PEX16

Existing Annotations Review

GO Term	Evidence	Action	Reason
GO:0007031 peroxisome organization	IBA GO_REF:0000033	ACCEPT	Summary: PEX16 is one of three early peroxins (PEX3, PEX16, PEX19) required for peroxisome membrane biogenesis in mammals. Loss of PEX16 leads to complete absence of peroxisomes. Peroxisome organization is a well-supported core function, though the more specific term peroxisome membrane biogenesis (GO:0016557) better captures PEX16's primary role. This IBA annotation at the broader level is appropriate and phylogenetically sound. Reason: IBA annotations undergo extensive phylogenetic review and this term accurately captures PEX16's role at the appropriate general level. PEX16 is essential for peroxisome organization as demonstrated by the complete loss of peroxisomes in PEX16-deficient cells (PMID:9837814, PMID:9922452, PMID:16717127). Supporting Evidence: PMID:9837814 HsPEX16 expression morphologically and biochemically restored peroxisome biogenesis only in fibroblasts from a CG-D patient with ZS PMID:9922452 expression of PEX16 restores the formation of new peroxisomes in PBD061 cells
GO:0005778 peroxisomal membrane	IBA GO_REF:0000033	ACCEPT	Summary: PEX16 is an integral peroxisomal membrane protein with two transmembrane helices. Both N- and C-terminal domains are exposed to the cytosol. Peroxisomal membrane localization is well established by immunofluorescence, cell fractionation, and topology studies. Reason: Peroxisomal membrane is the primary functional localization of PEX16, confirmed by multiple studies including topology determination (PMID:12223482), immunofluorescence (PMID:9837814), and cell fractionation (PMID:9922452). IBA annotation is phylogenetically appropriate. Supporting Evidence: PMID:12223482 we have determined the membrane topology of Pex16p by differential permeabilization method: both N- and C-terminal parts are exposed to the cytosol PMID:9837814 Pex16p was localized to peroxisomes through expression study of epitope-tagged Pex16p
GO:0005778 peroxisomal membrane	IEA GO_REF:0000120	ACCEPT	Summary: Combined automated annotation for peroxisomal membrane. Consistent with extensive experimental evidence and IBA annotation for the same term. Reason: Redundant with experimentally supported annotations but correct. PEX16 is an integral peroxisomal membrane protein.
GO:0007031 peroxisome organization	IEA GO_REF:0000043	ACCEPT	Summary: IEA annotation based on UniProt keyword mapping for peroxisome organization. Consistent with IBA and experimental annotations for the same term. Reason: Correct and consistent with extensive experimental evidence. PEX16 is essential for peroxisome organization.
GO:0005778 peroxisomal membrane	TAS Reactome:R-HSA-9603775	ACCEPT	Summary: Reactome annotation for peroxisomal membrane localization in the context of PEX3:PEX19:class I PMP dissociation. PEX16 is located at the peroxisomal membrane where PEX3-PEX19-PMP complexes dock. Reason: Correct localization. PEX16 functions at the peroxisomal membrane as the receptor for PEX3-PEX19 complexes (PMID:19114594).
GO:0005778 peroxisomal membrane	TAS Reactome:R-NUL-9604086	ACCEPT	Summary: Reactome annotation for peroxisomal membrane in the context of PEX19:Pex3 binding PEX16. PEX16 serves as the membrane-anchored receptor at the peroxisomal membrane. Reason: Correct localization in context of the PEX3-PEX16 interaction at the peroxisomal membrane (PMID:19114594).
GO:0005778 peroxisomal membrane	TAS Reactome:R-NUL-9604116	ACCEPT	Summary: Reactome annotation for peroxisomal membrane in the context of PEX16:PEX19:Pex3 dissociation. Reason: Correct localization. Multiple Reactome entries for the same CC term are acceptable as they represent different reaction contexts.
