Limits...
Additional nitrogen fertilization at heading time of rice down-regulates cellulose synthesis in seed endosperm.

Midorikawa K, Kuroda M, Terauchi K, Hoshi M, Ikenaga S, Ishimaru Y, Abe K, Asakura T - PLoS ONE (2014)

Bottom Line: As a result, it was assessed that genes associated with molecular processes such as photosynthesis, trehalose metabolism, carbon fixation, amino acid metabolism, and cell wall metabolism were differentially expressed.Moreover, additional nitrogen fertilization caused accumulation of storage proteins and up-regulated Cys-poor prolamin mRNA expression.These data suggest that additional nitrogen fertilization at heading time changes the expression of some storage substance-related genes and reduces cellulose levels in endosperm.

View Article: PubMed Central - PubMed

Affiliation: Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan.

ABSTRACT
The balance between carbon and nitrogen is a key determinant of seed storage components, and thus, is of great importance to rice and other seed-based food crops. To clarify the influence of the rhizosphere carbon/nitrogen balance during the maturation stage of several seed components, transcriptome analysis was performed on the seeds from rice plants that were provided additional nitrogen fertilization at heading time. As a result, it was assessed that genes associated with molecular processes such as photosynthesis, trehalose metabolism, carbon fixation, amino acid metabolism, and cell wall metabolism were differentially expressed. Moreover, cellulose and sucrose synthases, which are involved in cellulose synthesis, were down-regulated. Therefore, we compared cellulose content of mature seeds that were treated with additional nitrogen fertilization with those from control plants using calcofluor staining. In these experiments, cellulose content in endosperm from plants receiving additional nitrogen fertilization was less than that in control endosperm. Other starch synthesis-related genes such as starch synthase 1, starch phosphorylase 2, and branching enzyme 3 were also down-regulated, whereas some α-amylase and β-amylase genes were up-regulated. On the other hand, mRNA expression of amino acid biosynthesis-related molecules was up-regulated. Moreover, additional nitrogen fertilization caused accumulation of storage proteins and up-regulated Cys-poor prolamin mRNA expression. These data suggest that additional nitrogen fertilization at heading time changes the expression of some storage substance-related genes and reduces cellulose levels in endosperm.

Show MeSH
Significantly enriched categories were identified using QuickGO.In response to additional fertilization, 1,365 genes were up- or down-regulated; FDR-corrected P-values of categories at the deepest hierarchical level are shaded; *P<0.05.
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4048278&req=5

pone-0098738-g005: Significantly enriched categories were identified using QuickGO.In response to additional fertilization, 1,365 genes were up- or down-regulated; FDR-corrected P-values of categories at the deepest hierarchical level are shaded; *P<0.05.

Mentions: Furthermore, DEGs were identified between the control and N-fertilized samples using the rank products method. DEGs with FDR<0.05 were extracted, revealing 678 significantly up-regulated genes and 687 significantly down-regulated genes due to additional fertilization (Tables S2 and S3). The extracted DEGs were classified into functional categories according to gene ontology (GO) terms. Significantly enriched categories of DEGs (FDR<0.05) are shown in Fig. 5. The hierarchical GO structure indicated a more specific category with a deeper hierarchy. Therefore, most important categories appeared at the lower end of the tree (depth of hierarchy is shown in shadowed areas; Fig. 5). Furthermore, six functional categories were significantly enriched in DEGs. These included “photosynthesis, light harvesting,” “trehalose biosynthetic process,” “carbon fixation,” “cell wall organization,” “cellulose biosynthetic process,” and “cellular amino acid biosynthetic process.” Genes that were predicted to be involved in the synthesis of storage substances were also identified from the list of DEGs (Table 1). The “photosynthesis, light harvesting” category included genes that encode chlorophyll-binding proteins, and Rubisco was identified from the “carbon fixation” category (Table 2). Consistent with these results, the leaf blades of the N-fertilized samples were clearly darker in color than those of the control blades (Fig. S1). Because DNA microarray samples were collected from 15-DAF seeds with green pericarps, the molecules mentioned above are likely localized to the pericarp.


