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The expression of the genes encoding the ferredoxin-thioredoxin system including the ferredoxin-thiore-doxin reductase (FTR) genes ftrC and ftrV and the four different thioredoxin genes trxA (m-type; slr0623), trxB (x-type; slr1139), trxC (sll1057) and trxQ (y-type; slr0233) of the cyanobacterium Synechocystis sp. PCC 6803 has been studied according to changes in the photosynthetic conditions. Experiments of light-dark transition indicate that the expression of all these genes except trxQ decreases in the dark in the absence of glucose in the growth medium. The use of two electron transport inhibitors, 3-(3,4-dichlorophenyl)-1,1-dimethylurea (DCMU) and 2,5-dibromo-3-methyl-6-isopropyl-p-benzoquinone (DBMIB), reveals a differential effect on thioredoxin genes expression being trxC and trxQ almost unaf-fected, whereas trxA, trxB, and the ftr genes are down-regulated. In the presence of glucose, DCMU does not affect gene expression but DBMIB still does. Analysis of the single TrxB or TrxQ and the double TrxB TrxQ Synechocystis mutant strains reveal different functions for each of these thioredoxins under different growth conditions. Finally, a Synechocystis strain was generated containing a mutated version of TrxB (TrxBC34S), which was used to identify the potential in-vivo targets of this thioredoxin by a proteomic analysis.