Department of Botany, Christian-Albrechts-University, Olshausenstr. 40, 24098, Kiel, Germany.
Present address: Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India.
BMC Plant Biol. 2020 May 12;20(1):209. doi: 10.1186/s12870-020-02418-z.
Flowering is a crucial stage during plant development. Plants may respond to unfavorable conditions by accelerating reproductive processes like flowering. In a recent study, we showed that PRECOCIOUS1 (POCO1) is a mitochondrial pentatricopeptide repeat (PPR) protein involved in flowering time and abscisic acid (ABA) signaling in Arabidopsis thaliana. Here, we use RNA-seq data to investigate global gene expression alteration in the poco1 mutant.
RNA-seq analysis was performed during different developmental stages for wild-type and poco1 plants. The most profound differences in gene expression were found when wild-type and poco1 plants of the same developmental stage were compared. Coverage analysis confirmed the T-DNA insertion in POCO1, which was concomitant with truncated transcripts. Many biological processes were found to be enriched. Several flowering-related genes such as FLOWERING LOCUS T (FT), which may be involved in the early-flowering phenotype of poco1, were differentially regulated. Numerous ABA-associated genes, including the core components of ABA signaling such as ABA receptors, protein phosphatases, protein kinases, and ABA-responsive element (ABRE) binding proteins (AREBs)/ABRE-binding factors (ABFs) as well as important genes for stomatal function, were mostly down-regulated in poco1. Drought and oxidative stress-related genes, including ABA-induced stress genes, were differentially regulated. RNA-seq analysis also uncovered differentially regulated genes encoding various classes of transcription factors and genes involved in cellular signaling. Furthermore, the expression of stress-associated nuclear genes encoding mitochondrial proteins (NGEMPs) was found to be altered in poco1. Redox-related genes were affected, suggesting that the redox state in poco1 might be altered.
The identification of various enriched biological processes indicates that complex regulatory mechanisms underlie poco1 development. Differentially regulated genes associated with flowering may contribute to the early-flowering phenotype of poco1. Our data suggest the involvement of POCO1 in the early ABA signaling process. The down-regulation of many ABA-related genes suggests an association of poco1 mutation with the ABA signaling deficiency. This condition further affects the expression of many stress-related, especially drought-associated genes in poco1, consistent with the drought sensitivity of poco1. poco1 mutation also affects the expression of genes associated with the cellular regulation, redox, and mitochondrial perturbation.
开花是植物发育的关键阶段。植物可能会通过加速生殖过程（如开花）来应对不利条件。在最近的一项研究中，我们发现 PRECOCIOUS1（POCO1）是一种参与拟南芥开花时间和脱落酸（ABA）信号的线粒体五肽重复（PPR）蛋白。在这里，我们使用 RNA-seq 数据来研究 poco1 突变体的全局基因表达变化。
在不同的发育阶段对野生型和 poco1 植物进行了 RNA-seq 分析。当比较同一发育阶段的野生型和 poco1 植物时，发现基因表达的差异最为显著。覆盖分析证实了 POCO1 中的 T-DNA 插入，这与截断的转录本同时发生。发现许多生物过程被富集。一些与开花相关的基因，如 FLOWERING LOCUS T（FT），可能参与了 poco1 的早花表型，它们的表达受到了差异调控。许多 ABA 相关基因，包括 ABA 信号的核心成分，如 ABA 受体、蛋白磷酸酶、蛋白激酶和 ABA 反应元件（ABRE）结合蛋白（AREBs）/ABRE 结合因子（ABFs）以及与气孔功能有关的重要基因，在 poco1 中大多下调。干旱和氧化应激相关基因，包括 ABA 诱导的应激基因，也受到差异调控。RNA-seq 分析还揭示了各种转录因子编码基因和参与细胞信号转导的基因的差异调控。此外，还发现编码线粒体蛋白的应激相关核基因（NGEMPs）的表达在 poco1 中发生改变。与氧化还原相关的基因受到影响，这表明 poco1 中的氧化还原状态可能发生了改变。
各种富集的生物过程的鉴定表明，poco1 发育涉及复杂的调控机制。与开花相关的差异调控基因可能有助于 poco1 的早花表型。我们的数据表明 POCO1 参与了早期 ABA 信号转导过程。许多与 ABA 相关基因的下调表明 poco1 突变与 ABA 信号缺陷有关。这种情况进一步影响了 poco1 中许多与应激相关的基因的表达，尤其是与干旱相关的基因，这与 poco1 的干旱敏感性一致。poco1 突变还影响与细胞调控、氧化还原和线粒体扰动相关的基因的表达。
