ASP1 The Gene of the Decade

By:Katie Wright and Blair Hamilton

1)What is the standard name, systematic name, and name description for your gene (from SGD)?

2)What is the gene ID (identifier) for your gene in all four databases (SGD, NCBI Gene, Ensembl, UniProt)?

3)What is the DNA sequence of your gene?

              ATGAAAAGCGATTCAGTTGAAATCACTACCATCTGCCCAGATGTTGAAAATTCTCAGTTT
              GTTGTGCAAAGCAACTGTCCAGAGACTATTCCAGAGATTCTAAAGTCTCAAAATGCCGCT
              GTGAATGGCAGCGGCATCGCTTGCCAACAACGTAGCTTACCAAGAATCAAAATCTTGGGT
              ACCGGTGGTACTATTGCATCGAAAGCTATAGACTCCTCTCAAACTGCCGGCTATCATGTT
              GACCTGACCATCCAAGATCTATTGGATGCCATTCCAGATATATCCAAGGTCTGTGACATT
              GAATATGAGCAACTATGCAACGTGGATTCTAAAGACATAAACGAGGATATTCTTTATAAA
              ATTTATAAGGGCGTCTCAGAATCGTTGCAGGCTTTTGACGGTATAGTTATTACCCATGGG
              ACTGATACGCTATCTGAAACTGCATTCTTTATTGAAAGTACTATTGATGCTGGCGACGTT
              CCTATTGTTTTTGTTGGTTCGATGCGTCCTTCAACCAGCGTTTCTGCTGATGGCCCTATG
              AACCTTTACCAAGCAATTTGCATTGCTTCAAATCCAAAATCTAGAGGAAGAGGTGTTCTT
              GTTTCCTTGAATGACCAAATTTCCTCTGGTTACTACATTACTAAGACGAATGCAAATAGT
              TTGGATTCTTTTAATGTTAGACAAGGCTATTTAGGAAATTTTGTCAACAATGAAATTCAC
              TACTATTATCCTCCTGTGAAACCGCAAGGTTGCCACAAATTCAAACTGAGAGTGGACGGT
              AAGCATTTTAAATTACCAGAGGTTTGCATTTTATATGCTCACCAAGCCTTTCCGCCAGCT
              ATAGTCAACTTAGTGGCAGATAAGTATGATGGTATTGTTCTTGCTACCATGGGTGCTGGT
              TCATTGCCGGAGGAGGTCAATGAAACCTGCATGAAATTGAGTTTGCCGATCGTATATTCC
              AAGAGATCGATGGATGGTATGGTGCCTATTGCCAACGTACCAAAGAAAGGTTCAAAGGAG
              GATAATCTCATCGCATCTGGTTATCTAAGCCCTGAAAAGAGCAGAATCTTGTTACAATTA
              TGTTTGGCAGGTAACTACACGTTGGAAGAAATTAAACATGTTTTCACTGGCGTCTATGGT
              GGGTGA
            

• SGD ASP1 Sequence

4)What is the protein sequence corresponding to your gene?

              MKSDSVEITTICPDVENSQFVVQSNCPETIPEILKSQNAAVNGSG
              IACQQRSLPRIKILGTGGTIASKAIDSSQTAGYHVDLTIQDLLDA
              IPDISKVCDIEYEQLCNVDSKDINEDILYKIYKGVSESLQAFDGI
              VITHGTDTLSETAFFIESTIDAGDVPIVFVGSMRPSTSVSADGPM
              NLYQAICIASNPKSRGRGVLVSLNDQISSGYYITKTNANSLDSFN
              VRQGYLGNFVNNEIHYYYPPVKPQGCHKFKLRVDGKHFKLPEVCI
              LYAHQAFPPAIVNLVADKYDGIVLATMGAGSLPEEVNETCMKLSL
              PIVYSKRSMDGMVPIANVPKKGSKEDNLIASGYLSPEKSRILLQL
              CLAGNYTLEEIKHVFTGVYGG
           

• NCBI Protein Sequence

5)What is the function of your gene?

• ASP1 codes for L-ASPase, an enzyme that depletes levels of asparagine in the blood when expressed in humans.
• SGD Blog Article

6)What was different about the information provided about your gene in each of the parent databases? Were there differences in content, the information or data itself? Were there differences in presentation of the information?

