Red Tides

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Red Tides
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Marine Organisms
Trichodesmium erythraeum
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Microscopic view

• Present in the form of colonies
• Responsible for increased nitrogen
  fixation in the presence of Iron.

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Analysis of possible regulatory motifs

• Fe2/Zn2 uptake regulation proteins (FUR)

• Bacterioferritin ( cytochrome b1)

• ABC-type Fe3 transport system periplasmic
  component

9 known proteins known for iron regulation
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Upstream Sequences of Iron regulatory proteins
1) Periplasmic protein upstream sequence 2)
Bacterioferritin upstream sequence 3) FUR
upstream sequence
T T T T A C T T C A C G G G T C A A G A T T T T T
T C T C T C T C C C T T T T C C T T T T C T T C
C T A A A T T C G G A C A T T T T A T C A C T C C
T T A T A G C T T T T A A C C C A A G A T T G A
G G T G A T T T G A T T T C C C T T T T T C
A T rich sequence
What about similar genes in other organisms ?
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Upstream sequences of orthologs with similar
motifs
Organism Gene Position Upstream Sequence
Anabaena A7120.all1691 89 T C T T
T C A A G A A C T T C C T C A A G G C G A A C A C
C T G A G T G C A G A A G A T T T A T A T
Trichodesmium e. Tery.Te?4228 32 T T
T T T C A A A A C C T G C C A A A A G G C A A T C
A T C T G A G T G C C G A A G A T C T T T A T
Synechococcus e. S7942.ser2269 86
T C T T T C A A A A T C T C C C A G C A G G T G A
A C A C C T C A G T G C T G A G G A C C T T T A C
Anabaena v. A29413.Av?0480 89 T C T
T T C A A G A A C T T C C T C A A G G C G A A C A
C C T G A G C G C A G A A G A T T T A T A T
Nostoc p. S6803.sll0567 89 T T T T
T C A A A A T T T G C C G G A G G G G G A A C A T
C T C A G T G C C G A G G A G T T A C A C
Thermosynechococcus e. TeBP1.tll0048 125 T T T
T C C A G A A T C T G C C T A A G G G C A A T C A
C C T G A G T G C T G A A G A C C T C T A C
Crocosphaera w. Cwat.Cw?5989 161 T A
C T T C A T G C T C A A C A A G T G G G A G A A A
T T T T G A C T G G T T T A G A A G G C C A T
Anabaena A7120.all3940 161
T A C T C C A T G C T C A A C A A G T A G G A
G A A A T T C T C A C A G G T T T A G A T G G A C
A T Anabaena v. A29413.Av?3012 161
T A C T T C A T G C C C A A C A A G T G G G A G
A A A T T C T C A C A G G A T T A G A T G G A C A
T Crocosphaera w. Cwat.Cw?4935 89
TC T T C C A A A A T C T C C C T A G G G G G A A
T C A T T T G A G T G C T G A G G A A T T G T T T
Nostoc p. Npun.NpF6212 161
T A C T T C A T G C T G A A C A A G T A G G A
G A A A T T C T T A C C G G T T T A G A T G G G C
A T Trichodesmium e. Tery.Te?3328 170
T A C T T C A T G C T C A A C A A G C A G G A G
A A A T A T T A A C A G G T T T A G A A G G T C A
T Gloeobacter v. Gvi.glr3304 98
T G T T C C A G G A G T T G C C G G A G G G C
A A T C A C C T C A A T G C C G A G G A G C T G C
A C Prochlorococcus m. PMED4.PMM0637 104 T A T
T T G A G A A T A T T G G A G C A G G T A A T C A
T T T A A G T G C G G A A G A A G T T C A T
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What can we conclude from the information ?

• Matches with 2 Trichodesmium genes
• Already knew

• Matches with 2 nostoc and 4 anabaena genes not
  a surprise.. Both are rich in A and T
  nucleotides

What are other matches ?........
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Other matches ?

• Synechococcus e.
• Thermosynechococcus e.
• Crocosphaera w. (2 Genes)
• Gloeobacter v.
• Prochlorococcus m.

Iron regulatory upstream sequences somewhat
similar to Trichodesmium
Where else can we look for such matches ?
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Finding FE regulatory genes ?

• Intergenic sequences in the genome of
  Trichodesmium
• Orthologs of the other promising iron regulatory
  genes in Trichodesmium.

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• Thanks To

Dr. Jeff Elhai Bioinformatics VCU
Presented by Sukalpa Dutta