GO:0005829 cytosol	TAS Reactome:R-HSA-9603775	REMOVE	Summary: Reactome annotation placing PEX16 in the cytosol. However, PEX16 is an integral membrane protein that is never found in the cytosol. Cell fractionation shows PEX16 resides only in the membrane fraction (PMID:16717127). This Reactome annotation likely refers to the cytosolic face of PEX16 (both N- and C-termini are cytosolic) or to other participants in the reaction, not to PEX16 itself being a cytosolic protein. Reason: The Reactome pathway models PEX16 as a class I PMP, i.e. one synthesised in the cytosol, captured by PEX19 and delivered to PEX3, which would give it a transient cytosolic pool. That step does not apply to PEX16: Kim et al. (2006) showed by protease-protection and glycosylation assays that PEX16 is inserted cotranslationally into the ER, and by fractionation that PEX16-GFP partitions entirely into the non-soluble fraction with no soluble pool. A protein that never leaves a membrane after synthesis should not carry located_in cytosol. Note this is a point of deliberate divergence from the sibling PEX13 review, where the same Reactome cytosol rows are kept as non-core: PEX13 is a genuine post-translationally inserted class I PMP with PEX19-bound cytosolic intermediates, whereas PEX16 is not. Supporting Evidence: PMID:16717127 Cell fractionation and immunoblot analysis of PEX16-GFP-transformed COS-7 cells performed 24 h after transfection to allow for protein overexpression revealed that PEX16-GFP resided only in the membrane (or nonsoluble fraction), in contrast to GFP expressed alone, which was primarily in the soluble fraction
GO:0005829 cytosol	TAS Reactome:R-HSA-9603784	REMOVE	Summary: Reactome annotation placing PEX16 in cytosol for the PEX19:class I PMP binds PEX3 reaction. PEX16 is an integral membrane protein and is not cytosolic. Reason: Same rationale as the R-HSA-9603775 cytosol row: PEX16 is cotranslationally inserted into the ER and has no soluble pool, so the class I PMP cytosolic intermediate the Reactome reaction models does not apply to it (PMID:16717127, PMID:12223482). Supporting Evidence: PMID:16717127 The data thus confirmed that PEX16 undergoes cotranslational insertion into the ER
GO:0005829 cytosol	TAS Reactome:R-HSA-9603804	REMOVE	Summary: Reactome annotation placing PEX16 in cytosol for the PEX19 binds class I PMPs reaction. PEX16 is an integral membrane protein and is not cytosolic. Reason: Same rationale as the other two Reactome cytosol rows. PEX16 is a two-TM integral membrane protein with both termini facing the cytosol (PMID:12223482); cytosolic exposure of its soluble domains is not the same as residing in the cytosol, and the class I PMP cytosolic intermediate the reaction models does not apply to a cotranslationally inserted protein (PMID:16717127).
GO:0106101 ER-dependent peroxisome localization	IDA PMID:19479899 Pex3p-dependent peroxisomal biogenesis initiates in the endo...	ACCEPT	Summary: Toro et al. (2009) showed that Pex3p requires Pex16p for ER location and that Pex3p-dependent peroxisomal biogenesis initiates in the ER. Cross-expression experiments demonstrated that Pex3p requires Pex16p for ER location. This annotation captures PEX16's role in ER-dependent peroxisome localization. Reason: Direct evidence from cross-expression experiments showing PEX16's role in ER-dependent peroxisome biogenesis. PEX16 localizes to the ER and recruits other PMPs there for subsequent transport to peroxisomes. Supporting Evidence: PMID:19479899 Cross-expression experiments of Pex3p in GM623 cells lacking Pex16p or Pex16p in MR cells lacking Pex3p, showed evidence that Pex3p requires Pex16p for ER location but is dispensable for the ER location of Pex16p
GO:0016020 membrane	HDA PMID:19946888 Defining the membrane proteome of NK cells.	ACCEPT	Summary: High-throughput mass spectrometry study of NK cell membrane proteome identified PEX16 in the membrane fraction. The term 'membrane' is very generic; PEX16 is specifically localized to peroxisomal membrane and ER membrane. Reason: While very generic, this HDA annotation from a proteomics study is not incorrect -- PEX16 is indeed a membrane protein. More specific terms (peroxisomal membrane, ER membrane) are already annotated. This broad term from a large-scale study is acceptable as supporting evidence.
