CDC28/YBR160W Week 3

Database Summary

Known as cyclin-dependent kinase, or CDK, and is the master regulator of mitotic and meiotic cell cycles. CDK is associated with regulation of the G1, S, and G2/M phase cyclins, metabolism regulation, DNA to mRNA transcription regulation, chromosome changes/movement, and cellular morphogenesis. CDK also plays a role in osmostress by initiating transcription as a response. The CDC28 gene is translated into cyclin-dependent kinase 1 of Saccharomyces Cerivisiae. CDK1 is needed for initiation and controlling events in the cell cycle. It is also involved in various biological processes including, but not limited to, 7-methylguanosine mRNA capping, DNA double-strand break processing & repair via nonhomologous end joining, G1/S transition of the mitotic cell cycle, mitotic sister chromatid biorientation, mitotic spindle assembly, and negative regulation of meiotic & mitotic cell cycle. CDK1 interacts with CKS1 protein and with cyclin by forming a stable non-covalent complex.

Additional Information

Standard Name

CDC28

Systematic Name

YBR160W

Name Description

Cell Division Cycle

Gene ID

• CDC28 YBR160W Ensembl
• P00546 (CDK1_YEAST) Uniprot
• SGD:S000000364 SGD
• 852457 NCBI

Nucleotide Sequence

1 ATGAGCGGTG AATTAGCAAA TTACAAAAGA CTTGAGAAAG TCGGTGAAGG TACATACGGT

61 GTTGTTTATA AAGCGTTAGA CTTAAGACCT GGCCAAGGTC AAAGAGTAGT CGCATTGAAG

121 AAAATAAGAC TAGAGAGTGA AGACGAGGGT GTTCCCAGTA CAGCCATCAG AGAAATCTCA

181 TTATTGAAGG AATTAAAAGA CGATAATATT GTCAGATTAT ACGATATTGT TCACTCTGAT

241 GCACACAAGC TATATCTTGT TTTTGAGTTC CTCGATTTGG ACCTGAAAAG ATATATGGAG

301 GGTATTCCAA AGGACCAACC GTTAGGAGCT GATATTGTTA AGAAGTTTAT GATGCAACTT

361 TGTAAGGGTA TTGCATACTG CCACTCACAC CGTATTCTGC ATCGTGATTT AAAACCGCAG

421 AACTTATTGA TTAACAAAGA TGGGAATCTA AAACTAGGTG ATTTTGGCTT AGCGCGTGCT

481 TTTGGTGTTC CGTTGAGAGC TTACACACAT GAAATTGTTA CTCTATGGTA TAGAGCTCCG

541 GAGGTATTAC TGGGTGGAAA ACAATATAGT ACAGGTGTCG ATACATGGTC CATCGGCTGT

601 ATATTTGCCG AAATGTGTAA CAGGAAACCA ATCTTCAGTG GCGATAGTGA GATCGATCAG

661 ATTTTCAAGA TATTCAGAGT ATTGGGAACG CCGAATGAAG CTATATGGCC AGATATTGTC

721 TACTTGCCTG ATTTCAAGCC AAGCTTTCCT CAATGGCGCA GAAAAGACCT ATCACAAGTG

781 GTACCAAGTC TAGATCCACG CGGTATTGAT TTGTTGGACA AACTCCTCGC GTATGACCCT

841 ATTAACCGGA TTAGCGCCAG AAGAGCAGCC ATCCACCCCT ACTTCCAAGA ATCATAA

Amino Acid Sequence

MSGELANYKRLEKVGEGTYGVVYKALDLRPGQGQRVVALKKIRLESEDEGVPSTAIREIS LLKELKDDNIVRLYDIVHSDAHKLYLVFEFLDLDLKRYMEGIPKDQPLGADIVKKFMMQL CKGIAYCHSHRILHRDLKPQNLLINKDGNLKLGDFGLARAFGVPLRAYTHEIVTLWYRAP EVLLGGKQYSTGVDTWSIGCIFAEMCNRKPIFSGDSEIDQIFKIFRVLGTPNEAIWPDIV YLPDFKPSFPQWRRKDLSQVVPSLDPRGIDLLDKLLAYDPINRISARRAAIHPYFQES

CDC28 Amino Acid Sequence (Source: ExPASy)

Gene Functions

• Negative regulation of transcription
• Positive regulation of nuclear cell cycle DNA replication
• DNA double-strand break process
• DNA double-strand break repair via nonhomologous end joining
• Regulation of DNA double-strand break repair via homologous recombination
• 7-methylguanosine mRNA capping
• Protein phosphorylation
• Asymmetric cell division
• Response to cold
• Regulation of budding cell apical bud growth
• Regulation of filamentous growth
• Positive regulation of mitotic spindle pole separation
• Positive regulation of triglyceride catabolic process
• Regulation of vesicle-mediated transport
• Histone phosphorylation
• Peptidyl-serine phosphorylation
• Peptidyl-threonine phosphorylation
• Cell differentiation
• Regulation of telomere maintenance via telomerase
• Protein localization to nucleus
• Regulation of meiotic nuclear division
• Positive regulation of glycogen catabolic process
• Negative regulation of sister chromatid cohesion
• etc.

Difference Between Databases Used

• UniProt references Saccharomyces Genome Database, while Ensembl does not.
• UniProt includes all information in sections on a single page, while Ensembl requires lots of clicking around. This makes the CDC28 information on UniProt feel more complete rather than having several grey information headings with no links as seen in Ensembl.
• SGD contains less hyperlinks/annotations in the information than UniProt making SGD easier to read.
• UniProt includes images for the catalytic activity & subcellular location of the gene, which is not done in any other database.

Reason Why CDC28 Was Chosen

Since the last memory of a gene came from the Cell Function course that was taken during the Fall semester of 2018, David thought about the importance of the CDK2 gene that is found in human cells, which has a purpose of regulating the process during the cell cycle. It was soon discovered that CDC28 is the yeast equivalent to CDK2 in humans. CDC28 is critical in yeast cells because the presence initiates the start of the cell cycle by activating specific transcription factors that switches on transcription during the late G1 phase. We were interested how the CDC28 gene is translated to amino acids to make up the proteins that are used during the cell cycle.

References

1. SIB. (n.d.). Translate. Retrieved September 18, 2019, from https://web.expasy.org/translate/
2. UniProt Consortium. (2019). UniProtKB. Retrieved September 18, 2019, from https://www.uniprot.org/uniprot/P00546
3. Stanford U. (n.d.). Saccharomyces Genome Database. Retrieved September 18, 2019, from https://www.yeastgenome.org/locus/S000000364#protein
4. National Center for Biotechnology Information. (n.d.). Gene. Retrieved September 18, 2019, from https://www.ncbi.nlm.nih.gov/gene/852457
5. EMBL-EBI. (2019). Saccharomyces cerevisiae. Retrieved September 18, 2019, from https://uswest.ensembl.org/Saccharomyces_cerevisiae/Transcript/Sequence_Protein?db=core;g=YBR160W;r=II:560078-560974;t=YBR160W_mRNA

Acknowledgments

• Dr. Dahlquist for the continued support in assisting and answering our questions during the making of this assignment.

• Except for what is noted above, this individual journal entry was completed by me and not copied from another source. Dramir36 (talk) 18:17, 18 September 2019 (PDT)

Mavila9 (talk) 22:57, 18 September 2019 (PDT)