Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, PR China.
DNA Res. 2011 Oct;18(5):363-77. doi: 10.1093/dnares/dsr024. Epub 2011 Jul 27.
Autophagy is an intracellular degradation process for recycling macromolecules and organelles. It plays important roles in plant development and in response to nutritional demand, stress, and senescence. Organisms from yeast to plants contain many autophagy-associated genes (ATG). In this study, we found that a total of 33 ATG homologues exist in the rice [Oryza sativa L. (Os)] genome, which were classified into 13 ATG subfamilies. Six of them are alternatively spliced genes. Evolutional analysis showed that expansion of 10 OsATG homologues occurred via segmental duplication events and that the occurrence of these OsATG homologues within each subfamily was asynchronous. The Ka/Ks ratios suggested purifying selection for four duplicated OsATG homologues and positive selection for two. Calculating the dates of the duplication events indicated that all duplication events might have occurred after the origin of the grasses, from 21.43 to 66.77 million years ago. Semi-quantitative RT-PCR analysis and mining the digital expression database of rice showed that all 33 OsATG homologues could be detected in at least one cell type of the various tissues under normal or stress growth conditions, but their expression was tightly regulated. The 10 duplicated genes showed expression divergence. The expression of most OsATG homologues was regulated by at least one treatment, including hormones, abiotic and biotic stresses, and nutrient limitation. The identification of OsATG homologues showing constitutive expression or responses to environmental stimuli provides new insights for in-depth characterization of selected genes of importance in rice.
自噬是一种细胞内降解过程，用于回收大分子和细胞器。它在植物发育以及对营养需求、胁迫和衰老的响应中发挥重要作用。从酵母到植物的生物体都含有许多与自噬相关的基因（ATG）。在这项研究中，我们发现水稻[Oryza sativa L.（Os）]基因组中共有 33 个 ATG 同源物，它们分为 13 个 ATG 亚家族。其中有 6 个是选择性剪接基因。进化分析表明，10 个 OsATG 同源物的扩张是通过片段复制事件发生的，并且每个亚家族内这些 OsATG 同源物的发生是不同步的。Ka/Ks 比值表明，4 个复制的 OsATG 同源物受到纯化选择，而 2 个受到正选择。计算复制事件的日期表明，所有复制事件可能都发生在草类起源之后，时间在 2143 到 6677 百万年前。半定量 RT-PCR 分析和挖掘水稻数字表达数据库表明，在正常或应激生长条件下，各种组织的至少一种细胞类型中都可以检测到所有 33 个 OsATG 同源物，但它们的表达受到严格调控。10 个复制基因表现出表达差异。大多数 OsATG 同源物的表达受到至少一种处理的调节，包括激素、非生物和生物胁迫以及营养限制。鉴定出具有组成型表达或对环境刺激有反应的 OsATG 同源物，为深入研究水稻中重要基因提供了新的见解。
