Summary Macroautophagy (hereafter autophagy) is an evolutionarily conserved process in which portions of the cytoplasm are engulfed, degraded and subsequently recycled. The Atg17-Atg31-Atg29 complex translocates to the phagophore assembly site (PAS), where an autophagosome forms, at a very early stage of autophagy, playing a vital role in autophagy induction. Here, we identified a novel role of this complex in a late stage of autophagy where it coordinates with Atg11 to regulate autophagy-specific fusion with the vacuole. Atg17 and Atg11 interact with the vacuolar SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) Vam7 independent of each other. Several hydrophobic residues in helix 1 and helix 4 of Atg17 and the SNARE domain of Vam7 mediate the Atg17-Vam7 interaction. An F317D mutation of Atg17, which diminished its interaction with Vam7 without affecting its interaction with Atg13 or Atg31, leads to a defect in the fusion of autophagosomes with the vacuole and decreased autophagy activity. These results provide the first demonstration that the Atg17-Atg31-Atg29 complex functions in both early and late stages of autophagy, and provides a mechanistic explanation for the coordination of autophagosome completion and fusion with the vacuole.

Under high irradiance, most cyanobacteria induce a photoprotective mechanism that decreases the energy arriving at the photosynthetic reaction centers to avoid the formation of dangerous species of oxygen. This mechanism which rapidly increases the heat dissipation of excess energy at the level of the cyanobacterial antenna, the phycobilisomes, is triggered by the photoactivation of the Orange Carotenoid Protein (OCP). Under low light conditions, the Fluorescence Recovery Protein (FRP) mediates the recovery of the full antenna capacity by accelerating the deactivation of the OCP. Several FRP Synechocystis mutants were constructed and characterized in terms of the OCP-related photoprotective mechanism. Our results demonstrate that Synechocystis FRP starts at Met26 and not at Met1 (according to notation in Cyanobase) as was previously suggested. Moreover, changes in the genomic region upstream the ATG encoding for Met26 influenced the concentration of OCP in cells. A long FRP (beginning at Met1) is synthesized in Synechocystis cells when the frp gene is under the control of the psbA2 promoter but it is less active than the shorter protein. Overexpression of the short frp gene in Synechocystis enabled short FRP isolation from the soluble fraction. However, the high concentration of FRP in this mutant inhibited the induction of the photoprotective mechanism by decreasing the concentration of the activated OCP. Therefore, the amplitude of photoprotection depends on not only OCP concentration but also on that of FRP. The synthesis of FRP and OCP must be strictly regulated to maintain a low FRP to OCP ratio to allow efficient photoprotection.