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C10orf53

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Overview

Conceptual translation of C10orf53. The full nucleotide and amino acid sequence are shown and aligned to show the relationship between the sequences. Information regarding post translation modifications[1], exon boundaries[2], untranslated regions[2], and disordered regions[3] are emphasized in the translation.

C10orf53 is a protein in humans (Homo sapiens) that is encoded by the C10orf53 gene[2]. The gene is located on the positive strand of the DNA and is 30,611 nucleotides in length[4]. The protein is 157 amino acids and the gene has 3 exons[2]. C10orf53 orthologs are found in mammals, birds, reptiles, amphibians, fish, and invertebrates[5]. It is primarily expressed in the testes and at very low levels in the cerebellum, liver, placenta, and trachea[2].

Gene

Chromosome 10 open reading frame 53 (10orf53), also known as uncharacterized protein family 0728 (UPF0728), in humans, is encoded by Chromosome 10 (10q11.23)[2], spanning 30,611 nucleotides[4]. The gene is located on the positive strand[4] with 3 identified exons[2].

Transcript

Isoform Accession #[2] Length

(amino acids)[2]

Length (nucleotides)[2] Exons translated[2] Additional comments[2]
a NM_182554.4

NP_872360.2

157 30,611 3 Less common isoform
b NM_001042427.3

NP_001035892.1

93 17,882 3 More common isoform – alternative 3’ exon and distinct C-terminus

The table outlines the two identified isoforms of C10orf53. The most common isoform has 93 amino acids which is a shorter amino acid sequence due to an alternative 3’ terminal exon and distinct C-terminus[2]. Isoform A has a higher frequency of analysis due to it being the longer isoform[4]. The analysis in this article is focused on isoform A.

Protein

The molecular weight predicted was 17.6 kDa[6]. The isoelectric point for C10orf53 is estimated to be 6.36 pl[6].

Secondary Structure

Predicted tertiary structure through I-TASSER[7]. This is a predicted visual representation of the secondary structure including alpha-helices and beta-pleated sheets. 
MPKNAVVILRYGPYSAAGLPVEHHTFRLQGLQAVLAIDGHEVILEKIEDWNVVELMVNEEVIFHCNI         67

CCCCCSSSSSSCCCHHCCSSSSSCHHHHHHHHHHHHHCCCSSSSSSSCCCCSSSSSSCCCSSSSSCC         67

KDLEFGKLTPSSDKRTTSSSRLTFHQLSSPCRMKVSPLQQFPQKTQDLTCTVLAQIGSCIHFQTNLC         134

CCCCCCCCCHHHHHHHHHHHHHHHHCCCCHHHHCCCHHHHCCCCCCCSSSSSHHHHCCSSSSSCCCC         134

DLGWPGLDHMLISGLEKRGTQPY                                                     157

CCCCCCCHHHHHHHHHHCCCCCC                                                     157

The secondary structure above illustrates the estimated secondary structure for Isoform A of C10orf53[7]. The C that are italicized indicate that the amino acid is located within a coil, the bolded S is referring to the amino acid being in a strand, and the underlined H shows the amino acid is in a helix[7]. The strand and helix structures can then be translated into the predicted tertiary structure done through I-TASSER.

Tertiary Structure

The predicted tertiary structure of C10orf53 is shown. The tertiary structure contains the seven helix and 8 strand structures predicted through I-TASSER[7].

Regulation

This figure illustrates the evolution trend for the genes above. The amino acid sequences of C10orf53, Fibrinogen Alpha, and Cytochrome C in Homo sapiens were compared to the same sequences of Homo sapiens, Macaca fascicularis, Mus musculus, Monodelphis domestica, Ornithorhynchus anatinus, Gallus gallus, Xenopus tropicalis, and Danio rerio. C10orf53 is shown to have a quicker evolution compared to cytochrome C, but is slower than the fibrinogen alpha’s evolution.

Gene Level

C10orf53 is primarily expressed in the testes, but also has very low levels of expression in the cerebellum, liver, placenta, and trachea[2]. It is tissue-specific to the testes due to the low expression in other tissues compared to the testes. C10orf53 majorly is secreted in the cytoplasm of cells and has moderate levels in the nucleus and mitochondria[8].

Protein Level

C10orf53 was found to have two phosphorylation sites, two SUMOylation sites, and one lysine acetylation site[1] All of these regions are shown in the conceptual translation of C10orf53.

Homology/Evolution

This figure illustrates the orthologs of C10orf53 with the species, common name, taxonomic group, date of divergence[9], accession number[5], sequence length[5], sequence identity percentage[5], and sequence similarity percentage[5] using NCBI, Integrated Taxonomic Information System, and Time Tree.

Evolution

C10orf53 is predicted to have a slower evolution compared to the gene, fibrinogen alpha, but it also has a quicker evolution compared to cytochrome c. Fibrinogen alpha is considered as a gene that had evolved rather quickly when examining the gene in different organisms. When two organisms diverged into different taxa, the gene went through alterations that made it significantly different from other organisms, causing it to have a quick rate of evolution. In contrast, Cytochrome C is relatively conserved throughout different organisms, which shows that it has a slow rate of evolution. C10orf53 has a rate of evolution that is smaller than fibrinogen alpha, but larger than cytochrome c.

Homology

A group of distantly and closely related orthologs were chosen and categorized by their date of divergence from humans[9]. The percent similarity and percent identity in relation to humans showed the predicted conservation between C10orf53 in humans compared to their orthologs.

