIM23 complex. The annotation likely reflects its association with the inner membrane-bound TIM23 complex rather than intrinsic membrane localization.
Reason: GRPEL1 is primarily a soluble mitochondrial matrix protein that peripherally associates with the inner membrane through its interactions with the PAM/TIM23 complex. The annotation is not wrong per se, as GRPEL1 does associate with inner membrane complexes, but GO:0005759 (mitochondrial matrix) is the more accurate primary localization. The cited paper (PMID:10339406) predates the identification of GRPEL1 and describes the TIM23 translocase in general.
|
|
GO:0006886
intracellular protein transport
|
NAS
PMID:10339406 Genetic and structural characterization of the human mitocho... |
MODIFY |
Summary: NAS annotation from ComplexPortal. GRPEL1 is involved in intracellular protein transport as part of the mitochondrial import machinery. However, this term is overly broad; the more specific term GO:0030150 (protein import into mitochondrial matrix) better captures GRPEL1's role. The cited paper (PMID:10339406) describes the TIM23 translocase but predates GRPEL1's identification.
Reason: While GRPEL1 is involved in intracellular protein transport, this term is too general. The more specific term GO:0030150 (protein import into mitochondrial matrix) precisely describes GRPEL1's role in the TIM23/PAM-dependent import of preproteins into the matrix, and is already annotated via IBA.
Proposed replacements:
protein import into mitochondrial matrix
|
|
GO:0005739
mitochondrion
|
HTP
PMID:34800366 Quantitative high-confidence human mitochondrial proteome an... |
ACCEPT |
Summary: HTP annotation from a quantitative high-confidence human mitochondrial proteome study. GRPEL1 was identified in the mitochondrial proteome with high confidence. This is consistent with all other localization evidence.
Reason: High-throughput proteomic confirmation of GRPEL1 mitochondrial localization. Consistent with all other evidence (IDA from HPA, IDA from PMID:11311562, and functional studies).
|
|
GO:0051082
unfolded protein binding
|
IDA
PMID:11311562 Identification and characterization of a human mitochondrial... |
REMOVE |
Summary: This IDA annotation claims direct assay evidence for GRPEL1 binding unfolded proteins based on PMID:11311562 (Choglay et al., 2001). However, careful reading of the paper reveals that the experiments demonstrated GRPEL1 (HMGE) binding to Hsp70 proteins (DnaK, Hsc70, Mt-Hsp70) and inhibiting HSJ1b-enhanced Hsc70 ATPase activity, not direct binding to unfolded protein substrates. The study characterized GRPEL1 as a GrpE homolog that interacts with Hsp70 chaperones, which is nucleotide exchange factor activity, not unfolded protein binding. The annotation appears to be a misinterpretation of the co-chaperone's role in the chaperone cycle as direct substrate binding.
Reason: The cited paper (PMID:11311562) does not demonstrate direct binding of GRPEL1 to unfolded proteins. The experiments showed GRPEL1 binding to Hsp70 chaperones (DnaK, Hsc70, Mt-Hsp70) and inhibiting co-chaperone-stimulated ATPase activity. These are hallmarks of nucleotide exchange factor activity (GO:0000774), not unfolded protein binding. GRPEL1 acts on the nucleotide-binding domain of Hsp70 to catalyze ADP/ATP exchange; it does not directly engage unfolded polypeptide substrates. This annotation likely arose from conflating the system-level function (chaperone cycle handles unfolded proteins) with the specific molecular activity of this component.
Supporting Evidence:
PMID:11311562
HMGE expressed in E. coli as a GST fusion protein co-purified with the E. coli Hsp70 protein DnaK in the absence of ATP. DnaK could be released from the GST-HMGE with a Mg-ATP wash. ...HMGE was found to inhibit the HSJ1b-enhanced Hsc70 ATPase activity and may mediate this inhibition by binding the DnaJ-protein, HSJ1b.
|
|
GO:0005759
mitochondrial matrix
|
IDA
PMID:11311562 Identification and characterization of a human mitochondrial... |
ACCEPT |
Summary: IDA annotation based on subcellular fractionation and immunocytochemistry from the original characterization paper (Choglay et al., 2001). The paper demonstrates GRPEL1 (HMGE) is a mitochondrial protein using antisera and subcellular fractionation. This is further confirmed by Srivastava et al. (JBC 2017) showing matrix localization by microscopy with mitochondrial markers.
Reason: Well-supported by direct experimental evidence from subcellular fractionation and immunocytochemistry in the original characterization paper. Independently confirmed by Srivastava et al. (JBC 2017). Mitochondrial matrix is the specific subcellular location where GRPEL1 performs its NEF function within the PAM/TIM23 complex.
Supporting Evidence:
PMID:11311562
Subcellular fractionation and immunocytochemistry studies using antisera raized against HMGE show that it is a mitochondrial protein.
|
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BEFORE YOU BEGIN RESEARCH: You MUST verify you are researching the CORRECT gene/protein. Gene symbols can be ambiguous, especially for less well-characterized genes from non-model organisms.
DO NOT PROCEED WITH RESEARCH ON A DIFFERENT GENE. Instead:
- State clearly: "The gene symbol 'GRPEL1' is ambiguous or literature is limited for this specific protein"
- Explain what you found (e.g., "Found extensive literature on a different gene with the same symbol in a different organism")
- Describe the protein based ONLY on the UniProt information provided above
- Suggest that the protein function can be inferred from domain/family information
Please provide a comprehensive research report on the gene GRPEL1 (gene ID: GRPEL1, UniProt: Q9HAV7) in human.
The research report should be a detailed narrative explaining the function, biological processes, and localization of the gene product. Citations should be given for all claims.
You should prioritize authoritative reviews and primary scientific literature when conducting research. You can supplement
this with annotations you find in gene/protein databases, but these can be outdated or inaccurate.
We are specifically interested in the primary function of the gene - for enzymes, what reaction is catalyzed, and what is the substrate specificity? For transporters, what is the substrate? For structural proteins or adapters, what is the broader structural role? For signaling molecules, what is the role in the pathway.
We are interested in where in or outside the cell the gene product carries out its function.
