Zach and Hayden's Favorite Gene

Our Favorite Gene:BRO1


The Standard Name of our gene is BRO1(Saccharomyces Genome Database 2017).
The Systematic Name of our gene is YPL084W(Saccharomyces Genome Database 2017).
The Name Description of our gene is BCK1-like Resistance to Osmotic shock(Saccharomyces Genome Database 2017).

SGD Gene

Identifier: S000006005

Below is a link to the BRO1 SGD gene page

SGD Gene Page

UniProt Gene

Identifier: P48582

Below is a link to the BRO1 UniProt gene page

Uniprot Gene Page

NCBI Gene

Identifier: YPL084W

Below is a link to the BRO1 NCBI gene page

NCBI Gene Page

Ensembl Gene

Identifier: YPL084W

Below is a link to the BRO1 Ensembl gene page

Ensembl Gene Page

DNA Sequence

0001 ATGAAACCTT ACTTATTTGA CCTAAAGCTA AAAGACACAG AGAAGCTGGA TTGGAAAAAA
0061 GGCCTCTCCT CATATCTCAA GAAATCATAC GGCTCCTCAC AATGGAGAAC ATTTTATGAT
0121 GAGAAAGCTA CTTCAGAACT GGATCACTTA AGGAATAATG CAAATGGAGA ACTAGCACCT
0181 TCTTCATTGT CGGAACAAAA TCTAAAATAT TACTCATTTT TGGAGCATCT TTATTTTCGC
0241 CTGGGTAGCA AAGGATCAAG ATTAAAAATG GATTTCACTT GGTATGACGC AGAATACTCA
0301 TCGGCCCAGA AAGGATTGAA ATACACGCAA CATACGTTAG CATTTGAAAA GTCTTGTACT
0361 TTGTTCAACA TTGCTGTAAT CTTTACCCAA ATTGCGAGGG AGAATATCAA TGAGGACTAC
0421 AAAAACTCAA TCGCAAATTT GACAAAAGCT TTTTCCTGTT TTGAATATCT ATCAGAAAAT
0481 TTTTTGAACT CACCTTCAGT CGATCTTCAG TCAGAAAACA CTAGGTTTCT GGCTAATATT
0541 TGCCATGCAG AAGCTCAAGA ATTGTTTGTC TTGAAATTAT TAAATGATCA AATATCATCC
0601 AAGCAATATA CATTAATCAG TAAACTTTCT AGAGCCACGT GTAACCTCTT TCAGAAATGT
0661 CACGATTTTA TGAAAGAAAT AGATGACGAT GTGGCCATTT ATGGTGAACC CAAATGGAAA
0721 ACGACAGTTA CTTGCAAACT GCATTTCTAC AAATCGTTAA GCGCTTATTA TCACGGTTTA
0781 CACCTTGAAG AAGAAAATAG AGTTGGCGAA GCAATTGCTT TTCTCGATTT TTCTATGCAA
0841 CAATTGATTT CATCCCTTCC ATTCAAAACG TGGTTAGTGG AATTTATAGA CTTTGATGGG
0901 TTTAAAGAAA CTTTAGAAAA GAAACAAAAG GAGTTGATTA AAGATAACGA TTTTATATAT
0961 CATGAAAGCG TTCCAGCCGT TGTGCAGGTT GATTCCATTA AGGCGCTCGA TGCAATAAAA
1021 TCTCCAACAT GGGAGAAGAT ATTAGAACCA TATATGCAAG ATGTTGCAAA TAAATGTGAC
1081 TCTTTGTACA GAGGAATTAT TCCCCTAGAT GTCTATGAAA AGGAAAGTAT TTACTCAGAA
1141 GAAAAAGCGA CGCTGTTGAG AAAGCAAGTT GAAGAAACTG AGACAGCAAA TTTGGAATAT
1201 TCTTCCTTCA TCGAATTTAC AAATCTACCC AGGCTCTTGA GTGATTTGGA AAAACAATTT
1261 AGTGACGGAA ATATTTTCTC GAATACGGAT ACACAGGGAC AATTGATGAG GGACCAAATT
1321 CAGACATGGT GTAAATTTAT CCAAACAAAT GAATTTAGGG ATATAGAAGA ACAGATGAAC
1381 AAAATTGTTT TCAAAAGGAA ACAAATTTTA GAAATCCTTT CTGCCTTACC CAATGATCAA
1441 AAAGAAAATG TTACAAAACT AAAATCTTCT TTAGTAGCTG CTTCAAACTC AGACGAAAAA
1501 TTGTTCGCAT GCGTAAAACC ACATATTGTC GAGATCAATC TATTGAATGA CAATGGAAAA
1561 ATATGGAAGA AGTTTGACGA ATTTAATCGC AATACGCCTC CACAACCTAG CCTATTGGAT
1621 ATCGATGATA CCAAAAACGA CAAGATATTA GAGTTGTTAA AACAAGTAAA GGGCCATGCG
1681 GAAGACTTAA GAACATTGAA AGAGGAACGT TCGAGAAATT TGTCTGAACT AAGAGACGAA
1741 ATCAACAACG ATGATATCAC AAAATTATTA ATTATTAATA AGGGGAAATC CGATGTTGAG
1801 CTCAAAGATT TATTCGAGGT GGAACTGGAG AAATTCGAGC CTTTGAGCAC AAGAATAGAG
1861 GCGACAATTT ACAAACAATC TTCAATGATA GATGACATCA AAGCCAAGCT AGATGAAATT
1921 TTTCACCTTT CAAATTTCAA GGATAAATCT TCTGGGGAAG AAAAATTTTT AGAAGATCGT
1981 AAGAATTTTT TTGATAAGCT GCAAGAAGCA GTGAAATCAT TCAGTATTTT TGCATCCGAC
2041 TTGCCAAAAG GAATAGAGTT CTATGATTCA TTATTCAATA TGAGTAGAGA CTTAGCAGAA
2101 AGAGTGAGAG TTGCAAAGCA GACCGAGGAT TCAACAGCTA ATTCTCCCGC TCCTCCCCTC
2161 CCTCCACTTG ATTCTAAAGC GTCTGTCGTT GGGGGTCCTC CATTACTGCC CCAAAAAAGT
2221 GCAGCCTTTC AGTCATTATC TAGACAAGGG CTCAATTTAG GGGACCAATT TCAAAATCTC
2281 AAAATAAGTG CCGGCAGTGA TTTACCTCAA GGACCCGGTA TTCCACCAAG AACTTATGAA
2341 GCTTCGCCAT ATGCTGCAAC GCCTACTATG GCAGCCCCAC CAGTACCACC GAAACAATCG
2401 CAAGAGGATA TGTACGACTT GAGAAGACGT AAAGCAGTTG AAAACGAAGA ACGTGAACTG
2461 CAAGAGAATC CTACGTCCTT TTACAATAGA CCCTCTGTTT TTGATGAAAA TATGTACTCC
2521 AAATACAGCA GTTAG

