Creating Universal PSMD2 (Rpn1) Primers for a Range of Model Organisms and Homo sapiens
DOI:
https://doi.org/10.15330/jpnubio.10.34-44Keywords:
PSMD2, Rpn1, primer, sequence, oncogene, protein, nucleotide, model organism, conserved regionsAbstract
Protein degradation plays a key role in many cellular processes, degrading misfolded or abnormal proteins and thereby controlling cell proliferation, DNA repair, and stress response. For this reason, the ways of eliminating such proteins in the context of various human diseases are being actively investigated. The list of human diseases that involve protein degradation pathways includes a wide range of cancers. PSMD2 or Rpn1 (26S proteasome subunit, non-ATPase 2) is actively involved in the functioning of the ubiquitin-proteasome system. Expression of PSMD2 has been found to be upregulated in cancer cells and now it is actively studied as a potential therapeutic target and prognostic marker for several types of cancer. To explore a drug target, it is often necessary to use several model organisms at different stages of research. The goal of our study is to search for conserved PSMD2 sequences and create oligonucleotide sequences (primers) that would be suitable for conducting polymerase chain reaction (PCR) in a wide range of model organisms and humans. Gene sequences were obtained from the NCBI Nucleotide database. Next, we designed oligonucleotide sequences and optimized their parameters. The following candidate sequences were found: 5'-CTGGACATCATGGAGCCCAA-3' and 5'-CCACCATCCACATCCCACAG-3' for sense and antisense strands of PSMD2. The next step was to perform in silico PCR using an Online primer designing tool, which revealed that the PCR product was 266 nucleotides size in five organisms, including human. The PCR product was aligned and phylogenetic analysis was performed. Among organisms examined, the nucleotide sequence of golden hamster Mesocricetus auratus was found to be evolutionarily closest to the PSMD2 sequence in humans, and the sequence of Drosophila melanogaster was the most distant. The results of the study can be used for the screening of PSMD2 expression in different organisms. The approach of finding primers, which match genes of several organisms, can be applied for other genes that encode proteins with neighboring methionine, tryptophan, aspartic and glutamic acids, asparagine, glutamine, cysteine, histidine, lysine, tyrosine, and phenylalanine residues in their amino acid sequences.
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