Transcriptome-based network analysis of cell cycle-related genes in response to blue and red light in maize

Abstract

In maize, blue and red light are key environmental factors regulating cell-cycle progression. We used transcriptomics to investigate and compare differential gene expression under the four light conditions: red light, blue light, red converted to blue and blue converted to red. A total of 23 differentially expressed genes were identified. The gene-gene interaction analysis indicated a significant interaction between four unidentified genes, 100191551, pco143873, 100284747 and pco060490, and cell-cycle-related genes. Using multiple sequence alignment analysis and protein structure comparisons, we show here that these four unidentified genes were characterized as ALP1-like, ALP1, cyclin P1-1 and AEBP2, respectively. By constructing a protein-protein interaction network, we inferred that 100191551 and pco143873 are potentially regulated to avoid DNA damage by abiotic stress response factors in the cell cycle. The gene 100284747 regulates the cell cycle in response to phosphate starvation signalling. The gene pco060490 potentially negatively regulates the cell cycle through the mediation of Histone H3 and CYCD6 in response to red light. In conclusion, the cell-cycle-related genes are sensitive to blue and red light, and four novel functional genes may be involved in the cell cycle.

Keywords: Cell cycle; Zea mays L; cell division; light regulation; transcriptome.

Figure 1.

(A) The ratio of the number of DEGs in the total cell-cycle-related genes. (B) The RNA-seq expression of 23 DEGs of cell-cycle-related genes. (C) Comparison of 23 DEGs between six different groups among four light treatments.

Figure 2.

(A) Phylogenetic tree and GO functional annotation of 23 DEGs in cell cycle according to the NCBI and UniProt Database. (B) KEGG annotation of 23 DEGs in cell-cycle metabolic pathway.

Figure 3.

(A) Topological gene interaction network analysis using 23 cell cycle-related DEGs in total R-seq. (B) The RNA-seq expression of 130 DEGs within gene interaction network.

Figure 4.

Homologous comparison of conserved domain (A) and motif (B) of four unidentified proteins compared with Oryza sativa japonica (OsJ), Panicum hallii (Ph), and Sorghum bicolor (Sb). Prediction of secondary (C, D) and tertiary (D) structure of four unidentified proteins: 100191551, pco143873, 100284747 and pco060490.

Figure 5.

(A) Multiple sequence alignment profile of conserved domain of 10019551, pco143873 and 100284747 compared with Sorghum bicolor, Panicum hallii and Oryza sativa japonica. Black represents 100% sequence identity. Pink represents more than 75% while cyan represents less than 75% sequence identity. (B) Multiple sequence alignment profile of total sequence of pco060490 compared with S. bicolor, P. hallii and O. sativa japonica, the darker blue represents the highest identity.

Figure 6.

(A) PPI network of 35 proteins in cell-cycle functional pathway retrieved from STRING 11.0, and clustered by MCL method in inflation parameter 3. (B) The RNA-seq expression of four unidentified and seven directly related genes in the PPI of the cell cycle. (C) Ten DEGs randomly selected for qPCR validation.