Comparative genomic analysis of NAC transcriptional factors to dissect the regulatory mechanisms for cell wall biosynthesis.
Comparative genomic analysis of NAC transcriptional factors to dissect the regulatory mechanisms for cell wall biosynthesis.
复制标题
NAC转录因子的比较基因组分析，剖析细胞壁生物合成的调控机制
DOI：
10.1186/1471-2105-13-s15-s10
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发表时间：
2012
影响因子：
3
通讯作者：
Su Z
中科院分区：
文献类型：
--
作者：
Yao D;Wei Q;Xu W;Syrenne RD;Yuan JS;Su Z
背景NAC结构域转录因子是植物生长发育和逆境胁迫反应中重要的转录调控因子。最近的研究揭示了几类NAC转录因子对控制次生细胞壁生物合成至关重要。这些转录因子主要包括SND、NST和VND三类。尽管取得了进展，目前大多数分析是在模式植物拟南芥中进行的。此外，许多受这些转录因子调控的下游基因仍然不清楚。方法为了鉴定跨物种的关键同源基因，揭示控制细胞壁生物合成的网络，我们对NST进行了比较基因组分析，沿着19种高等植物的VND和SND基因，以及调控或协同调控基因的计算模型，结果比较基因组分析表明，次生壁相关NAC结构域转录因子在进化上最早出现于卷柏。事实上，在这三个类群中，只有摩氏链霉菌中出现了VND基因，它在进化上早于其他两个类群。拟南芥和水稻基因表达分析显示了与次生细胞壁相关的NAC基因（SND、NST和VND）的特定模式。它们大多数在茎中优先表达，尤其是在第二节间。进一步的共调控网络分析表明，SND和MYB基因是共调控的，这表明这些转录因子在调控细胞壁生物合成中具有协同作用。此外，共调控网络分析揭示了许多可能参与细胞壁生物合成及其调控的新基因和途径。基因本体分析还表明，碳水化合物的合成，运输和应激反应的过程，协调调节细胞壁biosynthesis. ConclusionsOverall，我们提供了一个新的见解的进化和基因调控网络的一个亚组的NAC基因家族控制细胞壁组成，通过生物信息学数据挖掘和实验室验证。我们的工作可能有助于阐明次生细胞壁生物合成调节网络的可能分子机制。
BackgroundNAC domain transcription factors are important transcriptional regulators involved in plant growth, development and stress responses. Recent studies have revealed several classes of NAC transcriptional factors crucial for controlling secondary cell wall biosynthesis. These transcriptional factors mainly include three classes, SND, NST and VND. Despite progress, most current analysis is carried out in the model plantArabidopsis. Moreover, many downstream genes regulated by these transcriptional factors are still not clear.MethodsIn order to identify the key homologue genes across species and discover the network controlling cell wall biosynthesis, we carried out comparative genome analysis of NST, VND and SND genes across 19 higher plant species along with computational modelling of genes regulated or co-regulated with these transcriptional factors.ResultsThe comparative genome analysis revealed that evolutionarily the secondary-wall-associated NAC domain transcription factors first appeared inSelaginella moellendorffii. In fact, among the three groups, only VND genes appeared inS. moellendorffii, which is evolutionarily earlier than the other two groups. TheArabidopsisand rice gene expression analysis showed specific patterns of the secondary cell wall-associated NAC genes (SND, NST and VND). Most of them were preferentially expressed in the stem, especially the second internodes. Furthermore, comprehensive co-regulatory network analysis revealed that the SND and MYB genes were co-regulated, which indicated the coordinative function of these transcriptional factors in modulating cell wall biosynthesis. In addition, the co-regulatory network analysis revealed many novel genes and pathways that could be involved in cell wall biosynthesis and its regulation. The gene ontology analysis also indicated that processes like carbohydrate synthesis, transport and stress response, are coordinately regulated toward cell wall biosynthesis.ConclusionsOverall, we provided a new insight into the evolution and the gene regulatory network of a subgroup of the NAC gene family controlling cell wall composition through bioinformatics data mining and bench validation. Our work might benefit to elucidate the possible molecular mechanism underlying the regulation network of secondary cell wall biosynthesis.