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1 Gene expressed in bebe3 ZmBEa Expression constructs 35S ZmBEa Pnos:Hygromycin r 35S Pnos:Hygromycin r 35S ctp YFP Pnos:Hygromycin r B -1 Chl YFP- Merge Supplemental Figure S1: Constructs Used for the Expression of Different Branching Enzyme Types in the rabidopsis bebe3 Double Mutant (), and the Correct Localization of E. coli GLGB (B). () Cartoon of the constructs used for the constitutive expression of different branching enzyme types. (B) Confocal laser scanning fluorescence microscopy of plants expressing YFP-tagged. The left-hand panel shows the chlorophyll auto-fluorescence. The middle panel shows YFP fluorescence. The right-hand panel shows the merged images confirming chloroplastic localization of the recombinant protein. White Bar = um

2 DP bebe3 DP3 B DP ZmBEa-1 DP3 ZmBEa C DP -1 DP3 D DP DP3-1 Retention time (min) Supplemental Figure S. MOS Composition From bebe3 Mutants Expressing Different Branching Enzyme Types. Neutralized soluble fractions of the - replicate plants of each line were analyzed by HPEC-PD. Maltose (DP ) and other linear glucans (DP 3-7) were identified by their retention time. Individual chromatograph for each line are shown. The peaks for DP 3-7 are show in the inset in each panel. Replicates for each line yielded comparable results. () Chromatographs of wild type (blue) and bebe3 mutant (black) (B) Chromatographs of bebe3 mutant expressing ZmBEa. ZmBEa-1 (pink), ZmBEa (blue), and (black) (C) Chromatographs of bebe3 mutant expressing. -1 (pink), (blue), and (black) (D) Chromatographs of bebe3 mutant expressing. -1(pink), (blue), and (black)

3 PHS bebe3 IS1-IS PHS1 tbe3 tbe Supplemental Figure S3. Native PGE (Zymograms) of Wild-Type rabidopsis () and bebe3 Mutants to Detect BE ctivities Soluble proteins were extracted from the indicated lines and separated by native PGE in gels containing.% (w/v) glycogen. Branching enzyme activity was detected by incubating the gels in a medium containing phosphorlyase a and its substrate, glucose-1-phosphate. Dark bands represent the endogenous α-glucan phosphorylases (PHS) in the cytosol (PHS) and plastid (PHS1). In this gel, BE3 is resolved from PHS1. pale band corresponds to the heteromultimeric IS1-IS debranching enzyme.

4 be be3 ZmBEa -1 ZmBEa ZmBEa -1 be be3-1 SS3 SS1 Supplemental Figure S. Native PGE (Zymograms) of Wild-Type rabidopsis () and bebe3 Mutants Expressing Different Branching Enzyme Types to Detect SS ctivities. Extracts of soluble protein from each line was loaded on native PGE gel containing.3% (w/v) glycogen. fter electrophoresis, the gels were incubated overnight in a solution containing. mm DP-glucose. Dark bands represent starch synthase activities SS1 and SS3. Pale bands represented glucan hydrolytic activities such as α- and β-amylases.

5 B E ZmBEa Degree of polymerization(dp) C F ZmBEa D G H I J Supplemental Figure S5. Chain Length Distribution of mylopectin from Wild-Type rabidopsis () and bebe3 Mutants Expressing Different Branching Enzyme Types. mylopectin fractions from the given lines were debranched and the resultant linear chains analyzed using HPEC-PD. Peak areas from DP 3 to DP 5 were summed and the relative peak area for each chain length was calculated. Values are the means ± SE from or 3 technical replicates. () CLD of amylopectin from the wild type (). (B-D) CLD of amylopectin from independent transgenic lines expressing ZmBEa (E-G) CLD of amylopectin from independent transgenic lines expressing (H-J) CLD of amylopectin from independent transgenic lines expressing

6 be ZmBEa ZmBEa ZmBEa be starch gbss deficient starch 7kDa 55kDa GBSS (7kDa) 55kDa Rubisco (5kDa) Supplemental Figure S. GBSS bundance in Total Protein Extracts of Wild-Type rabidopsis () and bebe3 Mutants Expressing Different Branching Enzyme Types. Total proteins were extracted from rosette leaves of each genotype harvested in the middle of day, by homogenization in a solution containing % SDS and subsequent boiled for 5 min. 1 mg of purified starch from and a mutant lacking GBSS were dissolved in 1 ml extraction solution and used as positive and negative controls. Protein extracts were loaded on a SDS-PGE gel, and subject to immunoblotting with GBSS-specific antibodies, as described in Seung et al. (15). Subsequently, the blots were stained with Coomassie blue to visualize the large subunit of the Rubisco protein, confirming equal protein loading for each lane, except those with proteins derived from pure starch samples (lower panel).

7 E 1 µm B F -1 C G D H Supplemental Figure S7. Various Granule Morphology in Line (-D), and in Different Expressing Lines (E-H). See Fig. and Materials and Methods for further details. Bar = 1µm.

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