Department of Plant Molecular Systems Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin 446-701, Korea; Graduate School of Biotechnology, Kyung Hee University, Yongin 446-701, Korea.
Department of Plant Molecular Systems Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin 446-701, Korea.
Mol Plant. 2015 Feb;8(2):276-89. doi: 10.1016/j.molp.2014.10.013. Epub 2014 Dec 17.
Genes that are expressed ubiquitously throughout all developmental stages are thought to be necessary for basic biological or cellular functions. Therefore, determining their biological roles is a great challenge. We identified 4034 of these genes in rice after studying the results of Agilent 44K and Affymetrix meta-anatomical expression profiles. Among 105 genes that were characterized by loss-of-function analysis, 79 were classified as members of gene families, the majority of which were predominantly expressed. Using T-DNA insertional mutants, we examined 43 genes and found that loss of expression of six genes caused developing seed- or seedling-defective phenotypes. Of these, three are singletons without similar family members and defective phenotypes are expected from mutations. Phylogenomic analyses integrating genome-wide transcriptome data revealed the functional dominance of three ubiquitously expressed family genes. Among them, we investigated the function of Os03g19890, which is involved in ATP generation within the mitochondria during endosperm development. We also created and evaluated functional networks associated with this gene to understand the molecular mechanism. Our study provides a useful strategy for pheonome analysis of ubiquitously expressed genes in rice.
在所有发育阶段都广泛表达的基因被认为是生物或细胞基本功能所必需的。因此，确定它们的生物学功能是一个巨大的挑战。在研究了 Agilent 44K 和 Affymetrix 元解剖表达谱的结果后，我们在水稻中鉴定了 4034 个这样的基因。在通过功能丧失分析进行特征描述的 105 个基因中，有 79 个被归类为基因家族成员，其中大多数为优势表达。我们使用 T-DNA 插入突变体，对 43 个基因进行了研究，发现有 6 个基因的表达缺失导致种子或幼苗发育缺陷表型。其中，有三个是没有类似家族成员的单基因，预计突变会导致缺陷表型。整合全基因组转录组数据的系统发育分析揭示了三个广泛表达的家族基因的功能主导地位。在这些基因中，我们研究了参与线粒体中胚乳发育过程中 ATP 生成的 Os03g19890 的功能。我们还创建和评估了与该基因相关的功能网络，以了解分子机制。我们的研究为水稻中广泛表达基因的表型分析提供了一种有用的策略。
