水稻对多种非生物胁迫的响应通过转录组荟萃分析揭示及新型遗传因子的鉴定-动脉网

Responses of rice plant to multiple abiotic stresses revealed by transcriptome meta-analysis and identification of novel genetic factors

Nature 等信源发布 2025-03-10 22:23

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可切换为仅中文

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Abstract

摘要

Plant responses to abiotic stresses have a complex polygenic nature including main and epistatic genetic factors. Several tolerant rice varieties were subjected to drought, salt and cold stresses and their transcriptomic responses were evaluated using affymetrix probe set. Meta-analysis of standardized microarray data was conducted to identify specific and common genes responding to multiple abiotic stresses.

植物对非生物胁迫的反应具有复杂的多基因性质，包括主要的和上位的遗传因素。对几种耐受性水稻品种进行了干旱、盐和冷胁迫处理，并使用Affymetrix探针组评估了它们的转录组反应。通过对标准化微阵列数据的荟萃分析，鉴定了响应多种非生物胁迫的特定基因和共同基因。

375 and 298 genes were up- and downregulated under drought stress, 281 and 313 genes were up- and downregulated under salt stress, and 1,273 and 2,996 genes were up- and downregulated under cold stress. In addition to many specific genes for each stress condition, common genes were identified for response to drought and salt (n=91), drought and cold (n=121), and salt and cold (n=108), while 14 genes were common for response to all 3 stresses.

干旱胁迫下，375个基因上调，298个基因下调；盐胁迫下，281个基因上调，313个基因下调；冷胁迫下，1,273个基因上调，2,996个基因下调。除了许多针对每种胁迫条件的特异性基因外，还鉴定了对干旱和盐胁迫共同响应的91个基因、对干旱和冷胁迫共同响应的121个基因、对盐和冷胁迫共同响应的108个基因，而对所有三种胁迫共同响应的基因为14个。

12 out of 14 genes were downregulated under the 3 stresses; however, only 2 upregulated genes (including an auxin-responsive protein and a LRR protein) were common among the 3 stresses. One of the common downregulated genes is a non-ABC transporter belonging to proton-dependent oligopeptide transport (POT) family protein which is novel and has a vital role in uptake of nutrients, particularly nitrate, and in recognizing plant defense compounds and hormones.

在三种胁迫下，14个基因中有12个被下调；然而，在三种胁迫中只有2个上调的基因是共同的（包括一个生长素响应蛋白和一个LRR蛋白）。其中一个共同下调的基因是一种属于质子依赖性寡肽转运蛋白（POT）家族的非ABC转运蛋白，它是新颖的，并在吸收营养物质（特别是硝酸盐）以及识别植物防御化合物和激素方面起着关键作用。

In addition, two other non-ABC transporters (.

此外，还有另外两个非ABC转运蛋白（。

OsAAP7C

and

和

OsGT1

) were identified which were downregulated under drought, salinity and cold stresses. This finding can explain why and how the uptake of necessary nutrients for growth and development of plants decreases under these oxidative stresses. Another novel downregulated gene under the 3 stresses is a TraB-related protein with vital role for normal mitochondrial function.

）被鉴定出在干旱、盐度和寒冷胁迫下下调。这一发现可以解释为什么以及在这些氧化胁迫下植物生长和发育所需营养的吸收会减少。另一个在三种胁迫下新发现的下调基因是一种与正常线粒体功能至关重要的TraB相关蛋白。

These results open new insights into genetic engineering and molecular breeding of plants for tolerance to abiotic stresses..

这些结果为植物耐受非生物胁迫的遗传工程和分子育种开辟了新的见解。

Introduction

简介

Abiotic stressors are thought to be serious agricultural challenges because they significantly reduce crop growth and productivity. Since plants are sessile and must endure harsh environmental conditions, they have evolved various responses to adapt

非生物胁迫被认为是严重的农业挑战，因为它们显著降低作物的生长和生产力。由于植物是固着的，必须忍受恶劣的环境条件，它们已经进化出各种响应机制来适应。

，

. Plants possess sophisticated sensory systems that detect subtle changes in growing conditions and trigger signal transduction cascades, leading to the activation of stress-responsive genes and subsequent physiological and biochemical changes

植物拥有复杂的感觉系统，能够检测生长条件的细微变化，并触发信号转导级联反应，从而激活应激响应基因以及随后的生理和生化变化。

，

. Understanding how plants respond to these challenges and the underlying mechanisms of stress tolerance can contribute to increasing global food supply.

了解植物如何应对这些挑战以及抗逆性的潜在机制，有助于增加全球粮食供应。

Over half of the world’s population depends on rice (

超过一半的世界人口依赖于水稻（

Oryza sativa

水稻

L.) as a staple crop, yet it is susceptible to several abiotic stresses, including salt, drought, and cold

L.) 作为主要作物，但它容易受到多种非生物胁迫的影响，包括盐、干旱和寒冷。

. With the projected increase in the frequency, intensity, and duration of these stresses due to climate change, rice productivity and global food security are at risk

由于气候变化，这些压力的频率、强度和持续时间预计会增加，水稻生产力和全球粮食安全面临风险。

. Many resources reported considerable damage of abiotic stresses to rice yield. For instance, severe drought stress in the flowering stage can cause more than 70% decrease in yield

许多资料报道，非生物胁迫对水稻产量造成了相当大的损害。例如，开花期的严重干旱胁迫可导致产量减少70%以上。

。

Abiotic stresses induce the production of reactive oxygen species (ROS) in plants, resulting in oxidative damage and reduced growth and yield. These ROS, including superoxide, OH

非生物胁迫会诱导植物产生活性氧（ROS），导致氧化损伤并降低生长和产量。这些活性氧包括超氧阴离子、羟基自由基等。

−

radicals, H

自由基，H

, and singlet oxygen, accumulate in cells due to various stress factors, disrupting cellular homeostasis

，单线态氧因各种压力因素在细胞内积累，破坏细胞稳态

. However, plants maintain a baseline ROS level essential for regulating vital cellular processes and metabolic pathways. To counteract ROS accumulation, plants have developed intricate antioxidative defense mechanisms, including enzymatic processes involving superoxide dismutase, catalase, peroxidase, and glutathione reductase, which help prevent or repair oxidative damage caused by stress.

