Evolutionary, structural and expression analysis of core genes involved in starch synthesis

Jianzhou Qu,Renhe Zhang,Zhengquan Zhang,Jiquan Xue,Linsan Liu,Yuyue Zhong,Dongwei Guo,Shutu Xu,Guangzhou Chen

doi:10.1038/s41598-018-30411-y

Jianzhou Qu, Renhe Zhang + Show 7 more

Open Access

https://doi.org/10.1038/s41598-018-30411-y

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Abstract

Starch is the main storage carbohydrate in plants and an important natural resource for food, feed and industrial raw materials. However, the details regarding the pathway for starch biosynthesis and the diversity of biosynthetic enzymes involved in this process are poorly understood. This study uses a comprehensive phylogenetic analysis of 74 sequenced plant genomes to revisit the evolutionary history of the genes encoding ADP-glucose pyrophosphorylase (AGPase), starch synthase (SS), starch branching enzyme (SBE) and starch de-branching enzyme (DBE). Additionally, the protein structures and expression patterns of these four core genes in starch biosynthesis were studied to determine their functional differences. The results showed that AGPase, SS, SBE and DBE have undergone complicated evolutionary processes in plants and that gene/genome duplications are responsible for the observed differences in isoform numbers. A structure analysis of these proteins suggested that the deletion/mutation of amino acids in some active sites resulted in not only structural variation but also sub-functionalization or neo-functionalization. Expression profiling indicated that AGPase-, SS-, SBE- and DBE-encoding genes exhibit spatio-temporally divergent expression patterns related to the composition of functional complexes in starch biosynthesis. This study provides a comprehensive atlas of the starch biosynthetic pathway, and these data should support future studies aimed at increasing understanding of starch biosynthesis and the functional evolutionary divergence of AGPase, SS, SBE, and DBE in plants.

Highlights

Starch is the predominant reserve form of carbohydrate and energy in plants and can be divided into two types, transitory starch and storage starch, based on biological function
SS can be further divided into granule-bound starch synthase (GBSS), which is responsible for the synthesis of amylose and the extra-long-chain fraction of amylopectin, and soluble starch synthase (SSS), which is mainly responsible for the synthesis of amylopectin[6,7]
When we compared maize GBSS isoforms with rice GBSSI, Agrobacterium tumefaciens glycogen synthase (AtGS) and Escherichia coli glycogen synthase (EcGS), we found that the binding sites for ADP and glucose were conserved in maize GBSS isoforms except for residues Lys[462], Phe[463], Asn[464] and Ile[490] (Fig. 6C and Supplementary Fig. 9)[29,30,31]

Summary

Introduction

Starch is the predominant reserve form of carbohydrate and energy in plants and can be divided into two types, transitory starch and storage starch, based on biological function. SSs share a highly conserved core region located in the C-terminus that generally consists of conserved starch catalytic glucosyl transferase family 5 (GT5) and GT1 domains, which mediate an inverting mode of glucosyl transfer during glucosyl transferase[11] Both the GT5 and GT1 domains belong to the GT-B superfamily according to the CAZy database (http://www.cazy.org/), and they possess conserved amino acid residues that can bind the glucosyl donor (ADP-Glc). These enzymes usually merge into the base catalytic region of starch synthases. SBEs have retained a C-terminal β-sheet catalytic domain (Aamy_C), while pullulanase (PUL) has a DUF3372 domain located in the N-terminal sequence, and this domain may play important roles in recognition and/or interaction with certain substrates or be involved in modulating PUL activity and interacting with other starch biosynthetic enzymes in specific environmental conditions[12,13]

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