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DNA motifs potentially related to Regulating genes in Response to Nitrogen in
Marine Cyanobacteria.
Created By David Long
VCU Biology Undergraduate
June 2005
Introduction: Locating DNA motifs in marine Cyanobacteria
Morphologically
Ex. Unicellular & Filamentous …
Ex. High-light adapted & Low-light adapted …
VariedEx. (Oceans, Fresh water, temperate soils, extreme environments ect )
Most concentrated at the first 100m depth 1
Effect Global Climate change 2
Regulate Atmospheric CO2 2
Remove 10 billion tons of carbon From atmosphereFigure 1:
Atmospheric View of Cyanobacteria Bloom. Baltic Sea System Study 1997
Introduction: Locating DNA motifs in marine Cyanobacteria
“ 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:
Question: Locating DNA motifs in marine Cyanobacteria:
Introduction: Locating DNA motifs in marine Cyanobacteria:
5’ 3’
• 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
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Procedure: Locating DNA motifs in marine Cyanobacteria:
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Machine Consisted of 7 Functions:
1. Bg-Count-Freq
2. Make Motif1 freq
3. Optimize tables
4. FastScore2
5. CB-FIND_NTCASearch
6. Find-NTCAScoreRepeated for each gene in each organism
• 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:
Results: Locating DNA motifs in marine Cyanobacteria:
•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"
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"
Results: Locating DNA motifs in marine Cyanobacteria:
Conclusion: Locating DNA motifs in marine Cyanobacteria:
Dr. Wolfgang HessProfessor of Experimental Bioinformatics University of Freiburg Institute of Biology
Ph(#49-(0)761-2032796
Email: [email protected]
Web: http://biochemie.biologie.uni-freiburg.de/hess/
Dr. Jeff ElhaiProfessor of Biology
Email: [email protected]
Web: www.people.vcu.edu/~elhai
David Long Bio351