然而，植物保持了一定的基础活性氧（ROS）水平，这对于调节关键的细胞过程和代谢途径至关重要。为了对抗活性氧的积累，植物进化出了复杂的抗氧化防御机制，包括涉及超氧化物歧化酶、过氧化氢酶、过氧化物酶和谷胱甘肽还原酶的酶促过程，这些机制有助于预防或修复由胁迫引起的氧化损伤。

，

。

Abiotic stress significantly impacts plant growth and productivity. Salt stress, for instance, not only affects the absorption of essential nutrients but also interacts with various metabolic processes in plants. Moreover, temperature fluctuations during critical growth stages can profoundly influence crop yield, especially in rice.

非生物胁迫显著影响植物的生长和生产力。例如，盐胁迫不仅影响必需营养元素的吸收，还与植物中的多种代谢过程相互作用。此外，在关键生长阶段的温度波动会深刻影响作物产量，尤其是在水稻中。

，

. On the other hand, the genetic regulation of stress responses offers potential strategies for enhancing plant resilience. On the other hand, the genetic regulation of stress responses offers potential strategies for enhancing plant resilience. The core components of strigolactone (SL) biosynthesis and signaling, MAX1–MAX4, are crucial for enhancing freezing tolerance in plants.

另一方面，胁迫反应的遗传调控为增强植物的适应力提供了潜在策略。另一方面，胁迫反应的遗传调控为增强植物的适应力提供了潜在策略。独脚金内酯（SL）生物合成与信号传导的核心组分MAX1-MAX4对提高植物的抗冻性至关重要。

Additionally, C-REPEAT BINDING FACTOR/DEHYDRATION RESPONSE ELEMENT BINDING FACTOR 1 (CBF/DREB1) transcription factors play essential roles in cold acclimation, with the F-box protein MAX2 facilitating the degradation of WRKY41 to enhance freezing tolerance.

此外，C-重复结合因子/脱水响应元件结合因子1（CBF/DREB1）转录因子在冷适应中发挥重要作用，F-box蛋白MAX2促进WRKY41的降解以增强抗冻性。

，

. Moreover, the involvement of genes like DEAR4 in stress responses is evident, as overexpression of DEAR4 leads to reduced seed germination rates under ABA and salt stress, along with decreased drought tolerance

此外，像DEAR4这样的基因参与胁迫反应的证据很明显，因为DEAR4的过表达会导致在ABA和盐胁迫下种子萌发率降低，同时抗旱性也下降。

. Likewise, in lettuce, RD29A and RD29B respond differently to various stresses, with RD29A being more responsive to drought and cold stresses, while RD29B is highly responsive to salt stress

同样，在生菜中，RD29A 和 RD29B 对各种胁迫的反应不同，其中 RD29A 对干旱和寒冷胁迫更敏感，而 RD29B 对盐胁迫高度敏感。

，

. Furthermore, carotenoid cleavage oxygenases (CCOs), including NCEDs (9-Cis-epoxycarotenoid dioxygenases), CCDs (Carotenoid cleavage dioxygenases), and CCD-like genes, are vital for rice’s response to stress

此外，类胡萝卜素裂解氧合酶（CCOs），包括NCEDs（9-顺式-环氧类胡萝卜素双加氧酶）、CCDs（类胡萝卜素裂解双加氧酶）和CCD-like基因，对水稻应对胁迫至关重要。

. Transcriptome analysis highlights the upregulation of OsNCED6 and OsNCED10 during abiotic stress, suggesting their potential for stress-resistant breeding

转录组分析强调了在非生物胁迫下OsNCED6和OsNCED10的上调，表明它们在抗逆育种中的潜力。

. Understanding the intricate genetic mechanisms underlying stress responses, such as those involving CBF/DREB1 transcription factors, WRKY41, DEAR4, RD29A, RD29B, and CCOs, provides insights into developing stress-resistant crop varieties. This knowledge can significantly contribute to improving agricultural productivity in the face of challenging environmental conditions..

理解与压力反应相关的复杂遗传机制，例如涉及CBF/DREB1转录因子、WRKY41、DEAR4、RD29A、RD29B和CCOs的机制，为开发抗压作物品种提供了见解。这一知识可以显著帮助提高在严峻环境条件下的农业生产力。

Rice is susceptible to various abiotic and biotic stresses, often occurring simultaneously within a single cropping season, significantly impacting rice growth and yield. To address this, rice mega varieties have been introduced, which exhibit tolerance to multiple stresses

水稻容易受到各种非生物和生物胁迫的影响，这些胁迫常常在单个种植季节内同时发生，显著影响水稻的生长和产量。为此，引入了对多种胁迫具有耐受性的水稻巨型品种。

，

. Yadav et al.

. Yadav 等人

developed the rice breeding line IR 91,648-B-1-B-3-1 using a funnel mating design to incorporate targeted QTLs and genes. Jamaloddin et al.

使用漏斗杂交设计，将目标QTL和基因融入，开发了水稻育种系IR 91,648-B-1-B-3-1。Jamaloddin等。

evaluated gene-pyramided rice lines TH-625-159 and TH-625-491, both showing resistance to blast and bacterial blight (BB) across multiple locations. These lines have the potential to become mega varieties for different agro-climatic zones and valuable resources in pre-breeding rice research.

评估了基因叠加的水稻品系TH-625-159和TH-625-491，这两个品系在多个地点均表现出对稻瘟病和细菌性枯萎病（BB）的抗性。这些品系有潜力成为适应不同农业气候区的超级品种，并在水稻预育种研究中成为宝贵的资源。

Meta-analysis, a statistical technique combining information from various genomic studies, offers a comprehensive understanding of the problem being studied

元分析是一种结合来自各种基因组研究信息的统计技术，提供了对所研究问题的全面理解。

. It helps identify candidate genes showing differential expression across studies

它有助于识别在不同研究中显示差异表达的候选基因

and elucidates the molecular mechanisms and crosstalk between individual and combined abiotic stresses by comparing transcriptome data

通过比较转录组数据，阐明了个体和复合非生物胁迫之间的分子机制及其相互作用。

. Meta-analyses are particularly suitable for such comparisons, offering greater power to discover genes with consistent responses that may be overlooked in individual studies or vary among them. For instance, a meta-analysis on drought stress response in cereal crops identified 69 conserved drought tolerant-related (CDT) genes, with 20 of these genes being potential novel candidates for drought tolerance.