We are also interested in the signaling or biochemical pathways in which the gene functions. We are less interested in broad pleiotropic effects, except where these elucidate the precise role.
Include evidence where possible. We are interested in both experimental evidence as well as inference from structure, evolution, or bioinformatic analysis. Precise studies should be prioritized over high-throughput, where available.
Question: You are an expert researcher providing comprehensive, well-cited information.
Provide detailed information focusing on:
1. Key concepts and definitions with current understanding
2. Recent developments and latest research (prioritize 2023-2024 sources)
3. Current applications and real-world implementations
4. Expert opinions and analysis from authoritative sources
5. Relevant statistics and data from recent studies
Format as a comprehensive research report with proper citations. Include URLs and publication dates where available.
Always prioritize recent, authoritative sources and provide specific citations for all major claims.
BEFORE YOU BEGIN RESEARCH: You MUST verify you are researching the CORRECT gene/protein. Gene symbols can be ambiguous, especially for less well-characterized genes from non-model organisms.
DO NOT PROCEED WITH RESEARCH ON A DIFFERENT GENE. Instead:
- State clearly: "The gene symbol 'GRPEL1' is ambiguous or literature is limited for this specific protein"
- Explain what you found (e.g., "Found extensive literature on a different gene with the same symbol in a different organism")
- Describe the protein based ONLY on the UniProt information provided above
- Suggest that the protein function can be inferred from domain/family information
Please provide a comprehensive research report on the gene GRPEL1 (gene ID: GRPEL1, UniProt: Q9HAV7) in human.
The research report should be a detailed narrative explaining the function, biological processes, and localization of the gene product. Citations should be given for all claims.
You should prioritize authoritative reviews and primary scientific literature when conducting research. You can supplement
this with annotations you find in gene/protein databases, but these can be outdated or inaccurate.
We are specifically interested in the primary function of the gene - for enzymes, what reaction is catalyzed, and what is the substrate specificity? For transporters, what is the substrate? For structural proteins or adapters, what is the broader structural role? For signaling molecules, what is the role in the pathway.
We are interested in where in or outside the cell the gene product carries out its function.
We are also interested in the signaling or biochemical pathways in which the gene functions. We are less interested in broad pleiotropic effects, except where these elucidate the precise role.
Include evidence where possible. We are interested in both experimental evidence as well as inference from structure, evolution, or bioinformatic analysis. Precise studies should be prioritized over high-throughput, where available.
Comprehensive Research Report: Human GRPEL1 (UniProt Q9HAV7)
Identity verification and key definitions
- Gene/protein identity: GRPEL1 encodes the human mitochondrial GrpE-like 1 protein (GrpEL1), a member of the GrpE family of nucleotide exchange factors (NEFs) that regulate Hsp70 chaperone cycles. Experimental studies in human cells identify GRPEL1 and its paralog GRPEL2 as mitochondrial NEFs for mortalin/mtHsp70 (HSPA9) and place them in the mitochondrial protein import and quality control machinery (Journal of Biological Chemistry, 2017; URL: https://doi.org/10.1074/jbc.m117.788463; published Nov 2017) (srivastava2017regulationofmitochondrial pages 1-1, srivastava2017regulationofmitochondrial pages 1-2).
- Organism and localization: Human (Homo sapiens). GRPEL1 localizes to mitochondria and partitions to the mitochondrial matrix by microscopy and subcellular fractionation in human cell lines (JBC 2017; URL above) (srivastava2017regulationofmitochondrial pages 2-3, srivastava2017regulationofmitochondrial pages 1-2).
- Family/domains: GRPEL1 belongs to the conserved GrpE family co-chaperones that catalyze nucleotide exchange on Hsp70/DnaK systems; reviews and primary work affirm its role as the human mitochondrial GrpE-like NEF (IJMS 2021; URL: https://doi.org/10.3390/ijms22158077; published Jul 2021) (havalova2021mitochondrialhsp70chaperone pages 26-27).
Biochemical function and pathway placement
- Primary function: GRPEL1 is a nucleotide exchange factor for mitochondrial Hsp70 (HSPA9). It accelerates ADP release and ATP rebinding on HSPA9, controlling substrate binding and release during protein folding and import. In vitro kinetics show tight binding of GRPEL1 to HSPA9 (KD ~39 nM) compared with GRPEL2 (~190 nM), and both NEFs inhibit single-turnover ATP hydrolysis at saturating concentrations as expected for NEF activity (JBC 2017; URL above; quantitative data within) (srivastava2017regulationofmitochondrial pages 2-3, srivastava2017regulationofmitochondrial pages 5-6).
- Import motor context (TIM23/PAM): GRPEL1 acts within the presequence translocase-associated motor (PAM) that powers import through the TIM23 channel. Co-immunoprecipitation in mitochondrial lysates shows GRPEL1/GRPEL2 associate with HSPA9 and TIMM44; ATP addition dissociates HSPA9–TIMM44 while the GRPEL1–GRPEL2 subcomplex remains stable, consistent with co-recruitment of the NEFs alongside HSPA9 at the import site (JBC 2017) (srivastava2017regulationofmitochondrial pages 5-6). Functionally, the GRPEL subcomplex fine-tunes import of preproteins and supports mitochondrial protein quality control and Fe–S cluster biogenesis downstream of HSPA9 (JBC 2017; URL above) (srivastava2017regulationofmitochondrial pages 1-1, srivastava2017regulationofmitochondrial pages 11-12).
Cellular localization and interaction partners
- Localization: Mitochondrial matrix (microscopy with mitochondrial markers and fractionation) (JBC 2017) (srivastava2017regulationofmitochondrial pages 2-3, srivastava2017regulationofmitochondrial pages 1-2).
- Interactors within the TIM23/PAM module: HSPA9/mtHsp70 and TIMM44; the J-protein co-chaperone module (DNAJC19/Tid1) and additional PAM factors (e.g., MAGMAS) operate in the same pathway context, with GRPEL1 functioning as the NEF for HSPA9 to drive the import motor (system-level reviews integrating these components) (IJMS 2021; URL above; Genes 2020; URL: https://doi.org/10.3390/genes11050563; published May 2020) (havalova2021mitochondrialhsp70chaperone pages 26-27).
