Brassinosteroid biosynthesis and signaling: Conserved and diversified functions of core genes across multiple plant species

Abstract

Brassinosteroids (BRs) are important regulators that control myriad aspects of plant growth and development, including biotic and abiotic stress responses, such that modulating BR homeostasis and signaling presents abundant opportunities for plant breeding and crop improvement. Enzymes and other proteins involved in the biosynthesis and signaling of BRs are well understood from molecular genetics and phenotypic analysis in Arabidopsis thaliana; however, knowledge of the molecular functions of these genes in other plant species, especially cereal crop plants, is minimal. In this manuscript, we comprehensively review functional studies of BR genes in Arabidopsis, maize, rice, Setaria, Brachypodium, and soybean to identify conserved and diversified functions across plant species and to highlight cases for which additional research is in order. We performed phylogenetic analysis of gene families involved in the biosynthesis and signaling of BRs and re-analyzed publicly available transcriptomic data. Gene trees coupled with expression data provide a valuable guide to supplement future research on BRs in these important crop species, enabling researchers to identify gene-editing targets for BR-related functional studies.

Keywords: Arabidopsis; Brachypodium; Setaria; brassinosteroids; maize; rice; soybean.

Figure 1

Phylogeny and transcript abundance across different tissues of SMT, SMO1, and SMO2 phytosterol biosynthetic enzyme families. Maximum-approximate-likelihood phylogenetic trees of (A) SMT, (B) SMO1, and (C) SMO2 amino acid sequences from maize (Zm), Setaria (Sevir), rice (Os), Arabidopsis (AT), soybean (Glyma), Brachypodium (Bradi), and the outgroup Physcomitrella (Pp) are shown. The relative transcript per million (TPM) values from re-analyzed publicly available datasets of different developmental tissues are represented as a heatmap next to each gene within the family. Yellow indicates the lowest individual transcript abundance in each tissue, and blue indicates the highest abundance in a given tissue. To compare transcript abundance across genes and species within the family, the average FPKM was determined across all tissues analyzed and is presented in the average-FPKM column (left) with the same color distribution described previously. See Supplemental Tables 1–6 for a description of tissue types.

Figure 2

Phylogeny and transcript abundance across different tissues of CPI, CYP51G1, HYD1, HYD2, and 3βHSD/D phytosterol biosynthetic enzyme families. Maximum-approximate-likelihood phylogenetic trees of (A) CPI, (B) CYP51G1, (C) HYD1, (D) HYD2, and (E) 3βHSD/D amino acid sequences from maize (Zm), Setaria (Sevir), rice (Os), Arabidopsis (AT), soybean (Glyma), Brachypodium (Bradi), and the outgroup Physcomitrella (Pp) are shown. The relative transcript per million (TPM) values from re-analyzed publicly available datasets of different developmental tissues are represented as a heatmap next to each gene within the family. Yellow indicates the lowest individual transcript abundance in each tissue, and blue indicates the highest abundance in a given tissue. To compare transcript abundance across genes and species within the family, the average FPKM was determined across all tissues analyzed and is presented in the average-FPKM column (left) with the same color distribution described previously. See Supplemental Tables 1–6 for a description of tissue types.

Figure 3

Phylogeny and transcript abundance across different tissues of DWF7, DWF5, DWF1, and DET2 phytosterol and brassinosteroid biosynthetic enzyme families. Maximum-approximate-likelihood phylogenetic trees of (A) DWF7, (B) DWF5, (C) DWF1, and (D) DET2 amino acid sequences from maize (Zm), Setaria (Sevir), rice (Os), Arabidopsis (AT), soybean (Glyma), Brachypodium (Bradi), and the outgroup Physcomitrella (Pp) are shown. The relative transcript per million (TPM) values from re-analyzed publicly available datasets of different developmental tissues are represented as a heatmap next to each gene within the family. Yellow indicates the lowest individual transcript abundance in each tissue, and the blue indicates the highest abundance in a given tissue. To compare transcript abundance across genes and species within the family, the average FPKM was determined across all tissues analyzed and is presented in the average-FPKM column (left) with the same color distribution described previously. See Supplemental Tables 1–6 for a description of tissue types. The expression boxes for ZmNA1 were left blank because there was not a gene annotation in the current maize genome version and the previous gene annotation version was therefore used for phylogenetic analysis.

