Comparative expression analysis of sucrose phosphate synthase gene family in a low and high sucrose Pakistani sugarcane cultivars

Abstract

Sugarcane is the world's largest cultivated crop by biomass and is the main source of sugar and biofuel. Sucrose phosphate synthase (SPS) enzymes are directly involved in the synthesis of sucrose. Here, we analyzed and compared one of the important gene families involved in sucrose metabolism in a high and low sucrose sugarcane cultivar. A comprehensive in silico analysis of the SoSPS family displayed their phylogenetic relationship, gene and protein structure, miRNA targets, protein interaction network (PPI), gene ontology and collinearity. This was followed by a spatial expression analysis in two different sugarcane varieties. The phylogenetic reconstruction distributed AtSPS, ZmSPS, OsSPS, SoSPS and SbSPS into three main groups (A, B, C). The regulatory region of SoSPS genes carries ABRE, ARE, G-box, and MYC as the most dominant cis-regulatory elements. The PPI analysis predicted a total of 14 unique proteins interacting with SPS. The predominant expression of SPS in chloroplast clearly indicates that they are the most active in the organelle which is the hub of photosynthesis. Similarly, gene ontology attributed SPS to sucrose phosphate synthase and glucosyl transferase molecular functions, as well as sucrose biosynthetic and disaccharide biological processes. Overall, the expression of SPS in CPF252 (high sucrose variety) was higher in leaf and culm as compared to that of CPF 251 (low sucrose variety). In brief, this study adds to the present literature about sugarcane, sucrose metabolism and role of SPS in sucrose metabolism thereby opening up further avenues of research in crop improvement.

Keywords: Amino acid; Arabidopsis; Gene; High level; Physiochemical; Protein; Sucrose; Sucrose phosphate synthase enzymes; Sugar cane; synthesis.

Figure 1. ML phylogenetic reconstruction of SPS family.

The cladogram grouped SPS protein sequences of rice, maize, sorghum, Arabidopsis, and sugarcane into consisting of three main clusters (A, blue; B, green; C, yellow). The figure was drawn from the aligned SPS protein sequences using MEGAX.

Figure 2. Exon-intron assembly of SoSPS. genes.

The structure of SoSPS genes was visualzed using the online tool GSDS by submitting their genomic and CDS sequences SoSPS and tree in Newick format. The yellow boxes indicate exons (coding sequences) and black lines denote introns (non-coding sequences). The UTRs (untranslated regions) are also shown in blue color. A cladogram has also been shown (left side).

Figure 3. Cis motifs in the promoter sequences of SoSPS genes.

(A) Name, sequence and feature of important cis motifs. (B) The frequency of occurrence of each cis motif is shown in various colors.

Figure 4. SoSPS protein motifs.

Ten motifs were detected in SoSPS proteins using online MEME tool. (A) Motifs, (B) motif sequence and (C) logo can be seen.

Figure 5. Protein interaction network of SPS.

The PPI of SoSPS proteins was predicted through the orthologous sequences of Sorghum using the STRING database.

Figure 6. Subcellular expression of SoSPS.

SoSPS proteins to be highly active in nucleus, cytoplasm, mitochondria, and chloroplast, while show less or no expression at all in the rest of organelles.

Figure 7. Gene ontology analysis of SoSPS.

All the terms in molecular functions (MF) and biological process (BP) indicate the role of SoSPS in sucrose synthesis.

Figure 8. Collinearity analysis of SoSPS with SbSPS and OsSPS.

The synteny/collinearity of sugarcane is higher with sorghum compared to rice.

Figure 9. Spatialexpression profile of SoSPS gene family in two cultivars.

The expression is shown in three different tissues including leaf (L), top internode (TI) and bottom internode (BI). Overall, CPF252 shows higher expression of SoSPS genes as compared to CPF252.