TCP Transcription Factors in Moso Bamboo (Phyllostachys edulis): Genome-Wide Identification and Expression Analysis

Abstract

TEOSINTE BRANCHED 1, CYCLOIDEA, and PROLIFERATING CELL FACTORS (T), members of a plant-specific gene family, play significant roles during plant growth and development, as well as in response to environmental stress. However, knowledge about this family in moso bamboo (Phyllostachys edulis) is limited. Therefore, in this study, the first genome-wide identification, classification, characterization, and expression pattern analysis of the TCP transcription factor family in moso bamboo was performed. Sixteen TCP members were identified from the moso bamboo genome using a BLASTP algorithm-based method and verified using the Pfam database. Based on a multiple-sequence alignment, the members were divided into two subfamilies, and members of the same family shared highly conserved motif structures. Subcellular localization and transactivation activity analyses of four selected genes revealed that they were nuclear localized and had self-activation activities. Additionally, the expression levels of several PeTCP members were significantly upregulated under abscisic acid, methyl jasmonate, and salicylic acid treatments, indicating that they play crucial plant hormone transduction roles in the processes of plant growth and development, as well as in responses to environmental stresses. Thus, the current study provides previously lacking information on the TCP family in moso bamboo and reveals the potential functions of this gene family in growth and development.

Keywords: TCP transcription factors; expression patterns; moso bamboo (Phyllostachys edulis); subcellular localization; transcription activity.

FIGURE 1

Phylogenetic analysis and statistical analysis of TCP members in different species. (A) Phylogenetic analysis of TCP members from moso bamboo, rice, Brachypodium distachyon, Sorghum, Arabidopsis thaliana, and poplar. Geometric figures of different colors and shapes are used to mark the TCP members from different species. (B) Statistical analysis of TCP members from moso bamboo, rice, Brachypodium distachyon, Sorghum, Arabidopsis thaliana, and poplar.

FIGURE 2

Multiple sequence analysis of TCP domain. Multiple sequence alignment was carried out with Clustal X 2.0.

FIGURE 3

Gene structures of TCPs in moso bamboo. Gene structures were performed using the GSDS online tool. Exons, introns, and untranslated regions (UTRs) are indicated by yellow rectangles, gray lines, and blue rectangles, respectively.

FIGURE 4

Schematic representation of the 10 conserved motifs in PeTCPs. Conserved motifs of the PeTCPs were identified using the online MEME program based on 16 full-length amino acid sequences with the following parameters: maximum number of motifs, 10; maximum width, 100. The lengths and positions of different motifs in the protein sequences are identified by the lengths and positions of the different color blocks.

FIGURE 5

cis-Acting elements related to ABA, Me-JA, and SA in the promoter regions of PeTCPs. A colored block with a number represents the cis-element number of PeTCPs.

FIGURE 6

Scatter plot statistics of Ka and Ks values among grass species. The black dotted line with slope one is used to show Ka/Ks = 1. A circle of different colors exhibits homologous pairs of different types. Pe-Pe: paralogous pairs of PeTCPs; Pe-Os: orthlogous pairs of TCPs between moso bamboo and rice; Pe-Bd: orthlogous pairs of TCPs between moso bamboo and Brachypodium distachyon; Pe-Sb: orthlogous pairs of TCPs between moso bamboo and Sorghum.

FIGURE 7

Expression patterns of TCP genes in different tissues and developmental stages of moso bamboo. Lanes: YL, young leaf; L, mature leaf; S, stem; Sh, shoot; Rh, rhizome; R, root. The mean values and SDs were obtained from three biological and three technical replicates.

FIGURE 8

Subcellular localization of four PeTCPs. The four PeTCP-GFP fusion proteins (PeTCP4-GFP, PeTCP5-GFP, PeTCP10-GFP, and PeTCP11-GFP) and GFP as a control were transiently expressed in N. tabacum leaves and observed under a fluorescence microscope.

FIGURE 9

Transactivational analyses of PeTCP proteins in yeast Y2HGold strain. The positive constructs, negative constructs, and fusion constructs were transformed into yeast Y2HGold strain and successively incubated in SD/-Trp media and SD-His/-Ade/-Trp plate supplemented with X-α-GAL.

FIGURE 10

Expression levels of PeTCPs under ABA, Me-JA, and SA treatment by qRT-PCR. The Y-axis and X-axis indicate the relative expression levels and the time courses of plant hormone treatments, respectively. Error bars, 6 ± SE. Asterisks indicate significant difference compared to the transcription level of control groups, as determined by Student’s t-test (^∗p < 0.05, ^∗∗p < 0.01).