Download Locating NTCA Binding Sites In Cyrano Bacteria

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 …
Varied
Ex. (Oceans, Fresh water, temperate soils, extreme
environments ect )
Most concentrated at the first 100m depth 1
Introduction: Locating DNA motifs in marine Cyanobacteria
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:
“ 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.
Question: Locating DNA motifs in marine Cyanobacteria:
Introduction: Locating DNA motifs in marine Cyanobacteria:
5’
3’
Introduction: Locating DNA motifs in marine Cyanobacteria:
• Prochlorococcus Marinus
SS120
• Prochlorococcus Marinus
PMED4
• Prochlorococcus Marinus
MIT9313
• Synechococcus sp.
WH8102
All Cyanobacteria images from: www.cyanosite.bio.purdue.edu/images/images.html
Procedure: Locating DNA motifs in marine Cyanobacteria:
100
50
East
0
West
1st 2nd 3r d 4th
Qtr Qtr Qtr Qtr
Nor th
Machine Consisted of 7
Functions:
1. Bg-Count-Freq
100
50
East
0
West
1st 2nd 3rd 4th
2. Make Motif1 freq
3. Optimize tables
North
Qtr Qtr Qtr Qtr
4. FastScore2
5. CB-FIND_NTCASearch
Repeated for each
gene in each
organism
6. Find-NTCAScore
Results: Locating DNA motifs in marine Cyanobacteria:
• 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
"Glutamine
urea
synthetase“
synthetase,
ABC transporter,
glutamate--ammonia
substrate binding
ligase“
protein”NtcA like
protein
promoter sequence"
•2. "putative
“Glutamine
"Uncharacterized
urea
synthetase,
ABC
protein“
transporter,
glutamate--ammonia
urea bindingligase“
protein NtcA like
promoter
•2.
"Global
sequence
nitrogen regulatory protein, CRP family of transcriptional
•3. "Predicted
“SAM (andprotein“
some other nucleotide) binding motif: Generic methyl-...“
regulators“
•3. "possible transcription regulator“
•4. "Predicted
“putative hydrogenase
protein family
accessory
PM-27“protein”
•3. "Short-chain dehydrogenase/reductase (SDR) superfamily"
•4. "UDP-N-glucosamine 1-carboxyvinyltransferase“
•5. "Uncharacterized
”possible NAD(P)protein“
transhydrogenase beta subunit”
•4. "Sulfatase Signal predicted by SignalP 2.0 HMM (Signal peptide
•5. "hypothetical“
•6. "Predicted
probabilty
“Global1.000)
nitrogen
protein“
withregulatory
cleavage site
protein,
probability
CRP family
0.884 of
at transcriptional
residue 24
regulators”
•6.
"conserved hypothetical protein short orf found near phage integrases“
•7.“hosphoribosylaminoimidazolesuccinocarboxamidePhosphoribosylami
•5.
"Type II alternative RNA polymerase sigma factor, sigma-70 family"
noimidazolesuccinocarboxamide“
•7.
"two-component response regulator“
•8. "hypothetical"
Results: Locating DNA motifs in marine Cyanobacteria:
Conclusion: Locating DNA motifs in marine Cyanobacteria:
Dr. Wolfgang Hess
Professor 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 Elhai
Professor of Biology
Email: [email protected]
Web: www.people.vcu.edu/~elhai
David Long Bio351