元分析特别适合进行这样的比较，它提供了更大的能力来发现具有持续响应的基因，这些基因可能在个别研究中被忽略或在不同研究之间存在差异。例如，一项关于谷类作物干旱胁迫响应的元分析鉴定了69个保守的与耐旱性相关的（CDT）基因，其中20个基因是潜在的新型耐旱候选基因。

. Meta-analysis of transcriptome studies reveals key regulatory hub genes, such as NSP2, DRE1D, ERF61, CDF1, and TLP3 for drought and TLP1, TLP, ERF109, ELF4, and ATHB7 for salt stress, which are associated with significant differential expression and offer potential candidate genes for improving

. 转录组研究的荟萃分析揭示了关键的调控枢纽基因，如干旱相关的NSP2、DRE1D、ERF61、CDF1和TLP3，以及盐胁迫相关的TLP1、TLP、ERF109、ELF4和ATHB7，这些基因与显著的差异表达相关，并为改良提供了潜在的候选基因。

Gossypium hirsutum

陆地棉

genotype selection against drought and salt stress conditions. In this study, we explored the expression pattern of rice genes in response to drought, salt, and cold stresses using a large-scale meta-analysis based on publicly accessible microarray data. This study aims to open new insights into genetic engineering and molecular breeding of plants for tolerance to abiotic stresses..

针对干旱和盐胁迫条件的基因型选择。在本研究中，我们利用基于公开可用的微阵列数据的大规模荟萃分析，探讨了水稻基因在应对干旱、盐和冷胁迫下的表达模式。本研究旨在为植物耐受非生物胁迫的遗传工程和分子育种提供新的见解。

Material and method

材料与方法

Microarray data

微阵列数据

The Gene Expression Omnibus (

基因表达综合数据库 (

https://www.ncbi.nlm.nih.gov/geo/

) was used to download microarray datasets from the Affymetrix platform Rice Genome Array, which were obtained from rice (

）用于从Affymetrix平台的水稻基因组阵列下载微阵列数据集，这些数据集是从水稻（

Oryza sativa

水稻

) seedlings grown under normal conditions and subjected to different stresses including drought, salinity and cold. Totally, ten GEO datasets were used in the study (Table

在正常条件下生长并受到不同胁迫（包括干旱、盐度和寒冷）的幼苗。总共，研究中使用了十个GEO数据集（表）。

). The expression data sets were processed separately using different methods depending on the platform used

）。根据所使用的平台，表达数据集采用不同的方法分别进行处理。

. The raw data was preprocessed with quantile normalization and Robust Multi-Array Average background correction, and then probes with low intensity and non-informative data were removed based on the program’s standard settings. The probes were also transformed to their corresponding genes.

原始数据经过分位数归一化和鲁棒多阵列平均背景校正进行预处理，然后根据程序的标准设置移除低强度和无信息的数据探针。这些探针还被转换为其相应的基因。

Table 1 Characteristics of the individual studies included in study.

表1 研究中包含的各个研究的特征。

Full size table

全尺寸表格

Differential gene expression and meta-analysis

差异基因表达与荟萃分析

Gene expression analysis was conducted for three treatment conditions versus normal condition. R specific pakages including edgeR and Limma were used for detection of differentially expressed genes (DEGs). A linear model was fitted to the data and a simple empirical Bayes model was used to adjust the standard errors.

针对三种处理条件与正常条件进行了基因表达分析。使用了包括 edgeR 和 Limma 在内的 R 语言特定包来检测差异表达基因 (DEGs)。对数据拟合了一个线性模型，并使用了一个简单的经验贝叶斯模型来调整标准误差。

For each contrast in every gene, moderated t-statistic and log-odds of differential expression were calculated. Genes with a q-value cut-off of ≤ 0.05 and − 1 ≥ log2 fold change ≥ 1 were identified as differentially expressed genes (DEG) in each of the 3 stresses..

对于每个基因中的每个对比，计算了适度的t统计量和差异表达的对数几率。在每种压力下，q值截止点为≤0.05且-1≥log2倍变化≥1的基因被确定为差异表达基因（DEG）。

RNA-seq profiling of DEGs under three stresses

三种胁迫下差异表达基因的RNA-seq分析

To validate the meta-analysis of microarray data, three independent RNA-seq data sets (including GSE8081: drought, PRJEB4671: salt, PRJNA506503: cold) were retrieved from GEO/SRA data bases and subjected to DEG analysis using edgeR and Limma packages in R. The gene expressions with |log2 fold change| ≥ 1 and FDR < 0.05 were considered significant..

为了验证微阵列数据的荟萃分析，从GEO/SRA数据库中获取了三个独立的RNA-seq数据集（包括GSE8081：干旱，PRJEB4671：盐，PRJNA506503：寒冷），并使用R中的edgeR和Limma包进行了差异表达基因（DEG）分析。基因表达变化满足|log2 fold change| ≥ 1且FDR < 0.05的被认为是显著的。

Validation of candidate genes by qRT-PCR

通过qRT-PCR验证候选基因

In order to validate the results of identifying candidate genes by meta-analysis, the genes were subjected to real-time PCR under drought stress in rice cultivar Neda. This cultivar is a high-yielding breeding line with relatively low water demand that is cultivated in Northern Iran. The seeds of this cultivar were obtained from Rice Research Institute of Iran.

为了验证通过荟萃分析鉴定候选基因的结果，在水稻品种Neda的干旱胁迫下对这些基因进行了实时PCR分析。该品种是一个高产育种系，需水量相对较低，种植于伊朗北部。该品种的种子由伊朗水稻研究所提供。

All the plant experiments/protocols were performed with relevant institutional, national, and international guidelines and legislation. Relevant permissions were obtained for plant sample collection. The plants were raised up to 5–6 leaf stage in hydroponic conditions with 4 replicates and the drought stress was treated for 6 h via imposing the roots to air and then leaf samples were collected under both normal and stress conditions.

所有植物实验/协议均按照相关的机构、国家和国际指南及法规进行。已获得植物样品采集的相关许可。植物在水培条件下生长至5-6叶期，设置4个重复，通过将根部暴露于空气中施加干旱胁迫6小时，然后在正常和胁迫条件下收集叶片样品。

In addition, another experiment was conducted for examining salinity response, so that seedlings (at 5–6 leaf stage) were imposed to salinity stress (150 mM NaCl) for 24 h and then the leaf samples (in 3 replicates) were collected. Furthermore, in another experiment, the cold response of rice was examined.

