BPIFA3

Last updated
BPIFA3
Identifiers
Aliases BPIFA3 , C20orf71, SPLUNC3, BPI fold containing family A member 3
External IDs MGI: 1920638 HomoloGene: 52268 GeneCards: BPIFA3
Orthologs
SpeciesHumanMouse
Entrez

128861

73388

Ensembl

ENSG00000131059

ENSMUSG00000027482

UniProt

Q9BQP9

Q9D9J8

RefSeq (mRNA)

NM_001042439
NM_178466

NM_001291079
NM_028528

RefSeq (protein)

NP_001035904
NP_848561

NP_001278008
NP_082804

Location (UCSC) Chr 20: 33.22 – 33.23 Mb Chr 2: 153.97 – 153.98 Mb
PubMed search [3] [4]
Wikidata
View/Edit Human View/Edit Mouse

BPI fold containing family A, member 3 (BPIFA3) is a protein that in humans is encoded by the BPIFA3 gene. [5] The gene is also known as SPLUNC3 and C20orf71 in humans and the orthologous gene in mice is 1700058C13Rik. [6] There are multiple variants of the BPIFA3 projected to be a secreted protein. [7] It is very highly expressed in testis with little or no expression in other tissues. The Human Protein Atlas project [8] and Mouse ENCODE Consortium [9] report RNA-Seq expression at RPKM levels (reads per kilobases of transcript per 1 million mapped reads ) of 29.1 for human testis and 69.4 for mouse, but 0 for all other tissues. [5] [6] Similarly, the Bgee consortium, [10] using multiple techniques in addition to RNA-Seq, reports a relative Expression Score of 95.8 out of 100 for testis and 99.0 for sperm in humans; however low levels of BPIFA3 between 20 and 30 were seen for a variety of tissues such as muscle, glands, prostate, nervous system, and skin. [11]

Contents

Superfamily

BPIFA3 is a member of a BPI fold protein superfamily defined by the presence of the bactericidal/permeability-increasing protein fold (BPI fold) which is formed by two similar domains in a "boomerang" shape. [12] This superfamily is also known as the BPI/LBP/PLUNC family or the BPI/LPB/CETP family. [13] The BPI fold creates apolar binding pockets that can interact with hydrophobic and amphipathic molecules, such as the acyl carbon chains of lipopolysaccharide found on Gram-negative bacteria, but members of this family may have many other functions.

BPIFA3 is a member of the BPI-fold gene family and the BPI/LBP/PLUNC protein superfamily BPIFfamily-BPIF-A3.png
BPIFA3 is a member of the BPI-fold gene family and the BPI/LBP/PLUNC protein superfamily

Genes for the BPI/LBP/PLUNC superfamily are found in all vertebrate species, including distant homologs in non-vertebrate species such as insects, mollusks, and roundworms. [14] [15] Within that broad grouping is the BPIF gene family whose members encode the BPI fold structural motif and are found clustered on a single chromosome, e.g., Chromosome 20 in humans, Chromosome 2 in mouse, Chromosome 3 in rat, Chromosome 17 in pig, Chromosome 13 in cow. The BPIF gene family is split into two groupings, BPIFA and BPIFB. In humans, BIPFA consists of 3 protein encoding genes BPIFA1 , BPIFA2 , BPIFA3, and 1 pseudogene BPIFA4P ; while BPIFB consists of 5 protein encoding genes BPIFB1 , BPIFB2 , BPIFB3 , BPIFB4 , BPIFB6 and 2 pseudogenes BPIFB5P , BPIFB9P . What appears as pseudogenes in humans may appear as fully functional genes in other species.

In humans, the BPIFA3 gene was first identified as a human PLUNC-related gene [16] and later in mouse as 1700058C13Rik. [17] Both were recognized as BPIF gene family members and were renamed BPIFA3 and Bpifa3, respectively.

