Genome-wide analysis of VQ motif-containing proteins in Moso bamboo (Phyllostachys edulis)

Abstract

29 Moso bamboo VQ proteins were genome-wide identified for the first time, and bioinformatics analysis was performed to investigate phylogenetic relationships and evolutionary divergence. The qRT-PCR data show that PeVQ genes response to different stress treatments. Accumulating evidence suggests that VQ motif-containing proteins in rice (Oryza sativa), Arabidopsis (Arabidopsis thaliana), and maize (Zea mays) play fundamental roles in response to various biotic and abiotic stresses. However, little is known about the functions of VQ family proteins in Moso bamboo (Phyllostachys edulis). In this study, we performed a genome-wide bioinformatic analysis and expression profiling of PeVQ genes. A total of 29 VQ genes was identified and divided into seven subgroups (I-VII) based on phylogenetic analysis. Gene structure and conserved motif analysis revealed that 25 of 29 VQ genes contained no introns. Multiple sequence alignment showed that Moso bamboo VQ motif-containing proteins contained five variations of the conserved motif. The time of duplication and divergence of Moso bamboo from rice and maize was calculated using K analysis. A heat map was generated using microarray data from 29 Moso bamboo VQ genes suggesting that these genes were expressed in different tissues or developmental stages. Quantitative real-time PCR (qRT-PCR) and promoter analysis indicated that PeVQ genes were differentially regulated following treatment with polyethylene glycol, abscisic acid and salicylic acid. Our results provide a solid foundation for further research of the specific functions of VQ motif-containing proteins in Moso bamboo.

Genome-Wide Identification of the VQ Protein Gene Family of Tobacco (Nicotiana tabacum L.) and Analysis of Its Expression in Response to Phytohormones and Abiotic and Biotic Stresses

“…Structural predictions indicated that most NtVQ genes (83.1%) in tobacco lack introns (Supplementary Figure S1), consistent with VQ protein gene structure in other plants (e.g., 88.2%, 90%, and 92.3% of the VQ protein genes in Arabidopsis [11], Chinese Cabbage [14], and tomato [24], respectively, lack introns). It was reported that a large number of introns might be lost in VQ genes during evolution [18]. The distribution of NtVQ genes among clades based on protein sequence conservation appears to follow the pattern observed in other plant species as well.…”

“…Analysis of the phylogenic tree of tobacco VQ proteins has shown that the clades are similar to those described for Arabidopsis [11] and tomato [24]. Tobacco NtVQ protein has an average of 223.5 amino acids, which is similar to the known VQ protein in many plants, where most of the VQ genes encode fewer than 300 amino acids, including Arabidopsis [11], rice [12], maize [16], Moso bamboo [18], apple [20], poplar [15], Chinese Cabbage [14], soybean [22], tomato [24], tea [23], and so on. On the contrary, four genes (NtVQ11, NtVQ12, NtVQ20, and NtVQ23) encode protein of more than or equal to 400 amino acids.…”

“…There are six variations of the conserved VQ motif among the 59 NtVQ proteins: FxxxVQxLTG (33/59), FxxxVQxFTG (10/59), FxxxVQxVTG (4/59), FxxxVQxYTG (3/59), FxxxVQxLTA (6/59), FxxxVQxLTV (2/59). In previous studies, it was known that there are six types of motifs in Arabidopsis (LTG, FTG, VTG, YTG, LTS, and LTD) [11], six types in maize (LTG, FTG, VTG, ITG, ATG, and LTA) [16], four types in rice (LTG, FTG, VTG, and ITG) [13], six types in Chinese cabbage (LTG, FTG, VTG, YTG, LTV, and LTS) [14], five types in Moso bamboo (LTG, FTG, VTG, ITG, and LTA) [18], five types in soybean (LTG, FTG, VTG, LTS, and LTR) [22], four types in apple(LTG, FTG, VTG, and LTC) [20], three types in grapevine (LTG, FTG, and VTG) [13] and seven in tomato (LTG, FTG, VTG, LTS, LTA, YTG, and HTG) [24]. Comparing the different variations of conserved VQ domain in the above plant species, we can see LTG, FTG, and VTG are the three most common ones for the VQ domain in plants.…”

“…Among the major transcriptional regulators found in plants are the VQ motif-containing proteins (designated as VQ proteins) that work independently or in combination with other TFs to regulate diverse plant growth and developmental processes and responses to biotic and abiotic stresses [10]. The VQ proteins, identified by the presence of a conserved FxxhVQxhTG amino acid motif, have been found in many plant species including both monocotyledons and dicotyledons [11][12][13][14][15][16][17][18][19][20][21][22][23][24][25]. These proteins are further classified into several types based on the terminal three amino acids in the conserved motifs.…”

Genome-Wide Analysis of the NAC Domain Transcription Factor Gene Family in Theobroma cacao

“…Bioinformatic analysis of TcNAC gene sequences and the calculation of coding sequence (CDS) length, molecular weight (MW), isoelectric point (pI), and open reading frame (ORF) lengths was performed using the Compute pI/MW tool at the Expert Protein Analysis System (ExPAsy) site (http://au.expas y.org/tools/pi_tool.html). We used the GSDS (Gene Structure Display Server) tool to analyze the exon/intron organization for individual NAC genes of Theobroma cacao [41,42]. MEME (v.12.0; http://meme-suite.org/tools/meme) was used to analyze the motifs of TcNAC proteins with the following parameters: minimum width of motifs, six; maximum width of motifs, 50; and number of motifs, 10.…”