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Additional file 1. Supplementary data, Haderbache et al, qPCR, ddPCR and cytometry sensitivity and reproducibility

International audience; Starch is vital in human nutrition and its unique physical properties are widely used in industrial applications. It accumulates in plants as water-insoluble, semi-crystalline granules. Plants produce and consume their starch over time scales from hours to years. Leaf starch is metabolized in chloroplasts during the diel cycle. The synthesis and degradation rates are under photoperiodic control. Starch is comprised of two glucan polymers (amylose and amylopectin) and its physicochemical properties are defined by their organization within the granule. It has been assumed that the polymers self-organize to form the granule matrix. Recently, however, two conserved but uncharacterized proteins, Early Starvation 1 (ESV1) and Like Early Starvation 1 (LESV), were proposed to organize the polysaccharides within the granules. The mechanism by which this occurs is unknown. We report here preliminary results on the structural organization of LESV from Arabidopsis thaliana.

International audience; Starch synthesis requires several enzymatic activities including branching enzymes (BEs) responsible for the formation of α(1→6) linkages. Distribution and number of these linkages are further controlled by debranching enzymes (DBEs) that cleave some of them, rendering the polyglucan water-insoluble and semi-crystalline. Although the activity of BEs and DBEs is mandatory to sustain normal starch synthesis, the relative importance of each in the establishment of the plant storage polyglucan (i.e. water-insolubility, crystallinity, presence of amylose) is still debated. Here, we have substituted the activity of BEs in Arabidopsis with that of the Escherichia coli glycogen branching enzyme (GlgB). The latter is the BE counterpart in the metabolism of glycogen, a highly branched water-soluble and amorphous storage polyglucan. GlgB was expressed in the be2 be3 double mutant of Arabidopsis that is devoid of BE activity and consequently free of starch. The synthesis of a water-insoluble, partly crystalline, amylose-containing starch-like polyglucan was restored in GlgB-expressing plants, suggesting that BEs origin only have a limited impact on establishing essential characteristics of starch. Moreover, the balance between branching and debranching is crucial for the synthesis of starch, as an excess of branching activity results in the formation of highly branched, water-soluble, poorly crystalline polyglucan.

Typical two-cysteine peroxiredoxines are involved in cell resistance against H2O2-induced oxidative stress, by reducing H2O2 in H2O. Furthermore, these enzymes take part in H2O2 signalling, which is transmitted and regulated by their redox state. The eukaryotic typical 2-Cys Prxs are subject to post-translational modification under sulfinic acid oxidation state, which inactivates have lost their peroxidase activity and thus regulates allows the passage of H2O2-dependent cellular message. Reduction of the sulfinic acid oxidation state is essential for the cell viability. Sulfiredoxin (Srx) catalyzes this reduction. These research studies demonstrated that the catalytic mechanism of Srx occurs in three steps: first, the sulfinic acid is activated as a sulfinyl phosphoryl anhydride intermediate by a direct transfer of the ?-phosphate of ATP; second, the activated sulfinic acid intermediate is reduced via attack of the catalytic Cys of Srx, which leads to formation of a thiosulfinate intermediate and; third Srx, is recycled with concomitant release of the PrxSOH product of the reaction. Two classes of Srx could be defined depending on the mechanism of Srx recycling. The class comprising yeast Srxs have one recycling Cys. This Cys attacks the thiosulfinate intermediate, resulting in PrxSOH release and formation of an oxidized Srx intermediate. This oxidized species, with an intramolecular disulfide bond, is recognized and reduced by thioredoxin. In the class comprising Srx devoid of recycling Cys, which includes the mammalian Srxs, Srx is recycled by a reducer distinct from thioredoxin, which reduces directly the thiosulfinate function.; Les peroxyrédoxines à deux cystéines typiques (2-Cys Prx) sont impliquées dans la résistance des cellules au stress oxydant associé à H2O2, en réduisant H2O2 en H2O. En parallèle, ces enzymes participent à la transduction du signal dépendant de H2O2 en tant que second messager, via leur état rédox. La suroxydation sous forme d'acide sulfinique des 2-Cys Prx typiques eucaryotes est une modification posttraductionnelle qui inactive l'activité peroxydase, permettant de réguler le passage du message cellulaire H2O2-dépendant. La réduction de cette espèce oxydée est essentielle pour la viabilité des cellules. Cette réaction est catalysée par les sulfirédoxines (Srx). Les études réalisées ont permis de caractériser le mécanisme catalytique de Srx de S. cerevisiae qui consiste en : 1) l'activation de la fonction acide sulfinique sous forme d?anhydride phosphoryl sulfinique, par transfert direct du phosphate y de l'ATP ; 2) la réduction de la fonction acide sulfinique activée par attaque de la Cys catalytique de Srx, ce qui conduit à un intermédiaire covalent thiosulfinate Prx/Srx ; 3) le recyclage de Srx avec la libération de PrxSOH. Au niveau du recyclage de l'activité Srx, deux classes de Srx peuvent être définies, celle à deux Cys et celle à une Cys. La classe de Srx à deux Cys, composée jusqu'à présent de Srx de levures, possède une Cys de recyclage qui attaque le thiosulfinate au niveau de la Cys de Srx, libérant la PrxSOH et la Srx oxydée sous forme de pont disulfure intramoléculaire. Cette forme oxydée de Srx est ensuite reconnue et réduite par la thiorédoxine. La classe de Srx à une Cys dont font partie les Srx de mammifères, ne possédant pas de Cys de recyclage, passe par un mécanisme de recyclage impliquant un réducteur autre que la Trx, qui reduit directement la fonction thiosulfinate, et dont la nature reste à déterminer.

