The Alignment of Pirin

 

The Sequence of Pirin

NCBI is a biotechnical database that has amassed a gamut of qualitative and quantitative biological research. I will be using NCBI’s conserved domain and nucleotide databases to conduct the following research on the amino acid sequencing of Pirin as well as the nucleotide sequence of the PIR gene that encodes it.  


The NCBI summary for pirin is as follows: 

“This family consists of Pirin proteins from both eukaryotes and prokaryotes. The function of Pirin is unknown but the gene coding for this protein is known to be expressed in all tissues in the human body although it is expressed most strongly in the liver and heart. Pirin is known to be a nuclear protein, exclusively localized within the nucleoplasma and predominantly concentrated within dot-like subnuclear structures. A tomato homolog of human Pirin has been found to be induced during programmed cell death. Human Pirin interacts with Bcl-3 and NFI and hence is probably involved in the regulation of DNA transcription and replication. It appears to be an Fe(II)-containing member of the Cupin superfamily” (“Pirin,” 2020).


According to the NCBI file “Homo sapiens pirin (PIR), transcript variant 1, mRNA”

the locus of PIR (The gene that encodes pirin) is categorized by NCBI with the tag NM_003662. The aforementioned file’s accession number is identical to its locus tag (NM_003662). The file is on its fourth iteration (Version NM_003662.4) and contains the following comment: 

           "REVIEWED REFSEQ: This record has been curated by NCBI staff. 

           The reference sequence was derived from DA686501.1,

           DT217415.1, Y07868.1 and BC002517.2. On Aug 13, 2020 this 

           sequence version replaced NM_003662.3.

            

            Summary: This gene encodes a member of the cupin superfamily.

            The encoded protein is an Fe(II)-containing nuclear protein

            Expressed in all tissues of the body and concentrated within dot-like

            subnuclear structures. Interactions with nuclear factor I/CCAAT box

            transcription factor as well as B cell lymphoma 3-encoded

            oncoprotein suggest the encoded protein may act as a

            transcriptional cofactor and be involved in the regulation of DNA

            transcription and replication. Alternatively spliced transcript

            variants have been described. [provided by RefSeq, Jul 2008].

            

            Transcript Variant: This variant (1) represents the longer

            transcript. Variants 1 and 2 encode the same protein.

            

            Publication Note:  This RefSeq record includes a subset of the

            publications that are available for this gene. Please see the Gene

            record to access additional publications” (“Homo sapiens pirin                

(PIR)”, 2020)."


The two files convey a similar function of pirin, but go into different levels of detail. While both link pirin as a cofactor for DNA transcription based on interactions with Bcl-3-encoded oncoproteins, only the first file links pirin to nuclear factor κB and only the latter file links pirin to nuclear factor I/CCAAT. Furthermore, only the second file notes pirin’s roles as a ligand of ferrous iron. 

The following data on the amino sequences of pirin in the species Homo sapiens, Mus musculus, Caenorhabditis elegans, and Drosophila melanogaster was retrieved from the NCBI's BLAST tool (Altschul, Madden, Schäffer, et al., 1997).



     


            The data provided indicates a lack of homologous amino sequences between human 

pirin and Caenorhabditis elegans/Drosophila melanogasterare. However, Mus musculus 

(House mice) was indicated to have several amino sequences with relatively low E-values, a 

100% query cover, and a percentage identity of 97.37%, indicating the presence of potential 

homologues or orthologues amino, and by extension nucleotide, sequences between humans

and house mice relating to pirin in humans and the PIR gene.

        A primer is a short strand of nucleic acid allows DNA to replicate itself. During replication,

DNA "unzips" itself through catabolic reaction, and then attaches itself to the RNA primers

through an anabolic reaction facilitated by the enzymes polymerase (Rychlik, 1993). The NCBI

allows us to create our own provided for the PIR gene that encode piren (Ye, Coulouris, 

Zaretakaya, Cutcutache, et al., 2012):







References

Conserved Domains Database [Internet]. Bethesda (MD): National Library of Medicine
(US), National Center for Biotechnology Information; 2004 – [cited 2021 Oct 12].
Available from: https://www.ncbi.nlm.nih.gov/cdd/


Conserved Domains Database [Internet]. Bethesda (MD): National Library of Medicine (
 US), National Center for Biotechnology Information; [2020] – . Accession No.
pfam02678-396999, Pirin; [cited 2021 Oct 12]. Available from:
https://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=396999


Nucleotide [Internet]. Bethesda (MD): National Library of Medicine (US), National
Center for Biotechnology Information; 2004 – [cited 2021 Oct 12]. Available
from: https://www.ncbi.nlm.nih.gov/nuccore/


Nucleotide [Internet]. Bethesda (MD): National Library of Medicine (US), National
Center for Biotechnology Information; [2020] – . Accession No.
NM_003662, Homo sapiens pirin (PIR), transcript variant 1, mRNA; [cited 2021
Oct 13]. Available from: https://www.ncbi.nlm.nih.gov/nuccore/NM_003662.4.


Rychlik W. Selection of primers for polymerase chain reaction. Methods Mol Biol. 1993;15:31-

        40. doi: 10.1385/0-89603-244-2:31. PMID: 21400260.


Stephen F. Altschul, Thomas L. Madden, Alejandro A. Schäffer, Jinghui Zhang, Zheng Zhang, 

        Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new                 

        generation of protein database search programs", Nucleic Acids Res. 25:3389-3402.


Ye J, Coulouris G, Zaretskaya I, Cutcutache I, Rozen S, Madden T (2012).
        Primer-BLAST: A tool to design target-specific primers for polymerase chain reaction.
        BMC Bioinformatics. 13:134.

Comments

  1. EricaOctober 18, 2021 at 6:52 AM

    Exceptional work, Josiah! I am truly impressed— are you sure we can’t convert you to a biologist? 🤣

    ReplyDelete

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