Table 3 |
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|
Presence and copy number of iron-regulated genes in the genomes of ecologically distinct diatoms |
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|
Gene |
Product |
Destination |
Mutual substitution at low-iron |
Putative role in iron uptake |
To |
Tp |
Pt |
Fc |
|
|
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|
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. |
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|
Lommer et al. Genome Biology 2012 13:R66 doi:10.1186/gb-2012-13-7-r66 |
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