Ding Anming, Marowa Prince, Kong Yingzhen
Key Laboratory for Tobacco Gene Resources, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, Shandong, People's Republic of China.
Mol Genet Genomics. 2016 Oct;291(5):1891-907. doi: 10.1007/s00438-016-1226-8. Epub 2016 Jun 21.
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.
扩展蛋白是一类依赖pH值的细胞壁松弛蛋白，在植物中构成一个大家族。研究表明，它们参与了各种发育过程，有助于植物从土壤中吸收养分，并赋予植物抗生物和非生物胁迫的能力。因此，它们显然可以成为作物改良基因工程中的潜在靶点。烟草（Nicotiana tabacum）是一种主要的作物品种，也是一种模式生物。鉴于目前仅对少数烟草扩展蛋白进行了研究，有必要对烟草扩展蛋白基因家族进行全基因组分析。在本研究中，我们在烟草中鉴定出52个扩展蛋白，它们被分为四个亚家族：36个NtEXPAs、6个NtEXPBs、3个NtEXLAs和7个NtEXLBs。与其他物种相比，NtEXLB亚家族的规模相对较大。系统发育分析表明，这52个烟草扩展蛋白被分为13个亚组。基因结构分析显示，亚家族/亚组内的基因表现出相似的特征，如基因结构和蛋白质基序排列。全基因组复制和串联复制事件可能在烟草扩展蛋白的扩增中发挥了重要作用。顺式作用元件分析表明，每个扩展蛋白基因或几个扩展蛋白基因受到内部和环境因素的共同调控。根据微阵列分析，其中35个基因被鉴定为有表达。与大多数在幼嫩器官中表达水平较高的NtEXPAs不同，NtEXLAs和NtEXLBs在成熟或衰老组织中优先表达，这表明它们可能在不同器官或不同发育阶段发挥不同的作用。作为烟草扩展蛋白基因家族全基因组分析的第一步，我们的工作提供了与烟草扩展蛋白的结构、进化、表达以及调控顺式作用元件相关的坚实背景信息。这些信息将为烟草扩展蛋白基因的克隆和功能探索提供有力的基础。