GO:0005515 protein binding	IPI PMID:19114594 The peroxisomal membrane protein import receptor Pex3p is di...	MODIFY	Summary: Matsuzaki and Fujiki (2008) demonstrated that PEX16 functions as the membrane receptor for PEX3-PEX19 complexes. PEX16 directly binds to PEX3 (shown by co-immunoprecipitation of cell-free synthesized proteins) and serves as the docking site for PEX3-PEX19 complexes at the peroxisomal membrane. The term 'protein binding' is uninformative; a more specific molecular function term should be used. Reason: The physical PEX16-PEX3 interaction is well established, but 'protein binding' says nothing about what PEX16 does with it. The earlier draft of this review proposed GO:0022615 (protein to membrane docking) as the replacement; that is a biological process term and cannot substitute for a molecular function annotation, so it has been corrected. The molecular activity is adaptor/receptor activity: membrane-anchored PEX16 binds PEX3 through a cytosolic loop while PEX19 binds PEX3 on the opposite face, so PEX16 holds the PEX3-PEX19 carrier at the membrane where PMPs can be delivered. GO:0060090 (molecular adaptor activity) is the term carried in core_functions and is already proposed as a NEW annotation below; GO:0022615 remains correctly annotated separately as the process. Proposed replacements: molecular adaptor activity Supporting Evidence: PMID:19114594 we demonstrate that Pex16p functions as the Pex3p-docking site and serves as the peroxisomal membrane receptor that is specific to the Pex3p-Pex19p complexes
GO:0022615 protein to membrane docking	IDA PMID:19114594 The peroxisomal membrane protein import receptor Pex3p is di...	ACCEPT	Summary: Matsuzaki and Fujiki (2008) showed using semi-intact cell import assays and co-immunoprecipitation that PEX16 functions as the membrane receptor for PEX3-PEX19 complexes. Ectopic expression of EGFP-Pex16p specifically enhanced targeting of Pex3p to peroxisomes 5-6 fold. Knockdown of Pex16p abrogated Pex3p targeting. This term captures PEX16's core molecular function of docking PEX3 at the peroxisomal membrane. Reason: This is a core molecular function annotation for PEX16. The paper provides strong direct evidence that PEX16 serves as the membrane docking receptor for PEX3-PEX19 complexes through in vitro import assays, co-IP, and siRNA knockdown experiments. Supporting Evidence: PMID:19114594 Pex16p functions as a membrane receptor for Pex3p-Pex19p complexes PMID:19114594 thereby indicating that Pex16p functions as a receptor for cytosolic Pex3p-Pex19p complexes PMID:19114594 Pex16p was a prerequisite for peroxisomal targeting of newly synthesized Pex3p in vivo, functioning as the Pex3p membrane receptor
GO:0005777 peroxisome	IDA PMID:21768384 Sec16B is involved in the endoplasmic reticulum export of th...	ACCEPT	Summary: Yonekawa et al. (2011) showed PEX16-GFP localizes to peroxisomes and that Sec16B regulates the ER-to-peroxisome transport of PEX16. The more specific term peroxisomal membrane (GO:0005778) is already annotated with stronger evidence. Reason: Peroxisome localization is correct. While the more specific peroxisomal membrane term is preferred and already annotated, this annotation is not wrong. Supporting Evidence: PMID:21768384 peroxisomal membrane biogenesis factors peroxin 3 (Pex3) and Pex16 were redistributed from peroxisomes to Sec16B-positive ER membranes
GO:0005783 endoplasmic reticulum	IDA PMID:21768384 Sec16B is involved in the endoplasmic reticulum export of th...	ACCEPT	Summary: Yonekawa et al. (2011) demonstrated that PEX16 transits through the ER en route to peroxisomes. Knockdown of Sec16B caused redistribution of PEX16-GFP to the ER, and overexpression of Sec16B also caused PEX16 redistribution to ER membranes. PEX16 ER localization is an intermediate in its trafficking pathway. Reason: PEX16 is found at the ER as an intermediate during its biogenesis and trafficking. This is well established by multiple studies. Supporting Evidence: PMID:21768384 Knockdown of Sec16B but not Sec16A by RNAi affected the morphology of peroxisomes, inhibited the transport of Pex16 from the ER to peroxisomes
