NBPF1

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NBPF1
Identifiers
Ensembl

ENSG00000219481

n/a

UniProt

Q3BBV0

n/a

RefSeq (mRNA)

NM_017940

n/a

RefSeq (protein)

NP_060410

n/a

Location (UCSC)Chr 1: 16.56 – 16.61 Mbn/a
PubMed search[2]n/a
Wikidata
View/Edit Human

Neuroblastoma breakpoint family, member 1, or NBPF1, is a protein that is encoded by the

neuroblastoma breakpoint family of proteins, a group of proteins that are thought to be involved in the development of the nervous system.[3]

Gene

The NBPF1 gene in humans is located on the minus strand of 1p36.3 in humans and is 51179 base pairs long including

CROCC. NBPF1 is one of the 26 known members of the Neuroblastoma Breakpoint Family genes and pseudogenes. The NBPF2 pseudogene and NBPF3 gene are the most similar genes located close to NBPF1 and they reside on the chromosomal location 1p36.12. Most members of the NBPF gene family are located on chromosomal location 1q21.1-1q23.3 in humans, and these genes are more similar to each other in sequence than they are to NBPF1.[4]

Location of NBPF1 in relation to other genes on chromosome 1

Transcript

The transcript for NBPF1 in humans is a 6183 base pair mRNA that is made of 28 exons. There are more than 14 alternative splicing forms of NBPF1 predicted, but only seven of the splice forms have been observed. Out of all of the possible transcripts, only two are known to code proteins. One of these transcripts is 1139 amino acids long with 23 coding exons, while and the other is 1095 amino acids long and 23 coding exons. The noncoding transcripts are processed, but their function is unknown.[3][5][6]

Protein

NBPF1 is a 1214 amino acid long protein in humans that weighs 139 kD and has an

DUF1220 domains. NBPF1 contains three coiled coil domains and nine DUF1220 domains in humans. The coiled coil domains are 60-100 amino acids long, while the DUF1220 domains are approximately 65 base pairs long with high sequence similarity.[9]

Amino acid sequence of NBPF1 that shows the locations DUF1220 domains(blue) and coiled coil domains(yellow).

Interactions

Human NBPF1 has been shown to interact with

Wnt signaling for cell proliferation.[12] Additionally, two hybrid screen have shown that NBPF1 interacted with bacterial proteins, such as an Oxidoreductase iron/ascorbate family protein from the bacterium Francisella tularensis and an uncharacterized protein from the bacterium Bacillus anthracis.[13]

Functional and clinical significance

Although the function of the NBPF1 protein in unknown, its physical and chemical properties can give insight about its function. Like other NBPF proteins, the NBPF1 protein product contains a repeated domain called

Autism severity, which often results from an excess of neurons that do not under synaptic pruning.[17]

Predicted Structure of Stat-1 and Stat3b-like DNA binding domains in NBPF1 using Phyre2

The NBPF1 protein is also found to be disrupted by a

oligomerization with other proteins.[19] Based on the interactions listed above, NBPF1 is shown to interact with the coiled coil domain of CBY1, which represses Wnt signaling.[18] Aberrant Wnt signaling in the brain is a common cause of tumor growth and drug resistance in neuroblastomas,[20]
further suggesting that NBPF1 could act as a tumor suppressor gene in the brain if it directly affects this pathway.

NBPF1 seems to be involved in proliferation during human neurogenesis, and growth suppression during adulthood. Showing that the DUF1220 and coiled coil domains may be important during different life stages. The DUF1220 domains are important in neurogenesis, while the coiled coil domains involved with the binding of cell proliferation inhibitors. Although there are no known differences between Autism and neuroblastoma rates are known, a study has shown the existence of

comorbid microcephaly and neuroblastoma conditions, although more research is needed to show this.[21]
Based on these predictions, the lack of NBPF1 during could prevent fetal neurogenesis and postnatal tumor suppression in the brain, although this connection is not well understood.

Expression

NBPF1 is ubiquitously expressed in all tissues in humans, but shows the highest levels of expression in the bone marrow, skeletal muscle, brain, and spinal cord. It is expressed at slightly lower levels in other tissues such as the pancreas, kidney, and lung.

orthologs in related species is most likely to be localized in the nucleus.[24]

Expression for NBPF1 based on NCBI GEO Profiles, whole tissue expression profile

Predicted Localization of NBPF1 and its Orthologs[24]

Species %Nuclear %Vacuolar %Cytoplasmic %Cytoskeletal
Human 87.0 4.3 4.3 4.3
Macaque 65.2 4.3 17.4 4.3
Baboon 82.6 0.0 13.0 0.0
Cow 65.2 0.0 17.4 0.0
Armadillo 65.2 0.0 13.0 0.0

Expression studies have shown changes in NBPF1 under different experimental conditions

tight junctions such as those of the blood–brain barrier, causes a sharp decline in NBPF1 expression[28]

