Genome-wide analysis of the plant-specific VQ motif-containing proteins in tomato (Solanum lycopersicum) and characterization of SlVQ6 in thermotolerance

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

“…Phylogenetic analysis of the NtVQ proteins based upon their nucleotide sequence, gene structure (exon-intron organization) and organization of conserved protein domains showed that the tobacco NtVQ proteins cluster into eight main groups ( Figure 1A). When compared with the VQ proteins across species, the NtVQ clustering pattern and clades in our analysis ( Figure 1B) exhibited high similarities to those previously reported in Arabidopsis and tomato with only minor differences [11,24]. For example, the Arabidopsis AtVQ2 alone was clustered in one branch, while in our analysis it was clustered with AtVQ3.…”

“…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.…”

“…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.…”