In Chlamydomonas reinhardtii, the presence of a defective STA11 locus results in significantly reduced granular starch deposition displaying major modifications in shape and structure. This defect simultaneously leads to the accumulation of linear malto-oligosaccharides (MOS). The mutants of STA11 were showed to lack d-enzyme, a plant ␣-1,4 glucanotransferase analogous to the Escherichia coli amylomaltase. We have cloned and characterized both the cDNA and gDNA corresponding to the C. reinhardtii d-enzyme. We now report allele-specific modifications of the d-enzyme gene in the mutants of STA11. These allele-specific modifications cosegregate with the corresponding sta11 mutations, thereby demonstrating that STA11 encodes d-enzyme. MOS production and starch accumulation were investigated during day and night cycles in wild-type and mutant C. reinhardtii cells. We demonstrate that in the algae MOS are produced during starch biosynthesis and degraded during the phases of net polysaccharide catabolism.Until recently plant starch was believed to be synthesized from ADP-Glc solely through a combination of starch synthases and branching enzymes. However the finding of low-starch or starchless mutants defective for a particular form of debranching enzyme in four different plant systems established that other enzymes of starch metabolism are equally important in ensuring normal starch granule biogenesis (James et al., 1995;Mouille et al., 1996;Nakamura et al., 1996;Zeeman et al., 1998). This came as a surprise because debranching enzymes were initially thought to be enzymes involved solely in starch breakdown. Mutants of the corresponding activities in yeast (Teste et al., 2000) or Escherichia coli (I. Kinderf, Z. Li, M.S. Samuel, B. Koshar-Hashezmi, S. Ball, L. Rampling, and M. Morell, unpublished data) are clearly glycogen over-producers, confirming the initial suspicion. Although the detailed interpretation of the results obtained with the plant mutants vary somewhat, there is now a general agreement that isoamylases, the particular form of debranching enzyme affected in these studies, are enzymes required during starch biosynthesis exclusively. It has been comforting to realize that all mutants affected in starch metabolism behaved in a similar fashion in plants as different as Chlamydomonas reinhardtii, Arabidopsis, pea (Pisum sativum), maize (Zea mays), or rice (Oryza sativa). Some discrepancies in expressivity of mutant phenotypes could be easily explained most of the time by subtle differences in the pathways. For instance, the presence of extraplastidial and plastidial ADP-Glc pyrophosphorylases in cereals easily explains why mutants of cereals lacking the major enzyme form displayed reduced expressivity in their starch accumulation phenotype (for review, see Kossmann and Lloyd, 2000). The starch accumulation phenotypes of the Arabidopsis or C. reinhardtii mutants defective for the catalytic subunit of their sole plastidial ADP-Glc pyrophosphorylase were much more severe (Lin et al., 1988;Zabawinski et al., 2001...