真核生物信使RNA（mRNA）上存在多种化学修饰，这些修饰本身不改变RNA序列信息，但却能精准调控RNA的结构、稳定性、翻译效率等多种生物学过程。近年来，越来越多的实验证据证实了mRNA化学修饰，如m⁶A（N⁶-甲基腺嘌呤）、Ψ（假尿嘧啶）和m⁵C（5-甲基胞嘧啶）等，在调控高等植物基因表达，调节生长发育，逆境生理等生物过程中发挥关键作用。前期，本课题组在植物中鉴定到一种全新的广泛存在的mRNA化学修饰- N⁴-乙酰化胞嘧啶（ac⁴C）修饰，该修饰可稳定靶标转录本，调控叶片发育进程。然而，该新型化学修饰在植物进化过程中是否参与更加保守的生物学过程尚不得而知。本研究以六种代表性高等植物（拟南芥、甘菊、草莓、大豆、水稻、番茄）为研究对象，结合RNA乙酰化免疫共沉淀测序（acRIP-seq）、翻译组学（Ribo-seq）、遗传学与多种生物化学研究手段，联合分析可知ac⁴C修饰保守地参与高等植物光合作用过程。此外，我们还初步探索了RNA乙酰化修饰（ac⁴C）调控植物光合效率的分子机制，为将来人工分子育种提供理论基础和基因储备。本论文主要研究结果如下：

六种植物全转录本ac⁴C修饰图谱的绘制与解析

利用acRIP-seq技术，本项目绘制了拟南芥、甘菊、草莓、大豆、水稻和番茄六种植物全转录本乙酰化图谱，详细描述了该修饰在各个植物细胞核、叶绿体及线粒体编码转录本上的ac⁴C修饰位点。六种植物RNA乙酰化修饰位点比较分析可知：叶绿体编码转录本ac⁴C修饰比例显著高于其他细胞器（如拟南芥叶绿体转录本ac⁴C修饰占比达28.57%）；并且该修饰广泛存在于光合系统相关基因转录本上。保守基序分析表明，所测序物种的ac⁴C修饰位点均普遍分布于富含胞嘧啶（C）的序列中，且主要富集于编码区（CDS），尤其靠近5'或3'UTR区域，提示其可能通过调控翻译起始或终止过程影响基因表达。基因本体（GO）富集分析进一步证实，ac⁴C修饰显著富集于“photosynthesis”，“chloroplast membrane”及“photosynthesis，light harvesting”等通路中，暗示其可能参与光合作用调控。

ACYR介导的ac⁴C修饰促进植物光合效率

分别检测并比较拟南芥和水稻RNA乙酰化转移酶（ACYR）缺失突变体与各自野生型植株的光合参数可知，ACYR缺失会导致植株光合速率（Fv/Fm）、电子传递效率（ETR）、单位反应中心吸收（ABS/RC）以及电子传递能力（ET₀/RC）显著下降；超微结构观察显示突变体类囊体结构完完整，基粒排布整齐；但高光强刺激实验结果却表明受调控能量耗散的量子产率 (Φ_(NPQ))降低，非调控能量耗散的量子产率 (Φ(_NO))增加。

RNA乙酰化促进靶标转录本翻译效率提升光合相关蛋白表达量

通过翻译组学，转录组学以及表观组学联合分析显示，具有ac⁴C修饰的光合转录本翻译效率（TE）显著高于未修饰的转录本。在拟南芥RNA乙酰化酶缺失突变体中，光合作用相关转录本的TE显著下调，尤其值得关注的是电子传递链相关转录本（包括光捕捉蛋白家族（Light-Harvesting Complex，LHC家族）成员LHCB2、LHCB3和LHCB4）的TE显著降低。蛋白质定量检测结果显示上述靶标转录本所编码蛋白质含量显著下降。组学数据分析联合生物化学手段检测结果表明LHC家族中多个转录本（LHCA4，LHCB2.2，LHCB3和LHCB4.2）上ac⁴C修饰丰度在ACYR突变体中显著下降（65%~97%）。该结果表明ACYR介导的RNA乙酰化通过促进光合靶标转录本（特别是电子传递链中LHC家族）翻译效率，进而增强其蛋白表达量，提升光捕捉效率和植物光合能力。

       综上所述，本研究系统构建了六种高等植物的RNA乙酰化修饰图谱，全面揭示了ac⁴C修饰在不同细胞器中的分布和调控特点。研究表明ac⁴C修饰在调控光合作用中的普遍性和保守性，这为进一步理解表观转录组调控机制提供了有力支持。通过一系列遗传学和生物化学实验，研究证实ACYR介导的ac⁴C修饰能够显著提升靶标转录本的翻译效率，从而有效调控光捕捉复合体及相关电子传递链成员的蛋白表达水平。总体而言，这些发现不仅阐明了ac⁴C在植物光合作用调控中的核心作用，也为未来利用分子育种手段优化光合效率提供了坚实的理论基础。