(Retrieved from Saccharomyces Genome Database 2017).

Amino Acid Sequence

001 MKPYLFDLKL KDTEKLDWKK GLSSYLKKSY GSSQWRTFYD EKATSELDHL RNNANGELAP
061 SSLSEQNLKY YSFLEHLYFR LGSKGSRLKM DFTWYDAEYS SAQKGLKYTQ HTLAFEKSCT
121 LFNIAVIFTQ IARENINEDY KNSIANLTKA FSCFEYLSEN FLNSPSVDLQ SENTRFLANI
181 CHAEAQELFV LKLLNDQISS KQYTLISKLS RATCNLFQKC HDFMKEIDDD VAIYGEPKWK
241 TTVTCKLHFY KSLSAYYHGL HLEEENRVGE AIAFLDFSMQ QLISSLPFKT WLVEFIDFDG
301 FKETLEKKQK ELIKDNDFIY HESVPAVVQV DSIKALDAIK SPTWEKILEP YMQDVANKCD
361 SLYRGIIPLD VYEKESIYSE EKATLLRKQV EETETANLEY SSFIEFTNLP RLLSDLEKQF
421 SDGNIFSNTD TQGQLMRDQI QTWCKFIQTN EFRDIEEQMN KIVFKRKQIL EILSALPNDQ
481 KENVTKLKSS LVAASNSDEK LFACVKPHIV EINLLNDNGK IWKKFDEFNR NTPPQPSLLD
541 IDDTKNDKIL ELLKQVKGHA EDLRTLKEER SRNLSELRDE INNDDITKLL IINKGKSDVE
601 LKDLFEVELE KFEPLSTRIE ATIYKQSSMI DDIKAKLDEI FHLSNFKDKS SGEEKFLEDR
661 KNFFDKLQEA VKSFSIFASD LPKGIEFYDS LFNMSRDLAE RVRVAKQTED STANSPAPPL
721 PPLDSKASVV GGPPLLPQKS AAFQSLSRQG LNLGDQFQNL KISAGSDLPQ GPGIPPRTYE
781 ASPYAATPTM AAPPVPPKQS QEDMYDLRRR KAVENEEREL QENPTSFYNR PSVFDENMYS
841 KYSS

(Retrieved from Saccharomyces Genome Database 2017).


