Download - Red Tides
Red Tides
Trichodesmium erythraeum
Microscopic view Present in the form of colonies
Responsible for increased nitrogen fixation in the presence of Iron.
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
1) Periplasmic protein upstream sequence 2) Bacterioferritin upstream sequence3) 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
Upstream Sequences of Iron regulatory proteins
A & T rich sequenceA & T rich sequence
What about similar genes in other organisms ?
Upstream sequences of orthologs with similar motifs
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
Organism Gene Position Upstream Sequence
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
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 ?........What are other matches ?........
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 ?
Finding FE+ regulatory genes ?
Intergenic sequences in the genome of Trichodesmium
Orthologs of the other promising iron regulatory genes in Trichodesmium.
Dr. Jeff Elhai
Bioinformatics
VCU
Presented by : Sukalpa Dutta
Thanks To :