Distinctions versus paralog GRPEL2
- Binding and stability: GRPEL1 binds HSPA9 more tightly (KD ~39 nM) than GRPEL2 (~190 nM). Purified GRPEL1 or GRPEL2 alone tend to aggregate at 37 °C, whereas the GRPEL1–GRPEL2 hetero-oligomer (~150–160 kDa by native sizing) is more stable and retains robust NEF activity, indicating hetero-oligomerization stabilizes the NEFs in cells (JBC 2017) (srivastava2017regulationofmitochondrial pages 5-6).
- Redox/stress specialization: GRPEL2, not GRPEL1, forms a redox-sensitive disulfide-bonded dimer via Cys87 under oxidative stress; GRPEL2 knockout clones are viable in HEK293 cells, whereas no GRPEL1 knockout clones were obtained. Population genetics support essentiality of GRPEL1 (ExAC pLI ~0.90) versus tolerance for GRPEL2 (pLI ~0.01) (Redox Biology 2018; URL: https://doi.org/10.1016/j.redox.2018.07.024; published Oct 2018) (konovalova2018redoxregulationof pages 3-5). Together, data suggest GRPEL1 provides the basal essential NEF function, while GRPEL2 confers stress-adaptive regulation.
Essentiality, phenotypes, and quantitative data
- Essentiality indicators: Failure to recover GRPEL1 knockout clones in HEK293 cells and high LoF constraint (pLI ~0.90) indicate essentiality/LoF intolerance for GRPEL1 in humans, contrasting with GRPEL2 (pLI ~0.01) (Redox Biology 2018; URL above) (konovalova2018redoxregulationof pages 3-5).
- Quantitative mechanistic data: GRPEL1–HSPA9 KD ~39 nM vs GRPEL2 ~190 nM; EL1–EL2 hetero-oligomer ~150–160 kDa; EL1 shows greater aggregation propensity than EL2 at 37 °C unless in hetero-complex; assays used single-turnover [γ-32P]ATP hydrolysis and biolayer interferometry (JBC 2017; URL above) (srivastava2017regulationofmitochondrial pages 2-3, srivastava2017regulationofmitochondrial pages 5-6).
Recent developments (2023–2024) and stress signaling links
- Mitochondrial UPR activation (2023): Human UPRmt is activated by two integrated cytosolic signals generated by mitochondrial misfolding: (i) release of mtROS to the cytosol and (ii) accumulation of mitochondrial precursor proteins in the cytosol due to import defects (c-mtProt). Oxidation of cytosolic DNAJA1 enhances HSP70 engagement with c-mtProt, liberating HSF1 to drive UPRmt gene expression. These data implicate the TIM23/PAM import axis—including HSPA9 and its NEF system (GRPEL1/2)—as central in stress signaling when import is compromised (Nature, 2023; URL: https://doi.org/10.1038/s41586-023-06142-0; published Jun 2023) (srivastava2017regulationofmitochondrial pages 5-6).
- Mitophagy upon import motor perturbation (2022, relevant to 2023–2024 context): A genome-wide CRISPR screen and proteomics show that dissociation of the PAM complex from the import machinery during mitochondrial misfolding reduces protein import and induces mitophagy in polarized mitochondria. The study reports decreased levels of HSPA9 and GrpEL1 under such stress conditions, consistent with import-motor remodeling as a mitophagy trigger (Nature Communications, 2022; URL: https://doi.org/10.1038/s41467-022-32564-x; published Sep 2022) (srivastava2017regulationofmitochondrial pages 5-6).
Biological processes and pathways
- Protein import and folding: GRPEL1 regulates HSPA9 cycling during presequence protein import via TIM23/PAM and assists folding/refolding of matrix proteins, maintaining mitochondrial proteostasis (JBC 2017) (srivastava2017regulationofmitochondrial pages 1-1, srivastava2017regulationofmitochondrial pages 5-6).
- Fe–S cluster biogenesis: Modulation of HSPA9 by GRPEL1 contributes to Fe–S protein biogenesis in the matrix, placing GRPEL1 in the ISC pathway context (JBC 2017; Reviews on Fe–S assembly also list GRPEL1 among matrix factors surrounding IscU/HSPA9) (srivastava2017regulationofmitochondrial pages 1-1) (srivastava2017regulationofmitochondrial pages 1-1).
- Mitochondrial protein quality control (MPQC): GRPEL1 operates in the HSPA9/TIM23 import and chaperone system that underlies MPQC; reviews summarize NEFs (GRPEL1/2) as accelerating ADP/ATP exchange to initiate substrate release by Hsp70, integrating with J-proteins and other co-chaperones (Genes 2020; URL above; IJMS 2021; URL above) (havalova2021mitochondrialhsp70chaperone pages 26-27).
Current applications, real-world implementations, and expert analyses
- Research applications: The mechanistic framework places GRPEL1 as a prospective node to probe mitochondrial import stress, UPRmt induction, and mitophagy. System-level studies perturbing PAM/TIM23 or HSPA9 levels are used as experimental proxies for mitochondrial proteostasis stress and quality control, where GRPEL1 participates as the NEF controlling HSPA9 turnover on substrates (Nat Commun 2022; Nature 2023; URLs above) (srivastava2017regulationofmitochondrial pages 5-6).
- Expert syntheses: Recent expert reviews on the mtHsp70 system and MPQC underscore the collaborative action of J-proteins, HSPA9, and GrpE-like NEFs (GRPEL1/2) in import and proteostasis and highlight disease associations when these systems fail (IJMS 2021; Genes 2020; URLs above) (havalova2021mitochondrialhsp70chaperone pages 26-27).
Statistics and datasets
- Binding affinity: GRPEL1–HSPA9 KD ~39 nM; GRPEL2 ~190 nM (biolayer interferometry) (JBC 2017) (srivastava2017regulationofmitochondrial pages 2-3).
- Oligomeric state: GRPEL1–GRPEL2 hetero-oligomer migrates at ~150–160 kDa; individual polypeptides ~25 kDa (JBC 2017) (srivastava2017regulationofmitochondrial pages 5-6).
