The DUF221 domain-containing (DDP) genes identification and expression analysis in tomato under abiotic and phytohormone stress

The domain of unknown function (DUF221 domain-containing) proteins regulates various aspects of plant growth, development, responses to abiotic stresses, and hormone transduction pathways. To understand the role of DDP proteins in tomato, a comprehensive genome-wide analysis was performed in the tomato genome. A total of 12 DDP genes were identified and distributed in 8 chromosomes in the tomato genome. Phylogenetically all SlDDPs were clustered into four clades, subsequently supported by their gene structure and conserved motifs distribution. The SlDDPs contained various cis-acting elements involved in plant responses to abiotic and various phytohormones stresses. The tissue-specific expression profile analysis revealed the constitutive expression of <i>SlDDPs</i> in roots, leaves, and developmental phases of fruit. It was found that <i>SlDDP1, SlDDP3, SlDDP4, SlDDP9, SlDDP10</i>, and <i>SlDDP12</i> exhibited high expression levels in fruits at different development stages. Of these genes, <i>SlDDP12</i> contained ethylene (ERE) responsive elements in their promoter regions, suggesting its role in ethylene-dependent fruit ripening. It was found that a single SlDDP induced by two or more abiotic and phytohormone stresses. These include, <i>SlDDP1, SlDDP2, SlDDP3, SlDDP4, SlDDP7, SlDDP8</i>, and <i>SlDDP10</i> was induced under salt, drought, ABA, and IAA stresses. Moreover, tomato SlDDPs were targeted by multiple miRNA gene families as well. In conclusion, this study predicted that the putative DDP genes might help improve abiotic and phytohormone tolerance in plants, particularly tomato, rice, and other economically important crop plant species.

含未知功能结构域221（DUF221）的蛋白可调控植物生长发育、非生物胁迫响应以及激素信号转导通路的诸多方面。为明确DDP蛋白在番茄中的功能，本研究对番茄基因组开展了全基因组范围的综合分析。研究共鉴定出12个DDP基因，它们分布于番茄基因组的8条染色体上。系统发育分析显示，所有番茄DDP（SlDDP）均可聚类为4个进化支，该结果后续得到了基因结构与保守基序分布特征的验证。SlDDP基因的启动子区域包含多种参与植物非生物胁迫及多种植物激素响应的顺式作用元件（cis-acting elements）。组织特异性表达谱分析结果显示，SlDDP基因在番茄根、叶以及果实发育阶段均组成型表达。研究发现，SlDDP1、SlDDP3、SlDDP4、SlDDP9、SlDDP10及SlDDP12在不同发育阶段的果实中均呈现高表达水平。其中，SlDDP12的启动子区域含有乙烯响应元件（ethylene responsive element, ERE），表明其可能参与依赖乙烯的果实成熟过程。研究发现，单个SlDDP可受两种及以上非生物胁迫与植物激素胁迫的诱导。具体而言，SlDDP1、SlDDP2、SlDDP3、SlDDP4、SlDDP7、SlDDP8及SlDDP10均可在盐胁迫、干旱胁迫、脱落酸（abscisic acid, ABA）及吲哚乙酸（indole-3-acetic acid, IAA）处理下被诱导表达。此外，番茄SlDDP还可被多个miRNA基因家族靶向调控。综上，本研究预测，这些潜在的DDP基因可有助于提升植物（尤其是番茄、水稻及其他经济重要作物）对非生物胁迫与植物激素胁迫的耐受性。