GO_REF:0000002

Gene Ontology annotation through association of InterPro records with GO terms

InterPro2GO mapped the PEPC InterPro signatures (IPR021135, IPR022805) to tricarboxylic acid cycle and carbon fixation; both mappings are too coarse for the anaplerotic housekeeping isozyme and are recommended for modification to oxaloacetate metabolic process.

GO_REF:0000043

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

SwissProt keyword-derived (SPKW) annotations present in the Sept 2025 goa_uniprot_gcrp snapshot but removed from the current GOA release after GOA retired the keyword2GO pipeline for cellular organisms.
The SPKW "photosynthesis" annotation for PPC16 derived from the family-level UniProt keyword "Photosynthesis"; its removal by GOA was justified because soybean is a C3 plant and PPC16 is the non-photosynthetic housekeeping PEPC isozyme.

GO_REF:0000033

Annotation inferences using phylogenetic trees

IBA annotation from the PEPC phylogenetic group correctly assigns cytosolic localization, consistent with plant-type PEPCs being cytosolic Class-1 homotetramers.

GO_REF:0000044

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

Subcellular-location mapping assigned cytoplasm, consistent with the curated UniProt location and with the IBA cytosol annotation.

GO_REF:0000120

Combined Automated Annotation using Multiple IEA Methods

Combined IEA methods (ARBA, InterPro, RHEA, EC) correctly assigned phosphoenolpyruvate carboxylase activity, the core molecular function of the protein.

PMID:1450389

cDNA sequence and expression of a phosphoenolpyruvate carboxylase gene from soybean.

The PEPC cDNA was isolated from soybean, explicitly described as a C3 plant.
The encoded protein resembles C3-type PEPC proteins, not the C4 or CAM photosynthetic isoforms.
The PEPC mRNA is present at similar levels in leaf, stem, root and developing seed, a ubiquitous housekeeping expression pattern.
Two potential start codons exist and the protein may be subject to regulation by protein kinase (consistent with the conserved N-terminal phosphoserine site).

PMID:21524275

The remarkable diversity of plant PEPC (phosphoenolpyruvate carboxylase); recent insights into the physiological functions and post-translational controls of non-photosynthetic PEPCs.

PEPC catalyses the irreversible beta-carboxylation of PEP to form oxaloacetate and Pi and sits at the core of plant carbon metabolism.
Beyond the C4/CAM photosynthetic role, PEPC fulfils non-photosynthetic functions, particularly anaplerotic replenishment of TCA-cycle intermediates consumed during biosynthesis and nitrogen assimilation.
Plant genomes encode several plant-type PEPCs (PTPCs, ~110 kDa, homotetrameric Class-1 PEPCs with conserved serine-phosphorylation sites) plus a distantly related bacterial-type PEPC (BTPC); PPC16/Q02909 is a PTPC.

PMID:36309625

Role of C4 photosynthetic enzyme isoforms in C3 plants and their potential applications in improving agronomic traits in crops.

All genes of the C4 photosynthetic pathway are present in C3 plants but the C3 isoforms perform diverse non-photosynthetic functions.
Non-photosynthetic PEPC isoforms support major metabolic pathways including the TCA cycle, cellular pH maintenance, and nutrient uptake/assimilation.

PMID:29240945

Transcript profiling indicates a widespread role for bacterial-type phosphoenolpyruvate carboxylase in malate-accumulating sink tissues.

Plant genomes encode several plant-type PEPC (PTPC) isozymes plus a distantly related bacterial-type PEPC (BTPC); the two are separate genes.
PEPC in biosynthetically active sink tissues maintains rapid anaplerotic PEP carboxylation and respiratory CO2 refixation rather than autotrophic carbon fixation.

PMID:10938812

Weather and nodule mediated variations in delta 13C and delta 15N values in field-grown soybean (Glycine max L.) with special interest in the analyses of xylem fluids.

In field-grown soybean, the contribution of PEPC-mediated CO2 fixation in root nodules to whole-plant carbon incorporation was not significant, consistent with an anaplerotic rather than net autotrophic carbon-fixing role for PEPC.

file:SOYBN/PPC16/PPC16-deep-research-falcon.md

Deep research report (falcon / Edison Scientific Literature) on soybean PPC16 (Q02909) phosphoenolpyruvate carboxylase.

Soybean primary literature (Sugimoto et al. 1992) cloned gmppc16 as a full-length PEPC cDNA from a developing-seed library and concluded the encoded protein resembles C3-type/housekeeping PEPCs more than C4/CAM photosynthetic forms; the report confirms PPC16 is the broadly expressed housekeeping isozyme of a C3 plant with no photosynthetic role.
gmppc16 mRNA was detected by Northern blot at similar levels in leaf, stem, root and developing seed, supporting a constitutive housekeeping rather than tissue-specialized expression pattern.
The report places the housekeeping/C3 PEPC reaction (PEP + HCO3- -> oxaloacetate + Pi, EC 4.1.1.31, irreversible, Mg2+-dependent) in cytosolic anaplerotic carbon metabolism, replenishing TCA-cycle C4 intermediates and supplying carbon skeletons for nitrogen assimilation and amino-acid/storage-protein synthesis during seed filling.
Genome-wide analysis (Wang et al. 2016) shows soybean has 10 PEPC genes (7 plant-type, 3 bacterial-type) predicted predominantly cytosolic; a later seed-development study (Yamamoto et al. 2020) identifies Gmppc16 as Glyma.12g161300, a plant-type PEPC isogene, supporting its classification as a PTPC paralog within the family.
The nodule-enhanced GmPEPC7 is 92.5% identical at the amino-acid level to gmppc16 (Hata et al. 1998), confirming gmppc16 is a close paralog representing the broadly-expressed housekeeping lineage and consistent with cytosolic localization stated for soybean nodule PEPCs.