GO:0005515 protein binding	IPI PMID:14709540 PEX19 is a predominantly cytosolic chaperone and import rece...	MARK AS OVER ANNOTATED	Summary: Jones et al. (2004) showed PEX19 binds to mPTS regions of PEX16 (amino acids 221-336 and 59-219). PEX19 functions as a chaperone and import receptor for class 1 PMPs including PEX16. The interaction is specific and functionally relevant, as PEX19 controls subcellular distribution of PEX16 mPTS-containing fragments. However, 'protein binding' is uninformative. Reason: The PEX19-PEX16 interaction is real and functionally important, but here PEX16 is the cargo, not the actor: PEX19 recognises PEX16's two mPTS regions (aa 59-219 and aa 221-336) in the course of chaperoning and targeting it. Being recognised by a receptor is not a molecular function of the substrate, and there is no GO MF term for it, so MODIFY has no valid target - the earlier draft proposed the BP term GO:0045046, which cannot replace an MF annotation. Marked as an over-annotation instead: the biology is already captured by PEX16's peroxisomal/ER membrane localisations and by GO:0045046 annotated as a process from PMID:12223482. Supporting Evidence: PMID:14709540 PEX19 binds multiple PMP targeting signals PMID:14709540 Both PMP34aa244-307/3xmyc and PEX16aa221-336/3xmyc were imported into peroxisomes in the majority of control cells (88% and 91%, respectively)
GO:0005778 peroxisomal membrane	HDA PMID:21525035 PEX14 is required for microtubule-based peroxisome motility ...	ACCEPT	Summary: Bharti et al. (2011) established a procedure for isolating native peroxisomal membrane protein complexes from human cells and identified PEX14-associated proteins by mass spectrometry. PEX16 was identified as a constituent of peroxisomal membrane complexes, confirming its peroxisomal membrane localization. Reason: High-throughput proteomic identification of PEX16 in peroxisomal membrane complexes is consistent with extensive experimental evidence for peroxisomal membrane localization. Supporting Evidence: PMID:21525035 Using mass spectrometric analysis, almost all known human peroxins involved in protein import were identified as constituents of the PEX14 complexes
GO:0007031 peroxisome organization	IMP PMID:19479899 Pex3p-dependent peroxisomal biogenesis initiates in the endo...	ACCEPT	Summary: Toro et al. (2009) showed using cross-expression experiments in Zellweger syndrome cell lines that PEX16 is required for peroxisome biogenesis. Pex3p requires Pex16p for ER location during de novo peroxisome formation. Reason: Direct mutant phenotype evidence demonstrates PEX16 is required for peroxisome organization. PEX16 is essential for de novo peroxisome biogenesis from the ER. Supporting Evidence: PMID:19479899 Cross-expression experiments of Pex3p in GM623 cells lacking Pex16p or Pex16p in MR cells lacking Pex3p, showed evidence that Pex3p requires Pex16p for ER location but is dispensable for the ER location of Pex16p
GO:0005783 endoplasmic reticulum	IDA PMID:19479899 Pex3p-dependent peroxisomal biogenesis initiates in the endo...	ACCEPT	Summary: Toro et al. (2009) showed that PEX16 localizes to the ER when expressed in ZS cells lacking PEX3 (MR cells), confirming that PEX16 targets the ER independently of PEX3. Reason: ER localization of PEX16 is established as an intermediate in its trafficking pathway, particularly during de novo peroxisome formation. PEX16 targets the ER independently of PEX3. Supporting Evidence: PMID:19479899 Pex3p requires Pex16p for ER location but is dispensable for the ER location of Pex16p
GO:0032581 ER-dependent peroxisome organization	IDA PMID:16717127 The origin and maintenance of mammalian peroxisomes involves...	ACCEPT	Summary: Kim et al. (2006) provided the first direct evidence in mammalian cells that the ER plays a central role in peroxisome biogenesis. They showed PEX16 is cotranslationally inserted into the ER and recruits other PMPs to ER membranes, driving de novo peroxisome formation. PEX16-GFP with an appended signal anchor sequence could complement PEX16-deficient cells, proving the ER pathway is sufficient. Reason: This is a core function annotation. Kim et al. (2006) provided landmark evidence that PEX16 regulates ER-dependent peroxisome formation, recruiting PMPs including PEX3 and PMP34 to ER membranes for subsequent transport to peroxisomes. Supporting Evidence: PMID:16717127 We provide direct evidence that peroxisomes can arise de novo from the ER in both normal and peroxisome-less mutant cells. We further show that PEX16 regulates this process by being cotranslationally inserted into the ER and serving to recruit other peroxisomal membrane proteins to membranes. PMID:16717127 when PEX16-Venus was coexpressed with either PEX3- or PMP34-Cerulean, both PMPs colocalized with PEX16-Venus in the ER