Function

Little is known about BPIFA3's function. Due to its high degree of similarity to other members of the BPI/LBP/PLUNC superfamily, it is predicted to have binding activity to lipids such as phospholipids and lipopolysaccharides but this has never been confirmed. [18]

A putative function of BPIFA3 in bacterial host defense has been suggested. Despite a near-exclusive expression of BPIFA3 in testis, only a single report implicates it in any normal or pathological states and that involves Otitis media (OM) in the ear. [19] OM is a common disease of early childhood characterized by inflammation of the middle ear cavity and an effort was made to identify genetic risk factors. A genome-wide association study was done in the "Raine Study," a longitudinal birth cohort of 2,868 children in which 1532 blood samples drawn at 1,2, and 3 years of age were analyzed for gene expression correlated to a susceptibility to OM. Unexpectedly, BPIFA3 and BPIFA1 were the top hits, along with CAPN14 and GALNT14 genes, none of which has previously been implicated in OM. The investigators noted that BPIF gene family members encode proteins involved in the early recognition of bacterial pathogens as part of the host defense at the nasopharyngeal, oral and lung entrances, and that expression of BPIFA3 and BPIFA1 may be a logical consequence of chronic bacterial presence in the pus filled, OM infected ear.

Related Research Articles

<span class="mw-page-title-main">Chromosome 20</span> Human chromosome

Chromosome 20 is one of the 23 pairs of chromosomes in humans. Chromosome 20 spans around 66 million base pairs and represents between 2 and 2.5 percent of the total DNA in cells. Chromosome 20 was fully sequenced in 2001 and was reported to contain over 59 million base pairs. Since then, due to sequencing improvements and fixes, the length of chromosome 20 has been updated to just over 66 million base pairs.

<span class="mw-page-title-main">BPIFA1</span> Protein-coding gene in the species Homo sapiens

BPI fold containing family A, member 1 (BPIFA1), also known as Palate, lung, and nasal epithelium clone (PLUNC), is a protein that in humans is encoded by the BPIFA1 gene. It was also formerly known as "Secretory protein in upper respiratory tracts" (SPURT). The BPIFA1 gene sequence predicts 4 transcripts ; 3 mRNA variants have been well characterized. The resulting BPIFA1 is a secreted protein, expressed at very high levels in mucosa of the airways and salivary glands; at high levels in oropharyneal epithelium, including tongue and tonsils; and at moderate levels many other tissue types and glands including pituitary, testis, lung, bladder, blood, prostate, pancreas, levels in the digestive tract and pancreas. The protein can be detected on the apical side of epithelial cells and in airway surface liquid, nasal mucus, and sputum.

<span class="mw-page-title-main">CST9L</span> Protein-coding gene in the species Homo sapiens

Cystatin-9-like is a protein that in humans is encoded by the CST9L gene.

<span class="mw-page-title-main">BPIFB2</span> Protein-coding gene in the species Homo sapiens

BPI fold-containing family B, member 2, (BPIFB2) also known as bactericidal/permeability-increasing protein-like 1, is a protein that in humans is encoded by the BPIFB2 gene.

<span class="mw-page-title-main">TSBP1</span> Protein found in humans

TSBP1 is a protein that in humans is encoded by the TSBP1 gene. C6orf10 is an open reading frame on chromosome 6 containing a protein that is ubiquitously expressed at low levels in the adult genome and may play a role during fetal development. C6orf10 has been found to be linked to both neurodegenerative and autoimmune diseases in adults. Expression of this gene is highest in the testis but is also seen in other tissue types such as the brain, lens of the eye and the medulla. TSBP1 was previously known as C6orf10.

<span class="mw-page-title-main">FAM185A</span> Gene of the species Homo sapiens

The FAM185A is a protein that in humans is encoded by the FAM185A gene. The FAM185A gene is found on the positive strand of Chromosome 7 at 7q22.1. The gene begins 102,389,399bp from the p-terminus of the chromosome and ends at 102,449,672bp from the p-terminus; it covers a total of 73,308 basepairs. The protein encoded by this gene is characterized by the presence of multiple copies of DUF4098 near its C-terminus. It is described as a Long Interspersed Nuclear Element (LINE), a subclass of penaeid repetitive elements (PREs).

