DNA motifs potentially related to Regulating genes in Response to Nitrogen in Marine Cyanobacteria.

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 Cyanobacteria Universe Extremely Diverse Morphologically Ex. Unicellular & Filamentous … Ex. High-light adapted & Low-light adapted … Habitat: Varied Ex. (Oceans, Fresh water, temperate soils, extreme environments ect ) Most concentrated at the first 100m depth 1 Oxygen Photosynthesis

3. Introduction: Locating DNA motifs in marine Cyanobacteria Cyanobacteria Universe Importance? Effect Global Climate change 2 Regulate Atmospheric CO2 2 Environment Remove 10 billion tons of carbon From atmosphere Figure 1: Atmospheric View of Cyanobacteria Bloom. Baltic Sea System Study 1997 www.io-warnemuende.de/.../newslett/news7.n

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

5. Question: Locating DNA motifs in marine Cyanobacteria: Question Specific Goal Ultimate Goal What Genes are Of the Genes, Which are responsible for Likely regulated by Understanding The ? NTCA binding sites using comparitive genomics N2 Fixing Heterocyst Molecular Machinery of: N2 Fixing Heterocyst Cryanobacteria

6. Introduction: Locating DNA motifs in marine Cyanobacteria: upstream sequences marine cyanobacteria ntcA promotor? Captured: Intergenetic region 3’ 5’

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

8. Procedure: Locating DNA motifs in marine Cyanobacteria: Orthologs of Meme applicaiton A7120

9. 1. Genone of Organism: PSSM bg-freq table • Machine Consisted of 7 Functions: • Bg-Count-Freq • Make Motif1 freq • Optimize tables • FastScore2 • CB-FIND_NTCASearch • Find-NTCAScore Meme applicaiton Repeated for each gene in each organism DATA

10. Results: Locating DNA motifs in marine Cyanobacteria: DATA • 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

11. Results: Locating DNA motifs in marine Cyanobacteria: Consensus NtcA binding Site

12. Results: Locating DNA motifs in marine Cyanobacteria: Genes Found PMED4 SS120 WH8102 MIT9313 • 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.“hosphoribosylaminoimidazolesuccinocarboxamidePhosphoribosylaminoimidazolesuccinocarboxamide“ • 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" • 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: Matching Proteins PMED4 Global nitrogen regulatory protein, CRP family... SS120 Glutamine synthetase, glutamate--ammonia ligase WH8102 Punative Urea ABC transport, binding protein... MIT9313

14. Conclusion: Locating DNA motifs in marine Cyanobacteria: Possible Motif? 5-NT 5-NT AA... Rich AT... Rich Begin End

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