此外，还进行了另一项实验以检测盐度响应，将幼苗（处于5-6叶期）置于盐度胁迫（150 mM NaCl）下24小时，然后收集叶片样品（3个重复）。此外，在另一项实验中，检测了水稻的冷响应。

For this, the seedlings (at 5–6 leaf stage) were subjected to low temperature (4 °C) for 24 h and then leaf samples (in 3 replicates) were collected for RNA extraction. RNA was extracted from samples using QIAGENE extraction kit. The cDNA was synthesized using a commercial kit (ParsTous cDNA synthesis kit, Iran).

为此，将幼苗（处于5-6叶期）置于低温（4°C）下24小时，然后收集叶片样品（3个重复）用于RNA提取。使用QIAGENE提取试剂盒从样品中提取RNA。使用商业试剂盒（ParsTous cDNA合成试剂盒，伊朗）合成cDNA。

Primer pairs for 2 and 6 up- and downregulated DEGs were designed using Primer 3.0 online tool (.

使用Primer 3.0在线工具设计了2个和6个上调和下调的差异表达基因（DEGs）的引物对。

https://www.primer3plus.com/index.html

) (Supplementary Table S1). The

)（补充表 S1）。该

OsActin

gene was used as housekeeping reference gene. Real-time qRT-PCR was conducted on cDNA samples and the statistical analysis of Ct values of selected genes was done using REST software

基因被用作看家参考基因。实时qRT-PCR在cDNA样品上进行，使用REST软件对所选基因的Ct值进行了统计分析。

. The relative expression in stressful condition vs. normal condition was calculated using 2

. 通过2计算了在压力条件与正常条件下的相对表达量

−∆∆Ct

method

方法

。

Network analysis

网络分析

Protein-protein Interaction (PPI) network was drawn by Cytoscape software ver. 3.9.1 and information derived from the website STRING (

蛋白质-蛋白质相互作用（PPI）网络由Cytoscape软件3.9.1版绘制，并从STRING网站获取信息（

https://string-db.org

). The minimum required interaction score was set to 0.40 for more confidence.

）。为了更有信心，最低要求的交互分数设定为0.40。

Results

结果

Differential gene expression analysis

差异基因表达分析

Meta-analysis was used to find out the most probable genes responsible for tolerance of rice to drought, salinity and cold stresses (Table

荟萃分析用于找出最可能负责水稻耐旱、耐盐和耐寒胁迫的基因（表

). The analysis was conducted on more than 57,000 probes set, and 2-sided clustering showed adequate resolution between samples and genes under different stress conditions, especially under drought stress (Supplementary Fig.

）。分析是在超过57,000个探针组上进行的，双向聚类显示在不同胁迫条件下样本和基因之间有足够分辨率，尤其是在干旱胁迫下（补充图。

A–C). Meta-analysis of standardized microarray data was conducted to identify specific and common genes responding to multiple abiotic stresses. In the DEG analysis it was obtained 3,607 downregulated and 1,929 upregulated genes under all conditions (Table

A–C). 进行了标准化微阵列数据的荟萃分析，以识别响应多种非生物胁迫的特定和共同基因。在差异表达基因分析中，所有条件下获得了3,607个下调基因和1,929个上调基因（表）。

). Drought stress resulted in up- and downregulation of 375 and 298 genes, respectively. 281 and 313 genes were up- and downregulated under salt stress, and 1,273 and 2,996 genes were up- and downregulated under cold stress) Table

）。干旱胁迫导致375个基因上调和298个基因下调。盐胁迫下，281个基因上调，313个基因下调；冷胁迫下，1,273个基因上调，2,996个基因下调）表

; Supplementary Table S2. The identified DEGs showed a discrete relative expression pattern under 3 stresses as revealed by Volcano plot analysis (Fig.

; 补充表S2。通过火山图分析（图）揭示了在3种胁迫下鉴定的差异表达基因显示出离散的相对表达模式。

A–C). Ten top specific DEGs for each stress condition were depicted in Table

A-C）。每种压力条件下的十个最具体的差异表达基因（DEGs）在表中进行了描述。

. As seen, 7 genes (including

。如图所示，7个基因（包括

OsEnS-22

，

OsPP2C51

，

OsCAF1A

，

BZIP12

，

OsRLCK243

and two

和二

DUF581

) were upregulated in drought stress; 3 genes (

）在干旱胁迫中上调；3个基因（

OsRCCR1

，

OsLTPd1

and

和

OsLTPd6

) were upregulated in salt stress, and 3 genes (

在盐胁迫下上调，3个基因（

CDKC

，

OSNPB_030848600

and

和

OsCML22

) were upregulated in cold stress.

）在冷胁迫下上调。

Table 2 The number of down- and upregulated genes (DEGs) under three stresses in rice microarray data.

表2 水稻微阵列数据中三种胁迫下差异表达基因（DEGs）的数量。

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Table 3 Ten top specific annotated DEGs for each stress condition in rice seedlings identified using microarray data analysis. Significant relative expression values (in view of LogFC) are presented in last column.

表3 通过微阵列数据分析鉴定的水稻幼苗在每种胁迫条件下的十个最显著特异性注释差异表达基因（DEGs）。最后一列展示了显著的相对表达值（以LogFC为参考）。

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Common genes were identified for response to drought and salt (91), drought and cold (121), and salt and cold (108), while 14 genes were common for response to all 3 stresses (Fig.

鉴定出对干旱和盐分（91个）、干旱和寒冷（121个）、以及盐分和寒冷（108个）共同响应的基因，而有14个基因是对这三种胁迫共同响应的（图。

D). Heatmap analysis indicated the discriminated expression pattern of all DEGs under the studied stress conditions (Fig.

D). 热图分析显示了在研究的胁迫条件下所有差异表达基因的区分表达模式（图。

A). The meta-analysis revealed that 12 out of 14 common genes were downregulated, and only 2 genes were upregulated (Fig.

A). 荟萃分析显示，14个常见基因中有12个被下调，只有2个基因被上调（图。

B). Notably, two genes

B). 值得注意的是，两个基因

Os01g0741900

(

IAA6

) and

) 和

Os03g0221800

（a

LRR-like

类LRR

) were upregulated, and three non-ABC transporters including

）被上调，包括三个非ABC转运蛋白在内的

Os10g0111700

，

Os02g0102200

and

和

Os06g0125500

(

POT

锅

，

OsAAP7C

and

和

OsGT1

, respectively) were downregulated under all three stresses.