<span class="mw-page-title-main">BPIFB4</span> Protein-coding gene in the species Homo sapiens

BPI fold containing family B, member 4 (BPIFB4) is a protein that in humans is encoded by the BPIFB4 gene. It was formerly known as "Long palate, lung and nasal epithelium carcinoma-associated protein 4" encoded by the LPLUNC4 gene. The BPIFB4 gene sequence predicts 4 transcripts ; 3 isoforms have been well characterized. In a variety of mammals, BPIFB4 is generally expressed in very high levels in the olfactory epithelium, high levels in the gonads and pituitary, moderate levels in white blood cells (monocytes) It can occur either localized in the cytoplasm of cells or secreted and circulated systemically in blood plasma.

<span class="mw-page-title-main">BPIFB1</span> Protein-coding gene in the species Homo sapiens

BPI fold-containing family B member 1 (BPIFB1) is a protein that in humans is encoded by the BPIFB1 gene. BPIFB1 is a secreted protein, expressed at very high levels in mucosa of the airways and salivary glands, and at moderate levels in the digestive tract and pancreas.

<span class="mw-page-title-main">C8orf48</span> Protein-coding gene in the species Homo sapiens

C8orf48 is a protein that in humans is encoded by the C8orf48 gene. C8orf48 is a nuclear protein specifically predicted to be located in the nuclear lamina. C8orf48 has been found to interact with proteins that are involved in the regulation of various cellular responses like gene expression, protein secretion, cell proliferation, and inflammatory responses. This protein has been linked to breast cancer and papillary thyroid carcinoma.

<span class="mw-page-title-main">FAM71E1</span> Mammalian protein found in Homo sapiens

FAM71E1, also known as Family With Sequence Similarity 71 Member E1, is a protein that in humans is encoded by the FAM71E1 gene. It is thought to be ubiquitously expressed at low levels throughout the body, and it is conserved in vertebrates, particularly mammals and some reptiles. The protein is localized to the nucleus and can be exported to the cytoplasm.

<span class="mw-page-title-main">C19orf44</span> Mammalian protein found in Homo sapiens

Chromosome 19 open reading frame 44 is a protein that in humans is encoded by the C19orf44 gene. C19orf44 is an uncharacterized protein with an unknown function in humans. C19orf44 is non-limiting implying that the protein exists in other species besides human. The protein contains one domain of unknown function (DUF) that is highly conserved throughout its orthologs. This protein is most highly expressed in the testis and ovary, but also has significant expression in the thyroid and parathyroid. Other names for this protein include: LOC84167.

<span class="mw-page-title-main">C12orf50</span> Protein-coding gene in humans

Chromosome 12 Open Reading Frame 50 (C12orf50) is a protein-encoding gene which in humans encodes for the C12orf50 protein. The accession id for this gene is NM_152589. The location of C12orf50 is 12q21.32. It covers 55.42 kb, from 88429231 to 88373811, on the reverse strand. Some of the neighboring genes to C12orf50 are RPS4XP15, LOC107984542, and C12orf29. RPS4XP15 is upstream C12orf50 and is on the same strand. LOC107984542 and C12orf29 are both downstream. LOC107984542 is on the opposite strand while C12orf29 is on the same strand. C12orf50 has six isoforms. This page is focusing on isoform X1. C12orf50 isoform X1 is 1711 nucleotides long and has a protein with a length of 414 aa.

<span class="mw-page-title-main">C13orf42</span> C13orf42 gene page

C13orf42 is a protein which, in humans, is encoded by the gene chromosome 13 open reading frame 42 (C13orf42). RNA sequencing data shows low expression of the C13orf42 gene in a variety of tissues. The C13orf42 protein is predicted to be localized in the mitochondria, nucleus, and cytosol. Tertiary structure predictions for C13orf42 indicate multiple alpha helices.

