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Gene & Protein in Disease Bioinformatics study of PCNP

molecular functions, ubiquitin protein ligase activity,
small conjugating protein ligase activity, amino acid ligase
activity, and ligase activity forming carbon nitrogen bonds
showed P < 0.05. The network of molecular functions
constructed by Cytoscape software is presented in
Figure 3B. Similarly, the cellular components results show
the distribution of PCNP solely in the nucleus of the cell
(Table S1). Furthermore, the pathway enrichment analysis
was performed using the Network Analyst server. There
were no results for the PCNP protein when searching broad
queries on both servers (Network Analyst and Enrichr) for
the Kyoto Encyclopedia of Genes and Genomes (KEGG)
Reactome, and WikiPathways.
3.5. Coexpression and PPI analysis
Co-expression of PCNP was investigated by GeneMANIA
server. The outcomes of GeneMANIA were subjected to
Cytoscape software to construct the network based on Figure 4. Coexpression network of 10 common targets of PCNP
their coexpression score. The coexpression results reveal constructed with Cytoscape software. In the network, the size of the node
that PCNP has significant expression with MORF4LI and corresponds to the coexpression affinity level with the PCNP. The bigger the
RSL24D1 genes, and the least association of coexpression size of the node, the greater the coexpression level with the respective gene.
with ATF1, NFYB, and CMPK1 genes (Figure 4). MORF4
(mortality factor on chromosome 4) is a senescence-
inducing gene in tumor cells. The previous research
has demonstrated that MORF4 protein is found both
in the cytoplasm and the nucleus of cells . In addition,
[44]
RSL24D1 is a NP involved in ribosomal biogenesis .
[45]
Hence, these findings are the first to confirm that PCNP
is a NP, and it might be a potent protein that plays a role
in the regulation of tumor cell progression and ribosomal
biogenesis through influencing the expression of MORF4
and RSL24D1 genes.
Moreover, in the present study, the PPI was determined
based on the data of tandem affinity purification Figure 5. The protein-protein interaction network of PCNP protein based
assay, affinity chromatography technology assay, and on the experimental models constructed with Cytoscape software. The
coimmunoprecipitation assay. From the results, four proteins in the green color nodes were collected from the tandem affinity
proteins, namely, TRAM1, PSMC6, SRP9, and PRKRIR, purification assay and coimmunoprecipitation assays, and the proteins
in the pink color nodes were filtered from the affinity chromatography
were extracted using tandem affinity purification technology assay.
and coimmunoprecipitation assays. Using the affinity
chromatography technology assay, two proteins, UHRF2 PSMC6 promotes the apoptosis of osteoblasts by halting
and BMI1, were found to have an interaction with PCNP the PI3K/AKT signal transduction pathway. Interestingly,
protein (Figure 5). TRAM1 (Translocating chain-associated a previous research study demonstrated PCNP activity
membrane protein 1) and SRP9 (Signal Recognition Particle through the PI3K/AKT signal transduction pathway.
9) are involved in the translocation of nascent secretory Therefore, these results suggest that the cross-talk between
proteins by facilitating proper chain folding into or through PCNP and PSMC6 is needed to regulate vital functions
the endoplasmic reticulum membrane . To this end, of the cell through the PI3K/AKT signal transduction
[46]
it can be speculated that PCNP might be associated with pathway . Moreover, UHRF2 is also a NP involved in cell
[47]
endoplasmic reticulum protein transport by making direct cycle regulation. It halts cell proliferation and acts as a tumor
or indirect interaction with TRAM1 or SRP9. In addition, suppressor factor. BMI1 is a member of polycomb-repressive
PSMC6 is located in the base region of the proteasome 19S complex 1 that is necessary for chromatin remodeling or
regulatory particle and is involved in the translocation of the silencing. Importantly, it also plays a role in the self-renewal
substrates to the core particle. A recent study reported that of somatic stem cells . Apart from these PPI findings,
[48]

Volume 1 Issue 1 (2022) 7 https://doi.org/10.36922/gpd.v1i1.65