分别在三种胁迫下均被下调。

Fig. 1

图1

Volcano plots showing differential expression under 3 stresses. (

显示在三种胁迫下的差异表达的火山图。 (

) drought, (

`) 干旱，(`

) Salinity, (

) 盐度，(

) cold. (

) 冷。(

) Venn diagram showing the number of unique and common DEGs between 3 stresses.

) 显示3种胁迫之间独特和共同差异表达基因数量的维恩图。

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Fig. 2

图2

(

) Heat map of all identified DEGs in the study under 3 stresses. (

) 在三种压力下，研究中所有已鉴定的差异表达基因 (DEGs) 的热图。(

) A heat map showing expression pattern of 14 common DEGs between 3 stresses.

显示3种胁迫之间14个常见差异表达基因表达模式的热图。

AFC

亚洲足球联合会

: average fold change under stress.

：压力下的平均倍数变化。

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RNA-seq profiling of common DEGs under three stresses

三种胁迫下常见差异表达基因的RNA-seq分析

To further validate the DEG identification obtained by meta-analysis on microarray data, the RNA-seq profiling of the 14 common DEGs was conducted. In overall a good consistency existed between the two data sets, particularly a high consistency detected between DEGs under drought stress (Table

为了进一步验证通过微阵列数据的荟萃分析获得的差异表达基因（DEG）识别结果，对14个常见的差异表达基因进行了RNA-seq分析。总体而言，两组数据之间存在良好的一致性，尤其是在干旱胁迫下的差异表达基因之间检测到高度一致性（表）。

). The correlation between results of two assays was 0.919 (drought), 0.843 (salt) and 0.873 (cold). Among 14 common DEGs,

）。两种检测方法结果之间的相关性为0.919（干旱）、0.843（盐）和0.873（冷）。在14个常见的差异表达基因中，

IAA6

(

Os01g0741900

) which is an auxin-responsive protein

) 它是一种生长素响应蛋白

was significantly upregulated under severe drought, salt and cold stresses. Additionally, a LRR protein coding gene (

在严重的干旱、盐和冷胁迫下显著上调。此外，一个LRR蛋白编码基因（

Os03g0221800

), was significantly upregulated only under drought and cold stresses. However, eight genes including

），仅在干旱和寒冷胁迫下显著上调。然而，包括八个基因在内的

Os03g0221700

(serine/threonine protein kinase),

（丝氨酸/苏氨酸蛋白激酶），

Os01g0619900

(

OsTCL2

Os10g0111700

(POT family protein),

（POT家族蛋白），

Os04g0387900

(AT.I.24-6 protein),

(AT.I.24-6 蛋白),

Os05g0481100

，

Os04g0531750

，

Os06g0125500

(

OsGT1

) and

) 和

Os08g0545700

(TraB protein-related) are among the downregulated genes under all 3 stresses. A non-ABC transporter (

(TraB蛋白相关)基因是在所有三种压力下均被下调的基因之一。一种非ABC转运蛋白(

OsAAP7C

) and

) 和

Os12g0438400

(hypothetical protein) were downregulated under drought and cold stresses. Two other genes (

（假设蛋白）在干旱和寒冷胁迫下被下调。另外两个基因（

Os08g0174500

and

和

Os12g0583500

) showed downregulation under both drought and salt stresses.

）在干旱和盐胁迫下均显示出下调。

Table 4 RNA-seq profiling of DEGs under three stresses in rice supported by public results, retrieved from GEO/SRA databases. Significant up/dowregulated DEGs in view of log2 fold change are presented in bold and italics colors, respectively.

表4 在三种胁迫下水稻中DEGs的RNA-seq表达谱，由公共结果支持，数据来源于GEO/SRA数据库。显著上调/下调的DEGs根据log2倍数变化分别以粗体和斜体颜色表示。

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Validation of meta-analysis results by qRT-PCR

qRT-PCR验证元分析结果

The expression of selected genes of up- and downregulated classes that were identified in meta-analysis, were examined using real-time qRT-PCR, and the obtained results are depicted in Fig.

通过实时qRT-PCR检测了在荟萃分析中鉴定的上调和下调类别中选定基因的表达，所得结果如图所示。

. As seen in the figure, both direction and magnitude of expression of the studied genes are comparable to meta-analysis results. Two upregulated DEGs (

。如图所示，所研究基因的表达方向和大小与荟萃分析结果具有可比性。两个上调的差异表达基因 (

IAA6

and

和

LRR-like

类似LRR

) showed 4.4 and 2.9 fold changes under drought stress, and 3.1 and 1.9 fold changes under salinity stress, and 1.6 and 2.3 fold changes under cold stress, respectively. Six downregulated DEGs showed − 2.8 to − 4.3 fold changes under drought stress. Similarly, the DEGs showed − 3.9 to − 7.0, and − 2.0 to − 4.6 fold changes, respectively, under salinity and cold stresses.

）在干旱胁迫下显示出4.4和2.9倍的变化，在盐胁迫下显示出3.1和1.9倍的变化，在冷胁迫下分别显示出1.6和2.3倍的变化。六个下调的差异表达基因在干旱胁迫下显示出-2.8至-4.3倍的变化。同样，这些差异表达基因在盐胁迫和冷胁迫下分别显示出-3.9至-7.0和-2.0至-4.6倍的变化。

With these results, real-time qRT-PCR confirmed the DEGs identified by meta-analysis..

通过这些结果，实时qRT-PCR验证了通过荟萃分析鉴定的差异表达基因（DEGs）。

Fig. 3

图 3

Relative expression results of 2 upregulated and 6 downregulated DEGs under abiotic stresses in rice seedlings. A: under drought stress; B: under salinity stress. C: under cold stress. * and ** represent the significance of relative expression at

水稻幼苗在非生物胁迫下2个上调和6个下调的差异表达基因的相对表达结果。A：干旱胁迫下；B：盐胁迫下；C：冷胁迫下。* 和 ** 代表相对表达的显著性水平。

≤ 0.05 and

小于等于0.05且

≤ 0.01 levels, respectively.

