Genome-wide identification of the expansin gene family in tobacco (Nicotiana tabacum)

Abstract

Expansins are pH-dependent cell wall loosening proteins which form a large family in plants. They have been shown to be involved in various developmental processes and been implicated in enabling plants' ability to absorb nutrients from the soil as well as conferring biotic and abiotic stress resistances. It is therefore clear that they can be potential targets in genetic engineering for crop improvement. Tobacco (Nicotiana tabacum) is a major crop species as well as a model organism. Considering that only a few tobacco expansins have been studied, a genome-wide analysis of the tobacco expansin gene family is necessary. In this study, we identified 52 expansins in tobacco, which were classified into four subfamilies: 36 NtEXPAs, 6 NtEXPBs, 3 NtEXLAs and 7 NtEXLBs. Compared to other species, the NtEXLB subfamily size was relatively larger. Phylogenetic analysis showed that the 52 tobacco expansins were divided into 13 subgroups. Gene structure analysis revealed that genes within subfamilies/subgroups exhibited similar characteristics such as gene structure and protein motif arrangement. Whole-genome duplication and tandem duplication events may have played important roles in the expanding of tobacco expansins. Cis-Acting element analysis revealed that each expansin gene was regulated or several expansin genes were co-regulated by both internal and environmental factors. 35 of these genes were identified as being expressed according to a microarray analysis. In contrast to most NtEXPAs which had higher expression levels in young organs, NtEXLAs and NtEXLBs were preferentially expressed in mature or senescent tissues, suggesting that they might play different roles in different organs or at different developmental stages. As the first step towards genome-wide analysis of the tobacco expansin gene family, our work provides solid background information related to structure, evolution and expression as well as regulatory cis-acting elements of the tobacco expansins. This information will provide a strong foundation for cloning and functional exploration of expansin genes in tobacco.

In silicoanalysis of 3 expansin gene promoters reveals 2 hubs controlling light and cytokinins response during bud outgrowth

“…Many common light-responsive elements were identified between the 3 promoters as previously observed in tobacco expansin promoters. 22 The high occurrence of these motifs (40/33/26) is consistent with the high transcript levels of the 3 genes in response to light treatment ( Fig. 2A).…”

“…The opposite situation was reported for tobacco and strawberry expansin promoters. 22,24 Additionally, the promoter regions of expression genes in response to CK treatment in darkness (Fig. 2B).…”

Genome-wide analysis of expansin superfamily in wild Arachis discloses a stress-responsive expansin-like B gene

“…The majority of the EXPA members (82%) had three exons, while EXLB genes presented the largest number of exons, ranging from four to six, similar to Malus x Domestica and G. max (Zhang et al 2014b; Zhu et al 2014). The EXLA members had the same gene structure (4-exon/3-intron) in both Arachis species which differs from the usual 5-exon/4-intron EXLA structure of other plants (Ding et al 2016; Krishnamurthy et al 2014; Sampedro et al 2005). …”

Decrease in cell size and cell wall components under ectopic expression of the CaRLK1 gene

“…Cell elongation is controlled by cell extensibility, which is regulated by cell wall-loosening proteins and enzymes, including expansin and xyloglucan endotransglycosylase (XET) [31]. It was reported that EXPA4 was highly expressed in germinating seeds and that EXPA3 was highly expressed in young roots and germinating seeds in tobacco [32].…”