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C5orf22

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C5orf22
Identifiers
AliasesC5orf22, chromosome 5 open reading frame 22
External IDsMGI: 1925127; HomoloGene: 10149; GeneCards: C5orf22; OMA:C5orf22 - orthologs
Orthologs
SpeciesHumanMouse
Entrez

55322

77877

Ensembl

ENSG00000082213

ENSMUSG00000022195

UniProt

Q49AR2

Q8BGC1

RefSeq (mRNA)

NM_018356

NM_001166360
NM_029998
NM_001357761

RefSeq (protein)

NP_060826

NP_001159832
NP_084274
NP_001344690

Location (UCSC)Chr 5: 31.53 – 31.56 MbChr 15: 12.81 – 12.82 Mb
PubMed search[3][4]
Wikidata
View/Edit HumanView/Edit Mouse

Chromosome 5 open reading frame 22 (c5orf22) is a protein-coding gene of poorly characterized function in Homo sapiens.[5] The primary alias is unknown protein family 0489 (UPF0489).[5]

Gene

C5orf22 is located on the positive strand of Chromosome 5 at 5P13.3, spanning 22,779 nucleotides, from base pair 31532275 to 31555053.[6] C5orf22 encodes 9 total exons and contains 7 isoforms.[5] Isoform variants differ in their exon configuration and untranslated region. Transcript variant 1 is the canonical isoform, encoding 442 amino acids across 9 exons.[7]

Annotated human chromosome 5. Retrieved from NCBI Gene.[5]
C5orf22 gene diagram. Human C5orf22 is located on chromosome 5 (5p13.3) at base pair 31,532,275 to 31,555,053. Transcript variant 1 (depicted above) encodes 9 exons.1 Promoter prediction is from Genomatix.[8] The GXP# for the promoter is GXP_55076. Pro1, is the assigned promoter for all transcript variants. This promoter lies directly upstream from the 5’ UTR and spans 1,081 base pairs. Promoter is labeled in green. Exons (Ex) are denoted in dark blue. Illustration was created using Domain Illustrator.21  

Expression and regulation

C5orf22 displays ubiquitous RNA expression across tissue types from all 3 germ layers and from all phases of development in humans, mice, chickens, and zebrafish.[5] There are statistically significant differences in RNA expression between select tissues, with skeletal muscle containing the greatest abundance (7.8 RPKM)[5][9]

C5orf22 contains 1 predicted promoter directly upstream of the gene (GXP_55076).[8] This promoter is 1,081 base pairs and partially overlaps with the 5’ untranslated region.[8] GXP_55076 is assigned to all transcript variants.[8] Transcription factor binding elements consist of TATA box binding elements, SMAD transcription factors, MAF/AP1 binding factors, and several others.[8]

Neighboring elements

C5orf22 closest neighboring element is Drosha, a ribonuclease which is encoded by the minus strand proximal to C5orf22.[5][10] Drosha is a double stranded endoribonuclease that assists with the first step of microRNA biogenesis.[11]

Structure

C5orf22 contains 2 globular domains and 3 small disordered regions.[12] The molecular-weight is approximately 50 kDa.[13] The isoelectric point is 4.7.[13] C5orf22 contains relatively average amino acid proportions compared to most proteins.[14] There were no significant outliers in abundance of individual amino acids. C5orf22 contains several predicted post-translational modifications including phosphorylation sites, ubiquitination sites, glycosylation sites, SH2 domain, and a myristylation site.[12]

C5orf22 protein structure contains 2 globular domains and 3 disordered regions.

Subcellular distribution

C5orf22 is most likely to exist as a soluble protein located within the cytoplasm and nucleus.[15] Amino acid sequence predictions and immunohistochemical staining support the localization of C5orf22 to cytoplasm and nucleus.[9][16] Furthermore, amino acid sequence analysis indicated a predicted partial nuclear localization signal (NLS) from AA 175-185.[17]

Function

The precise function of C5orf22 is still unknown however it is hypothesized to be a component of a DNA splicing complex.[18] Proteomic research implicated the protein product as a novel component of the WBP11/PQBP1 splicing complex which regulates expression of genes involved in a spectrum of processes ranging from DNA repair to immunomodulation.[18] C5orf22 knockdown was associated with downregulation of alternative splicing events that led to aberrant gene expression of select genes and ultimately cell cycle dysfunction.[18] Cell localization evidence and the presence of a NLS further support this hypothesized function.