Function of BRO1

The function of BRO1 is to recruit Doa4p to deubiquitinate proteins which are travelling through the Multivesicular Body Pathway. The process of deubiquitination is to reactivate the proteins by removing the ubiquitin which is bound to them(Saccharomyces Genome Database 2017).


Differences in Biological Databases

Most of the information about BRO1 found in the biological databases was similar, except for the gene identifiers, the sources the database used and the descriptions of the process of BRO1. However, the rest of the information that we needed for this assignment was agreeable between the databases. As for the format, the databases exhibited numerous differences. We found that SGD is the easiest website to follow(Saccharomyces Genome Database 2017) for the laymen geneticist. We found NCBI to have the information we needed, but not as easily accessible due to the amount of content available on NCBI(NCBI 2017). This amount of content however serves as a positive trait of NCBI, giving the user many possible avenues of education whether it be through articles or books etc. We found UniProt to be concise and not as visually pleasing as SGD, but had all the information of BRO1 available and easily accesible. Ensembl was the least navigatiable of the four databases. It also was the least visually pleasing. It should be noted though that Ensembl can be used for comparitive research(Ensembl 2017).

Gene Summary

The BRO1 Gene is a gene that helps with deubiquitination. Pulling from the function of the gene, the recruitment of the Doa4p causes the deubiquitination process to start for proteins. Basically, when proteins are outside of the cell, a ubiquitin is attached to the protein that “puts it asleep” or deactivates it causing the protein to last longer. This is called ubiquitination. When the protein reenters the cell, the protein needs to be deubiquitinated so the protein can be active again. The BRO1 gene helps by ridding the sleeper chemical from the targeted protein as it passes back into the cell(Saccharomyces Genome Database 2017).



Why is BRO1 our Favorite?

I mean bro....it's BRO1.

Overall structure of BRO1
Here is a computer generated image of the overall structure of BRO1(NCBI 2017).






SGD and UniProt Data download


YeastMine (SGD)

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UniProt

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References

  1. Saccharomyces Genome Database (2017). BRO1 / YPL084W Overview. Retrieved October 12, 2017, https://www.yeastgenome.org/locus/S000006005
  2. UniProt (2017). UniProtKB-P48582 (BRO1_YEAST). Retrieved October 12, 2017, http://www.uniprot.org/uniprot/P48582
  3. NCBI (2017). Genes and Expression, Gene, BRO1. Retrieved October 12, 2017, https://www.ncbi.nlm.nih.gov/gene/856021
  4. Ensembl (2017). Gene: BRO1. Retrieved October 12, 2017, https://www.ensembl.org/Saccharomyces_cerevisiae/Gene/Summary?db=core;g=YPL084W;r=XVI:394038-396572;t=YPL084W
  5. Bootstrap (2017). Introduction. Retrieved October 12, 2017, https://getbootstrap.com/docs/4.0/getting-started/introduction/
  6. LMU BioDB 2017. (2017). Week 4. Retrieved September 25, 2017, https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_4
  7. LMU BioDB 2017. (2017). Week 7. Retrieved October 12, 2017, https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_7
  8. Microsoft(2017). Visual Studio (Version 1.17) [Software]. Available from https://code.visualstudio.com/
  9. Node.js Foundation(2017). Node.js (Version 8.7.0) [Software]. Availaible from https://nodejs.org/en/.
  10. GitHub (2017). Atom (Version 1.21.1) [Software]. Availaible from https://atom.io/.
  11. NCBI (2017). Journal Lists, Structural Basis for Endosomal Targeting by the Bro1 Domain [Computer generated image of the general structure of BRO1]. Retrieved October 13, 2017, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2862258/bin/nihms197164f1.jpg

Acknowledgements

  1. Hayden and Zach worked together on multiple occasions in the computer lab and on Campus to synthesize our favorite gene page.
  2. We utilized the Bootstrap documentation section.
  3. We used information from the biological databases listed in references.
  4. Utilized Week 4 assignment webpage for assignment direction.
  5. We utilized the Week 7 assignment webpage for assignment direction.
  6. Dr. Dionisio helped explain the functions of Node.js in class.