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==Protein==
==Protein==
NBPF1 is a 1214 amino acid long protein in humans that weighs 139 kD and has an isoelectric point of 4.74. One interesting feature about this protein's composition is that it is much richer than most other proteins in both glutamine and glutamic acid residues. Additionally, it contains amino acid repeats that are present in humans, other primates, and even armadillos.<ref>{{cite web|last1=Brendel|first1=V|last2=Bucher|first2=P|last3=Nourbakhsh|first3=I.R.|last4=Blaisdell|first4=B.E.|last5=Karlin|first5=S|title=Methods and algorithms for statistical analysis of protein sequences|url=http://seqtool.sdsc.edu/CGI/BW.cgi#!|website=SDSC Biology Workbench|publisher=National Academy of Sciences|accessdate=4 May 2015}}</ref> Another interesting feature is that the NBPF1 protein contains residues that are predicted to have [[post-translational modifications]], including [[glycation]], [[N-linked glycosylation]], [[O-GlcNAc]] attachment, [[O-linked glycosylation]], [[Phosphorylation]], and [[Sumoylation]].<ref>{{cite web|title=ExPASy Proteomics: Post-Translational Modification Tools|url=http://www.expasy.org/proteomics/post-translational_modification|website=ExPASy: Bioinformatics Resource Portal|accessdate=4 May 2015}}</ref> The two most important domain types in the NBPF1 protein are the coiled coil domains and [[DUF1220]] domains. NBPF1 contains three coiled coil domains and nine DUF1220 domains. The coiled coil domains are 60-100 amino acids long, while the DUF1220 domains are approximately 65 base pairs long with high sequence similarity.<ref>{{cite web|title=Q3BBV0 - NBPF1_HUMAN|url=http://www.uniprot.org/uniprot/Q3BBV0|website=Uniprot|accessdate=4 May 2015}}</ref>
NBPF1 is a 1214 amino acid long protein in humans that weighs 139 kD and has an [[isoelectric point]] of 4.74. One interesting feature about this protein's composition is that it is much richer than most other proteins in both glutamine and glutamic acid residues. Additionally, it contains amino acid repeats that are present in humans, other primates, and even armadillos.<ref>{{cite web|last1=Brendel|first1=V|last2=Bucher|first2=P|last3=Nourbakhsh|first3=I.R.|last4=Blaisdell|first4=B.E.|last5=Karlin|first5=S|title=Methods and algorithms for statistical analysis of protein sequences|url=http://seqtool.sdsc.edu/CGI/BW.cgi#!|website=SDSC Biology Workbench|publisher=National Academy of Sciences|accessdate=4 May 2015}}</ref> Another interesting feature is that the NBPF1 protein contains residues that are predicted to have [[post-translational modifications]], including [[glycation]], [[N-linked glycosylation]], [[O-GlcNAc]] attachment, [[O-linked glycosylation]], [[Phosphorylation]], and [[Sumoylation]].<ref>{{cite web|title=ExPASy Proteomics: Post-Translational Modification Tools|url=http://www.expasy.org/proteomics/post-translational_modification|website=ExPASy: Bioinformatics Resource Portal|accessdate=4 May 2015}}</ref> The two most important domain types in the NBPF1 protein are the [[coiled coil]] domains and [[DUF1220]] domains. NBPF1 contains three coiled coil domains and nine DUF1220 domains. The coiled coil domains are 60-100 amino acids long, while the DUF1220 domains are approximately 65 base pairs long with high sequence similarity.<ref>{{cite web|title=Q3BBV0 - NBPF1_HUMAN|url=http://www.uniprot.org/uniprot/Q3BBV0|website=Uniprot|accessdate=4 May 2015}}</ref>