Interacting proteins

Experimental evidence has indicated over 20 interactors with C5orf22. [19][20][21] Interactants are localized to both the nucleus and cytoplasm.[22] The most likely interactors are WBP11, OSM, Surf2, ELOF1, and DDITL4.[20]

Evolution & homology

C5orf22 initially appeared in invertebrates approximately 797 million years ago.[23] It is the only member of its gene family. Human UPF0489 C5orf22 is conserved through invertebrates.[23] C5orf22 orthologs showed conservation of the two globular domains through bony fish and conservation of 1 globular domain within arthropods.[12] Isoelectric point and molecular weights of C5orf22 orthologs were within ∓ 0.15 and ∓ 3kDa through bony fish.[12] There are no paralogs to c5orf22 in humans.[23]

UPF0489 C5orf22 is slow evolving protein, based on comparisons of the percent corrected divergence of orthologous proteins.[24]

Table 1: C5orf22 orthologs[24]
Taxonomic Class Common Name Genus species Date of Divergence

Millions of Years Ago (MYA)

Sequence

Identity (%)

Sequence

Similarity (%)

Sequence

Length (AA)

Query Coverage

(%)

Accession Number
Mammal Human Homo sapiens N/A 100 100 442 100 NP_060826.2
Mouse Mus musculus 90 78 86 442 100 NP_084274.1
Whale Balaenoptera musculus 96 89 94 467 100 XP_036705025.1
Aves Chicken Gallus gallus 312 68 79 446 98 XP_418996.3
Reptile Tiger rattlesnake Crotalus tigris 312 65 75 476 98 XP_039212189.1
Amphibian African clawed frog Xenopus laevis 352 67 78 459 95 XP_018121838.1
Fish Zebrafish Danio rerio 435 57 71 439 95 NP_956625.1
Sea lamprey Petromyzon marinus 615 51 69 589 89 XP_032827184.1
Invertebrate Fruit fly Drosophila suzukii 797 33 50 481 95 XP_036671373.1
Conceptual translation of human C5orf22 isoform X1. C5orf22 isoform 1 nucleotide sequence overlying protein translation. Features and sequences are indicated in respective colors. Figure legend is listed here: Start: First ATG encoding methionine. Disordered: Disordered region. GlobD: globular domain.  Ex*|ex*: border of two exons. M-alt term: Alternate methionine N-terminus. Phos site: Phosphorylation site. Ubq site: Ubiquitination site. Sumo site: Sumoylation site. SNP: single nucleotide polymorphism. Myrstyl: myristoylation site. PDphos: Proline dependent phosphorylation site. MAPK: MAPK domain. A-hlx: alpha-helix. B-sheet:Beta-pleated sheet. NLS:Nuclear localization signal.Stop: Stop codon. miRNA site: miRNA site with target score of 98%, indicated by miRDB.[25] PolyA signal: Polyadenylation regulatory signal.

Clinical significance

Recent studies on miRNA’s role in breast cancer pathogenesis has correlated upregulation of C5orf22 with reduced survival of breast cancer patients.[26]

Patient's with tibial muscular dystrophy, exhibit decreased expression of C5orf22. [27] Patient's with non-ischemic cardiomyopathy exhibit increased expression of C5orf22.

