Gene expression profile of grass shrimp Palaemonetes pugio exposed to chronic hypoxia
Gene expression profile of grass shrimp Palaemonetes pugio exposed to chronic hypoxia
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DOI：
10.1016/j.cbd.2009.03.004
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发表时间：
2009-09-01
影响因子：
3
通讯作者：
Brouwer, Marius
中科院分区：
文献类型：
--
作者：
Li, Tiandao;Brouwer, Marius
DNA微阵列技术已成为研究环境胁迫和毒物引起的基因表达变化和遗传途径的重要工具。在该研究中，从先前研究中产生的表达序列标签的六个文库设计并构建cDNA微阵列（Li，T.，Brouwer，M.，2009.暴露于环境胁迫的草虾Palaemonetes pugio表达序列标签的生物信息学分析。Comp. Biochem. Physiol. Part D Genomics Proteomics. doi：10.1016/cbd.2009.03.001）。采用基因芯片技术检测慢性缺氧（溶解氧1.5 mg/L）6 h（H6）、12 h（H12）、24 h（H24）、48 h（H48）、120 h（H120）和240 h（H240）时缺氧组与常氧组基因表达的差异。对缺氧的最初反应是29个基因的上调。仅6 h后，观察到47个基因的显著下调。24 h时有19个基因表达上调，无基因表达下调。在第2天和第5天，分别有34和22个基因上调，到第10天，有24个基因下调，6个基因上调。聚类分析证实了两种反应模式，一种是由上调为主的簇组成，包括H6，H24和H120，另一种是由下调为主的簇组成，包括H12，H48和H240。差异表达基因的维恩图显示，没有基因上调或下调共同的所有六组。24、48和120 h后血蓝蛋白转录上调，12 h后下调。一些基因在特定的时间点上是独特的。磷酸烯醇式丙酮酸羧激酶在H120和H240组中上调。细胞色素c氧化酶亚基I和C型凝集素在H12中独特地上调，而卵黄蛋白原和trachealess在H48中独特地下调。来自R的GOstats和org.Dm.eg.db包用于将GO术语分配给显著表达的基因。共有291，129和219个基因被分配到生物过程，细胞成分和分子功能，分别。最丰富的基因组与运输，代谢过程，防御反应和蛋白水解。使用KEGG数据库中的果蝇代谢途径分析途径。氧化磷酸化/柠檬酸循环和核糖体是慢性低氧暴露最丰富的类别。在微阵列上显示差异表达的19个选定基因中，17个在微阵列和qPCR中显示出相似的上调或下调模式。因此，定制的cDNA微阵列是一个有效的和有用的工具，研究基因表达的变化，在慢性缺氧暴露的草虾。一些基因，如编码血蓝蛋白，ATP合成酶，磷酸烯醇式丙酮酸羧激酶，卵黄蛋白原，trachealess，细胞色素c氧化酶亚基1，溶酶体巯基还原酶和C型凝集素，可以作为慢性缺氧在特定时间点的分子指标。然而，这些显着的基因的变化太动态，作为一般的生物标志物的缺氧应激在草虾的整个持续时间的慢性缺氧暴露。(C)2009 Elsevier Inc. All rights reserved.
DNA microarrays have become an important toot to measure global gene expression changes and genetic pathways involved in response to environmental stressors and toxicants. In this study a cDNA microarray was designed and constructed from six libraries of expressed sequence tags generated in a previous study (Li, T., Brouwer, M., 2009. Bioinformatic analysis of expressed sequence tags from grass shrimp Palaemonetes pugio exposed to environmental stressors. Comp. Biochem. Physiol. Part D Genomics Proteomics. doi:10.1016/j. cbd.2009.03.001). The microarrays were used to examine differentially expressed genes in hypoxic vs. normoxic groups at 6 (H6),12 (H12), 24 (H24),48 (H48),120 (H120), and 240 (H240) h exposure to chronic hypoxia (dissolved oxygen (DO) 1.5 mg/L). The initial response to hypoxia was an up-regulation of 29 genes. Only 6 h later, a dramatic down-regulation of 47 genes was observed. There was another reversal with 19 genes being up-regulated and none down-regulated at 24 h. After 2 and 5 days 34 and 22 genes were up-regulated, respectively, and 24 genes were down-regulated and 6 up-regulated by day 10. Cluster analysis confirmed two response patterns, one composed of an up-regulated dominated cluster, including H6, H24, and H120, the other composed of a down-regulated dominated cluster, including H12, H48, and H240. Venn diagrams of differentially expressed genes showed there was no gene up- or down-regulated common to all six groups. Hemocyanin transcription was up-regulated after 24, 48, and 120 h, but down-regulated after 12 h. Some genes appeared unique for specific time points. Phosphoenolpyruvate carboxykinase was up-regulated in the H120 and H240 groups. Cytochrome c oxidase subunit I and C-type lectin were uniquely up-regulated in H12, whereas vitellogenin and trachealess were uniquely down-regulated in H48. GOstats and org.Dm.eg.db packages from R were used to assign GO terms to significantly expressed genes. A total of 291, 129, and 219 genes were assigned to biological process, cellular components, and molecular function, respectively. The most abundant groups of genes were associated with transport, metabolic process, defense response, and proteolysis. Pathways were analyzed using Drosophila metabolic pathways in the KEGG database. Oxidative phosphorylation/Citrate cycle and Ribosome were the most abundant categories for chronic hypoxic exposure. Of 19 selected genes that showed differential expression on the microarrays, 17 showed similar up- or down-regulated patterns in both microarray and qPCR. In conclusion, the custom cDNA microarray is a valid and useful tool to investigate the changes in gene expression of grass shrimp during chronic hypoxia exposure. Some genes, such as those coding for hemocyanin, ATP synthase, phosphoenolpyruvate carboxykinase, vitellogenin, trachealess, cytochrome c oxidase subunit 1, lysosomal thiol reductase, and C-type lectin, could be used as molecular indicators of chronic hypoxia at specific time points. However, changes of these significant genes were too dynamic to serve as generic biomarkers of hypoxia stress in grass shrimp for the whole duration of the chronic hypoxia exposure. (C) 2009 Elsevier Inc. All rights reserved.