PAAT (protein)

PAAT (protein associated with ABC transporters), also known as C10orf88 (chromosome 10 open reading frame 88), is a protein in the human genome, encoding by the gene of the same name.^[5] It is predicted to be associated with ABC transporters, containing an ABC transporter domain, specifically Type II ABC Transporters.^[6] PAAT physically interacts with mitochondrial inner membrane ABC transporters, and plays a functional role in ferric nutrient transport and heme biosynthesis. The gene has been strongly associated with a rare form of Alzheimer's disease, and is primarily expressed in the cerebral cortex, testis, and thymus. It is mainly localized in the cytoplasm and nucleus.

PAAT is assessed to have first appeared in genomic data in the subphylum Cephalochordata, specifically in the European lancelet (Branchiostoma lanceolatum).^[7] This organism represents one of the most basal chordates and is believed to have diverged from the vertebrate lineage approximately 588 million years ago (MYA), likely during the Cambrian period, though some phylogenetic models propose divergence as late as the Cretaceous period.

Comparative sequence analysis indicates that the European lancelet ortholog of PAAT shares only 21% sequence ID and 38% similarity with the human protein, alongside a corrected sequence divergence (CSD) of 156%, suggesting a high rate of molecular evolution or substantial domain restructuring over deep evolutionary time. This is similar in the Brook lamprey (Lampetra planeri), which is another early-branching cordate.^[8]

Sequence identity and similarity increase progressively in more closely related species (resulting in lower corrected sequence divergence, CSD), with the highest conservation observed in mammals (~80% average identity). This pattern suggests strong purifying selection on PAAT in lineages reliant on hemoglobin-based oxygen transport, consistent with its proposed role as a heme transporter in circulatory systems. Notably, mammals—which depend heavily on heme-bound iron for oxygen delivery—exhibit the lowest CSD values, reflecting functional constraint.^[9]

Notably, PAAT is found in Actinopterygii but not Sarcopterygii, which differ in the presence of subcutaneous muscular limb buds supported by articulated appendicular skeletons.^[10] Additionally, there were no orthologs detected in invertebrates or prokaryotes, suggesting a chordate-specific origin.

Upon comparison of the evolution of PAAT to other model proteins (Cytochrome C; slow evolving and Fibrinogen A; fast evolving), the gene exhibits a rapid evolutionary pattern, exhibiting a CSD of much higher the further away from humans the species is, having a rate closer to Fibrinogen alpha rather than Cytochrome C. This rapid evolutionary pattern suggests that the function of the PAAT is likely significantly changed depending on the species, as suggested by the function of it in humans being a ferric transporter.

PAAT is located on chromosome 10 at the cytogenetic locus 10q26.13. The gene spans 2,913 base pairs and comprises six exons and five introns, encoding a 445-amino acid protein with no known isoforms or splice variants. The mature mRNA is 1,497 nucleotides after splicing.

The PAAT gene contains binding sites for transcription factors (TFs) linked to neural, immune, and reproductive functions, consistent with its expression in the brain, thymus, and testis. Key TFs include NRF1, NR2C2, ELK4 & ETV4, TFAP2A, and IRF3.

The protein exists as a novel ATPase, meaning it interacts with ATP catalysis and transport. It has no known isoforms. It contains two domains, with one being the primary functional PAAT-like site, and the other being a domain associated with other ABC Transporters, known as the "ABC Transport 1" domain.

It functions via ATP hydrolysis, regulating homeostasis through balancing iron concentrations.^[11] It has a theoretical isoelectric point of 6, and a predicted molecular weight of 49.2 kDa.^[12] The ABC Transporter 1 domain mainly consists of beta sheets, while the C-terminus consists of mostly secondary structure and alpha helices. PAAT also has no disulfide bonds or oligomerization.

Computational tools PSORT II^[13] and DeepLoc^[14] both predicted PAAT to be primarily localized in the nucleus, with approximately 60% confidence. However, their secondary predictions differed: PSORT II suggested mitochondrial (17.4%) and cytoplasmic (13%) localization, while DeepLoc indicated a stronger cytoplasmic signal (41%). The absence of mitochondrial targeting signals and cleavage sites supports nuclear localization as the most probable. These predictions are consistent across orthologs.

Further analysis was completed using WoLF PSORT^[15] and an analysis of the interacting proteins. Interacting proteins revealed nuclear and cytoplasmic localization, with the most relevant proteins being localized in those regions. WoLF also predicted for the nuclear and cytoplasm to be the highest. This would support the prediction that the protein is localized in both the cytoplasm and nucleus, with mitochondria being a potentially relevant localization as well.

The protein is experimentally known to interact with other specific ABC transporters, mainly ABCB7, ABCB8, and ABCB10.^[11] Additionally, the STRING database identified 10 proteins interacting with PAAT, including five with experimental evidence (CLTC, GDI2, CCDC91, NCKAP1, and LILRB4).^[16] Most showed co-expression, except TEX9, NADSYN1, and LILRB4, while all but POLR3F were supported by text-mining. Key interactors CLTC, NADSYN1, CYP2R1, and POLR3F were selected based on strong co-expression (via GEO microarray data) and functional links, particularly CLTC, which had consistent co-expression across studies.^[17] NADSYN1 and CYP2R1 may associate through the vitamin D pathway.^[18]

PAAT is predicted to undergo several post-translational modifications, including phosphorylation at multiple serine residues (e.g., S11, S150, S201),^[19] lysine acetylation at K25,^[20] and both N- and O-linked glycosylation.^[21] Degron motifs suggest regulation by SCF-βTrCP1 and APC/C complexes.^[22] Functional motifs include 14-3-3 and SH2 binding sites, a PP1 phosphatase docking site,^[23] and a nuclear export signal.^[24] No signal peptides, lipid anchors, or organelle-targeting sequences were detected.