- Essentiality constraint: GRPEL1 pLI ~0.90 (loss-of-function intolerant) vs GRPEL2 pLI ~0.01 (tolerant) in ExAC; GRPEL2 knockout viable, GRPEL1 knockout not recovered in HEK293 (Redox Biology 2018) (konovalova2018redoxregulationof pages 3-5).
Conclusions
GRPEL1 (Q9HAV7) is the primary human mitochondrial GrpE-like NEF that localizes to the matrix and functions within the TIM23/PAM import motor to regulate HSPA9 chaperone cycling, thereby supporting presequence protein import, matrix proteostasis, and Fe–S cluster biogenesis. Compared with its paralog GRPEL2, GRPEL1 shows tighter HSPA9 binding and essentiality, whereas GRPEL2 confers redox-responsive modulation. Emerging studies tie perturbations of the import motor and HSPA9/GRPEL axis to human UPRmt activation and mitophagy, emphasizing GRPEL1’s central role in mitochondrial stress responses and quality control (JBC 2017; Redox Biology 2018; Nature Communications 2022; Nature 2023; URLs and dates above) (srivastava2017regulationofmitochondrial pages 1-1, srivastava2017regulationofmitochondrial pages 2-3, srivastava2017regulationofmitochondrial pages 11-12, srivastava2017regulationofmitochondrial pages 5-6, konovalova2018redoxregulationof pages 3-5, srivastava2017regulationofmitochondrial pages 1-2, srivastava2017regulationofmitochondrial pages 14-15, havalova2021mitochondrialhsp70chaperone pages 26-27).
References
(srivastava2017regulationofmitochondrial pages 1-1): Shubhi Srivastava, Mohammad Azharuddin Savanur, Devanjan Sinha, Abhijit Birje, Vigneshwaran R, Prasenjit Prasad Saha, and Patrick D'Silva. Regulation of mitochondrial protein import by the nucleotide exchange factors grpel1 and grpel2 in human cells. Journal of Biological Chemistry, 292:18075-18090, Nov 2017. URL: https://doi.org/10.1074/jbc.m117.788463, doi:10.1074/jbc.m117.788463. This article has 72 citations and is from a domain leading peer-reviewed journal.
(srivastava2017regulationofmitochondrial pages 1-2): Shubhi Srivastava, Mohammad Azharuddin Savanur, Devanjan Sinha, Abhijit Birje, Vigneshwaran R, Prasenjit Prasad Saha, and Patrick D'Silva. Regulation of mitochondrial protein import by the nucleotide exchange factors grpel1 and grpel2 in human cells. Journal of Biological Chemistry, 292:18075-18090, Nov 2017. URL: https://doi.org/10.1074/jbc.m117.788463, doi:10.1074/jbc.m117.788463. This article has 72 citations and is from a domain leading peer-reviewed journal.
(srivastava2017regulationofmitochondrial pages 2-3): Shubhi Srivastava, Mohammad Azharuddin Savanur, Devanjan Sinha, Abhijit Birje, Vigneshwaran R, Prasenjit Prasad Saha, and Patrick D'Silva. Regulation of mitochondrial protein import by the nucleotide exchange factors grpel1 and grpel2 in human cells. Journal of Biological Chemistry, 292:18075-18090, Nov 2017. URL: https://doi.org/10.1074/jbc.m117.788463, doi:10.1074/jbc.m117.788463. This article has 72 citations and is from a domain leading peer-reviewed journal.
(havalova2021mitochondrialhsp70chaperone pages 26-27): Henrieta Havalová, Gabriela Ondrovičová, Barbora Keresztesová, Jacob A. Bauer, Vladimír Pevala, Eva Kutejová, and Nina Kunová. Mitochondrial hsp70 chaperone system—the influence of post-translational modifications and involvement in human diseases. International Journal of Molecular Sciences, 22:8077, Jul 2021. URL: https://doi.org/10.3390/ijms22158077, doi:10.3390/ijms22158077. This article has 68 citations and is from a poor quality or predatory journal.
(srivastava2017regulationofmitochondrial pages 5-6): Shubhi Srivastava, Mohammad Azharuddin Savanur, Devanjan Sinha, Abhijit Birje, Vigneshwaran R, Prasenjit Prasad Saha, and Patrick D'Silva. Regulation of mitochondrial protein import by the nucleotide exchange factors grpel1 and grpel2 in human cells. Journal of Biological Chemistry, 292:18075-18090, Nov 2017. URL: https://doi.org/10.1074/jbc.m117.788463, doi:10.1074/jbc.m117.788463. This article has 72 citations and is from a domain leading peer-reviewed journal.
(srivastava2017regulationofmitochondrial pages 11-12): Shubhi Srivastava, Mohammad Azharuddin Savanur, Devanjan Sinha, Abhijit Birje, Vigneshwaran R, Prasenjit Prasad Saha, and Patrick D'Silva. Regulation of mitochondrial protein import by the nucleotide exchange factors grpel1 and grpel2 in human cells. Journal of Biological Chemistry, 292:18075-18090, Nov 2017. URL: https://doi.org/10.1074/jbc.m117.788463, doi:10.1074/jbc.m117.788463. This article has 72 citations and is from a domain leading peer-reviewed journal.
(konovalova2018redoxregulationof pages 3-5): Svetlana Konovalova, Xiaonan Liu, Pooja Manjunath, Sundar Baral, Nirajan Neupane, Taru Hilander, Yang Yang, Diego Balboa, Mügen Terzioglu, Liliya Euro, Markku Varjosalo, and Henna Tyynismaa. Redox regulation of grpel2 nucleotide exchange factor for mitochondrial hsp70 chaperone. Redox Biology, 19:37-45, Oct 2018. URL: https://doi.org/10.1016/j.redox.2018.07.024, doi:10.1016/j.redox.2018.07.024. This article has 39 citations and is from a domain leading peer-reviewed journal.
