Phospholipase D3, also known as PLD3, is a protein that in humans is encoded by the PLD3 gene. PLD3 belongs to the phospholipase D superfamily because it contains the two HKD motifs common to members of the phospholipase D family, however, it has no known catalytic function similar to PLD1 or PLD2. PLD3 serves as a ssDNA 5' exonuclease in antigen presenting cells. PLD3 is highly expressed in the brain in both humans and mice, and is mainly localized in the endoplasmic reticulum (ER) and the lysosome.
PLD3 may play a role in regulating the lysosomal system, myogenesis, late-stage neurogenesis, inhibiting insulin signal transduction, and amyloid precursor protein (APP) processing. The involvement in PLD3 in the lysosomal system and in APP processing and the loss-of-function mutations in PLD3 are thought to be linked to late-onset Alzheimer's disease (LOAD). However, there are also studies that challenge the association between PLD3 and Alzheimer's disease (AD).
How APP processing is affected by PLD3 during AD still remains unclear, and its role in the pathogenesis of AD is ambiguous. PLD3 may contribute to the onset of AD by a mechanism other than by influencing APP metabolism, with one proposed mechanism suggesting that PLD3 contributes to the onset of AD by impairing the endosomal-lysosomal system. In 2017, PLD3 was shown to have an association with another neurodegenerative disease, spinocerebellar ataxia.
Genetics
PLD3 was first characterized as a human homolog of the HindIII K4L protein in the vaccinia virus, having a DNA sequence 48.1% similar to the viral gene. The PLD3 gene in humans is located at chromosome 19q13.2, with a sequence comprising at least 15 exons and is alternatively spliced at the low GC 5' UTR into 25 predicted transcripts. Translation of the 490 amino acid-long PLD3 protein is initiated around exons 5 to 7, and ends at the stop codon in exon 15.
Structure
PLD3 is a 490 amino acid-long type 2 transmembrane protein, unlike PLD1 and PLD2 which do not contain a transmembrane protein domain in their protein structure.
The cytosolic N-terminal of the protein faces towards the cytoplasm of the cell, and lacks consensus sites for N-glycosylation. The N-terminus is also predicted to contain a transmembrane domain.
The bulk of the protein is located in the ER lumen, containing the C-terminal domain. The C-terminal domain contains seven glycosylation sites along with a prenylation motif and two HXKXXXXD/E (HKD) motifs. In PLD1 and PLD2, this is the catalytic domain or active site of the protein, which is why PLD3 was assigned to the phospholipase D superfamily. However, PLD3 has no known catalytic activity and aside from presence of the HKD motifs, PLD3 has no structural commonalities with PLD1 or PLD2.
Tissue and subcellular distribution
Expression of PLD3 in tissues differs with the transcript size of its mRNA. The longer 2200 base pair transcript is ubiquitously expressed in the body, exhibiting higher expression levels in the heart, skeletal muscle, and the brain. Meanwhile, the shorter 1700 base pair transcript is found in abundance in the brain, but at low expression in non-nervous tissue. PLD3 expression is especially pronounced in mature neurons in the mammalian forebrain. High expression of PLD3 is specifically seen in the hippocampus and the frontal, temporal, and occipital lobes in the cerebral cortex. The PLD3 gene is also found with high expression in the cerebellum.
Subcellular localization of PLD3 is thought to primarily be in the endoplasmic reticulum (ER), as it has been shown to co-localize with protein disulfide-isomerase, a protein known to be a marker for the ER. PLD3 may also be localized in lysosomes, co-localizing with lysosomal markers LAMP1 and LAMP2 in lysosomes in separate studies. PLD3 was identified as a protein in insulin secretory granules derived from pancreatic beta cells.
Function
PLD3 is a member of the phospholipase D protein family, however, unlike phospholipase PLD1 and PLD2, it serves as a 5' exonuclease that specifically degrade ssDNA in the endolysosome, which is similar to the function of PLD4. Both PLD3 and PLD4 are essential for the clearance of nucleic acid product in antigen presenting cells. Deletion of PLD3 and PLD4 leads to accumulation of ssDNA and RNA in the endosome, which activates various nucleic acid sensors including TLR9, TLR7 and cGAS-STING and triggers inflammation and elevated secretion of cytokines. It is shown that mitochondrial DNA (mtDNA) is the major physiological substrate for PLD3 to degrade.