≤ 0.01 水平，分别。

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Protein–protein interaction (PPI) network of meta DEGs

差异表达基因（DEGs）的蛋白质-蛋白质相互作用（PPI）网络

The predicted protein-protein interaction network of

预测的蛋白质-蛋白质相互作用网络

Os10g0111700

(POT protein, which is a non-ABC crucial peptide/nutrient transporter) and

(POT蛋白，这是一种非ABC关键肽/营养转运蛋白) 和

Os08g0545700

(TraB protein, which plays a crucial role in autophagic degradation and is vital for the recycling process) was generated using the STRING database (Fig.

（TraB蛋白，其在自噬降解中起关键作用，并且对回收过程至关重要）是使用STRING数据库生成的（图。

). It is predicted that

）。据预测，

Os10g0111700

interacts with manganese-dependent ADP-ribose/CDP-alcohol diphosphatase (

与锰依赖性ADP-核糖/CDP-醇二磷酸酶相互作用 (

OsJ_25650

) and calcineurin-like phosphoesterase (

`) 和钙调磷酸酶样磷酸酯酶 (`

OsJ_34100

). On the other hand, the protein of the downregulated gene

). 另一方面，下调基因的蛋白质

OS08g0545700

shows more diverse interactions. The most confident interaction is between

展示了更多样化的互动。最自信的互动存在于

Os08g0545700

and molybdenum cofactor sulfurase 3 (

和钼辅因子硫化酶3 (

Os08g0545000

). Additionally, inositol-1-monophosphatase, transcription initiation factor IIA subunit 2, and cytochrome P450 703A2 are predicted to interact with

此外，肌醇-1-单磷酸酶、转录起始因子IIA亚基2和细胞色素P450 703A2被预测与

Os08g0545700

. However, the database could not find any connection between these two downregulated genes (Fig.

然而，数据库无法找到这两个下调基因之间的任何联系（图。

）。

Fig. 4

图4

Predicted protein-protein interaction network of

预测的蛋白质-蛋白质相互作用网络

Os10g0111700

(POT protein) and

（POT蛋白）和

Os08g0545700

(TraB protein). The first network contains 8 nodes, and the second contains 3 nodes. Line thickness indicates the strength of data support.

（TraB蛋白）。第一个网络包含8个节点，第二个网络包含3个节点。线条粗细表示数据支持的强度。

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Discussion

讨论

As shown in this microarray-based meta-analysis,

正如这项基于微阵列的荟萃分析所示，

IAA6

and an LRR protein were upregulated under three abiotic stresses including drought, salinity and cold. Aux/IAA genes are known to play a crucial role in the tolerance of plants to abiotic stresses

一种LRR蛋白在包括干旱、盐度和寒冷在内的三种非生物胁迫下被上调。Aux/IAA基因已知在植物对非生物胁迫的耐受性中起关键作用。

. Studies have reported differential expression of many Aux/IAA genes under stress conditions such as salinity and cold in soybean

研究表明，在大豆中许多Aux/IAA基因在盐度和寒冷等胁迫条件下表现出差异表达。

. A transcriptomic profiling study conducted on rice grown under abiotic stress showed that several OsIAA proteins, including OsIAA9 and OsIAA20 (XP_015641983.1), were significantly upregulated under salt and drought stresses

一项针对在非生物胁迫下生长的水稻进行的转录组分析研究表明，包括OsIAA9和OsIAA20（XP_015641983.1）在内的几种OsIAA蛋白在盐胁迫和干旱胁迫下显著上调。

. Recent research has revealed that auxin-sensitive Aux/IAA proteins such as IAA5, IAA6, and IAA19 regulated aliphatic GLS levels in Arabidopsis plants exposed to drought conditions, and loss of IAA5/6/19 resulted in decreased drought tolerance

最近的研究表明，对生长素敏感的Aux/IAA蛋白（如IAA5、IAA6和IAA19）在干旱条件下调控拟南芥植物中的脂肪族GLS水平，而IAA5/6/19的缺失导致抗旱能力下降。

. Additionally, these IAAs were found to be involved in stomatal regulation and drought stress response. The OsIAA20 gene was also found to display increased expression levels under drought stress, salt stress, and ABA treatment

此外，这些IAAs被发现参与气孔调节和干旱胁迫响应。OsIAA20基因在干旱胁迫、盐胁迫和ABA处理下也表现出表达水平的上升。

. A study found that drought stress induces the rice gene

一项研究发现，干旱胁迫会诱导水稻基因

OsIAA6

, which plays a key role in the response to drought stress and the regulation of tiller growth. Overexpression of

，它在干旱胁迫的响应和分蘖生长的调节中起着关键作用。过表达

OsIAA6

in transgenic rice plants improves drought tolerance by regulating auxin biosynthesis genes. The gene is specifically expressed in the axillary meristem of the basal stem, which gives rise to tillers. A knock-down mutation of

在转基因水稻植株中，通过调控生长素生物合成基因提高抗旱性。该基因在茎基部腋生分生组织中特异性表达，这部分组织会产生分蘖。一个敲减突变导致了

OsIAA6

resulted in abnormal tiller outgrowth, suggesting that

导致了异常的分蘖生长，这表明

OsIAA6

is involved in the control of tiller growth through the regulation of

参与通过调节控制分蘖生长的

OsPIN1

and

和

OsTB1

. Many studies have demonstrated the importance of auxin biosynthesis genes in improving drought tolerance. Overexpression of

许多研究已经证明了生长素生物合成基因在提高抗旱性方面的重要性。过度表达

OsIAA6

and

和

OsABF1/57

in rice resulted in drought tolerance

在水稻中导致了抗旱性

，

. In tobacco, overexpression of iiaH and iiaM genes, involved in auxin biosynthesis, led to improved heat tolerance and water retention capacity. These findings suggest that auxin biosynthesis plays a crucial role in enhancing plant drought tolerance

在烟草中，过表达参与生长素生物合成的iiaH和iiaM基因，可提高耐热性和保水能力。这些发现表明，生长素的生物合成在增强植物抗旱性方面起着关键作用。

。

LRR (leucine-rich repeat) proteins play a crucial role in the response of plants to abiotic stress conditions. These proteins are involved in various signaling pathways that regulate plant growth, development, and stress responses. LRR proteins act as receptors or co-receptors, perceiving external signals and transmitting them to downstream signaling components.