(srivastava2017regulationofmitochondrial pages 14-15): Shubhi Srivastava, Mohammad Azharuddin Savanur, Devanjan Sinha, Abhijit Birje, Vigneshwaran R, Prasenjit Prasad Saha, and Patrick D'Silva. Regulation of mitochondrial protein import by the nucleotide exchange factors grpel1 and grpel2 in human cells. Journal of Biological Chemistry, 292:18075-18090, Nov 2017. URL: https://doi.org/10.1074/jbc.m117.788463, doi:10.1074/jbc.m117.788463. This article has 72 citations and is from a domain leading peer-reviewed journal.
id: Q9HAV7
gene_symbol: GRPEL1
product_type: PROTEIN
status: IN_PROGRESS
taxon:
id: NCBITaxon:9606
label: Homo sapiens
description: >-
GRPEL1 encodes the primary human mitochondrial GrpE-like nucleotide exchange factor (NEF) that functions
within the TIM23/PAM import motor complex. It accelerates ADP release from mitochondrial HSP70 (HSPA9/mortalin),
enabling the chaperone to rebind ATP and release substrate proteins. GRPEL1 is essential for mitochondrial
protein import, matrix protein folding, and Fe-S cluster biogenesis. It binds HSPA9 with high affinity
(KD ~39 nM) and forms a stable hetero-oligomer with its paralog GRPEL2. GRPEL1 is the essential basal NEF
(pLI ~0.90), while GRPEL2 provides stress-adaptive redox regulation.
existing_annotations:
- term:
id: GO:0000774
label: adenyl-nucleotide exchange factor activity
evidence_type: IBA
original_reference_id: GO_REF:0000033
review:
summary: >-
GRPEL1 is a nucleotide exchange factor (NEF) for mitochondrial HSP70 (HSPA9). It accelerates ADP
release and ATP rebinding on HSPA9, which is the defining biochemical activity of an adenyl-nucleotide
exchange factor. Quantitative binding data show GRPEL1 binds HSPA9 with KD ~39 nM and inhibits
single-turnover ATP hydrolysis at saturating concentrations, consistent with NEF activity
(Srivastava et al., JBC 2017). The IBA annotation is phylogenetically well-supported, as GrpE family
members across bacteria and eukaryotes share this conserved NEF function. This is the core molecular
function of GRPEL1.
action: ACCEPT
reason: >-
Adenyl-nucleotide exchange factor activity is the defining molecular function of GRPEL1. This is
strongly supported by in vitro biochemical data (Srivastava et al., JBC 2017) showing direct NEF
activity on HSPA9, as well as by conserved domain architecture (GrpE family) and phylogenetic inference.
supported_by:
- reference_id: PMID:11311562
supporting_text: >-
HMGE expressed in E. coli as a GST fusion protein co-purified with the E. coli Hsp70 protein DnaK
in the absence of ATP. DnaK could be released from the GST-HMGE with a Mg-ATP wash.
- term:
id: GO:0001405
label: PAM complex, Tim23 associated import motor
evidence_type: IBA
original_reference_id: GO_REF:0000033
review:
summary: >-
GRPEL1 is a component of the PAM (presequence translocase-associated motor) complex. Co-immunoprecipitation
experiments in mitochondrial lysates show GRPEL1 associates with HSPA9 and TIMM44 (Srivastava et al.,
JBC 2017). UniProt lists GRPEL1 as a component of the TIM23 complex (ComplexPortal CPX-6129 and CPX-6130).
The IBA annotation is phylogenetically well-supported from the yeast Mge1p ortholog.
action: ACCEPT
reason: >-
Multiple lines of evidence confirm GRPEL1 as a PAM complex component: co-immunoprecipitation with
HSPA9 and TIMM44 (Srivastava et al., JBC 2017), functional conservation with yeast Mge1p in the
import motor, and ComplexPortal entries for TIM23 complexes listing GRPEL1.
supported_by:
- reference_id: PMID:11311562
supporting_text: >-
Subcellular fractionation and immunocytochemistry studies using antisera raized against HMGE show
that it is a mitochondrial protein.
- term:
id: GO:0030150
label: protein import into mitochondrial matrix
evidence_type: IBA
original_reference_id: GO_REF:0000033
review:
summary: >-
GRPEL1 participates in protein import into the mitochondrial matrix as the NEF for HSPA9 within the
PAM/TIM23 import motor. By cycling HSPA9 between ADP- and ATP-bound states, GRPEL1 enables the
ratchet mechanism that drives preprotein translocation through the TIM23 channel (Srivastava et al.,
JBC 2017; Havalova et al., IJMS 2021). The IBA annotation from yeast Mge1p is well-supported.
action: ACCEPT
reason: >-
GRPEL1 is directly involved in mitochondrial protein import as the NEF component of the PAM import
motor. This is the primary biological process in which GRPEL1 functions, supported by its PAM complex
membership and essential role in HSPA9 cycling during preprotein translocation.
- term:
id: GO:0051082
label: unfolded protein binding
evidence_type: IBA
original_reference_id: GO_REF:0000033
review:
summary: >-
This annotation attributes direct unfolded protein binding to GRPEL1. However, GRPEL1 is a nucleotide
exchange factor, not a substrate-binding chaperone. The unfolded protein binding activity in the
Hsp70 system resides with HSPA9 itself (via its substrate-binding domain) and J-protein co-chaperones
that deliver substrates. GRPEL1 acts on the nucleotide-binding domain of HSPA9 to accelerate ADP
release, which indirectly causes substrate release. There is no evidence that GRPEL1 directly
binds unfolded polypeptide substrates. The IBA annotation propagates from an IDA (PMID:11311562)
that conflated the co-chaperone's role in the chaperone cycle with direct substrate binding.
action: REMOVE
reason: >-
GRPEL1 is a nucleotide exchange factor that acts on the ATPase domain of HSPA9; it does not directly
bind unfolded protein substrates. The chaperone system as a whole handles unfolded proteins, but
GRPEL1's specific role is nucleotide exchange. This annotation confuses the system-level function
with the molecular-level activity of this specific component. The core MF annotation should be
GO:0000774 (adenyl-nucleotide exchange factor activity). The underlying IDA (PMID:11311562) does
not demonstrate direct unfolded protein binding by GRPEL1.
supported_by:
- reference_id: PMID:11311562
supporting_text: >-
HMGE expressed in E. coli as a GST fusion protein co-purified with the E. coli Hsp70 protein DnaK
in the absence of ATP. DnaK could be released from the GST-HMGE with a Mg-ATP wash.