References

  1. ^ a b c GRCh38: Ensembl release 89: ENSG00000082213 – Ensembl, May 2017
  2. ^ a b c GRCm38: Ensembl release 89: ENSMUSG00000022195 – Ensembl, May 2017
  3. ^ "Human PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
  4. ^ "Mouse PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
  5. ^ a b c d e f g "C5orf22 chromosome 5 open reading frame 22 [Homo sapiens (human)] - Gene - NCBI". www.ncbi.nlm.nih.gov. Retrieved 2021-12-18.
  6. ^ "Human C5orf22". www.genecards.org. Archived from the original on 2011-11-26. Retrieved 2021-09-20.
  7. ^ "Transcript: ENST00000325366.14 (C5orf22-201) - Summary - Homo_sapiens - Ensembl genome browser 105". useast.ensembl.org. Retrieved 2021-12-18.
  8. ^ a b c d e "Genomatix Annotation (ElDorado)". Genomatix. Archived from the original on 2012-01-14.
  9. ^ a b "Tissue expression of C5orf22 - Summary - The Human Protein Atlas". www.proteinatlas.org. Retrieved 2021-12-18.
  10. ^ "DROSHA drosha ribonuclease III [Homo sapiens (human)] - Gene - NCBI". www.ncbi.nlm.nih.gov. Retrieved 2021-12-18.
  11. ^ "DROSHA - Ribonuclease 3 - Homo sapiens (Human) - DROSHA gene & protein". www.uniprot.org. Retrieved 2021-12-18.
  12. ^ a b c d "ELM - Search the ELM resource". elm.eu.org. Retrieved 2021-12-18.
  13. ^ a b "C5orf22 - UPF0489 protein C5orf22 - Homo sapiens (Human) - C5orf22 gene & protein". www.uniprot.org. Retrieved 2021-12-18.
  14. ^ "SAPS < Sequence Statistics < EMBL-EBI". www.ebi.ac.uk. Retrieved 2021-12-18.
  15. ^ "PSORT II Prediction". psort.hgc.jp. Retrieved 2021-12-18.
  16. ^ "DeepLoc1.0 C5orf22". DTU Health Services. Archived from the original on 2020-08-15.
  17. ^ "NLS Mapper". nls-mapper.iab.keio.ac.jp. Archived from the original on 2021-11-22. Retrieved 2021-12-18.
  18. ^ a b c Zi Z, Zhang Y, Zhang P, Ding Q, Chu M, Chen Y, et al. (January 2020). "A Proteomic Connectivity Map for Characterizing the Tumor Adaptive Response to Small Molecule Chemical Perturbagens". ACS Chemical Biology. 15 (1): 140–150. doi:10.1021/acschembio.9b00694. PMC 7268550. PMID 31846293.
  19. ^ "IntAct Portal". www.ebi.ac.uk. Retrieved 2021-12-18.
  20. ^ a b "C5orf22 Result Summary | BioGRID". thebiogrid.org. Retrieved 2021-12-18.
  21. ^ "Results - mentha: the interactome browser". www.mentha.uniroma2.it. Retrieved 2021-12-18.
  22. ^ "Motif Scan". myhits.sib.swiss. Retrieved 2021-12-18.
  23. ^ a b c "BLAST: Basic Local Alignment Search Tool". blast.ncbi.nlm.nih.gov. Retrieved 2021-12-18.
  24. ^ a b "Protein BLAST: search protein databases using a protein query". blast.ncbi.nlm.nih.gov. Retrieved 2021-12-18.
  25. ^ "miRDB - MicroRNA Target Prediction Database". www.mirdb.org. Retrieved 2021-12-18.
  26. ^ Shinden Y, Hirashima T, Nohata N, Toda H, Okada R, Asai S, et al. (May 2021). "Molecular pathogenesis of breast cancer: impact of miR-99a-5p and miR-99a-3p regulation on oncogenic genes". Journal of Human Genetics. 66 (5): 519–534. doi:10.1038/s10038-020-00865-y. PMID 33177704. S2CID 226312590.
  27. ^ "GDS4843 / 1552660_a_at". www.ncbi.nlm.nih.gov. Retrieved 2021-12-18.
UPF0489 C5orf22 rate of evolution. Estimated time of divergence from human C5orf22 (millions of years ago; MYA) versus % corrected divergence of orthologous protein (m; total # of AA changes/100 residues). Slopes for fibrinogen alpha, C5orf22, and cytochrome C are 0.24, 0.09, and 0.03, respectively. Orthologs are monkey (Callithrix jacchus), mouse (Mus musculus), bird (Merops nubicus), frog (Xenopus laevis), and fish (Danio rerio). Data points for C5orf22 are displayed in blue. Data points for cytochrome C are shown in red. Data points for fibrinogen alpha are indicated in yellow. All data was collected from NCBI BLASTP.
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