Interacting Proteins

Protein[10] Protein Name[10] Identification[10] Function[11]
PIGR Polymeric Immunoglobulin Receptor Affinity chromatography Aids in the movement of polymeric IgA and IgM across mucosal epithelial cells
DSCC1 DNA Replication And Sister Chromatid Cohesion 1 Affinity chromatography Loads PCNA onto primed templates to manipulate replication forks
UXT Ubiquitously Expressed Prefoldin Like Chaperone Affinity chromatography Regulates androgen receptor transcription
ZG16B Zymogen Granule Protein 16B Affinity chromatography Located in the extracellular exosome and enables carbohydrate binding activity
SPECC1L Sperm Antigen With Calponin Homology And Coiled-Coil Domains 1 Like Affinity chromatography Helps with spindle organization and cytokinesis
MNAT1 CDK Activating Kinase Affinity chromatography Creates the CDK-activating kinase enzyme complex
SPTB Spectrin Beta, Erythrocytic Affinity chromatography Composes the cytoskeletal network in erythrocyte membranes

The table contains all predicted proteins that were found to interact with C10orf53[10]. It includes the protein acronym and name, the means that identification occurred, and the function of each protein. Due to the related function of some of the proteins, this provides evidence that these interactions coincide with the predicted location.

Clinical Significance

A study was conducted that compared the relative spermatogenesis in humans to the relative expression of RNAs correlated to teratozoospermia. In non-afflicted humans, there is a relatively high expression of C10orf53 across the RNAs tested. However, when a human had teratozoospermia, those levels dropped to almost zero[12] Another study examined the expression of C10orf53 in spermatogenesis and testis development in mice during development. C10orf53 is only highly expressed from day 30-56 of mice development, with the expression decreasing slightly on each five-day period until 56 days were reached[13]. The final study looked at research done within the past five years has correlated African American prostate cancer patients with the presence of C10orf535. When examining the exosome found in Caucasian populations associated with prostate cancer (PCC) against the African American exosome (PAA), C10orf53 was unique only to PAA [14].

References

  1. ^ a b "GPS 5.0 - Kinase-specific Phosphorylation Site Prediction". gps.biocuckoo.cn. Retrieved 2022-12-16.
  2. ^ a b c d e f g h i j k l m n "C10orf53 chromosome 10 open reading frame 53 [Homo sapiens (human)] - Gene - NCBI". www.ncbi.nlm.nih.gov. Retrieved 2022-12-16.
  3. ^ "ELM - unknown". elm.eu.org. Retrieved 2022-12-17.
  4. ^ a b c d "C10orf53 Gene - GeneCards | CJ053 Protein | CJ053 Antibody". www.genecards.org. Retrieved 2022-12-16.
  5. ^ a b c d e "BLAST: Basic Local Alignment Search Tool". blast.ncbi.nlm.nih.gov. Retrieved 2022-12-16.
  6. ^ a b "SAPS < Sequence Statistics < EMBL-EBI". www.ebi.ac.uk. Retrieved 2022-12-16.
  7. ^ a b c d "I-TASSER server for protein structure and function prediction". zhanggroup.org. Retrieved 2022-12-16.
  8. ^ "PSORT II Prediction". psort.hgc.jp. Retrieved 2022-12-16.
  9. ^ a b "TimeTree :: The Timescale of Life". www.timetree.org. Retrieved 2022-12-17.
  10. ^ a b c d "PSICQUIC View". www.ebi.ac.uk. Retrieved 2022-12-16.
  11. ^ "GeneCards - Human Genes | Gene Database | Gene Search". www.genecards.org. Retrieved 2022-12-16.
  12. ^ Platts, Adrian E.; Dix, David J.; Chemes, Hector E.; Thompson, Kary E.; Goodrich, Robert; Rockett, John C.; Rawe, Vanesa Y.; Quintana, Silvina; Diamond, Michael P.; Strader, Lillian F.; Krawetz, Stephen A. (2007-04-01). "Success and failure in human spermatogenesis as revealed by teratozoospermic RNAs". Human Molecular Genetics. 16 (7): 763–773. doi:10.1093/hmg/ddm012. ISSN 0964-6906. PMID 17327269.
  13. ^ Shima, James E.; McLean, Derek J.; McCarrey, John R.; Griswold, Michael D. (2004-07). "The murine testicular transcriptome: characterizing gene expression in the testis during the progression of spermatogenesis". Biology of Reproduction. 71 (1): 319–330. doi:10.1095/biolreprod.103.026880. ISSN 0006-3363. PMID 15028632. {{cite journal}}: Check date values in: |date= (help)
  14. ^ Panigrahi, Gati K.; Praharaj, Prakash P.; Kittaka, Hiroki; Mridha, Asit R.; Black, Olen M.; Singh, Rakesh; Mercer, Roger; van Bokhoven, Adrie; Torkko, Kathleen C.; Agarwal, Chapla; Agarwal, Rajesh; Abd Elmageed, Zakaria Y.; Yadav, Hariom; Mishra, Santosh K.; Deep, Gagan (2019-01-08). "Exosome proteomic analyses identify inflammatory phenotype and novel biomarkers in African American prostate cancer patients". Cancer Medicine. 8 (3): 1110–1123. doi:10.1002/cam4.1885. ISSN 2045-7634. PMC 6434210. PMID 30623593.
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