GO:0005777 peroxisome	IDA PMID:9837814 Mutation in PEX16 is causal in the peroxisome-deficient Zell...	ACCEPT	Summary: Honsho et al. (1998) showed Pex16p localized to peroxisomes using epitope-tagged expression studies. This was the original identification of human PEX16. Reason: Original characterization of human PEX16 showing peroxisomal localization. Well supported by subsequent studies. Supporting Evidence: PMID:9837814 Pex16p was localized to peroxisomes through expression study of epitope-tagged Pex16p
GO:0006625 protein targeting to peroxisome	IMP PMID:9837814 Mutation in PEX16 is causal in the peroxisome-deficient Zell...	MODIFY	Summary: Honsho et al. (1998) showed that PEX16 expression restored peroxisome biogenesis in CG-D patient fibroblasts. This encompasses the targeting of peroxisomal proteins to the newly formed organelle. While PEX16 is more specifically involved in PMP targeting (membrane protein targeting rather than matrix protein targeting), the broader term is not incorrect since PEX16 function is prerequisite for all peroxisomal protein targeting. Reason: GO:0006625 covers directing proteins to the peroxisome generally, which for PEX16 lumps together what it does (PMP delivery to the membrane) with what merely fails downstream when it is absent (matrix protein import, for which the machinery is PEX5/PEX13/PEX14). The precise term is GO:0045046 protein import into peroxisome membrane, whose definition explicitly separates PMP targeting from matrix import; that term is already independently annotated as IMP from PMID:12223482, so the replacement is consistent with the rest of the record rather than novel. Proposed replacements: protein import into peroxisome membrane Supporting Evidence: PMID:9837814 HsPEX16 expression morphologically and biochemically restored peroxisome biogenesis only in fibroblasts from a CG-D patient with ZS
GO:0016557 peroxisome membrane biogenesis	IMP PMID:9837814 Mutation in PEX16 is causal in the peroxisome-deficient Zell...	ACCEPT	Summary: Honsho et al. (1998) demonstrated that mutation in PEX16 causes loss of peroxisomes in CG-D/CG-IX Zellweger syndrome. Introduction of wild-type PEX16 restores peroxisome biogenesis. This is the most specific and accurate core function annotation for PEX16. Reason: Peroxisome membrane biogenesis is the primary biological process function of PEX16. Patient cells with PEX16 mutations completely lack peroxisomal membranes, and complementation restores them. Supporting Evidence: PMID:9837814 HsPEX16 expression morphologically and biochemically restored peroxisome biogenesis only in fibroblasts from a CG-D patient with ZS
GO:0005515 protein binding	IPI PMID:15713480 Analysis of human Pex19p's domain structure by pentapeptide ...	MARK AS OVER ANNOTATED	Summary: Fransen et al. (2005) performed pentapeptide scanning mutagenesis of PEX19 and identified that PEX19's carboxy-terminal domain interacts with multiple PMPs including PEX16. This paper is primarily about PEX19's domain structure, and PEX16 is one of many PMPs tested as a binding partner. The 'protein binding' annotation is uninformative. Reason: Same situation as the PMID:14709540 row, and derived from a paper whose subject is PEX19's domain architecture rather than PEX16: PEX16 appears as one of six PMPs bound by the PEX19 C-terminal domain. PEX16 is the ligand of a chaperone here, which is not a molecular function of PEX16, so there is no MF term to MODIFY to (the earlier draft proposed the BP term GO:0045046, a branch mismatch). Flagged as over-annotated rather than removed: the interaction itself is genuine and the pentapeptide-scanning evidence is sound. Supporting Evidence: PMID:15713480 a carboxy-terminal domain that interacts with multiple PMPs including Pex3p, Pex11pbeta, Pex12p, Pex13p, Pex16p, and Pex26p
GO:0005789 endoplasmic reticulum membrane	IDA PMID:16717127 The origin and maintenance of mammalian peroxisomes involves...	ACCEPT	Summary: Kim et al. (2006) showed by fluorescence microscopy and cell fractionation that PEX16-GFP localizes to ER membranes in addition to peroxisomes. In cells lacking peroxisomes (PBD399-T1 or PBD400), PEX16-GFP was exclusively in the ER. In vitro assays confirmed cotranslational insertion into ER microsomes. FLIP experiments showed PEX16-GFP diffuses freely throughout the ER. Reason: ER membrane is a bona fide localization of PEX16, representing the site of its cotranslational insertion and a transit point during trafficking to peroxisomes. Strong experimental evidence from imaging, fractionation, and in vitro insertion assays. Supporting Evidence: PMID:16717127 The distribution of PEX16-GFP in these cells included the ER as well as peroxisomes PMID:16717127 a significant proportion of PEX16-glyc molecules underwent glycosylation during cotranslational targeting, whereas none did so during posttranslational targeting. The data thus confirmed that PEX16 undergoes cotranslational insertion into the ER