- term:
id: GO:0000774
label: adenyl-nucleotide exchange factor activity
evidence_type: IEA
original_reference_id: GO_REF:0000002
review:
summary: >-
IEA annotation from InterPro domain mapping (IPR000740, GrpE domain). The GrpE domain is the
defining structural feature of nucleotide exchange factors for DnaK/Hsp70 chaperones. This
electronic annotation is fully consistent with the IBA annotation and experimental evidence.
action: ACCEPT
reason: >-
Correct IEA mapping. The GrpE domain (IPR000740) is a reliable predictor of adenyl-nucleotide
exchange factor activity, and this is confirmed by both phylogenetic (IBA) and experimental evidence
for GRPEL1.
- term:
id: GO:0005759
label: mitochondrial matrix
evidence_type: IEA
original_reference_id: GO_REF:0000044
review:
summary: >-
IEA annotation from UniProtKB subcellular location vocabulary mapping. GRPEL1 is annotated in
UniProt as localizing to the mitochondrial matrix based on PMID:11311562. This electronic annotation
is consistent with the IDA annotation from the same publication.
action: ACCEPT
reason: >-
Correct IEA mapping consistent with experimental IDA evidence. Mitochondrial matrix localization
is well established for GRPEL1 by subcellular fractionation and immunocytochemistry (PMID:11311562)
and by the Srivastava et al. (JBC 2017) study.
- term:
id: GO:0006457
label: protein folding
evidence_type: IEA
original_reference_id: GO_REF:0000002
review:
summary: >-
IEA annotation from InterPro domain mapping. GrpE family proteins participate in the Hsp70 chaperone
cycle, which assists protein folding. GRPEL1 contributes to protein folding indirectly by enabling
HSPA9 to cycle through substrate binding and release, supporting folding of newly imported and
misfolded matrix proteins. However, GRPEL1 is not itself a folding chaperone; it is a co-chaperone
(NEF) that regulates the chaperone cycle.
action: KEEP_AS_NON_CORE
reason: >-
While GRPEL1 participates in the protein folding process through its NEF function in the HSPA9
chaperone cycle, protein folding is not its core evolved function. Its core function is nucleotide
exchange factor activity (GO:0000774) within the mitochondrial protein import system. Protein folding
is a downstream consequence of HSPA9 cycling that GRPEL1 facilitates, making it a non-core annotation.
- term:
id: GO:0042802
label: identical protein binding
evidence_type: IEA
original_reference_id: GO_REF:0000117
review:
summary: >-
IEA annotation from ARBA machine learning. GRPEL1 does form homo-oligomers as shown by size
exclusion chromatography and native gel experiments (Srivastava et al., JBC 2017), though the
physiologically relevant form appears to be the GRPEL1-GRPEL2 hetero-oligomer (~150-160 kDa).
The IPI annotation from PMID:32296183 provides experimental support for self-association.
action: ACCEPT
reason: >-
GRPEL1 self-association is experimentally supported by IPI data (PMID:32296183) and by biochemical
studies showing GRPEL1 homo-oligomerization (Srivastava et al., JBC 2017), though the heteromeric
complex with GRPEL2 is the predominant physiological form.
- term:
id: GO:0042803
label: protein homodimerization activity
evidence_type: IEA
original_reference_id: GO_REF:0000002
review:
summary: >-
IEA annotation from InterPro domain mapping. GrpE family members are known to dimerize. Bacterial
GrpE forms a homodimer. GRPEL1 can self-associate as shown by co-IP and Y2H data (PMID:32296183),
and purified GRPEL1 forms oligomers (Srivastava et al., JBC 2017), though the predominant
physiological form is the GRPEL1-GRPEL2 hetero-oligomer.
action: ACCEPT
reason: >-
Homodimerization is a conserved property of GrpE family proteins, and there is experimental evidence
that GRPEL1 can self-associate. However, note that in vivo the GRPEL1-GRPEL2 hetero-oligomer may
be the predominant species.
- term:
id: GO:0051087
label: protein-folding chaperone binding
evidence_type: IEA
original_reference_id: GO_REF:0000002
review:
summary: >-
IEA annotation from InterPro domain mapping. GRPEL1 directly binds the protein-folding chaperone
HSPA9/mortalin with high affinity (KD ~39 nM; Srivastava et al., JBC 2017). The original
characterization paper (PMID:11311562) also showed GRPEL1 binding to HSP70, HSC70, and HSJ1b.
This annotation accurately captures the binding interaction between GRPEL1 and its chaperone
partner HSPA9.
action: ACCEPT
reason: >-
GRPEL1 is a co-chaperone that directly binds the protein-folding chaperone HSPA9 with high affinity.
This binding is central to its nucleotide exchange factor function. Supported by multiple lines
of evidence including co-IP, biolayer interferometry, and functional assays.
supported_by:
- reference_id: PMID:11311562
supporting_text: >-
HMGE expressed in E. coli as a GST fusion protein co-purified with the E. coli Hsp70 protein DnaK
in the absence of ATP. DnaK could be released from the GST-HMGE with a Mg-ATP wash.
...HMGE also appears to bind the constitutive cytosolic Hsp70, Hsc70, in addition to
mitochondrial Hsp70, Mt-Hsp70.
- term:
id: GO:0005515
label: protein binding
evidence_type: IPI
original_reference_id: PMID:28514442
review:
summary: >-
High-throughput interactome study. The WITH/FROM field indicates interaction with HSPA9 (P38646),
which is the known physiological partner of GRPEL1. However, protein binding is uninformative
as a GO term; the specific interaction is better captured by GO:0051087 (protein-folding chaperone
binding) and GO:0000774 (adenyl-nucleotide exchange factor activity).
action: MARK_AS_OVER_ANNOTATED
reason: >-
Protein binding (GO:0005515) is uninformative per GO curation guidelines. The GRPEL1-HSPA9
interaction is better captured by more specific terms already annotated (GO:0051087 and GO:0000774).
- term:
id: GO:0005515
label: protein binding
evidence_type: IPI
original_reference_id: PMID:30021884
review:
summary: >-
High-throughput crosslinking mass spectrometry study of histone interactions in cell nuclei.
The WITH/FROM field indicates interaction with HSPA9 (P38646). The study context (histone
interaction landscapes in nuclei) is not directly relevant to GRPEL1's mitochondrial function.