LRR（富含亮氨酸重复）蛋白在植物对非生物胁迫条件的响应中起着至关重要的作用。这些蛋白参与各种信号通路，调控植物的生长、发育和胁迫响应。LRR蛋白充当受体或共受体，感知外部信号并将其传递给下游信号组分。

四十三

. During abiotic stress, such as drought, salinity, extreme temperatures, or oxidative stress, LRR proteins are known to participate in stress perception and signal transduction. They can activate specific defense pathways, regulate gene expression, and modulate physiological and biochemical responses to help plants adapt and survive under adverse conditions.

在干旱、盐碱、极端温度或氧化压力等非生物胁迫下，LRR蛋白参与胁迫感知和信号转导。它们能激活特定的防御途径，调控基因表达，调节生理和生化反应，帮助植物在不利条件下适应和生存。

. The specific mechanisms through which LRR proteins function in abiotic stress responses can vary depending on the plant species and the nature of the stress. Some LRR proteins are involved in the perception of stress signals and the activation of defense-related genes, while others participate in stress tolerance by regulating ion homeostasis, osmotic adjustment, or antioxidant defense systems.

LRR蛋白在非生物胁迫响应中的具体作用机制可能因植物种类和胁迫性质而异。一些LRR蛋白参与胁迫信号的感知和防御相关基因的激活，而另一些则通过调节离子稳态、渗透调节或抗氧化防御系统来参与胁迫耐受。

，

。

Our meta-analysis on microarray data showed that

我们的微阵列数据的荟萃分析显示

Os10g0111700

(POT family protein), which is a non-ABC crucial peptide/nutrient transporter, was downregulated under three abiotic stresses. Furthermore, two additional non-ABC transports (viz.

（POT家族蛋白）是一种非ABC关键肽/营养转运蛋白，在三种非生物胁迫下被下调。此外，还有另外两种非ABC转运蛋白（即

OsGT1

and

和

OsAAP7C

) that are involved in amino acid/oligopeptide transport, were downregulated under 3 stresses that their expression was validated under drought/salt/cold by RNAseq analysis (Table

) 参与氨基酸/寡肽转运的基因在三种胁迫下被下调，其表达通过RNAseq分析在干旱/盐/冷条件下得到验证 (表

). The import of nutrients from outside the cell is crucial for the survival of all living organisms. While some nutrients can cross the cellular membrane by passive diffusion, others require specific transport proteins for facilitated transport. These transport processes can be powered by either primary or secondary energy sources.

）。从细胞外部输入营养物质对所有生物的生存至关重要。虽然有些营养物质可以通过被动扩散穿过细胞膜，但其他一些则需要特定的转运蛋白来辅助运输。这些转运过程可以由主要或次要能源驱动。

The uptake of nitrogen from the surroundings through the peptide transport is a significant pathway for cells.

通过肽转运从周围环境中吸收氮是细胞的重要途径。

. Disruption of the absorption and transfer of nutrients, especially nitrogen (which is crucial for synthesis of amino acids and peptides) into cells and tissues will reduce cell growth and proliferation. The downregulation of the abovementioned genes under abiotic stresses can explain why and how the leaves of stressed plants turn yellow.

营养物质尤其是氮（对氨基酸和肽的合成至关重要）的吸收和转运受到干扰，会减少细胞和组织的生长与增殖。上述基因在非生物胁迫下的下调表达，可以解释受胁迫植物叶片为何以及如何变黄。

The POTs, also known as PTR2s uses the electrochemical proton gradient for the uptake of their substrate. The proton-dependent oligopeptide transporters from different kingdoms of life can generally be classified into two groups: the PEPT-like POTs and the PHTs. The PEPT1-like POTs are the most abundant and can be found in bacteria, fungi, protists, and plants.

POTs，也称为PTR2s，利用电化学质子梯度来吸收其底物。来自不同生物界的依赖质子的寡肽转运蛋白通常可以分为两类：PEPT样POTs和PHTs。PEPT1样POTs是最丰富的，存在于细菌、真菌、原生生物和植物中。

The POT family is included in the major facilitator superfamily (MFS) in the Transporter Classification Database.

POT家族包含在转运蛋白分类数据库的主要促进因子超家族（MFS）中。

. The PTR system in

。PTR系统在

S. cerevisiae

酿酒酵母

is composed of three genes that are mutually dependent. Ptr2, the most well-known member of the PTR family, is encoded by

由三个相互依赖的基因组成。Ptr2，PTR家族中最著名的成员，由

PTR2

and is an integral membrane transporter. Isoforms of Ptr2 have also been found in

并且是一种完整的膜转运蛋白。Ptr2的同工型也在

Candida albicans

白色念珠菌

and

和

A. thaliana

拟南芥

，

. The ability to transport other nitrogen sources, for example, by nitrate permease

通过硝酸盐透性酶运输其他氮源的能力

AtCHL1

在

(A) thaliana

(A) 拟南芥

, has been acquired by members of the POT family in plants

，已被植物中的POT家族成员获取

. The NPF family, a vital group of NRTs in plants, is not only regulated by nitrate but also by other nutrients, playing roles in various signaling pathways. In

NPF家族是植物中重要的NRT家族，不仅受硝酸盐调控，还受其他营养物质的调控，在多种信号通路中发挥作用。

Brassica napus

甘蓝型油菜

，

BnaNPFs

respond to nitrogen (N), phosphorus (P), potassium (K) stresses, and NH

响应氮 (N)、磷 (P)、钾 (K) 胁迫，以及 NH

toxicity in both leaves and roots, suggesting their involvement in nutrient sensing and crosstalk. Moreover,

叶片和根部的毒性，表明它们参与了营养感知和串扰。此外，

BnaA05.NPF1;1

emerges as a key regulator under diverse nutrient conditions, including NH

在包括NH在内的多种营养条件下，成为一个关键的调节因子，

加号

toxicity, highlighting its role in

毒性，强调其在

(B) napus

(B) 油菜

resistance

抵抗

. In rice, maize, sorghum, peanut, soybean, and Arabidopsis, PTR genes (part of the NPF family) are involved in N uptake and utilization, especially under low N conditions. They are distributed across various genomic regions and may interact to regulate N metabolism, particularly through hub genes like protein kinases.

