EJ Kochis.  Regulatory sequences found in intergenic regions of DNA  There are different types!  Repressor  Promoter  DNAa Sites.

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Presentation transcript:

EJ Kochis

 Regulatory sequences found in intergenic regions of DNA  There are different types!  Repressor  Promoter  DNAa Sites

Article by Vogel et Al published in 2003 about PrMED4 Intergenic DNA Near Transcription Site Effects on Transcription   ??? Attempt to find this sequence in other organisms and try to discern it’s significance

I used the code below to find the sequence Nucleotide sequence Organism Results of function, highlighted nucleotides are matches of Vogels conserved sequence I examined 25 organisms all Prochlrococcus and Synechococus

Prochlororcocus Marinius as GCTTGACTTATAAGTACTTAATGAAGCATTCTTCGGATTGAACAT MED GCTTGACTTATCAGTACGTTATGGACCATTCTTCGGATTGAACAT MIT GCTTGACTTATAAGTACTTAATGAAGCATTCTTCGAATTGAACAT MIT GCTTGACGGAAGGATGGGCTGCAGAGCATTGTCCATTGCGAACAT MIT GCTTGACGGAAGTTGCCTGCGCAGAGCATTCTCCTTCCCGAACAT MIT GCTTGACTTATAAGTACGTTATGGACCATTCTTCCAATTGAACAT Synechococcus Carboxylase promoters: Bl GCTTGACGGCGAGGGTCTTGGCAGAGCAATGTCCCGAGCGAACAT CC GCTTGACGAGTTGGCCTCCGGCAGACCAATGTCATCGGCGAACAT CC GCTTGACGGGAAGGGTTCTGGCGAAGCAATGTCCCCAGCGAACAT CC GCTTGACGGCGAGGGTCTTGGCAGAGCAATGTCCCGAGCGAACAT WH GCTTGACGGCCAGGCCTCTGGCAGAGCAGTCTCGGCGGCGAACAT WH GCTTGACGGGAAGGGATCTGGCGGACCAATGTCCCGAGCGAACAT Total 12 promoters found out of 25 organisms queried

I found them…so what? They are ALL upstream of a gene coding for Carboxylase Carboxylase Gene My Sequence

 GCTTGACGGATATGGGA [T/C] [T/G] TGGC [A/G] GAGCATT [G/C] TCCCGAGCGAACAT  TSS My sequences have the characteristics of a promoter sequence Using an alignment I formed a consensus sequence from my 12 matches

 Consensus 35 region-  Experimental 35 region - GCTTGAC  Consensus -10 region- TATAATG  Experimental 10 region- GAGCAGT TTGACA

Carboxylase is in every cyanobacteria found thus far. Why isn’t this possible promoter? List of organisms that the consensus sequence was found in 100+

 Hawley, D. K. & McClure, W. R. (1983) Nucleic Acids Res. 11,  Gary M. STUDNICKA. "Escherichia Coli Promoter -10 and -35 Region Homologies Correlate with Binding and Isomerization Kinetics."Biochem. (1988) 252, (n.d.): n. pag. Web. 14 Apr  Kinney, James N., et al. "Elucidating essential role of conserved carboxysomal protein CcmN reveals common feature of bacterial microcompartment assembly." Journal of Biological Chemistry (2012):  "Transcription in Prokaryotes." Transcription in Prokaryotes. CliffsNotes, n.d. Web. 27 Apr  Vogel, Jörg, et al. "Experimental and computational analysis of transcriptional start sites in the cyanobacterium Prochlorococcus MED4." Nucleic acids research (2003):