===Interactions===
NBPF1 has been shown to interact with [[UBC]] via both [[protein complex immunoprecipitation]]<ref>{{cite journal|last1=Nathan|first1=James A|last2=Tae Kim|first2=Hyoung|last3=Ting|first3=Lily|last4=Gygi|first4=Steven P|last5=Goldberg|first5=Alfred L|title=Why do cellular proteins linked to K63-polyubiquitin chains not associate with proteasomes?|journal=The EMBO Journal|date=11 January 2013|volume=32|issue=4|pages=552–565|doi=10.1038/emboj.2012.354}}</ref> and [[affinity chromatography]].<ref>{{cite journal|last1=Kim|first1=Woong|last2=Bennett|first2=Eric J.|last3=Huttlin|first3=Edward L.|last4=Guo|first4=Ailan|last5=Li|first5=Jing|last6=Possemato|first6=Anthony|last7=Sowa|first7=Mathew E.|last8=Rad|first8=Ramin|last9=Rush|first9=John|last10=Comb|first10=Michael J.|last11=Harper|first11=J. Wade|last12=Gygi|first12=Steven P.|title=Systematic and Quantitative Assessment of the Ubiquitin-Modified Proteome|journal=Molecular Cell|date=October 2011|volume=44|issue=2|pages=325–340|doi=10.1016/j.molcel.2011.08.025}}</ref> Additionally, [[Two-hybrid screening]] assays have shown that NBPF1 interacts with an [[Oxidoreductase]] iron/ascorbate family protein from the bacterium [[Francisella tularensis]] and an uncharacterized protein from the bacterium [[Bacillus anthracis]].<ref>{{cite journal|last1=Dyer|first1=Matthew D.|last2=Neff|first2=Chris|last3=Dufford|first3=Max|last4=Rivera|first4=Corban G.|last5=Shattuck|first5=Donna|last6=Bassaganya-Riera|first6=Josep|last7=Murali|first7=T. M.|last8=Sobral|first8=Bruno W.|last9=Rénia|first9=Laurent|title=The Human-Bacterial Pathogen Protein Interaction Networks of Bacillus anthracis, Francisella tularensis, and Yersinia pestis|journal=PLoS ONE|date=9 August 2010|volume=5|issue=8|pages=e12089|doi=10.1371/journal.pone.0012089}}</ref>

===Functional Relevance===
The physical and chemical properties of the NBPF1 protein can give insight to figure out its function. The NBPF1 gene, especially in the DUF1220 domains, is very rich in [[glutamic acid]]. Glutamic acid rich domains are found to be important in the [[ion channel]] organization of [[photoreceptors]].<ref name="nih3">{{cite web|url=http://www.ncbi.nlm.nih.gov/pubmed/21813684|title=In situ visualization of protein interactions in sensory neurons: g... - PubMed - NCBI|publisher=ncbi.nlm.nih.gov|accessdate=2015-02-05}}</ref> Additionally, NBPF1 contains three [[coiled coil|coiled coil domains]]. Coiled coil structures are commonly involved in [[oligomerization]] with other proteins.<ref name="nih4">{{cite web|url=http://www.ncbi.nlm.nih.gov/pubmed/11166216|title=Coiled coils: a highly versatile protein folding motif. - PubMed - NCBI|publisher=ncbi.nlm.nih.gov|accessdate=2015-02-05}}</ref>


==Expression==
==Expression==

Revision as of 05:42, 4 May 2015

Template:PBB Neuroblastoma Breakpoint Family, Member 1, or NBPF1 is a protein that is encoded by the gene NBPF1 in humans. This protein is member of the neuroblastoma breakpoint family proteins, a group of proteins that are thought to be involved in the development of the nervous system.[1]

Gene

The NBPF1 gene in humans is located on the minus strand of 1p36.3 in humans and is 51179 base pairs long including exons and introns. It is located between the protein coding genes NECAP2 and 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.[2]

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 which 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.[1][3][4]

File:Alternative Transcripts.png
Alternative Transcripts for NBPF1 Gene

Protein

NBPF1 is a 1214 amino acid long protein in humans that weighs 139 kD and has an isoelectric point of 4.74. One interesting feature about this protein's composition is that it is much richer than most other proteins in both glutamine and glutamic acid residues. Additionally, it contains amino acid repeats that are present in humans, other primates, and even armadillos.[5] Another interesting feature is that the NBPF1 protein contains residues that are predicted to have post-translational modifications, including glycation, N-linked glycosylation, O-GlcNAc attachment, O-linked glycosylation, Phosphorylation, and Sumoylation.[6] The two most important domain types in the NBPF1 protein are the coiled coil domains and DUF1220 domains. NBPF1 contains three coiled coil domains and nine DUF1220 domains. The coiled coil domains are 60-100 amino acids long, while the DUF1220 domains are approximately 65 base pairs long with high sequence similarity.[7]

Interactions

NBPF1 has been shown to interact with UBC via both protein complex immunoprecipitation[8] and affinity chromatography.[9] Additionally, Two-hybrid screening assays have shown that NBPF1 interacts with an Oxidoreductase iron/ascorbate family protein from the bacterium Francisella tularensis and an uncharacterized protein from the bacterium Bacillus anthracis.[10]

