Genome-wide co-expression analysis predicts protein kinases as important regulators of phosphate deficiency-induced root hair remodeling in Arabidopsis.
Genome-wide co-expression analysis predicts protein kinases as important regulators of phosphate deficiency-induced root hair remodeling in Arabidopsis.
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DOI：
10.1186/1471-2164-14-210
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发表时间：
2013-04-01
期刊：
影响因子：
4.4
通讯作者：
Schmidt W
中科院分区：
文献类型：
--
作者：
Lan P;Li W;Schmidt W
磷(P)是植物生长的必需元素之一，但往往是限制性元素。基于转录谱分析，我们之前报道了3000多个基因在磷（Pi）缺乏和磷充足的拟南芥根中差异表达（MCP 11(11): 1156-1166, 2012）。目前的研究扩展了这些发现，重点分析了编码蛋白激酶（PK）和磷酸酶（PP）的基因，挖掘了在缺磷反应中差异表达的PK和PP基因。根据拟南芥基因组的TAIR10释放，挖掘了1118个和205个带注释的PK和PP基因亚群。RNA-seq数据分析显示，根中未检出92个PK基因和19个PP基因（3个生物重复序列为零）；96 PK和10 PP丰度较低（≤10 reads）。基因本体分析表明，188个在拟南芥根中不表达或低表达的PK基因主要参与花粉识别、花粉管生长或其他与根毛形成无关的过程。超过50%的富含半胱氨酸的RLK（受体样蛋白激酶）亚家族基因属于这一群体。29个无表达或低表达的PP基因中，紫色酸磷酸酶、卤酸去卤酶样水解酶和具有RNA聚合酶II c端结构域去磷酸化和mRNA capping功能的PP2C基因富集。在pi缺乏条件下，173个PK和35个PP基因亚群差异表达。基于MACCU工具箱的共表达分析，构建了这些PK和PP基因的推定功能模块（簇）。共表达网络包括65个已知或注释的PK和PP基因（分别为60个PK基因和5个PP基因），被细分为几个高度共表达的基因亚簇。最大的亚簇由22个基因组成，其中大部分属于RLK超家族，与细胞壁代谢、花粉管和/或根毛发育和生长有关。我们在此提供了拟南芥根系中PK和PP基因的全面“数字化”转录信息。从我们的数据挖掘方法衍生的共表达网络为后续实验奠定了基础，有助于完成我们对Pi缺陷诱导的根毛形态发生变化的翻译后调控的理解。
Phosphorus (P) is one of the essential but often limiting elements for plants. Based on transcriptional profiling we reported previously that more than 3,000 genes are differentially expressed between phosphate (Pi)-deficient and Pi-sufficient Arabidopsis roots (MCP 11(11):1156–1166, 2012). The current study extends these findings by focusing on the analysis of genes that encode protein kinases (PK) and phosphatases (PP) by mining PK and PP genes that were differentially expressed in response to Pi deficiency. Subsets of 1,118 and 205 annotated PK and PP genes were mined on the basis of the TAIR10 release of the Arabidopsis genome. Analysis of RNA-seq data showed that 92 PK and 19 PP genes were not detected in roots (zero reads in three biological repeats); 96 PK and 10 PP showed low abundance (≤ 10 reads). Gene ontology analysis revealed that the 188 PK genes with no or low expression level in Arabidopsis roots are mainly involved in pollen recognition, pollen tube growth or other processes not relevant for root hair formation. More than 50% of the cysteine-rich RLK (receptor-like protein kinase) subfamily genes belong to this group. Among the 29 PP genes with no or low expression level, purple acid phosphatases, haloacid dehalogenase-like hydrolases, and PP2C genes with functions in the dephosphorylation of RNA polymerase II C-terminal domain and mRNA capping were enriched. Subsets of 173 PK and 35 PP genes were differentially expressed under Pi-deficient conditions. Putative functional modules (clusters) of these PK and PP genes were constructed based on co-expression analysis using the MACCU toolbox. A co-expression network comprising 65 known or annotated PK and PP genes (60 PK and 5 PP genes, respectively) was subdivided into several highly co-expressed gene sub-clusters. The largest sub-cluster was composed of 22 genes, most of which have been assigned to the RLK superfamily and were associated with cell wall metabolism, pollen tube and/or root hair development and growth. We here provide comprehensive ‘digital’ transcriptional information on PK and PP genes in Arabidopsis roots. The co-expression network derived from our data mining approach sets the stage for follow-up experimentation that helps to complete our understanding of the post-translational regulation of Pi deficiency-induced changes in root hair morphogenesis.
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影响因子：
5.1
作者：
Hwang, Indeok;Kim, Soo Young;Kim, Cheol Soo;Park, Yoonkyung;Tripathi, Giri Raj;Kim, Seong-Ki;Cheong, Hyeonsook
通讯作者：
Cheong, Hyeonsook
影响因子：
4.5
作者：
Bruex A;Kainkaryam RM;Wieckowski Y;Kang YH;Bernhardt C;Xia Y;Zheng X;Wang JY;Lee MM;Benfey P;Woolf PJ;Schiefelbein J
通讯作者：
Schiefelbein J
影响因子：
5.1
作者：
Chen, KG;Du, LQ;Chen, ZX
通讯作者：
Chen, ZX
影响因子：
7
作者：
Lan, Ping;Li, Wenfeng;Schmidt, Wolfgang
通讯作者：
Schmidt, Wolfgang
DOI：
10.1098/rstb.2012.0003
发表时间：
2012-09-19
影响因子：
6.3
作者：
Lehti-Shiu, Melissa D.;Shiu, Shin-Han
通讯作者：
Shiu, Shin-Han