<span class="mw-page-title-main">BPIFB3</span> Protein-coding gene in the species Homo sapiens

BPI fold containing family B, member 3 (BPIFB3) is a protein that in humans is encoded by the BPIFB3 gene. Two variants have been detected in humans.

<span class="mw-page-title-main">BPIFB5P</span> Pseudogene in the species Homo sapiens

BPI fold containing family B, member 5 is a non-human protein encoded by the Bpifb5 gene, also known as Lplunc5. The BPIFB5 protein and Bpifb5 gene have been characterized in mammals such as rodents and even-toed ungulates but are apparently lacking in primates and other vertebrates such as birds, reptiles, and amphibians. The protein in rodents is expressed at moderately high levels in mucosa of the airways and at moderate levels in salivary glands, esophagus, and gonads ; in even-toed ungulates expression is high in testis, moderate in brain and striated muscle, and low in kidney.

<span class="mw-page-title-main">BPIFB6</span> Protein-coding gene in the species Homo sapiens

BPI fold containing family B, member 6 (BPIFB6), also known as bactericidal/permeability-increasing protein-like 3 (BPIL3), is a protein that in humans is encoded by the BPIFB6 gene, also known as BPIL3 and LPLUNC6. It is expressed at high levels in hypertrophic tonsils, at relatively moderate levels in oronasal epithelium including nasal mucosa, tongue, and salivary gland, as well as esophageal mucosa at lesser levels. Orthologs are present in many vertebrate species including mammals, birds, reptiles, and amphibians.

<span class="mw-page-title-main">BPIFB9P</span> Pseudogene in the species Homo sapiens

Vomeromodulin is a non-human protein also known as BPI fold containing family B, member 9 (BPIFB9) in the rat encoded by the Bpifb9/RYF3 gene, and as BPI fold containing family B, member 9A (BPIFB9A) encoded by the Bpifb9a gene in the mouse. This protein has been characterized in mammals such as rodents, carnivores, even-toed ungulates, insectivores, bats, lagomorphs, and shrews but is apparently absent in primates and other vertebrates such as birds, reptiles, and amphibians. Its function is associated with detection of chemical odorant pheromone molecules.

<span class="mw-page-title-main">BPIFA2</span> Protein-coding gene in the species Homo sapiens

BPI fold containing family A, member 2 (BPIFA2), also known as Parotid Secretory Protein (PSP), is a protein that in humans is encoded by the BPIFA2 gene. The BPIFA2 gene sequence predicts multiple transcripts ; 2 mRNA variants have been well characterized. The resulting BPIFA2 is a secreted protein, expressed at very high levels in the parotid (salivary) gland; at high levels in oropharyngeal mucosa, including tongue; and at moderate levels many other tissue types and glands including mammary gland, testis, lung, bladder, blood, prostate, adrenal gland, kidney, and pancreas.

<span class="mw-page-title-main">BPIFA4P</span> Pseudogene in the species Homo sapiens

BPI fold containing family A, member 4 (BPIFA4) is a non-human protein encoded by the Bpifa4 gene in mammals such as monkey, cat, and cow but does not appear in rodents and humans. It is also known as Latherin in horse, encoded by the Lath/Bpifa4 gene but is somewhat divergent from the other species. Latherin/BPIFA4 is a secreted protein found in saliva and sweat.

<span class="mw-page-title-main">ARMH1</span> Novel human gene

Armadillo-like Helical Domain Containing 1 (ARMH1) is a protein which in humans is encoded by chromosome 1 open reading frame 228, also known as the ARMH1 gene. The gene shows expression levels significantly higher in bone marrow, lymph nodes, and testis. Currently the function of the gene and subsequent protein is still uncertain.