Functional Relevance

The physical and chemical properties of the NBPF1 protein can give insight to figure out its function. The NBPF1 gene, especially in the DUF1220 domains, is very rich in glutamic acid. Glutamic acid rich domains are found to be important in the ion channel organization of photoreceptors.[11] Additionally, NBPF1 contains three coiled coil domains. Coiled coil structures are commonly involved in oligomerization with other proteins.[12]

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.[13] In the brain, NBPF1 expression is the highest in the frontal, temporal, and parietal lobes, and it lowest in the ventricles and cerebellum.[14] Based on protein composition, NBPF1 in humans and its orthologs in related species is most likely to be localized in the nucleus.[15]

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

Predicted Localization of NBPF1 and its Orthologs[15]

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 in vitro. First, the depletion of nervous system transcription factor SOX11 causes a slight increase in NBPF1 expression.[16] Additionally, the inactivation of Far upstream element-binding protein 1 causes a decrease in NBPF1, while the inactivation of Far Upstream Binding Elements 2 and 3 causes an increase in NBPF1 expression.[17] Far upstream binding elements are involved in transcriptional regulation using gene enhancers, each having different binding sites.[18] The overexpression of CLDN1, a protein that forms tight junctions such as those of the blood-brain barrier, causes a sharp decline in NBPF1 expression[19]

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.[12] Like other NBPF proteins, the NBPF1 protein product contains a repeated domain called DUF1220, a domain of unknown function that is thought to be related to human brain complexity.[20] 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.[21]

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

Selected Orthologs of NBPF1[22][23]

Species Common Name Date of Divergence (mya) NCBI Accession Number Sequence Length (Amino Acids) Protein Similarity mRNA Similarity
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 high similariy 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 Example 633 100% 75%

Functional Relevance

The physical and chemical properties of the NBPF1 protein can give insight to figure out its function. The isoelectric point of the protein is 4.742, meaning that it is rich in negatively charged amino acids. The NBPF1 gene, especially in the DUF1220 domains, is very rich in glutamic acid. Glutamic acid rich domains are found to be important in the ion channel organization of photoreceptors.[11] Additionally, NBPF1 contains three coiled coil domains. Coiled coil structures are commonly involved in oligomerization with other proteins.[12]

Disease and Relevance

This gene’s protein product contains a repeated domain called DUF1220, a domain of unknown function that is thought to be related to human brain complexity.[20] This domain is present nearly twice as much in humans as in chimpanzees. Additionally, higher copy numbers of the DUF1220 domain are associated with increasing Autism severity.[24] The NBPF1 protein is also found to be mutated in some cases of neuroblastoma.[25]

