Conservation and divergence of Starch Synthase III genes of monocots and dicots

Abstract

Starch Synthase (SS) plays an important role in extending the α-1,4 glucan chains during starch biosynthesis by catalyzing the transfer of the glucosyl moiety from ADP-glucose to the non-reducing end of a pre-existing glucan chain. SS has five distinct isoforms of which SSIII is involved in the formation of longer glucan chain length. Here we report identification and detailed characterization of ‘true’ orthologs of the well-characterized maize SSIII (ZmSSIII), among six monocots and two dicot species. ZmSSIII orthologs have nucleotide sequence similarity ranging from 56–81%. Variation in gene size among various orthologs ranged from 5.49 kb in Arabidopsis to 11.62 kb in Brachypodium and the variation was mainly due to intron size and indels present in the exons 1 and 3. Number of exons and introns were highly conserved among all orthologs however. While the intron number was conserved, intron phase showed variation at group, genera and species level except for intron 1 and 5. Several species, genera, and class specific cis-acting regulatory elements were identified in the promoter region. The predicted protein size of the SSIII orthologs ranged from 1094 amino acid (aa) in Arabidopsis to 1688 aa in Brachypodium with sequence identity ranging from 60%-89%. The N-terminal region of the protein was highly variable whereas the C-terminal region containing the Glycosyltransferase domain was conserved with >80% sequence similarity among the orthologs. In addition to confirming the known motifs, eleven novel motifs possibly providing species, genera and group specific functions, were identified in the three carbohydrate binding domains. Despite of significant sequence variation among orthologs, most of the motifs and their relative distances are highly conserved among the orthologs. The 3-D structure of catalytic region of SSIII orthologs superimposed with higher confidence confirming the presence of similar binding sites with five unidentified conserved regions in the catalytic (glycosyltransferase) domain including the pockets involved in catalysis and binding of ligands. Homeologs of wheat SSIII gene showed tissue and developmental stage specific expression pattern with the highest expression recorded in developing grains.

Loss of Starch Synthase IIIa changes starch molecular structure and granule morphology in grains of hexaploid bread wheat

“…Both iodine binding and SEC revealed substantial elevations of amylose in the triple mutant, and SEC also revealed smaller but signi cant elevation in the double mutants (iodine binding: 35.1% for triple mutants vs. 26.0% in sibling controls; SEC: 33.8% for triple mutants and 29.3% for double mutants vs. 25.5% in sibling controls). The double and triple mutants also had fewer long amylopectin chains; this was anticipated given the proposed role of SSIII in producing longer length amylopectin chains by extending short chains produced by SSI 39 . Prior studies of ssIIIa mutants in maize and rice also found that the mutants had fewer long amylopectin chains 18,21 .…”

Loss of starch synthase IIIa changes starch molecular structure and granule morphology in grains of hexaploid bread wheat

“…The different levels of amylose observed in double vs. triple mutants may be of particular interest for wheat breeding applications and open new possibilities for fine-tuning amylose levels in wheat using unique combinations of mutant ssIIIa homoeologues. The double and triple mutants also had fewer long amylopectin chains; this was anticipated given the proposed role of SSIII in producing longer length amylopectin chains by extending short chains produced by SSI 43 . Prior studies of ssIIIa mutants in maize and rice also found that the mutants had fewer long amylopectin chains 20 , 23 .…”

Soluble Starch Synthase Enzymes in Cereals: An Updated Review

“…There are either one or two coiled-coil (Cc) motifs in SSIII, SSIV, and SSV in the Nterminal region, which play an essential role in protein-protein interactions [84]. In SSIII, three conserved binding modules (CBM-25) are detected in the N-terminal region and play an important role in substrate binding [85]. The secondary structure of SS isoforms of maize was developed on the basis of the reference model of SSI in wheat, which showed 83% similarity to maize SSI [86].…”