GO:0005778 peroxisomal membrane	IDA PMID:12223482 The membrane biogenesis peroxin Pex16p. Topogenesis and func...	ACCEPT	Summary: Honsho et al. (2002) determined the membrane topology of PEX16 by differential permeabilization, showing it is an integral peroxisomal membrane protein with both N- and C-terminal domains exposed to the cytosol. They identified the topogenic sequence (residues 66-81 and the first transmembrane segment) essential for membrane integration. Reason: Direct experimental evidence for peroxisomal membrane localization and topology determination. This is a primary characterization study. Supporting Evidence: PMID:12223482 we have determined the membrane topology of Pex16p by differential permeabilization method: both N- and C-terminal parts are exposed to the cytosol
GO:0016557 peroxisome membrane biogenesis	IMP PMID:12223482 The membrane biogenesis peroxin Pex16p. Topogenesis and func...	ACCEPT	Summary: Honsho et al. (2002) showed that overexpression of dysfunctional PEX16 variants interfered with peroxisome membrane assembly. The C-terminal cytoplasmic part of PEX16 abrogated peroxisome restoration in pex3 mutants, implying PEX16 functions upstream of PEX3 in peroxisome membrane assembly. Reason: Functional evidence that PEX16 is required for peroxisome membrane biogenesis, acting upstream of PEX3 in the pathway. Supporting Evidence: PMID:12223482 Pex16p C-terminal cytoplasmic part severely abrogated peroxisome restoration in pex mutants such as matrix protein import-defective pex12 and membrane assembly impaired pex3 by respective PEX12 and PEX3 expression
GO:0045046 protein import into peroxisome membrane	IMP PMID:12223482 The membrane biogenesis peroxin Pex16p. Topogenesis and func...	ACCEPT	Summary: Honsho et al. (2002) showed that dysfunctional PEX16 variants interfered with localization of PMPs (Pex14p, Pex13p, PMP70) to peroxisomes, demonstrating that PEX16 is required for PMP import into the peroxisome membrane. Reason: Direct evidence that PEX16 function is required for import of PMPs (Pex14p, Pex13p, PMP70) into the peroxisome membrane. This is a core function annotation. Supporting Evidence: PMID:12223482 Localization to peroxisomes of membrane proteins such as Pex14p, Pex13p, and PMP70 was interfered with in CHO-K1 cells by a higher level expression of the pex16 patient-derived dysfunctional but topogenically active Pex16pR176ter
GO:0005777 peroxisome	IDA PMID:15813749 Requirement for microtubules and dynein motors in the earlie...	ACCEPT	Summary: Brocard et al. (2005) used PEX16-mutant cells for microinjection complementation studies examining microtubule requirements for peroxisome biogenesis. PEX16 was expressed and localized to newly formed peroxisomes in complemented cells. Reason: Peroxisome localization of PEX16 confirmed in the context of complementation experiments. Supporting Evidence: PMID:15813749 nuclear microinjection of plasmids expressing EGFP-SKL and Pex16p in PEX16-mutant cells resulted in the accumulation of EGFP-SKL into newly formed peroxisomes
GO:0007031 peroxisome organization	IMP PMID:15813749 Requirement for microtubules and dynein motors in the earlie...	ACCEPT	Summary: Brocard et al. (2005) showed that PEX16 complementation in PEX16-mutant cells restores peroxisome formation, and that this process requires microtubules and dynein motors. This demonstrates PEX16's role in peroxisome organization. Reason: Complementation of PEX16-mutant cells demonstrates PEX16 is required for peroxisome organization. The paper adds mechanistic context (microtubule dependence). Supporting Evidence: PMID:15813749 pretreatment of the cells with nocodazol, prior to microinjection, resulted in the inhibition of complementation of the PEX16 mutant