The GRPEL1-HSPA9 interaction is well established but protein binding is uninformative.
action: MARK_AS_OVER_ANNOTATED
reason: >-
Protein binding (GO:0005515) is uninformative. The GRPEL1-HSPA9 interaction is real but already
captured by more specific terms. The study context (nuclear histone interactions) is tangential
to GRPEL1's mitochondrial function.
- term:
id: GO:0005515
label: protein binding
evidence_type: IPI
original_reference_id: PMID:32296183
review:
summary: >-
Reference map of the human binary protein interactome (HuRI). Multiple interactors detected for
GRPEL1 including POLR1C (O15160), GALT (P07902), CCDC57 (Q2TAC2-2), and SPG21 (Q9NZD8). These
are high-throughput Y2H interactions. Some may represent artifacts from overexpression; GALT and
POLR1C are not established mitochondrial matrix proteins. Protein binding is uninformative.
action: MARK_AS_OVER_ANNOTATED
reason: >-
Protein binding (GO:0005515) is uninformative per GO curation guidelines. Several of the detected
interactors (GALT, POLR1C, CCDC57, SPG21) are from high-throughput Y2H and may not represent
physiologically relevant interactions for a mitochondrial matrix protein.
- term:
id: GO:0005515
label: protein binding
evidence_type: IPI
original_reference_id: PMID:33961781
review:
summary: >-
Dual proteome-scale network study detecting GRPEL1 interaction with HSPA9 (P38646). This confirms
the well-established GRPEL1-HSPA9 interaction, but protein binding is uninformative as a GO term.
action: MARK_AS_OVER_ANNOTATED
reason: >-
Protein binding (GO:0005515) is uninformative. The GRPEL1-HSPA9 interaction is the core functional
interaction already captured by more specific terms (GO:0051087, GO:0000774).
- term:
id: GO:0042802
label: identical protein binding
evidence_type: IPI
original_reference_id: PMID:32296183
review:
summary: >-
The HuRI binary interactome study detected GRPEL1 self-interaction (WITH/FROM: Q9HAV7). This is
consistent with the known oligomeric behavior of GrpE family proteins. Srivastava et al. (JBC 2017)
showed that purified GRPEL1 forms oligomers, though the physiologically predominant form is the
GRPEL1-GRPEL2 hetero-oligomer.
action: ACCEPT
reason: >-
Experimental IPI evidence for GRPEL1 self-interaction from a binary interactome study. This is
consistent with known GrpE family homodimerization and biochemical evidence of GRPEL1 oligomerization.
- term:
id: GO:0005739
label: mitochondrion
evidence_type: IDA
original_reference_id: GO_REF:0000052
review:
summary: >-
IDA annotation from HPA immunofluorescence data. GRPEL1 mitochondrial localization is well
established by multiple methods including subcellular fractionation and immunocytochemistry
(PMID:11311562), and microscopy with mitochondrial markers (Srivastava et al., JBC 2017).
This is a broader term than GO:0005759 (mitochondrial matrix) but still correct.
action: ACCEPT
reason: >-
Mitochondrial localization is firmly established for GRPEL1. While GO:0005759 (mitochondrial
matrix) is more specific, this broader IDA annotation from HPA immunofluorescence is also correct
and independently confirms the localization.
supported_by:
- reference_id: PMID:11311562
supporting_text: >-
Subcellular fractionation and immunocytochemistry studies using antisera raized against HMGE show
that it is a mitochondrial protein.
- term:
id: GO:0005743
label: mitochondrial inner membrane
evidence_type: NAS
original_reference_id: PMID:10339406
review:
summary: >-
NAS annotation from ComplexPortal based on Bauer et al. (1999) which characterized the human TIM23
translocase. The paper describes hTim44 localization in the matrix and TIM23/TIM17 in the inner
membrane. GRPEL1 itself was not characterized in this paper (it was identified later in 2001).
GRPEL1 is a soluble matrix protein that associates with the inner membrane via its interaction with
the PAM/TIM23 complex. The annotation likely reflects its association with the inner membrane-bound
TIM23 complex rather than intrinsic membrane localization.
action: KEEP_AS_NON_CORE
reason: >-
GRPEL1 is primarily a soluble mitochondrial matrix protein that peripherally associates with
the inner membrane through its interactions with the PAM/TIM23 complex. The annotation is
not wrong per se, as GRPEL1 does associate with inner membrane complexes, but GO:0005759
(mitochondrial matrix) is the more accurate primary localization. The cited paper (PMID:10339406)
predates the identification of GRPEL1 and describes the TIM23 translocase in general.
- term:
id: GO:0006886
label: intracellular protein transport
evidence_type: NAS
original_reference_id: PMID:10339406
review:
summary: >-
NAS annotation from ComplexPortal. GRPEL1 is involved in intracellular protein transport as part
of the mitochondrial import machinery. However, this term is overly broad; the more specific term
GO:0030150 (protein import into mitochondrial matrix) better captures GRPEL1's role. The cited
paper (PMID:10339406) describes the TIM23 translocase but predates GRPEL1's identification.
action: MODIFY
reason: >-
While GRPEL1 is involved in intracellular protein transport, this term is too general. The more
specific term GO:0030150 (protein import into mitochondrial matrix) precisely describes GRPEL1's
role in the TIM23/PAM-dependent import of preproteins into the matrix, and is already annotated
via IBA.
proposed_replacement_terms:
- id: GO:0030150
label: protein import into mitochondrial matrix
- term:
id: GO:0005739
label: mitochondrion
evidence_type: HTP
original_reference_id: PMID:34800366
review:
summary: >-
HTP annotation from a quantitative high-confidence human mitochondrial proteome study. GRPEL1
was identified in the mitochondrial proteome with high confidence. This is consistent with all
other localization evidence.
action: ACCEPT
reason: >-
High-throughput proteomic confirmation of GRPEL1 mitochondrial localization. Consistent with all
other evidence (IDA from HPA, IDA from PMID:11311562, and functional studies).
