The MYB-related gene plays key roles as transcriptional regulators,circadian clock-associated repressors, and telomeric repeat-binding proteins in diverse biological processes
MYB proteins are characterized by a conserved DNA-binding domain and constitute one of the largest families of transcription factors (TFs) in plants, which are classified into four major groups according to the number of adjacent repeats in the DNA-binding domain. All four groups are found in plants. The most common is the 2R-MYB group. The second group comprises a heterogeneous collection of R3- or 1R-MYB type proteins, hereafter referred to as MYB-related proteins, which usually contain a single MYB repeat. The third and fourth groups are composed of 3R-MYB and 4R-MYB type proteins, respectively. These latter groups consist of only 1–5 members.
The first plant MYB-encoding gene, C1 (2R-MYB), was isolated from maize (Zea mays). Accordingly, research on MYB genes has mainly focused on the 2R-MYB gene family because of its large size. In the last two decades, a vast number of plant 2R-MYB genes have been shown to play important roles in many plant-specific processes. The first plant MYB-related gene (MybSt1) was isolated from potato. The numerous MYB-related genes subsequently identified play key roles as transcriptional regulators, circadian clock-associated repressors,and telomeric repeat-binding proteins in diverse biological processes. To date, genome-wide analyses of 2R-MYB proteins have been conducted in numerous plant species based on sequenced genomes1, However, comprehensive analyses of MYB-related proteins in major land plants are still lacking. Accordingly, the evolutionary relationships between plant MYB-related proteins remain unknown, necessitating a detailed survey and classification of disparate evolutionary groups.
To understand the temporal and spatial expression patterns of MYB-related genes, we compared their expression patterns during maize and soybean development.
Microarray data of 60 different tissues/developmental conditions of maize were used (Fig. 1). Few genes were constitutively expressed in all organs and developmental stages. CCA-like/R-R genes were expressed in most organs examined, with the exception of seeds. However, six genes in a CCA1-like/R-R subgroup clade (ZmMYBR02, ZmMYBR11, ZmMYBR34, ZmMYBR42, ZmMYBR65, and ZmMYBR67) showed higher expression in seeds than in other organs, which indicated that they may play important roles in seed development (Fig. 1). Similar to CCA1-like/R-R proteins, the I-box-like genes were also expressed abundantly in many maize organs. This may indicate that these two subgroups predominantly contribute to maize development. The expression of I-box-like genes and most of the CCA1-like/R-R genes significantly decreased during seed development, further implying roles as negative regulators in seed development. A CPC-like gene, ZmMYBR20, was highly expressed in leaf tissues, which suggested that it may function in leaf development, or it may be restricted by 2R-MYB genes in other developmental stages .
The TRF-like subgroup included only two maize genes, which showed relatively high expression in seeds. Although no TRF-like genes have yet been functionally characterized in plants, their preferential expression in maize seed tissues implies their possible roles in seed development. The TBP-like subgroup, consisting of five clades, contained 14 maize genes. Although members of this subgroup displayed relatively low expression in all examined organs, TBP-like genes have wider expression in maize . Furthermore, closely related genes generally showed highly similar expression patterns, indicating that they may share similar or overlapping functions.
We next analysed the expression profiles of soybean MYB-related genes.The majority of the 127 soybean MYB-related genes showed wide expressions in the examined tissues. However, 22 soybean genes were not expressed in this dataset, suggesting that they might be pseudogenes. In most of the cases, the expression patterns of MYB-related genes in maize and soybean were very similar . The expression patterns of soybean genes divided into two main groups. Most of the CCA1-like/R-R genes showed prominent responses in the early stage of soybean development, while some TBP-like genes were expressed at higher levels in leaves and seeds. There were also minor differences in the expression patterns of I-box-like and CPC-like genes between maize and soybean. Some soybean I-box-like and CPC-like genes showed higher expression in more tissues, suggesting that these genes may play wider roles in soybean. The high similarity of MYB-related gene expression in maize and soybean indicates functional conservation of this gene family in plants.
To understand the evolutionary history of plant MYB-related genes, we identified MYB-related proteins at the genome-wide level and performed structural and evolutionary analyses across distantly related plant evolutionary lineages, including eudicots, monocots, a gymnosperm, a bryophyte, five chlorophyte species, and a rhodophyte. Subsequently, we assessed the origins, patterns of differentiation, and expansion of different phylogenetic subgroups of this gene family. In addition, we analysed the expressions of MYB-related genes in different tissues and developmental stages and under stress treatments.
To analyse the selective pressures acting during the expansion of plant MYB-related genes, we investigated the influences of selective constraints on the MYB domains. By globally fitting an evolutionary model, we first calculated the dN/dS ratios for each subgroup. The dN/dS values were substantially <1 in all subgroups, providing a crude indication that the strong purifying selection has been maintained across land plants . At the individual codon level, most of the residues were under significant negative selection (P < 0.05).
Because the CCA1-like/R-R and TBP-like subgroups subdivided into several clades (Fig. 2), the preceding method merely estimated the dN/dS ratio across each subgroup, without considering variations among clades in the large subgroups. Therefore, we estimated the dN/dS ratios for the clades of the CCA1-like/R-R and TBP-like subgroups .
In general, the dN/dS values of individual clades were lower than that of the subgroups. However, the dN/dS values of some individual clades were higher than that of the subgroups, and the number of residues under significant negative selection was reduced (P < 0.05). However, no clades showed dN/dS values >1, suggesting that different clades were subjected to different strengths of purifying selection. For example, in TBP-like subgroup clades, the dN/dS values ranged from 0.06 to 0.32, while in CCA1-like/R-R subgroup clades, the dN/dS values were <0.11. Thus, our dN/dS analysis suggests that selective constraints have remained stable throughout the evolution of MYB-related genes in land plants.
Labs working on this gene
1. Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region of Ministry of Agriculture, Maize Research Institute of Sichuan Agricultural University, Chengdu, Sichuan 611130, China
2. Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
3. Department of Plant and Environmental Sciences, Norwegian University of Life Sciences, PO Box 5003, Ås N-1432, Norway
4. Department of Food and Bioproduct Sciences, University of Saskatchewan, Saskatoon, SK, Canada, S7N 5A8
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