Cloning, characterisation and comparative analysis of a starch synthase IV gene in wheat: functional and evolutionary implications

Abstract

BackgroundStarch is of great importance to humans as a food and biomaterial, and the amount and structure of starch made in plants is determined in part by starch synthase (SS) activity. Five SS isoforms, SSI, II, III, IV and Granule Bound SSI, have been identified, each with a unique catalytic role in starch synthesis. The basic mode of action of SSs is known; however our knowledge of several aspects of SS enzymology at the structural and mechanistic level is incomplete. To gain a better understanding of the differences in SS sequences that underscore their specificity, the previously uncharacterised SSIVb from wheat was cloned and extensive bioinformatics analyses of this and other SSs sequences were done.ResultsThe wheat SSIV cDNA is most similar to rice SSIVb with which it shows synteny and shares a similar exon-intron arrangement. The wheat SSIVb gene was preferentially expressed in leaf and was not regulated by a circadian clock. Phylogenetic analysis showed that in plants, SSIV is closely related to SSIII, while SSI, SSII and Granule Bound SSI clustered together and distinctions between the two groups can be made at the genetic level and included chromosomal location and intron conservation. Further, identified differences at the amino acid level in their glycosyltransferase domains, predicted secondary structures, global conformations and conserved residues might be indicative of intragroup functional associations.ConclusionBased on bioinformatics analysis of the catalytic region of 36 SSs and 3 glycogen synthases (GSs), it is suggested that the valine residue in the highly conserved K-X-G-G-L motif in SSIII and SSIV may be a determining feature of primer specificity of these SSs as compared to GBSSI, SSI and SSII. In GBSSI, the Ile485 residue may partially explain that enzyme's unique catalytic features. The flexible 380s Loop in the starch catalytic domain may be important in defining the specificity of action for each different SS and the G-X-G in motif VI could define SSIV and SSIII action particularly.

Correlation analysis between starch properties and single nucleotide polymorphisms of waxy genes in common rye (Secale cereale L.)

“…The amino acid variations in the catalytic domain were predicted to be located in the α-helix and β-pleated sheet of A domain and irregular curls inside the crack. The above structure was consistent with the domains of TaSSIVb (Leterrier et al, 2008) and rice Wx protein and catalytic center prediction (Li et al, 2012). …”

Causal Relations Among Starch Biosynthesis, Structure, and Properties

“…It has been reported that two isoforms of SSIV exist in plants: SSIVa and SSIVb, which are expressed in the endosperm and leaves, respectively [39,112,158]. Recently, the role for the SSIV class has been primarily shown to be in starch granule initiation in Arabidopsis, although it may also be involved in producing short branches [145].…”

RNA interference-mediated silencing of the starch branching enzyme gene improves amylose content in rice

“…In recent years, cloning of starch enzyme genes has improved our understanding of starch synthesis (Jain et al, 2008b;Leterrier et al, 2008). Several cDNAs encoding SBEs have been isolated from rice, wheat, maize, and barley (Kim et al, 1998;Mutisya et al, 2003;Han et al, 2007).…”

“…Therefore, research aimed at regulating starch biosynthesis and improving starch quality is imperative. Developments in molecular biology have resulted in various starch biosynthesis management methods, ranging from genetic engineering to conventional breeding (Hirose and Terao, 2004;Song et al, 2004;Leterrier et al, 2008).…”