GO:0005778 peroxisomal membrane	IMP PMID:9922452 Peroxisome synthesis in the absence of preexisting peroxisom...	ACCEPT	Summary: South and Gould (1999) showed that PBD061 cells (PEX16-deficient) lack detectable peroxisome membranes and cannot import PMPs. Expression of PEX16 restores peroxisome membranes. This demonstrates PEX16 is required for peroxisomal membrane formation. However, the evidence type IMP with CC term is unusual -- this represents the mutant phenotype showing PEX16 is required for peroxisomal membrane existence. Reason: Mutant phenotype demonstrates PEX16 is essential for peroxisomal membrane formation. PEX16-deficient cells completely lack peroxisomal membranes. Supporting Evidence: PMID:9922452 we report here a Zellweger syndrome patient (PBD061) with an unusual cellular phenotype, an inability to import peroxisomal membrane proteins PMID:9922452 expression of PEX16 restores the formation of new peroxisomes in PBD061 cells
GO:0016558 protein import into peroxisome matrix	IMP PMID:9922452 Peroxisome synthesis in the absence of preexisting peroxisom...	KEEP AS NON CORE	Summary: South and Gould (1999) showed that PBD061 (PEX16-deficient) cells are unable to import peroxisomal matrix proteins because they lack peroxisomes entirely. After PEX16 complementation, matrix protein import was restored following membrane assembly. However, PEX16 is not directly involved in matrix protein import -- it is required for membrane biogenesis, which is prerequisite for matrix import. The MGI curator used the qualifier acts_upstream_of_or_within rather than involved_in, which is exactly the right encoding for a requirement that is real but indirect. Reason: Downgraded from the earlier draft's MARK_AS_OVER_ANNOTATED. PEX16 is genuinely not part of the matrix import machinery - that is the PEX5/PEX13/PEX14 DTM - and matrix import fails in PEX16-null cells only because there is no membrane to import into. But the GOA row carries the qualifier acts_upstream_of_or_within, not involved_in, so the curator has already recorded the relation as upstream/indirect and the annotation is not making the claim being objected to. The ordering South and Gould observed (membrane assembly and PMP import first, matrix import following) is precisely what acts_upstream_of_or_within is for. Keeping it as a correct non-core annotation; the direct function remains peroxisome membrane biogenesis (GO:0016557). Supporting Evidence: PMID:9922452 Peroxisome synthesis and peroxisomal membrane protein import could be detected within 2-3 h of PEX16 injection and was followed by matrix protein import
GO:0060090 molecular adaptor activity	IDA PMID:19114594 The peroxisomal membrane protein import receptor Pex3p is di...	NEW	Summary: PEX16 functions as a molecular adaptor/receptor at the peroxisomal membrane, bringing together PEX3 and PEX19 in a trimeric complex to enable PMP delivery. Matsuzaki and Fujiki (2008) demonstrated that PEX16 is the membrane receptor for PEX3-PEX19 complexes using semi-intact cell import assays. Lee et al. (2024) confirmed a specific PEX3-PEX16 interface (PEX16 loop residues 132-214) with PEX19 binding PEX3 on the opposite face, supporting a trimeric adaptor model. This MF term is not currently annotated in GOA but accurately describes PEX16's core molecular function of bridging PEX3 and PEX19 at the membrane. Reason: PEX16 acts as a molecular adaptor by bringing together PEX3 (via direct binding through its cytosolic loop) and PEX19 (indirectly, through the PEX3-PEX19 interaction) at the peroxisomal membrane. This adaptor/scaffold function is the core molecular activity of PEX16. The existing 'protein binding' annotations are uninformative, and 'protein to membrane docking' (GO:0022615) is a BP term. GO:0060090 (molecular adaptor activity) best captures PEX16's role as a membrane-anchored receptor that coordinates the PEX3-PEX16-PEX19 assembly for PMP delivery. The structural trimer model that makes the adaptor reading concrete (PEX16 anchoring PEX3 at the membrane while PEX19 binds PEX3 on the opposite face) comes from the deep-research synthesis of Lee et al. (2024), cited below; that paper is not itself in the GOA record for this gene. Supporting Evidence: PMID:19114594 we demonstrate that Pex16p functions as the Pex3p-docking site and serves as the peroxisomal membrane receptor that is specific to the Pex3p-Pex19p complexes PMID:19114594 Pex16p was a prerequisite for peroxisomal targeting of newly synthesized Pex3p in vivo, functioning as the Pex3p membrane receptor file:human/PEX16/PEX16-deep-research-falcon.md The authors propose a trimeric complex in which PEX16 anchors PEX3 at the peroxisomal membrane, while PEX19 binds PEX3 on the opposite face and can deliver PMPs

Gene Description

Existing Annotations Review

Core Functions

References

Deep Research

Falcon

📚 Additional Documentation

Notes

📄 View Raw YAML