Figure 4

Phylogeny and transcript abundance across different tissues of the CYP450 enzyme family involved in multiple steps of brassinosteroid biosynthesis. Maximum-approximate-likelihood phylogenetic tree of brassinosteroid biosynthetic CYP450 amino acid sequences from maize (Zm), Setaria (Sevir), rice (Os), Arabidopsis (AT), soybean (Glyma), Brachypodium (Bradi), and the outgroup Physcomitrella (Pp). The relative transcript per million (TPM) values from re-analyzed publicly available datasets of different developmental tissues are represented as a heatmap next to each gene within the family. Yellow indicates the lowest individual transcript abundance in each tissue, and blue indicates the highest abundance in a given tissue. To compare transcript abundance across genes and species within the family, the average FPKM was determined across all tissues analyzed and is presented in the average-FPKM column (left) with the same color distribution described previously. See Supplemental Tables 1–6 for a description of tissue types.

Figure 5

Phylogeny and transcript abundance across different tissues of BRI1 and BAK1 families involved in brassinosteroid perception. Maximum-approximate-likelihood phylogenetic trees of (A) BRI1 and (B) BAK amino acid sequences from maize (Zm), Setaria (Sevir), rice (Os), Arabidopsis (AT), soybean (Glyma), Brachypodium (Bradi), and the outgroup Physcomitrella (Pp) are shown. The relative transcript per million (TPM) values from re-analyzed publicly available datasets of different developmental tissues are represented as a heatmap next to each gene within the family. Yellow indicates the lowest individual transcript abundance in each tissue, and blue indicates the highest abundance in a given tissue. To compare transcript abundance across genes and species within the family, the average FPKM was determined across all tissues analyzed and is presented in the average-FPKM column (left) with the same color distribution described previously. See Supplemental Tables 1–6 for a description of tissue types.

Figure 6

Phylogeny and transcript abundance across different tissues of the BIN2/GSK family involved in brassinosteroid signal transduction. Maximum-approximate-likelihood phylogenetic tree of BIN2/GSK amino acid sequences from maize (Zm), Setaria (Sevir), rice (Os), Arabidopsis (AT), soybean (Glyma), Brachypodium (Bradi), and the outgroup Physcomitrella (Pp). The relative transcript per million (TPM) values from re-analyzed publicly available datasets of different developmental tissues are represented as a heatmap next to each gene within the family. Yellow color indicates the lowest individual transcript abundance in each tissue, and blue indicates the highest abundance in a given tissue. To compare transcript abundance across genes and species within the family, the average FPKM was determined across all tissues analyzed and is presented in the average-FPKM column (left) with the same color distribution described previously. See Supplemental Tables 1–6 for a description of tissue types.

Figure 7

Phylogeny and transcript abundance across different tissues of the BES1/BZR1 brassinosteroid transcription factor family. Maximum-approximate-likelihood phylogenetic tree of BES1/BZR1 amino acid sequences from maize (Zm), Setaria (Sevir), rice (Os), Arabidopsis (AT), soybean (Glyma), Brachypodium (Bradi), and the outgroup Physcomitrella (Pp). The relative transcript per million (TPM) values from re-analyzed publicly available datasets of different developmental tissues are represented as a heatmap next to each gene within the family. Yellow indicates the lowest individual transcript abundance in each tissue, and blue indicates the highest abundance in a given tissue. To compare transcript abundance across genes and species within the family, the average FPKM was determined across all tissues analyzed and is presented in the average-FPKM column (left) with the same color distribution described previously. See Supplemental Tables 1–6 for a description of tissue types.