Typical two-cysteine peroxiredoxines are involved in cell resistance against H2O2-induced oxidative stress, by reducing H2O2 in H2O. Furthermore, these enzymes take part in H2O2 signalling, which is transmitted and regulated by their redox state. The eukaryotic typical 2-Cys Prxs are subject to post-translational modification under sulfinic acid oxidation state, which inactivates have lost their peroxidase activity and thus regulates allows the passage of H2O2-dependent cellular message. Reduction of the sulfinic acid oxidation state is essential for the cell viability. Sulfiredoxin (Srx) catalyzes this reduction. These research studies demonstrated that the catalytic mechanism of Srx occurs in three steps: first, the sulfinic acid is activated as a sulfinyl phosphoryl anhydride intermediate by a direct transfer of the ?-phosphate of ATP; second, the activated sulfinic acid intermediate is reduced via attack of the catalytic Cys of Srx, which leads to formation of a thiosulfinate intermediate and; third Srx, is recycled with concomitant release of the PrxSOH product of the reaction. Two classes of Srx could be defined depending on the mechanism of Srx recycling. The class comprising yeast Srxs have one recycling Cys. This Cys attacks the thiosulfinate intermediate, resulting in PrxSOH release and formation of an oxidized Srx intermediate. This oxidized species, with an intramolecular disulfide bond, is recognized and reduced by thioredoxin. In the class comprising Srx devoid of recycling Cys, which includes the mammalian Srxs, Srx is recycled by a reducer distinct from thioredoxin, which reduces directly the thiosulfinate function., Les peroxyrédoxines à deux cystéines typiques (2-Cys Prx) sont impliquées dans la résistance des cellules au stress oxydant associé à H2O2, en réduisant H2O2 en H2O. En parallèle, ces enzymes participent à la transduction du signal dépendant de H2O2 en tant que second messager, via leur état rédox. La suroxydation sous forme d'acide sulfinique des 2-Cys Prx typiques eucaryotes est une modification posttraductionnelle qui inactive l'activité peroxydase, permettant de réguler le passage du message cellulaire H2O2-dépendant. La réduction de cette espèce oxydée est essentielle pour la viabilité des cellules. Cette réaction est catalysée par les sulfirédoxines (Srx). Les études réalisées ont permis de caractériser le mécanisme catalytique de Srx de S. cerevisiae qui consiste en : 1) l'activation de la fonction acide sulfinique sous forme d?anhydride phosphoryl sulfinique, par transfert direct du phosphate y de l'ATP ; 2) la réduction de la fonction acide sulfinique activée par attaque de la Cys catalytique de Srx, ce qui conduit à un intermédiaire covalent thiosulfinate Prx/Srx ; 3) le recyclage de Srx avec la libération de PrxSOH. Au niveau du recyclage de l'activité Srx, deux classes de Srx peuvent être définies, celle à deux Cys et celle à une Cys. La classe de Srx à deux Cys, composée jusqu'à présent de Srx de levures, possède une Cys de recyclage qui attaque le thiosulfinate au niveau de la Cys de Srx, libérant la PrxSOH et la Srx oxydée sous forme de pont disulfure intramoléculaire. Cette forme oxydée de Srx est ensuite reconnue et réduite par la thiorédoxine. La classe de Srx à une Cys dont font partie les Srx de mammifères, ne possédant pas de Cys de recyclage, passe par un mécanisme de recyclage impliquant un réducteur autre que la Trx, qui reduit directement la fonction thiosulfinate, et dont la nature reste à déterminer.