Transcriptome sequencing of Saccharina japonica sporophytes during whole developmental periods reveals regulatory networks underlying alginate and mannitol biosynthesis

Abstract

Background: Alginate is an important cell wall component and mannitol is a soluble storage carbon substance in the brown seaweed Saccharina japonica. Their contents vary with kelp developmental periods and harvesting time. Alginate and mannitol regulatory networks and molecular mechanisms are largely unknown.

Results: With WGCNA and trend analysis of 20,940 known genes and 4264 new genes produced from transcriptome sequencing of 30 kelp samples from different stages and tissues, we deduced that ribosomal proteins, light harvesting complex proteins and "imm upregulated 3" gene family are closely associated with the meristematic growth and kelp maturity. Moreover, 134 and 6 genes directly involved in the alginate and mannitol metabolism were identified, respectively. Mannose-6-phosphate isomerase (MPI2), phosphomannomutase (PMM1), GDP-mannose 6-dehydrogenase (GMD3) and mannuronate C5-epimerase (MC5E70 and MC5E122) are closely related with the high content of alginate in the distal blade. Mannitol accumulation in the basal blade might be ascribed to high expression of mannitol-1-phosphate dehydrogenase (M1PDH1) and mannitol-1-phosphatase (M1Pase) (in biosynthesis direction) and low expression of mannitol-2-dehydrogenase (M2DH) and Fructokinase (FK) (in degradation direction). Oxidative phosphorylation and photosynthesis provide ATP and NADH for mannitol metabolism whereas glycosylated cycle and tricarboxylic acid (TCA) cycle produce GTP for alginate biosynthesis. RNA/protein synthesis and transportation might affect alginate complex polymerization and secretion processes. Cryptochrome (CRY-DASH), xanthophyll cycle, photosynthesis and carbon fixation influence the production of intermediate metabolite of fructose-6-phosphate, contributing to high content of mannitol in the basal blade.

Conclusions: The network of co-responsive DNA synthesis, repair and proteolysis are presumed to be involved in alginate polymerization and secretion, while upstream light-responsive reactions are important for mannitol accumulation in meristem of kelp. Our transcriptome analysis provides new insights into the transcriptional regulatory networks underlying the biosynthesis of alginate and mannitol during S. japonica developments.

Keywords: Alginate; Development; Growth; Mannitol; Regulatory networks; Saccharina japonica; Transcriptome.

Fig. 1

Contents of alginate and mannitol detected in S. japonica samples collected from different developmental stages and tissue parts. a Content variations of alginate from March to June. b Content variations of mannitol from March to June

Fig. 2

Transcriptional patterns of the genes involved in alginate and mannitol metabolism. a Expression levels of alginate biosynthetic genes. b Expression levels of mannitol metabolic genes. The order of each row is: JaB, MhB, ApB, MyB, JuB, ApB, Ap1, Ap2, ApD. MPI1: GENE_021848; MPI2: GENE_013980; MPI3: GENE_013986; PMM1: GENE_007314; PMM2: GENE_006655; GMD1: GENE_022030; GMD2: GENE_008524; GMD3: GENE_022063; GT2: GENE_006305; MC5E1: GENE_007233; MC5E70: GENE_007019; MC5E122: XLOC_006798; M1PDH1: GENE_011959; M1PDH2: GENE_003979; M1Pase: XLOC_010181; M2DH1: GENE_006978; M2DH2: GENE_006979; FK: GENE_018623 MPI Mannose-6-phosphate isomerase, PMM Phosphomannomutase, GMD GDP-mannose 6-dehydrogenase, GT2 Beta-1,3-glucan synthases (family GT2), MC5E Mannuronate C5-epimerase, M1PDH Mannitol-1-phosphate dehydrogenase, M1Pase Mannitol-1-phosphatase, M2DH Mannitol-2-dehydrogenase, FK Fructokinase

Fig. 3

Module-trait correlations and gene expression patterns of the top 2 modules correlated with alginate and mannitol contents. a Module-trait relationships and corresponding p values. The color scale on the right shows correlations from − 1 (green) to 1 (red). Panels on the left represent alginate and mannitol content as traits. Other panels show the expression variations of each biosynthetic gene as a trait. b Expression patterns of each selected module. “Brown4” and “Darkgreen” were highly correlated with alginate content, whereas “Black” and “Darkslateblue” were highly correlated with mannitol content

Fig. 4

Expression levels of the genes involved in alginate and mannitol metabolism by RNA-Seq and real-time qPCR validation. The histogram shows the RT-qPCR results and the curve indicates the expression levels from RNA-Seq results

Fig. 5

Cytoscape representation of co-expressed genes with alginate and mannitol metabolisms selected by Pearson correlation coefficient ≥ 0.6 or ≤ − 0.6. a Protein interaction network for alginate biosynthesis. Genes involved in alginate pathway (red), DNA and protein regulation pathways (green), energy-producing metabolisms (purple) and transcription factor (blue) were indicated. b Protein interaction network for mannitol metabolism. Genes involved in mannitol biosynthesis (red), mannitol degradation (yellow), light-responsive reactions (green), energy-producing metabolisms (purple), carbon fixation (brown) and transcription factor (blue) were indicated. Full names for all genes were listed in Abbreviations

Fig. 6

Schematic representation of putative transcriptional regulatory model for alginate and mannitol metabolism in S. japonica. Pathways correlated with mannitol metabolism are colored in light orange, with involvement of photosynthesis, oxidative phosphorylation, carbon fixation, glycolysis and gluconeogenesis. Pathways correlated with alginate biosynthesis are colored in cyan, containing glyoxylate cycle, TCA cycle, gluconeogenesis, and RNA/protein synthesis and transportation. The predicted transcription factors are colored in lilac