References

  1. 1 2 3 GRCh38: Ensembl release 89: ENSG00000131059 - Ensembl, May 2017
  2. 1 2 3 GRCm38: Ensembl release 89: ENSMUSG00000027482 - 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. 1 2 "BPIFA3 BPI fold containing family A member 3 [Homo sapiens (human)] - Gene - NCBI". www.ncbi.nlm.nih.gov. Retrieved 17 February 2023.
  6. 1 2 "Bpifa3 BPI fold containing family A, member 3 [Mus musculus (house mouse)] - Gene - NCBI". www.ncbi.nlm.nih.gov. Retrieved 17 February 2023.
  7. ↑ "Q9BQP9 - BPIA3_HUMAN". www.uniprot.org. Retrieved 17 February 2023.
  8. ↑ Fagerberg L, Hallström BM, Oksvold P, Kampf C, Djureinovic D, Odeberg J, et al. (February 2014). "Analysis of the human tissue-specific expression by genome-wide integration of transcriptomics and antibody-based proteomics". Molecular & Cellular Proteomics. 13 (2): 397–406. doi: 10.1074/mcp.M113.035600 . PMC   3916642 . PMID   24309898.
  9. ↑ Yue F, Cheng Y, Breschi A, Vierstra J, Wu W, Ryba T, et al. (November 2014). "A comparative encyclopedia of DNA elements in the mouse genome". Nature. 515 (7527): 355–64. Bibcode:2014Natur.515..355.. doi:10.1038/nature13992. PMC   4266106 . PMID   25409824.
  10. ↑ Bastian FB, Roux J, Niknejad A, Comte A, Fonseca Costa SS, de Farias TM, et al. (January 2021). "The Bgee suite: integrated curated expression atlas and comparative transcriptomics in animals". Nucleic Acids Research. 49 (D1): D831–D847. doi:10.1093/nar/gkaa793. PMC   7778977 . PMID   33037820.
  11. ↑ "Gene: BPIFA3 - ENSG00000131059". bgee.org. The Bgee suite: integrated curated expression atlas and comparative transcriptomics in animals. Retrieved 17 February 2023.
  12. ↑ Beamer LJ, Carroll SF, Eisenberg D (April 1998). "The BPI/LBP family of proteins: a structural analysis of conserved regions". Protein Science. 7 (4): 906–914. doi:10.1002/pro.5560070408. PMC   2143972 . PMID   9568897.
  13. ↑ "CDD Conserved Protein Domain Family: BPI". www.ncbi.nlm.nih.gov.
  14. ↑ Beamer LJ, Fischer D, Eisenberg D (July 1998). "Detecting distant relatives of mammalian LPS-binding and lipid transport proteins". Protein Science. 7 (7): 1643–1646. doi:10.1002/pro.5560070721. PMC   2144061 . PMID   9684900.
  15. ↑ Bingle CD, Seal RL, Craven CJ (August 2011). "Systematic nomenclature for the PLUNC/PSP/BSP30/SMGB proteins as a subfamily of the BPI fold-containing superfamily". Biochemical Society Transactions. 39 (4): 977–983. doi:10.1042/BST0390977. PMC   3196848 . PMID   21787333.
  16. ↑ Bingle CD, Craven CJ (15 April 2002). "PLUNC: A novel family of candidate host defense proteins expressed in the upper airways and nasopharynx". Human Molecular Genetics. 11 (8): 937–943. doi:10.1093/hmg/11.8.937. PMID   11971875.
  17. ↑ Oakley MS, McCutchan TF, Anantharaman V, Ward JM, Faucette L, Erexson C, et al. (October 2008). "Host biomarkers and biological pathways that are associated with the expression of experimental cerebral malaria in mice". Infection and Immunity. 76 (10): 4518–29. doi:10.1128/IAI.00525-08. PMC   2546852 . PMID   18644885.
  18. ↑ "BPIFA3 Gene - GeneCards". www.genecards.org. Retrieved 17 February 2023.
  19. ↑ Rye MS, Warrington NM, Scaman ES, Vijayasekaran S, Coates HL, Anderson D, Pennell CE, Blackwell JM, Jamieson SE (2012). "Genome-wide association study to identify the genetic determinants of otitis media susceptibility in childhood". PLOS ONE. 7 (10): e48215. Bibcode:2012PLoSO...748215R. doi: 10.1371/journal.pone.0048215 . PMC   3485007 . PMID   23133572.
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