Homology and evolution

Orthologs

Although NBPF1 itself only exists in primates, a wide variety of NBPF like protein

orthologs exist in other mammals such as cattle, felines, and cetaceans. In non-primate mammals, the gene sequences of NBPF-like genes have little similarity to the primate NBPF genes. These genes appear to be entirely absent in model mammals such as mice and rats. The large amount of NBPF genes in the human genome is most likely due to recent duplications because all of the NBPF genes are so similar and repetitive that they easily recombine with each other, causing duplications. Variation in the number of repetitive sequences in the NBPF genes also varies even within humans.[29]
DUF1220 domains also vary greatly from humans in other species in their NBPF proteins. The further away a species is from humans, the fewer DUF1220 domains the species has. Humans have on average 272 DUF1220 domains in their NBPF genes, while chimpanzees have 125, macaques have 35, and dolphins only have 4.[30]

This shows the predicted relationship between NBPF1 similarity based on a multiple sequence alignment.

Selected Orthologs of NBPF1[31][32]

Species Common name Time of divergence from humans (mya) NCBI accession number Sequence length (amino acids) Protein similarity to human NBPF1 mRNA similarity to human NBPF1
Homo sapiens
 Human 0 AAX85114.1 1214 100% 100%
Pan troglodytes
 Chimpanzee 6.3 XP_009439437.1 656 93% 98%
Macaca fascicularis
 Crab-eating macaque 29 XP_005544713.1 1173 77% 87%
Tursiops truncates
 Bottle-nosed dolphin 94.2 XP_004329243.1 888 40% 37%
Bos taurus
 Cattle 94.2 XP_005197798.1 633 39% 36%
Felis catus
 Domestic cat 94.2 XP_011283477.1 813 38% 35%
Sus scrofa
 Pig 94.2 XP_005653139.1 567 36% 40%
Dasypus novemcinctus
 Nine-banded armadillo 104.2 XP_004469026 934 30% 34%

Paralogs

The

paralogs
for NBPF1 are other members of the NBPF protein family. The highest similarity between these paralogs further shows evidence of gene duplication during human evolution.

Rooted phylogenetic tree of NBPF1 paralogs based on multiple sequence alignment.

Selected Paralogs of NBPF1

Gene name NCBI accession number Sequence length (amino acids) Protein sequence identity Protein sequence similarity
NBPF1 NP_060410.2 1214 100% 100%
NBPF12 NP_001265070.1 1457 100% 93%
NBPF8 NP_001032590.2 942 100% 93%
NBPF14 NP_056198.2 2819 100% 92%
NBPF15 NP_775909.2 670 98% 93%
NBPF3 NP_115640.1 633 100% 75%

References

  1. ^ a b c GRCh38: Ensembl release 89: ENSG00000219481 – Ensembl, May 2017
  2. ^ "Human PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
  3. ^ a b "NBPF1 neuroblastoma breakpoint family, member 1 [Homo sapiens (human)] - Gene - NCBI". ncbi.nlm.nih.gov. Retrieved 2015-02-05.
  4. ^ "Neuroblastoma breakpoint family | HUGO Gene Nomenclature Committee". www.genenames.org. Archived from the original on 2013-09-09.
  5. ^ "Gene: NBPF1 (ENSG00000219481) - Summary - Homo_sapiens - Ensembl genome browser 106".
  6. ^ "NBPF1 - Neuroblastoma breakpoint family member 1 - Homo sapiens (Human)". uniprot.org. Retrieved 2015-02-05.
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  8. ^ "ExPASy Proteomics: Post-Translational Modification Tools". ExPASy: Bioinformatics Resource Portal. Retrieved 4 May 2015.
  9. ^ "Q3BBV0 - NBPF1_HUMAN". Uniprot. Retrieved 4 May 2015.
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  11. PMID 21906983
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  12. PMID 20096688
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  13. PMID 20711500
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  18. ^
    PMID 18493581
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  20. S2CID 24480929
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  21. PMID 8397936
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  22. ^ "GDS424 / 59465_r_at / NBPF1, Normal human tissue expression profiling". NCBI Geo Profiles. Retrieved 4 May 2015.
  23. ^ "Allen Brain Atlas: Human Brain Microarray". Allen Brain Atlas. Retrieved 4 May 2015.
  24. ^ a b Nakai, Kenta. "PSORT II". PSORT II Prediction. Archived from the original on 6 September 2021. Retrieved 4 May 2015.
  25. ^ "Neural transcription factor SOX11 depletion effect on mantle cell lymphoma cell line". NCBI Geo Profiles. Retrieved 4 May 2015.
  26. ^ "Far-upstream element binding protein inactivation". NCBI GEO Profiles. Retrieved 4 May 2015.
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  28. ^ "Claudin-1 overexpression effect on lung adenocarcinoma cell line". NCBI GEO Profiles. Retrieved 4 May 2015.
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  31. ^ "NCBI BLAST". NCBI. Retrieved 4 May 2015.
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