Week 13

 

Hello!

Protein: Q9BZP6 CHIA

This week I am researching my protein on EBI, which is Europe’s version of NCBI. I am using this database to cross-reference information on my protein.

This information is on the” Gene & Protein Summary for Q9BZP6.” I’m going to start with the “Gene” tab.

Gene

When I was researching on NCBI, I had searched CHIA (my protein’s gene) since NCBI was not allowing me to do a nucleotide search for Q9BZP6. The single RefSeq sequence I found was for the chromosome that contains my protein: Chromosome 1. EBI says the same. The cool thing about EBI, is it also says the CHIA gene spans 29716 bps, and even gives the range it spans.

Expression

This is the CHIA expression summary provided by EBI. UniProt did not get super detailed about expression, but said it is detected in the lungs at lower levels, and in high levels in the stomach. I’m not 100% on how to read this chart, so I don’t want to make any assumptions, but these seem to be CHIA expression results for different body parts, and they seem to be mostly consistent with UniProt.

Protein

The majority of this page is just a bunch of links and references to UniProt, so they’re definitely accurate. NCBI had consistent results with UniProt also. The protein function summary for Q9BZP6 has pretty much been a copy and paste on every resource. The amino acid sequence is 476 aa, identical to UniProt and NCBI, and molecular weight is 52271, identical to other resources.

Protein Structure

EBI shows the ribbon structure for only 2ybu. UniProt shows several different ribbon structures for this protein. I never looked at the structurs on NCBI. We haven’t done much research on the ribbon structures, so I’m not going to do a real detailed analysis.

 

    So for the next part of this week’s research, I looked up the gene-disease association. There were no results when I searched “Q9BZP6”, “Q9BZP5 CHIA,” or “acidic mammalian chitinase” but there was results when I searched CHIA. The first result did not have a text mining optio

The results are as follows:

CHIA - acute myeloid leukemia
Overall association score: 0.052890405

• ·        This result was listed differently than the others… It was the only “Open Targets Genetics” source for my search. I had to click a few links to find the page that had the “Text Mining” option, and there was nothing listed. It only listed a genetics association (acute myeloid leukemia).

CHIA - rhinitis
Overall association score: 0.0513

• Allergic Rhinitis - “Expression of AMCase mRNA in nasal mucosa of allergic rhinitis in SD rats.” Liu Y, Xing Z, Wang M. 31 Jan. 2015.

To examine AMCase (acidic mammalian chitinase) mRNA expression levels in nasal mucosa of allergic rhinitis SD rats. The experimental group was given intraperitoneal shots of ovalbumin. The control group was treated the same but with saline water. Allergic rhinitis was diagnosed based on accumulation score about nasal symptom. Results showed positive expression of AMCase mRNA in normal nasal mucosa. Expression increased significantly during nasal allergy. The increased expression of AMCase mRNA in allergic rhinitis are related with nasal symptoms score. Increased expression of AMCase mRNA in nasal mucosa in allergic rhinitis model might play roles in pathogenesis of AR.

•   Allergic Rhinitis – "Increased expression of acidic mammalian chitinase and chitotriosidase in the nasal mucosa of patients with allergic rhinitis.”-- Cho WS, Kim TH, Lee SH et al. – 30 Apr. 2010 

Acidic mammalian chitinase is an important mediator of allergic asthma in humans and animals. Chitotriosidase might play role in innate immunity due to phagocytic-specific expression. AMCase and chitotriosidase may play role in pathogenesis allergic nasal mucosa. Normal inferior turbinate mucosa obtained in patients admitted for augmentation rhinoplasty. Allergic turbinate mucosa obtained from patients who had perennial allergic rhinitis during septo-turbinate surgery. AMCase and and chitotriosidase mRNAs and proteins analyzed were found in normal and allergic turbinate mucosa. Levels of expression were higher in allergic turbinate. Since both are found in normal and allergic mucosa, suggests involvement in defense against chitin-containing pathogens. Upregulation of these chitinases in allergic condition suggests they may play role in nasal allergic reaction like other inflammatory mediators in allergic rhinitis.

CHIA - Otitis media
Overall association score: 0.0192

•     Otitis media with effusion – “Expression of chitinases in hypertrophies adenoids of children.” – Heo KW, hur DY, Park SK et al. – 24 May 2011.

Chronic rhinosinusitis, Otitis media with effusion, and allergic rhinitis has been associated with hypertrophied adenoids in children, and adenoidectomy is clinically recommended. Assayed expression levels and site of AMCase and chitotriosidase in hypertrophied adenoids of children to determine expression levels of 2 chitinases in relation to CRS, OME, and AR. Hypertrophied adenoids taken from children during adenoidectomy. mRNA and protein of AMCase and ChT present in adenoids of all subjects. CRS significant variable in AMCase mRNA and protein expression. CRS, OME, and AR significant in ChT mRNA and protein expression. AMCase and ChT expressed in histiocytes and vascular endothelial cells of adenoid tissues. Findings suggest that chitin-containing pathogens or dysregulated immune responses to them in the hypertrophied adenoids of children might be factors contributing to CRS, OME, and AR via AMCase and ChT overexpression.

 

Citations

Gene & protein summary for Q9BZP6. (n.d.) EMBL-EBI. Retrieved October 09, 2020. https://www.ebi.ac.uk/ebisearch/s4/summary/molecular?tab=gene&term=q9bzp6&spine=molecular&classification=9606&tid=protOrthCHIAHUMAN.

Liu Y, Xing Z, Wang M. [Expression of AMCase mRNA in nasal mucosa of allergic rhinitis in SD rats]. Lin Chuang er bi yan hou tou Jing wai ke za zhi = Journal of Clinical Otorhinolaryngology, Head, and Neck Surgery. 2015 Feb;29(3):267-9, 274.

Cho WS, Kim TH, Lee HM, et al. Increased expression of acidic mammalian chitinase and chitotriosidase in the nasal mucosa of patients with allergic rhinitis. The Laryngoscope. 2010 May;120(5):870-875. DOI: 10.1002/lary.20863.

Heo KW, Hur DY, Park SK, et al. Expression of chitinases in hypertrophied adenoids of children. Otolaryngology--head and Neck Surgery : Official Journal of American Academy of Otolaryngology-head and Neck Surgery. 2011 Oct;145(4):660-665. DOI: 10.1177/0194599811410656.