PAAT is characterized by ubiquitous expression across human tissues,^[25] with notably higher RNA levels in the testis, brain, and thymus. Data from the Human Protein Atlas (HPA) RNA-seq normal tissues indicate significant expression in the testis (RPKM: 4.006) and brain (RPKM: 1.916), while most other tissues also display detectable expression levels, reinforcing its widespread presence.^[26]

During human fetal development, analysis of tissue-specific circular RNA induction reveals early-stage expression of PAAT across tissues, suggesting a potential role in early developmental processes, though without substantial tissue-specific differences.^[27] Similarly, total RNA sequencing of 20 human tissues confirms significant expression in the cerebellum and thymus, further supporting the gene's broadly distributed, yet brain and immune-related, expression profile.^[28]

Additional insights from the NCBI Gene Expression Omnibus (GEO) datasets (GDS1096, GDS596, and GDS3113) corroborate these findings. GDS1096 shows general expression throughout the brain, particularly in the thalamus and amygdala, and strong expression in the testis. GDS596 further highlights notable expression in olivary ganglia, superior cervical ganglia, and dorsal root ganglia. GDS3113 emphasizes high expression in the fetal brain and testis, suggesting consistent gene activity across both developmental and adult stages.

Several expression quantitative trait loci (eQTLs) have been associated with PAAT, demonstrating regulatory influence in specific tissues. For instance, the variant chr10_123305622_C_A_b38 shows a strong negative normalized effect score (NES: -1.0) in EBV-transformed lymphocytes, while chr10_123424873_AT_A_b38 displays a positive NES (0.86) in the esophagus muscularis. Notably, variants in the brain, including the caudate and cerebellar hemisphere, show negative regulatory effects, consistent with the gene's regional expression patterns. Additionally, a positive effect in the testis (NES: 0.39) further supports its reproductive tissue specificity.

While some tissues affected by polar eQTLs (such as EBV-transformed lymphocytes and the esophagus) are not strongly represented in protein-level data, these regulatory variants may suggest disease-specific or context-dependent functions, particularly in immune or epithelial cell types.

Immunohistochemical staining data provide insight into PAAT protein localization, with strong cytoplasmic positivity observed in two tissues: the testis and pancreas. In the testis, expression is localized to subsets of cells within the seminiferous ducts, while in the pancreas, staining is prominent in exocrine glandular cells. These results suggest tissue-specific functional roles at the protein level, despite more ubiquitous gene expression.

Data from PaxDb^[29] indicate that PAAT protein abundance is approximately average relative to the human proteome, with higher levels in the brain, testis, lymph nodes, and ovaries. This aligns with RNA expression data, suggesting that PAAT maintains a consistent presence at both the transcript and protein levels across key tissues involved in neurological, reproductive, and immune functions.

PAAT expression appears sensitive to cellular differentiation and disease states. In redifferentiated podocytes derived from amniotic kidney progenitor cells, expression significantly increases, implying a role in renal cell maturation or kidney-specific functions.^[30]

In contrast, PAAT is downregulated in skeletal muscle tissues of individuals with Myotonic Dystrophy Type 2 (DM2), suggesting its potential involvement in muscular maintenance or its disruption in neuromuscular disorders.^[31]

Additionally, the gene is upregulated in peripheral blood mononuclear cells during Simian Immunodeficiency Virus (SIV) infection, particularly in response to PD-1 antibody treatment, indicating a likely function in immune activation, T cell signaling, or viral response pathways.^[32]

A study conducted by Yang et. al. (2014) identified that regulates mitochondrial ABC transporters, playing a critical role in iron homeostasis and heme biosynthesis. It localizes to both the cytoplasm and mitochondria, where its intrinsic ATPase activity enables functional interactions with specific mitochondrial ABC transporters—including ABCB7, ABCB8, and ABCB10, but not others such as ABCB1 or ABCG2.^[11]

By modulating ferric nutrient transport and heme synthesis, PAAT maintains mitochondrial integrity. Depletion of PAAT disrupts mitochondrial membrane potential, increases oxidative DNA damage, and triggers cell death, underscoring its role in cellular survival. These findings position PAAT as a trans-regulator linking mitochondrial ABC transporter activity to broader metabolic and stress-response pathways.

PAAT has been proposed to be a component in the Vitamin D cycle,^[33] specifically interacting with Cytochrome P450 during hydroxylation. As such, PAAT has been associated with Vitamin D deficiencies when disregulated.^[34]

As well as this, the protein is associated with the rare form of Alzheimer's Disease reported as AD15. This form presents with amyloid-ß plaques, but diverts from the typical expression wherein there are no neurofibrillary tangles.^[35]

GWAS links PAAT to lipid metabolism in humans (variants rs7904973 and rs12246352 associate with lower LDL and Apolipoprotein B)^[36][37] and to two rat phenotypes: 2-Methylbutyryl-CoA Dehydrogenase Deficiency (BCAA catabolism disorder) and craniosynostosis. The BCAA connection aligns with PAAT's role in neural and metabolic pathways.