Website Title	Presentation Differences	Content Differences
SGD	Easiest to find answers for and well-labeled when searching information. Multiple tabs for further knowledge and explaination of the gene.	Most thorough in content compared to the other four sites.
Ensembl	Inconvenient to reference other information about the gene, for example you have to change pages to access information.	Simple descriptions of the gene.
UniProt	Most aesthetically pleasing to read and follow. Also as thorough as SGD in terms of information on the gene. However, not as easy to maneuver between sections.	Different ID for finding the gene compared to SGD and Ensembl.
NCBI	Similar to Ensembl in amount of information, but accessing information is easier since it is all on one page. Focuses on sequencing and naming the parts of the gene for it's primary page.	Different ID for finding the gene compared to SGD and Ensembl.

While differences in formatting and presentation varied between each database, the overall information did not change, except for the IDs.

7)Why did you choose your particular gene? i.e., why is it interesting to you and your partner?

• We thought that ASP1 is a really interesting gene for a number of reasons when we first read about it on the SGD Blog. Both partners have had members of their family affected by cancer, so any advance in the fight against cancer is intriguing. In addition, Katie was a clinical research assistant for the University of Washington Division of Hematology in 2016. During her time there, Katie worked with teams researching AML, ALL, and other blood cancers. It is interesting for her to learn about another possible way to treat these cancers.
• SGD Blog Article

• ASP1 is a gene that codes for L-ASPase, an enzyme that takes asparagine (ASP) out of the blood. Most cells in the body can survive without additional ASP from the blood because cells can synthesize ASP independently. However, certain cancerous cells such as those of acute lymphoblastic leukemia (ALL) lose their ability to synthesize ASP and must take ASP from the blood. L-ASPase could be used as a therapy for certain cancers since lowering levels of ASP in individuals with ALL could effectively starve the cancerous cells. Currently, L-ASPase is sourced primarily from two different types of bacteria, E. Coli and E. chrysanthemi. The yeast version of L-ASPase may be a preferred alternative to the bacterial kind because “It may be able to kill cancer cells with fewer side effects.”

The following two databases are ajax sources one in XML and one in JSON file types.

• We referenced the Bootstrap Website for formatting headers, lists, grid layout, flex boxes, coloring and image location.
• We collaborated with eachother on homework questions as well as the cs file uploads. We met in person going over our website look and content to post. We met once more to revise, fix typos and add certain stylistic changes.
• We used Dr. Dionisio's starter zip file as a template for our website.

• ASP1 asparaginase ASP1 [Saccharomyces cerevisiae S288C] - Gene - NCBI. (2017, September 14). Retrieved September 25, 2017, from https://www.ncbi.nlm.nih.gov/gene/851920
• ASP1 [Saccharomyces cerevisiae] - Protein - NCBI. Retrieved September 25, 2017, from https://www.ncbi.nlm.nih.gov/protein/KZV12561.1?report=fasta
• ASP1. Retrieved September 25, 2017, from https://www.yeastgenome.org/locus/S000002729#reference
• Das Murtey, M., & Ramasamy, P. (2016, October 14). [SEM Image of Brewer's Yeast]. Retrieved September 25, 2017, from https://upload.wikimedia.org/wikipedia/commons/thumb/9/95/Saccharomyces_cerevisiae_SEM.jpg/640px-Saccharomyces_cerevisiae_SEM.jpg
• LMU BioDB 2017. (2017). Week 4. Retrieved September 21, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_4
• Gene: ASP1. (2017, August 9). Retrieved September 25, 2017, from https://www.ensembl.org/Saccharomyces_cerevisiae/Gene/Summary?db=core;g=YDR321W;r=IV:1108702-1109847;t=YDR321Wg
• L-asparaginase 1. (2017, July 05). Retrieved September 25, 2017, from http://www.uniprot.org/uniprot/P38986
• Starr, B. (2017, March 2). Feed a Cold, Starve a Cancer? Retrieved September 25, 2017, from https://www.yeastgenome.org/blog/feed-a-cold-starve-a-cancer