Regulation of gene expression in the protozoan parasite Entamoeba invadens: identification of core promoter elements and promoters with stage-specific expression patterns.
Regulation of gene expression in the protozoan parasite Entamoeba invadens: identification of core promoter elements and promoters with stage-specific expression patterns.
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DOI：
10.1016/j.ijpara.2014.06.008
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发表时间：
2014-10-01
影响因子：
4
通讯作者：
Singh, Upinder
中科院分区：
文献类型：
--
作者：
Manna, Dipak;Ehrenkaufer, Gretchen M.;Singh, Upinder
关键词：
在生命周期各阶段之间的发育转换是许多病原生物的共同特征。溶组织内阿米巴是一种重要的人类病原体，是全球主要的寄生虫致死原因。在其生命周期中，内阿米巴在包囊（疾病传播所必需的）和滋养体（负责组织入侵）之间转换。尽管是其生物学的核心，但参与这种寄生虫发育途径的触发因素还没有得到很好的理解。为了定义与阶段转换相关的转录网络，我们使用侵袭内阿米巴作为内阿米巴发育生物学的模型系统，并在不同的发育时间点进行RNA测序。在这项研究中，RNA-Seq数据被用来定义基本的转录控制元件，以及确定启动子调节阶段特异性基因表达模式。我们发现E.侵袭菌基因较短，中值分别为20个核苷酸（nt）和26个核苷酸。对起始密码子和终止密码子附近的DNA序列进行生物信息学分析，确定了两个保守的基序：（i）E.入侵种核心启动子基序-GAAC样（EiCPM-GL）（GAACTACAAA），和（ii）E.分别在5'和3'侧翼区中具有侵入体3 '-U-富集基序（Ei 3'-URM）（TTTGTT）。电泳迁移率变动分析表明，这两个基序特异性地结合E.侵入滋养体。此外，我们确定了阶段特异性表达模式的选择基因，并分析了每个基因启动子在发育周期中驱动荧光素酶报告基因的能力。该方法证实了三个滋养体特异性启动子，四个包囊特异性启动子和两个脱囊特异性启动子。这项工作奠定了使用阶段特异性启动子在特定生命周期阶段表达感兴趣蛋白质的框架，为E.并允许进一步解剖控制内阿米巴发育生物学的因素。
Developmental switching between life-cycle stages is a common feature among many pathogenic organisms. Entamoeba histolytica is an important human pathogen and is a leading parasitic cause of death globally. During its life cycle, Entamoeba converts between cysts (essential for disease transmission) and trophozoites (responsible for tissue invasion). Despite being central to its biology, the triggers that are involved in the developmental pathways of this parasite are not well understood. In order to define the transcriptional network associated with stage conversion we used Entamoeba invadens which serves as a model system for Entamoeba developmental biology, and performed RNA sequencing at different developmental time points . In this study RNA-Seq data was utilized to define basal transcriptional control elements as well as to identify promoters which regulate stage-specific gene expression patterns. We discovered that the 5’ and 3’ untranslated regions of E. invadens genes are short, a median of 20 nucleotides (nt) and 26 nt respectively. Bioinformatics analysis of DNA sequences proximate to the start and stop codons identified two conserved motifs: (i) E. invadens Core Promoter Motif - GAAC-Like (EiCPM-GL) (GAACTACAAA), and (ii) E. invadens 3’- U-Rich Motif (Ei3’-URM) (TTTGTT) in the 5’ and 3’ flanking regions, respectively. Electrophoretic mobility shift assays demonstrated that both motifs specifically bind nuclear protein(s) from E. invadens trophozoites. Additionally, we identified select genes with stage-specific expression patterns and analyzed the ability of each gene promoter to drive a luciferase reporter gene during the developmental cycle. This approach confirmed three trophozoite-specific, four encystation-specific and two excystation-specific promoters. This work lays the framework for use of stage-specific promoters to express proteins of interest in a particular life-cycle stage, adding to the molecular toolbox for genetic manipulation of E. invadens and allowing further dissection of factors controlling Entamoeba developmental biology.
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影响因子：
1.5
作者：
SANCHEZ, L;ENEA, V;EICHINGER, D
通讯作者：
EICHINGER, D
DOI：
10.1093/bioinformatics/btq033
发表时间：
2010-03-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Quinlan AR;Hall IM
通讯作者：
Hall IM
影响因子：
14.9
作者：
Hon CC;Weber C;Sismeiro O;Proux C;Koutero M;Deloger M;Das S;Agrahari M;Dillies MA;Jagla B;Coppee JY;Bhattacharya A;Guillen N
通讯作者：
Guillen N
影响因子：
7.7
作者：
López, C;Marchat, LA;Orozco, E
通讯作者：
Orozco, E
影响因子：
4.8
作者：
Pearson, Richard J.;Morf, Laura;Singh, Upinder
通讯作者：
Singh, Upinder