1. DNA motifs potentially related to Regulating genes in Response to Nitrogen in Marine Cyanobacteria. Created By David Long VCU Biology Undergraduate June 2005

2. Introduction: Locating DNA motifs in marine Cyanobacteria Morphologically Ex. Unicellular & Filamentous … Ex. High-light adapted & Low-light adapted … Varied Ex. (Oceans, Fresh water, temperate soils, extreme environments ect ) Most concentrated at the first 100m depth 1

3. Effect Global Climate change 2 Regulate Atmospheric CO2 2 Remove 10 billion tons of carbon From atmosphere Figure 1: Atmospheric View of Cyanobacteria Bloom. Baltic Sea System Study 1997 Introduction: Locating DNA motifs in marine Cyanobacteria

4. “ Turing sunlight and carbon into organic molecules ” “ Most abundant photosynthetic organisms on earth ” 1 Unique light harvesting complex Chlorophyll a and b binding protein Nutrient uptake less difficult because of small size for nutrients such a N & P2 Makes beneficial to larger growing organisms. Introduction: Locating DNA motifs in marine Cyanobacteria:

5. Question: Locating DNA motifs in marine Cyanobacteria:

6. Introduction: Locating DNA motifs in marine Cyanobacteria: 5’ 3’

7. Prochlorococcus Marinus SS120 Prochlorococcus Marinus PMED4 Prochlorococcus Marinus MIT9313 Synechococcus sp. WH8102 Introduction: Locating DNA motifs in marine Cyanobacteria: All Cyanobacteria images from : www.cyanosite.bio.purdue.edu/images/images.html

8. Procedure: Locating DNA motifs in marine Cyanobacteria:

9. Machine Consisted of 7 Functions: 1.Bg-Count-Freq 2.Make Motif1 freq 3.Optimize tables 4.FastScore2 5.CB-FIND_NTCASearch 6.Find-NTCAScore Repeated for each gene in each organism

10. Name & Description of: upstream gene Scores: –Common possibilities with Threshold 1.0 that sequence is a ntcA Promotor. Distance: from Upstream gene Direction & Position: along the Chromosome Results: Locating DNA motifs in marine Cyanobacteria:

12. 1. "putative urea ABC transporter, substrate binding protein” 2. “Glutamine synthetase, glutamate--ammonia ligase“ 3. “SAM (and some other nucleotide) binding motif: Generic methyl-...“ 4. “putative hydrogenase accessory protein” 5. ”possible NAD(P) transhydrogenase beta subunit” 6. “Global nitrogen regulatory protein, CRP family of transcriptional regulators” 1. "Glutamine synthetase“ 2. "Uncharacterized protein“ 3. "Predicted protein“ 4. "Predicted protein family PM-27“ 5. "Uncharacterized protein“ 6. "Predicted protein“ 7.“hosphoribosylaminoimidazolesuccinocarboxamidePhosphoribosylami noimidazolesuccinocarboxamide“ 1. "Glutamine synthetase, glutamate--ammonia ligase“ 2. "putative urea ABC transporter, urea binding protein NtcA like promoter sequence 3. "possible transcription regulator“ 4. "UDP-N-glucosamine 1-carboxyvinyltransferase“ 5. "hypothetical“ 6. "conserved hypothetical protein short orf found near phage integrases“ 7. "two-component response regulator“ 8. "hypothetical" Results: Locating DNA motifs in marine Cyanobacteria: 1. "putative urea ABC transporter, substrate binding protein NtcA like promoter sequence" 2. "Global nitrogen regulatory protein, CRP family of transcriptional regulators“ 3. "Short-chain dehydrogenase/reductase (SDR) superfamily" 4. "Sulfatase Signal predicted by SignalP 2.0 HMM (Signal peptide probabilty 1.000) with cleavage site probability 0.884 at residue 24 5. "Type II alternative RNA polymerase sigma factor, sigma-70 family"

13. Results: Locating DNA motifs in marine Cyanobacteria:

14. Conclusion: Locating DNA motifs in marine Cyanobacteria:

15. Dr. Wolfgang Hess Professor of Experimental Bioinformatics University of Freiburg Institute of Biology Ph(#49-(0)761-2032796 Email: wolfganghess@biologie.uni-freiburg.dewolfganghess@biologie.uni-freiburg.de Web: http://biochemie.biologie.uni-freiburg.de/hess/http://biochemie.biologie.uni-freiburg.de/hess/ Dr. Jeff Elhai Professor of Biology Email: elhaij@vcu.eduelhaij@vcu.edu Web: www.people.vcu.edu/~elhaiwww.people.vcu.edu/~elhai David Long Bio351