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 :