References

  1. ^ a b "NBPF1 neuroblastoma breakpoint family, member 1 [Homo sapiens (human)] - Gene - NCBI". ncbi.nlm.nih.gov. Retrieved 2015-02-05.
  2. ^ http://www.genenames.org/genefamilies/NBPF
  3. ^ http://useast.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000219481;r=1:16562319-16613562;t=ENST00000430580;redirect=no
  4. ^ "NBPF1 - Neuroblastoma breakpoint family member 1 - Homo sapiens (Human)". uniprot.org. Retrieved 2015-02-05.
  5. ^ Brendel, V; Bucher, P; Nourbakhsh, I.R.; Blaisdell, B.E.; Karlin, S. "Methods and algorithms for statistical analysis of protein sequences". SDSC Biology Workbench. National Academy of Sciences. Retrieved 4 May 2015.
  6. ^ "ExPASy Proteomics: Post-Translational Modification Tools". ExPASy: Bioinformatics Resource Portal. Retrieved 4 May 2015.
  7. ^ "Q3BBV0 - NBPF1_HUMAN". Uniprot. Retrieved 4 May 2015.
  8. ^ Nathan, James A; Tae Kim, Hyoung; Ting, Lily; Gygi, Steven P; Goldberg, Alfred L (11 January 2013). "Why do cellular proteins linked to K63-polyubiquitin chains not associate with proteasomes?". The EMBO Journal. 32 (4): 552–565. doi:10.1038/emboj.2012.354.
  9. ^ Kim, Woong; Bennett, Eric J.; Huttlin, Edward L.; Guo, Ailan; Li, Jing; Possemato, Anthony; Sowa, Mathew E.; Rad, Ramin; Rush, John; Comb, Michael J.; Harper, J. Wade; Gygi, Steven P. (October 2011). "Systematic and Quantitative Assessment of the Ubiquitin-Modified Proteome". Molecular Cell. 44 (2): 325–340. doi:10.1016/j.molcel.2011.08.025. {{cite journal}}: no-break space character in |first10= at position 8 (help); no-break space character in |first11= at position 3 (help); no-break space character in |first12= at position 7 (help); no-break space character in |first2= at position 5 (help); no-break space character in |first3= at position 7 (help); no-break space character in |first7= at position 7 (help)
  10. ^ Dyer, Matthew D.; Neff, Chris; Dufford, Max; Rivera, Corban G.; Shattuck, Donna; Bassaganya-Riera, Josep; Murali, T. M.; Sobral, Bruno W.; Rénia, Laurent (9 August 2010). "The Human-Bacterial Pathogen Protein Interaction Networks of Bacillus anthracis, Francisella tularensis, and Yersinia pestis". PLoS ONE. 5 (8): e12089. doi:10.1371/journal.pone.0012089.{{cite journal}}: CS1 maint: unflagged free DOI (link)
  11. ^ a b "In situ visualization of protein interactions in sensory neurons: g... - PubMed - NCBI". ncbi.nlm.nih.gov. Retrieved 2015-02-05.
  12. ^ a b c "Coiled coils: a highly versatile protein folding motif. - PubMed - NCBI". ncbi.nlm.nih.gov. Retrieved 2015-02-05. Cite error: The named reference "nih4" was defined multiple times with different content (see the help page).
  13. ^ "GDS424 / 59465_r_at / NBPF1, Normal human tissue expression profiling". NCBI Geo Profiles. Retrieved 4 May 2015.
  14. ^ "Allen Brain Atlas: Human Brain Microarray". Allen Brain Atlas. Retrieved 4 May 2015.
  15. ^ a b Nakai, Kenta. "PSORT II". PSORT II Prediction. Retrieved 4 May 2015.
  16. ^ "Neural transcription factor SOX11 depletion effect on mantle cell lymphoma cell line". NCBI Geo Profiles. Retrieved 4 May 2015.
  17. ^ "Far-upstream element binding protein inactivation". NCBI GEO Profiles. Retrieved 4 May 2015.
  18. ^ Davis-Smyth, T.; Duncan, R. C.; Zheng, T.; Michelotti, G.; Levens, D. (6 December 1996). "The Far Upstream Element-binding Proteins Comprise an Ancient Family of Single-strand DNA-binding Transactivators". Journal of Biological Chemistry. 271 (49): 31679–31687. doi:10.1074/jbc.271.49.31679. {{cite journal}}: |access-date= requires |url= (help)CS1 maint: unflagged free DOI (link)
  19. ^ "Claudin-1 overexpression effect on lung adenocarcinoma cell line". NCBI GEO Profiles. Retrieved 4 May 2015.
  20. ^ a b "DUF1220 domains, cognitive disease, and human brain evolution. - PubMed - NCBI". ncbi.nlm.nih.gov. Retrieved 2015-02-05.
  21. ^ Dumas, Laura J.; O’Bleness, Majesta S.; Davis, Jonathan M.; Dickens, C. Michael; Anderson, Nathan; Keeney, J.G.; Jackson, Jay; Sikela, Megan; Raznahan, Armin; Giedd, Jay; Rapoport, Judith; Nagamani, Sandesh S.C.; Erez, Ayelet; Brunetti-Pierri, Nicola; Sugalski, Rachel; Lupski, James R.; Fingerlin, Tasha; Cheung, Sau Wai; Sikela, James M. (September 2012). "DUF1220-Domain Copy Number Implicated in Human Brain-Size Pathology and Evolution". The American Journal of Human Genetics. 91 (3): 444–454. doi:10.1016/j.ajhg.2012.07.016. {{cite journal}}: no-break space character in |first12= at position 8 (help); no-break space character in |first16= at position 6 (help); no-break space character in |first18= at position 4 (help); no-break space character in |first19= at position 6 (help); no-break space character in |first1= at position 6 (help); no-break space character in |first2= at position 8 (help); no-break space character in |first3= at position 9 (help); no-break space character in |first4= at position 3 (help)
  22. ^ "NCBI BLAST". NCBI. Retrieved 4 May 2015.
  23. ^ Hedges, S. B.; Dudley, J.; Kumar, S. (4 October 2006). "TimeTree: a public knowledge-base of divergence times among organisms". Bioinformatics. 22 (23): 2971–2972. doi:doi:10.1093/bioinformatics/btl505. {{cite journal}}: Check |doi= value (help)
  24. ^ "PLOS Genetics: DUF1220 Dosage Is Linearly Associated with Increasing Severity of the Three Primary Symptoms of Autism". journals.plos.org. Retrieved 2015-02-05.
  25. ^ "Please enable Javascript and reload the page". dcc.icgc.org. Retrieved 2015-02-05.


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