Many mitochondrial and chloroplast proteins are encoded in the nucleus and subsequently imported into the organelles via active protein transport systems. While usually highly specific, some proteins are dual-targeted to both organelles. In tobacco (<i>Nicotiana tabacum L.</i>), the cDNA encoding the mitochondrial isoform of NADP+-dependent isocitrate dehydrogenase (NADP+-ICDH) contains two translational ATG start sites, indicating the possibility of two tandem targeting signals. In this work the putative mitochondrial and chloroplastic targeting signals from NADP+-ICDH were fused to a yellow fluorescent protein (YFP) to generate a series of constructs and introduced into tobacco leaves by <i>Agrobacterium</i>-mediated transient transfection. The subsequent sub-cellular locations of the ICDH:YFP fusion proteins were then examined under the confocal microscope. Constructs predicted to be targeted to the chlroplast all localized to the chloroplast. However, this was not the case for constructs that were predicted to be mitochondrial targeted. While some constructs localized to mitochondria, others appeared to be chloroplast localized. This was attributed to an additional 50 amino acid residues of the mature NADP+-ICDH protein which was present in those constructs. In addition, during the process of generating these constructs our sequence analysis indicated a stop codon present at amino acid position 161 of the mature NADP+-ICDH protein from both Xanthi and Petit Havana cultivars of tobacco. This was confirmed by multiple sequencing reactions and created discrepancies with the reported sequence present in the database. The results of this study raise interesting questions with regard to the targeting and processing of NADP+-ICDH.

Many mitochondrial and chloroplast proteins are encoded in the nucleus and subsequently imported into the organelles via active protein transport systems. While usually highly specific, some proteins are dual-targeted to both organelles. In tobacco (<i>Nicotiana tabacum L.</i>), the cDNA encoding the mitochondrial isoform of NADP+-dependent isocitrate dehydrogenase (NADP+-ICDH) contains two translational ATG start sites, indicating the possibility of two tandem targeting signals. In this work the putative mitochondrial and chloroplastic targeting signals from NADP+-ICDH were fused to a yellow fluorescent protein (YFP) to generate a series of constructs and introduced into tobacco leaves by <i>Agrobacterium</i>-mediated transient transfection. The subsequent sub-cellular locations of the ICDH:YFP fusion proteins were then examined under the confocal microscope. Constructs predicted to be targeted to the chlroplast all localized to the chloroplast. However, this was not the case for constructs that were predicted to be mitochondrial targeted. While some constructs localized to mitochondria, others appeared to be chloroplast localized. This was attributed to an additional 50 amino acid residues of the mature NADP+-ICDH protein which was present in those constructs. In addition, during the process of generating these constructs our sequence analysis indicated a stop codon present at amino acid position 161 of the mature NADP+-ICDH protein from both Xanthi and Petit Havana cultivars of tobacco. This was confirmed by multiple sequencing reactions and created discrepancies with the reported sequence present in the database. The results of this study raise interesting questions with regard to the targeting and processing of NADP+-ICDH.

La détection de potentielles cibles secondaires ou off-targets d’un ligand donné requiert la détermination de son site d’interaction et la recherche de sites d’interaction similaires sur d’autres protéines. Dans le but de mener à bien cette étude, nous avons développé PatchSearch : cet outil compare un patch requête, correspondant à un site d’interaction, avec la surface d’une cible potentielle. L’algorithme employé s’appuie sur une méthode originale de recherche de quasi-cliques dans un graphe produit : cette approche identifie des groupes d’atomes du patch appariés avec ceux de la surface ciblée avec des propriétés physico-chimiques conservées et dans des configurations proches. Nous montrons que PatchSearch trouve des patches qui correspondent à ceux qui sont connus sur les surfaces ciblées. De plus, les résultats de l’application de PatchSearch sur des protéines flexibles indiquent que l’approche des quasi-cliques permet de retrouver à la fois les parties rigides et flexibles des patches,contrairement à la recherche classique de cliques. Enfin, les performances de Patch-Search sont équivalentes à celles des autres outils de comparaison de sites de liaison.Nous avons également appliqué PatchSearch sur des off-targets de médicaments impliqués dans le traitement de cancers. Nos expériences suggèrent l’utilisation de PatchSearch dans la recherche des éventuelles off-targets d’un médicament. / Detection of putative off-targets for a ligand requires to search for some similarbinding sites onto other proteins surface. In order to achieve this goal, we developeda tool named PatchSearch. This program compares a query patch, whichcontains the binding site, with the surface a potentially targeted protein. Patch-Search’s algorithm is based on an original method searching for some quasi-cliquesin a graph product, which identifies some atoms both in the patch and in the surfacewith conserved physicochemical properties and in similar configurations. Weshow that PatchSearch efficiently finds known patches on protein surfaces. Moreover,application of PatchSearch on flexible proteins shows that, unlike the classiccliques approach, quasi-cliques method allows to find both rigid and flexible partsof the patches. PatchSearch gets similar results compared to the other binding sitecomparison tools. We also applied PatchSearch to find patches binding polypharmacologicaldrugs involved in cancer treatment, in order to identify them on knownoff targets. Our experiments suggest to employ PatchSearch in off-targets detectionprocess.