TAL effectors and activation of predicted host targets distinguish Asian from African strains of the rice pathogen Xanthomonas oryzae pv. oryzicola while strict conservation suggests universal importance of five TAL effectors.
TAL effectors and activation of predicted host targets distinguish Asian from African strains of the rice pathogen Xanthomonas oryzae pv. oryzicola while strict conservation suggests universal importance of five TAL effectors.
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DOI：
10.3389/fpls.2015.00536
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发表时间：
2015
影响因子：
5.6
通讯作者：
Bogdanove AJ
中科院分区：
文献类型：
--
作者：
Wilkins KE;Booher NJ;Wang L;Bogdanove AJ
米黄单胞菌 pv. oryzicola (Xoc) 引起日益重要的水稻细菌性叶斑病 (BLS)，部分原因是通过 III 型传递富含重复的转录激活因子样 (TAL) 效应子来上调宿主易感基因。通过病原体全基因组、单分子、实时测序和宿主 RNA 测序，我们比较了 10 个不同地理位置的 Xoc 菌株的 TAL 效应子含量和水稻转录反应。 TAL 效应子含量总体上令人惊讶地保守，但将亚洲分离株与非洲分离株区分开来。五个 TAL 效应子在所有菌株中都是保守的。在先前对水稻品种的实验室测定中。日本晴，只有两种对菌株 BLS256 的毒力有贡献，但严格的保守性表明所有五种可能在不同的水稻基因型或田间都很重要。跨菌株的 TAL 效应子内容串联并对齐，很大程度上反映了基于管家基因的关系，表明主要是垂直传播。水稻转录反应并未反映这些关系，平均而言，只有 28% 的菌株上调基因和 22% 的基因下调基因在所有菌株中（分别）上调和下调。然而，当仅考虑已知的 TAL 效应器目标时，这些关系类似于 TAL 效应器的关系。为了识别新靶标，我们使用 TAL 效应子 DNA 识别代码来预测每种菌株上调基因启动子中的效应子结合元件，但发现对于每种菌株，所有上调基因都至少有一个。使用我们之前开发的分类器进行过滤会减少整个基因组中预测的结合元件的数量，这表明它可能会减少上调基因中的假阳性。应用此过滤器并消除上调与相应 TAL 效应器的存在不严格相关的基因，我们为五个严格保守的 TAL 效应器中的四个生成了可测试数量的候选靶标。
Xanthomonas oryzae pv. oryzicola (Xoc) causes the increasingly important disease bacterial leaf streak of rice (BLS) in part by type III delivery of repeat-rich transcription activator-like (TAL) effectors to upregulate host susceptibility genes. By pathogen whole genome, single molecule, real-time sequencing and host RNA sequencing, we compared TAL effector content and rice transcriptional responses across 10 geographically diverse Xoc strains. TAL effector content is surprisingly conserved overall, yet distinguishes Asian from African isolates. Five TAL effectors are conserved across all strains. In a prior laboratory assay in rice cv. Nipponbare, only two contributed to virulence in strain BLS256 but the strict conservation indicates all five may be important, in different rice genotypes or in the field. Concatenated and aligned, TAL effector content across strains largely reflects relationships based on housekeeping genes, suggesting predominantly vertical transmission. Rice transcriptional responses did not reflect these relationships, and on average, only 28% of genes upregulated and 22% of genes downregulated by a strain are up- and down- regulated (respectively) by all strains. However, when only known TAL effector targets were considered, the relationships resembled those of the TAL effectors. Toward identifying new targets, we used the TAL effector-DNA recognition code to predict effector binding elements in promoters of genes upregulated by each strain, but found that for every strain, all upregulated genes had at least one. Filtering with a classifier we developed previously decreases the number of predicted binding elements across the genome, suggesting that it may reduce false positives among upregulated genes. Applying this filter and eliminating genes for which upregulation did not strictly correlate with presence of the corresponding TAL effector, we generated testable numbers of candidate targets for four of the five strictly conserved TAL effectors.