MSymond1 KMill104 Week 3

Summary

Our gene MSN1 is found in Sachharomyces cerevisiae, more commonly known as Baker’s yeast. It codes for a sequence-specific DNA-binding protein involved in positively regulating transcription in environments with stressors. By binding to a specific DNA sequence upstream of the transcription factor recognition sequence, RNA Polymerase II is signaled to start transcription. The protein is primarily found in the nucleus but can also localize to the cytoplasm.

Additional Information

1. The Standard name for the gene is MSN1, the systematic name for the gene is YOL116W, and the name description of the gene from SGD is Multicopy suppressor of SNF1 mutation (SGD).
2. The gene ID's from the differing databases are as follows
   • SGD:S000005476 SGD Page
   • NIH:854033 NIH Page
   • Ensembl:P22148 Ensembl page
   • UniProt:P22148 Uniprot Page
3. DNA sequence
4. Protein Sequence - MASNQHIGASNLNENEAILTNRVAELERRMSMFEGIFHALSNRLDLHFKKYDVVVNSQQQQINELTAFLSTLLNDQQRHAEILSEKLSGTLHGVSATSISLSQTLDPQGFTDGTTAPGAPRYTSVPMNNDQTAHPQNEGAVSNETLFEDILNGNSQENDKSQQQTNSSNSISQENNSTNPSVDTRFNKPQNYNSNLVPSLEEYSANPPNNDGGQSQGLYISSNSSQSRQSPNLQKVSPNHENAVESNAQESVPTFEEEQYETKTGLKRKRIVCTRPFEFIKSPHSVMEVWKEYTEGVNGQPSIRKMEALYQTAWRRDPAVNKRYSRRKVLWKAIQTGLNRGYSLNYVVEILENSRYVNDKQKVKQPIGWLCHSSHIPETLK The sequence is in reading frame 1
5. The primary function of our gene is to code for a protein that positively regulates transcription. The protein specifically acts in response to environmental stress so that transcription still occurs.
6. Each database had a section at the top with general information regarding the gene, like its name, organism, and other common descriptors. The UniProt and Ensembl databases had a more detailed summary of the protein our gene codes for. UniProt referenced other genes and proteins that our gene/protein may interact with in order to positively regulate transcription. The description also mentioned that a specifically iron deficient environment will have enhanced growth when MSN1 is present. The Ensembl database listed some processes of the protein in its description, like iron uptake and chromium accumulation. Both SGD and NCBI had less detailed summaries of the gene where they just listed its function as coding for a protein that positively regulates transcription. After going further down the page, each database had more detailed sections regarding specific functions, processes, and components. SGD had a large summary concerning regulation of the gene, while NCBI had a table summarizing the interactions between MSN1 and other genes. NCBI also provided related articles in PubMed. UniProt was the only database to provide an image of the protein’s structure. The presentation of information was different in the way that specific sections were organized and where they were placed on the page. Both SGD and NCBI has the gene sequence near the top of the page, while UniProt and Ensembl had it further down. SGD had a bar graph to illustrate expression of the gene, which was unique to its database. Ensembl was the only database where you had to click on links in the sidebar to get to certain sections. Ensembl also had a table dedicated to listing known variants of the gene and their alleles. NCBI had little images except for the gene sequence, while UniProt had images of both the nucleus and the protein’s structure.
7. We chose this gene because we were originally interested in proteins that could bind to DNA for some specific purpose. We thought it particularly interesting that this DNA-binding protein acted as a transcriptional regulator for cells that were in environmental stress. We wanted to learn more about how a protein can combat stressors so that transcription isn’t inhibited.
8. Picture of structure

Acknowledgements

• I worked with my homework partner Dean Symonds MSymond1 to complete this assignment. We worked together in class and texted once to ask a question. Except for what is noted above, this individual journal entry was completed by me and not copied from another source. Kmill104 (talk) 12:51, 31 January 2024 (PST)
• I worked with my homework partner, Katie Miller, we texted briefly. We also worked together in class to choose the gene. The picture of the structure was obtained using Jmol4 link Except for what is noted above, this individual journal entry was completed by me and not copied from another source. Msymond1 (talk) 13:47, 31 January 2024 (PST)

References

• LMU BioDb 2024. (2024). Week 3. Retrieved January 31, 2024, from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Week_3
• Saccharomyes Genome Database. (2024). MSN1 / YOLL16W. Retrieved January 31, 2024, from https://www.yeastgenome.org/locus/S000005476#resources
• National Center for Biotechnology Genome Database. (2024). MSN1 Msn1p [Saccharomyces cerevisiae S288C]. Retrieved January 31, 2024, from https://www.ncbi.nlm.nih.gov/gene/854033
• UniProt. (2024). P22148 · MSN1_YEAST. Retrieved January 31, 2024, from https://www.uniprot.org/uniprotkb/P22148/entry
• Ensembl. (2024). Gene: MSN1. Retrieved January 31, 2024, from http://useast.ensembl.org/Saccharomyces_cerevisiae/Gene/Summary?db=core;g=YOL116W;r=XV:99809-100957;t=YOL116W_mRNA