Additional nitrogen fertilization at heading time of rice down-regulates cellulose synthesis in seed endosperm.

Midorikawa K, Kuroda M, Terauchi K, Hoshi M, Ikenaga S, Ishimaru Y, Abe K, Asakura T - PLoS ONE (2014)

Significantly enriched categories were identified using QuickGO.In response to additional fertilization, 1,365 genes were up- or down-regulated; FDR-corrected P-values of categories at the deepest hierarchical level are shaded; *P<0.05.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4048278&req=5

pone-0098738-g005: Significantly enriched categories were identified using QuickGO.In response to additional fertilization, 1,365 genes were up- or down-regulated; FDR-corrected P-values of categories at the deepest hierarchical level are shaded; *P<0.05.
Mentions: Furthermore, DEGs were identified between the control and N-fertilized samples using the rank products method. DEGs with FDR<0.05 were extracted, revealing 678 significantly up-regulated genes and 687 significantly down-regulated genes due to additional fertilization (Tables S2 and S3). The extracted DEGs were classified into functional categories according to gene ontology (GO) terms. Significantly enriched categories of DEGs (FDR<0.05) are shown in Fig. 5. The hierarchical GO structure indicated a more specific category with a deeper hierarchy. Therefore, most important categories appeared at the lower end of the tree (depth of hierarchy is shown in shadowed areas; Fig. 5). Furthermore, six functional categories were significantly enriched in DEGs. These included “photosynthesis, light harvesting,” “trehalose biosynthetic process,” “carbon fixation,” “cell wall organization,” “cellulose biosynthetic process,” and “cellular amino acid biosynthetic process.” Genes that were predicted to be involved in the synthesis of storage substances were also identified from the list of DEGs (Table 1). The “photosynthesis, light harvesting” category included genes that encode chlorophyll-binding proteins, and Rubisco was identified from the “carbon fixation” category (Table 2). Consistent with these results, the leaf blades of the N-fertilized samples were clearly darker in color than those of the control blades (Fig. S1). Because DNA microarray samples were collected from 15-DAF seeds with green pericarps, the molecules mentioned above are likely localized to the pericarp.

Bottom Line: As a result, it was assessed that genes associated with molecular processes such as photosynthesis, trehalose metabolism, carbon fixation, amino acid metabolism, and cell wall metabolism were differentially expressed.Moreover, additional nitrogen fertilization caused accumulation of storage proteins and up-regulated Cys-poor prolamin mRNA expression.These data suggest that additional nitrogen fertilization at heading time changes the expression of some storage substance-related genes and reduces cellulose levels in endosperm.

View Article: PubMed Central - PubMed

Affiliation: Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan.

ABSTRACT
The balance between carbon and nitrogen is a key determinant of seed storage components, and thus, is of great importance to rice and other seed-based food crops. To clarify the influence of the rhizosphere carbon/nitrogen balance during the maturation stage of several seed components, transcriptome analysis was performed on the seeds from rice plants that were provided additional nitrogen fertilization at heading time. As a result, it was assessed that genes associated with molecular processes such as photosynthesis, trehalose metabolism, carbon fixation, amino acid metabolism, and cell wall metabolism were differentially expressed. Moreover, cellulose and sucrose synthases, which are involved in cellulose synthesis, were down-regulated. Therefore, we compared cellulose content of mature seeds that were treated with additional nitrogen fertilization with those from control plants using calcofluor staining. In these experiments, cellulose content in endosperm from plants receiving additional nitrogen fertilization was less than that in control endosperm. Other starch synthesis-related genes such as starch synthase 1, starch phosphorylase 2, and branching enzyme 3 were also down-regulated, whereas some α-amylase and β-amylase genes were up-regulated. On the other hand, mRNA expression of amino acid biosynthesis-related molecules was up-regulated. Moreover, additional nitrogen fertilization caused accumulation of storage proteins and up-regulated Cys-poor prolamin mRNA expression. These data suggest that additional nitrogen fertilization at heading time changes the expression of some storage substance-related genes and reduces cellulose levels in endosperm.

Show MeSH