RNA modifications refer to chemical changes that occur on RNA molecules without altering the RNA sequence information, but they can regulate RNA structure, stability, and function. In previous studies, modifications such as m⁶A, Ψ (pseudouridine), and m⁵C have been confirmed to play key roles in biological processes including gene expression regulation and RNA splicing. In recent years, RNA acetylation modification (ac⁴C) has gradually been recognized as an important component of epitranscriptomic regulation. It participates in the regulation of target genes in cells by affecting mRNA stability and translation efficiency. Although the functions of ac⁴C in animal cells have been widely reported, its functional mechanism in higher plant photosynthesis remains unclear. This study focuses on six representative higher plants (Arabidopsis, Chrysanthemum, Strawberry, Soybean, Rice, and Tomato) and uses a comprehensive approach combining ac⁴C-specific RNA immunoprecipitation sequencing (acRIP-seq), ribosome profiling (Ribo-seq), genetics, and biochemical methods. The aim is to preliminarily explore the molecular mechanism by which RNA acetylation modification (ac⁴C) regulates photosynthetic efficiency in plants, thus providing a theoretical foundation and gene reserves for future molecular breeding. The main research findings are as follows:

Mapping and analysis of the whole-transcriptome ac⁴C modification in six plants

Using acRIP-seq technology, this project generated the whole-transcriptome ac⁴C modification profiles for Arabidopsis, Chrysanthemum, Strawberry, Soybean, Rice, and Tomato. The ac⁴C modification sites were detailed for nuclear, chloroplast, and mitochondrial transcripts in each species. Comparative analysis of the ac⁴C modification sites across these six plants revealed that the proportion of ac⁴C-modified transcripts encoded by chloroplast genes was significantly higher than that in other organelles (for example, Arabidopsis chloroplast transcripts showed an ac⁴C modification ratio of 21.05%). Moreover, ac⁴C modification is widely present on transcripts of genes related to the photosynthetic system. Conserved motif analysis indicated that the ac⁴C modification sites in the species examined are generally distributed in cytosine-rich sequences and are mainly enriched in coding sequences (CDS), particularly near the 5’ or 3’ untranslated regions, suggesting that they may influence gene expression by regulating translation initiation or termination. Gene Ontology (GO) enrichment analysis further confirmed that ac⁴C modifications are significantly enriched in pathways such as “photosynthesis”, “chloroplast membrane”, and “photosynthesis, light harvesting”, indicating a central regulatory role in photosynthesis.

ACYR-mediated ac⁴C modification promotes plant photosynthetic efficiency

Comparison of photosynthetic parameters between acyltransferase (ACYR) deletion mutants and their respective wild-type plants in Arabidopsis and Rice showed that the absence of ACYR led to significant decreases in photosynthetic rate (Fv/Fm), electron transport efficiency (ETR), absorption per reaction center (ABS/RC), and electron transport capacity (ET_O/RC). Although ultrastructural observations revealed intact thylakoid structures and neatly arranged grana in the mutants, high light stress experiments indicated a reduction in the quantum yield of regulated energy dissipation (Φ_(NPQ)) and an increase in the quantum yield of non-regulated energy dissipation (Φ_(NO)).

RNA acetylation enhances target transcript translation efficiency and increases the expression of photosynthesis-associated proteins

Integrated analysis of translatomics, transcriptomics, and epitranscriptomics demonstrated that the translation efficiency (TE) of photosynthetic transcripts bearing ac⁴C modifications was significantly higher than those without modifications. In Arabidopsis RNA acetylation enzyme deletion mutants, the TE of photosynthesis-related transcripts was markedly downregulated, notably in transcripts related to the electron transport chain (including LHC family members LHCB2, LHCB3, and LHCB4). Protein quantification assays showed a significant decrease in the protein levels encoded by these target transcripts. Combined analysis of omics data and biochemical assays revealed that multiple transcripts of the Light-Harvesting Complex (LHC, LHCA4, LHCB2.2, LHCB3, and LHCB4.2) exhibited a significant decrease (65%–97%) in ac4C modification abundance in the ACYR mutants. These results indicate that ACYR-mediated RNA acetylation enhances the translation efficiency of photosynthetic target transcripts—especially those of the LHC family involved in the electron transport chain—thus increasing the corresponding protein expression levels, improving light capture efficiency, and ultimately enhancing plant photosynthetic capacity.

In summary, this study systematically constructed the RNA acetylation modification landscape in higher plants, comprehensively revealing the distribution and regulatory characteristics of ac⁴C in different organelles. The findings indicate that ac⁴C modification is both pervasive and conserved in the regulation of photosynthesis, providing strong support for further understanding of epitranscriptomic regulatory mechanisms. Through a series of genetic and biochemical experiments, the study confirmed that ACYR-mediated ac⁴C modification can significantly enhance the translation efficiency of target transcripts, thereby effectively regulating the protein expression levels of the light capture complex and related members of the electron transport chain. Overall, these discoveries not only elucidate the central role of ac⁴C in the regulation of photosynthesis in plants but also provide a solid theoretical foundation for optimizing photosynthetic efficiency through future molecular breeding strategies.

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