Table 3

Presence and copy number of iron-regulated genes in the genomes of ecologically distinct diatoms

Gene

Product

Destination

Mutual substitution at low-iron

Putative role in iron uptake

To

Tp

Pt

Fc


PETF

Ferredoxin

CP

Ferredoxin → flavodoxin (short)

1

1

1

1

FLDA(s)

Flavodoxin (short)

CP

Ferredoxin → flavodoxin (short)

2

0

1

1

FLDA(l)

Flavodoxin (long)

SP (ER?)

None (distinct functional context)

1

1

1

1

CYTC6 (type A)

Cytochrome c6

CP

Cytochrome c6 (type A) → plastocyanin

2

1

1

1

CYTC6 (type B)

Cytochrome c (?)

SP (ER?)

None (distinct functional context)

1

1

1

0

PETE/PCY

Plastocyanin

CP

Cytochrome c6 (type A) → plastocyanin

1

0

0

1

Class II FBA (type A)

Class II fructose-bisphosphate aldolase

CP pyrenoid (Pt FBAC1)

Class II FBA (type A) → class I FBA (type A)

1

1

1

1

Class II FBA (type B)

Class II fructose-bisphosphate aldolase

CP stroma (Pt FBAC2)

Class II FBA (type B) → class I FBA (type B)

1

1

1

1

Class II FBA (type C)

Class II fructose-bisphosphate aldolase

Cytosolic (Pt FBA3)

Class II FBA (type C) → class I FBA (type C)

1

1

1

1

Class I FBA (type A)

Class I fructose-bisphosphate aldolase

CP pyrenoid (Pt FBAC5)

Class II FBA (type A) → class I FBA (type A)

1

0

1

1

Class I FBA (type B)

Class I fructose-bisphosphate aldolase

CP stroma

Class II FBA (type B) → class I FBA (type B)

1

0

0

1

Class I FBA (type C)

Class I fructose-bisphosphate aldolase

Cytosolic (Pt FBA4)

Class II FBA (type C) → class I FBA (type C)

1

1

1

1

ISIP1

Iron starvation induced protein 1

Cell surface

Receptor (?)

2

0

1

3

ISIP3

Iron starvation induced protein 3

Cell surface

Co-receptor (?)

1

1

1

2


The coastal diatom species T. pseudonana (Tp) lacks several genes that are found in the genomes of diatoms with high tolerance to low-iron conditions (T. oceanica (To), P. tricornutum (Pt), F. cylindrus (Fc)). Listed are also the respective counterparts whose products are subject to substitution under iron-limited conditions. The conserved paralogous genes of FLDA and CYTC6 are predicted to contain a signal peptide and are assumed to act in a different functional context. CP chloroplast; ER endoplasmic reticulum; SP, secretory pathway.

Lommer et al. Genome Biology 2012 13:R66   doi:10.1186/gb-2012-13-7-r66

Open Data