- term:
id: GO:0051082
label: unfolded protein binding
evidence_type: IDA
original_reference_id: PMID:11311562
review:
summary: >-
This IDA annotation claims direct assay evidence for GRPEL1 binding unfolded proteins based on
PMID:11311562 (Choglay et al., 2001). However, careful reading of the paper reveals that the
experiments demonstrated GRPEL1 (HMGE) binding to Hsp70 proteins (DnaK, Hsc70, Mt-Hsp70) and
inhibiting HSJ1b-enhanced Hsc70 ATPase activity, not direct binding to unfolded protein substrates.
The study characterized GRPEL1 as a GrpE homolog that interacts with Hsp70 chaperones, which is
nucleotide exchange factor activity, not unfolded protein binding. The annotation appears to be
a misinterpretation of the co-chaperone's role in the chaperone cycle as direct substrate binding.
action: REMOVE
reason: >-
The cited paper (PMID:11311562) does not demonstrate direct binding of GRPEL1 to unfolded proteins.
The experiments showed GRPEL1 binding to Hsp70 chaperones (DnaK, Hsc70, Mt-Hsp70) and inhibiting
co-chaperone-stimulated ATPase activity. These are hallmarks of nucleotide exchange factor activity
(GO:0000774), not unfolded protein binding. GRPEL1 acts on the nucleotide-binding domain of Hsp70
to catalyze ADP/ATP exchange; it does not directly engage unfolded polypeptide substrates. This
annotation likely arose from conflating the system-level function (chaperone cycle handles unfolded
proteins) with the specific molecular activity of this component.
supported_by:
- reference_id: PMID:11311562
supporting_text: >-
HMGE expressed in E. coli as a GST fusion protein co-purified with the E. coli Hsp70 protein DnaK
in the absence of ATP. DnaK could be released from the GST-HMGE with a Mg-ATP wash.
...HMGE was found to inhibit the HSJ1b-enhanced Hsc70 ATPase activity and may mediate this
inhibition by binding the DnaJ-protein, HSJ1b.
- term:
id: GO:0005759
label: mitochondrial matrix
evidence_type: IDA
original_reference_id: PMID:11311562
review:
summary: >-
IDA annotation based on subcellular fractionation and immunocytochemistry from the original
characterization paper (Choglay et al., 2001). The paper demonstrates GRPEL1 (HMGE) is a
mitochondrial protein using antisera and subcellular fractionation. This is further confirmed
by Srivastava et al. (JBC 2017) showing matrix localization by microscopy with mitochondrial
markers.
action: ACCEPT
reason: >-
Well-supported by direct experimental evidence from subcellular fractionation and immunocytochemistry
in the original characterization paper. Independently confirmed by Srivastava et al. (JBC 2017).
Mitochondrial matrix is the specific subcellular location where GRPEL1 performs its NEF function
within the PAM/TIM23 complex.
supported_by:
- reference_id: PMID:11311562
supporting_text: >-
Subcellular fractionation and immunocytochemistry studies using antisera raized against HMGE show
that it is a mitochondrial protein.
core_functions:
- description: >-
GRPEL1 is the primary mitochondrial GrpE-like nucleotide exchange factor (NEF)
for HSPA9/mortalin. It accelerates ADP release from HSPA9, enabling ATP
rebinding and substrate release. This NEF activity is essential for the PAM
import motor that drives preprotein translocation through the TIM23 channel
into the mitochondrial matrix.
molecular_function:
id: GO:0000774
label: adenyl-nucleotide exchange factor activity
directly_involved_in:
- id: GO:0030150
label: protein import into mitochondrial matrix
locations:
- id: GO:0005759
label: mitochondrial matrix
in_complex:
id: GO:0001405
label: PAM complex, Tim23 associated import motor
supported_by:
- reference_id: PMID:11311562
supporting_text: >-
HMGE expressed in E. coli as a GST fusion protein co-purified with the E. coli Hsp70 protein DnaK
in the absence of ATP. DnaK could be released from the GST-HMGE with a Mg-ATP wash.
references:
- id: GO_REF:0000002
title: Gene Ontology annotation through association of InterPro records with GO
terms
findings: []
- id: GO_REF:0000033
title: Annotation inferences using phylogenetic trees
findings: []
- id: GO_REF:0000044
title: Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular Location
vocabulary mapping, accompanied by conservative changes to GO terms applied by
UniProt
findings: []
- id: GO_REF:0000052
title: Gene Ontology annotation based on curation of immunofluorescence data
findings: []
- id: GO_REF:0000117
title: Electronic Gene Ontology annotations created by ARBA machine learning models
findings: []
- id: PMID:10339406
title: Genetic and structural characterization of the human mitochondrial inner
membrane translocase.
findings:
- statement: >-
Describes the human TIM23/TIM17 translocase complex, including Tim44 matrix localization
and two TIM17 variants. GRPEL1 was not yet identified at the time of this study.
- id: PMID:11311562
title: Identification and characterization of a human mitochondrial homologue of
the bacterial co-chaperone GrpE.
findings:
- statement: >-
Original identification of GRPEL1 (HMGE). Demonstrated mitochondrial localization by
subcellular fractionation and immunocytochemistry. Showed binding to DnaK, Hsc70, and
Mt-Hsp70. Demonstrated inhibition of HSJ1b-enhanced Hsc70 ATPase activity. Modeled on
the E. coli GrpE crystal structure with significant structural conservation.
supporting_text: >-
HMGE expressed in E. coli as a GST fusion protein co-purified with the E. coli Hsp70 protein DnaK
in the absence of ATP. DnaK could be released from the GST-HMGE with a Mg-ATP wash.
...Subcellular fractionation and immunocytochemistry studies using antisera raized against HMGE show
that it is a mitochondrial protein.
- id: PMID:28514442
title: Architecture of the human interactome defines protein communities and disease
networks.
findings: []
- id: PMID:30021884
title: Histone Interaction Landscapes Visualized by Crosslinking Mass Spectrometry
in Intact Cell Nuclei.
findings: []
- id: PMID:32296183
title: A reference map of the human binary protein interactome.
findings: []
- id: PMID:33961781
title: Dual proteome-scale networks reveal cell-specific remodeling of the human
interactome.
findings: []
- id: PMID:34800366
title: Quantitative high-confidence human mitochondrial proteome and its dynamics
in cellular context.
findings: []