在水稻、玉米、高粱、花生、大豆和拟南芥中，PTR基因（属于NPF家族的一部分）参与氮的吸收和利用，尤其是在低氮条件下。它们分布于不同的基因组区域，可能通过枢纽基因（如蛋白激酶）相互作用来调节氮代谢。

. In cotton,

。在棉花中，

GhNPF

genes show differential expression under abiotic stresses, with

基因在非生物胁迫下表现出差异表达，

GhNPF8

exhibiting varied responses to cold, heat, salt, and drought stresses, suggesting their involvement in stress response mechanisms

对冷、热、盐和干旱胁迫表现出不同的反应，表明它们参与了胁迫响应机制。

. This research provides insights into the role of NPF genes in nutrient sensing, crosstalk and stress responses across different plant species

这项研究为NPF基因在不同植物物种中的营养感知、串扰和胁迫反应中的作用提供了见解。

。

Nitrogen is essential for plant growth and productivity, and rice growth relies heavily on the activity of PTR/NRT1 transporters

氮是植物生长和生产力所必需的，水稻的生长很大程度上依赖于PTR/NRT1转运蛋白的活性。

. Fan et al.

. 范等

suggest that upregulating the expression of

提示上调表达

OsPTR6

could enhance rice growth by increasing the expression of ammonium transporters and the activity of glutamine synthetase (GSA). When the

可以通过增加铵转运蛋白的表达和谷氨酰胺合成酶 (GSA) 的活性来促进水稻生长。当

OsPTR6

gene was overexpressed in the Nipponbare rice cultivar, it led to increased rice growth via increased ammonium transporter expression and GSA activity

该基因在日本晴水稻品种中过表达时，通过增加铵转运蛋白表达和GSA活性，导致水稻生长增加。

. The rice nitrate transporter 1/peptide transporter family 8.1 (

。水稻硝酸盐转运蛋白1/肽转运蛋白家族8.1 (

OsNPF8.1

) is an important peptide transporter that plays a significant role in the rebalancing of plant growth and tolerance to abiotic stresses like N deficiency, salt, drought, and ABA by facilitating stress-induced organic N transportation. Its activity helps in redistributing organic N during stress conditions, resulting in changes in water potential and proline levels that aid in stress tolerance.

）是一种重要的肽转运蛋白，通过促进胁迫诱导的有机氮运输，在植物生长的再平衡及对无机胁迫（如缺氮、盐分、干旱和脱落酸）的耐受性中发挥重要作用。其活性有助于在胁迫条件下重新分配有机氮，从而导致水势和脯氨酸水平的变化，增强对胁迫的耐受性。

。

The meta-analysis of multiple experiments examining plant transcriptional responses to drought, salinity and cold stresses revealed that

对多个研究植物干旱、盐碱和寒冷胁迫转录反应的实验进行的荟萃分析表明

Os10g0111700

, a member of the POT family of proteins, was consistently downregulated across all conditions. This finding strongly suggests that the suppression of this transporter protein is a key response of rice to oxidative stress. The recently solved crystal structure of

，属于POT蛋白家族的成员，在所有条件下均一致下调。这一发现强烈表明，该转运蛋白的抑制是水稻应对氧化应激的关键反应。最近解析的晶体结构

NRT1

。

indicates that

表明

Thr101

is located on 3rd transmembrane motif (TM3) and faces a hydrophobic pocket created by residues on TM2 and TM4, which make up the extracellular and intracellular gates, respectively. It is suggested that phosphorylation of this residue would interfere with the helix packing and allow

位于第三个跨膜基序（TM3）上，面向由TM2和TM4上的残基形成的疏水口袋，这些残基分别构成了细胞外和细胞内的门。据推测，该残基的磷酸化会干扰螺旋堆积并允许

NRT1

。

to cycle faster, potentially lowering the energy barrier for the return step in the transport cycle

加快循环速度，可能会降低传输循环中返回步骤的能量障碍

. This disruption may also trigger a transition from dimer to monomer in the membrane, which could subsequently impact the regulation of the nitrate signaling pathway that activates the high-affinity nitrate uptake system

。这种破坏还可能触发膜中二聚体向单体的转变，随后可能影响激活高亲和力硝酸盐吸收系统的硝酸盐信号通路的调控。

，

。

The interactions between the endoplasmic reticulum (ER) and mitochondria are crucial for mitochondrial division and the exchange of signals and substrates between these compartments. While animal proteins involved in this process have been extensively studied, only a few plant proteins have been identified as regulators of ER-mitochondrial interactions.

内质网 (ER) 和线粒体之间的相互作用对于线粒体分裂以及这些细胞器之间信号和底物的交换至关重要。尽管已对参与此过程的动物蛋白进行了广泛研究，但仅发现少数植物蛋白是 ER-线粒体相互作用的调节因子。

，

. Li et al.

李等人。

identified the evolutionarily conserved

识别出进化上保守的

TraB

运输B

family proteins as important regulators of two pathways: ER-mitochondrial interactions and mitophagy, the degradation of damaged mitochondria. They indicated that TRB1 has a critical role in maintaining mitochondrial homeostasis, and its dysfunction leads to an accumulation of damaged mitochondria and impaired mitochondrial function.

家族蛋白作为两条通路的重要调节因子：内质网-线粒体相互作用和线粒体自噬，即受损线粒体的降解。他们指出，TRB1在维持线粒体稳态方面具有关键作用，其功能障碍会导致受损线粒体的积累和线粒体功能受损。

。

TraB

传输蛋白B

is a DNA translocase similar to

是一种类似于的DNA转位酶

FtsK

and is accountable for the transfer of conjugative plasmids in Streptomyces. Unlike other conjugative systems that rely on a type IV secretion system, the transfer of the plasmid as double-stranded DNA in Streptomyces is only dependent on the TraB protein

并且负责链霉菌中接合质粒的转移。与其他依赖IV型分泌系统的接合系统不同，链霉菌中作为双链DNA的质粒转移仅依赖于TraB蛋白。

. Researchers have shown that TraB-family proteins, which act as mitophagy receptors, have been identified in plants.

研究人员表示，作为线粒体自噬受体的TraB家族蛋白已在植物中被鉴定出来。

TRB1

and

和

TRB2

play a crucial role in mitophagy by interacting with ATG8 to mark damaged mitochondria for autophagic degradation and are crucial for the recycling process. Unlike animal and yeast cells, plant cells have chloroplasts that can produce ATP, so a mild disturbance in mitochondrial function, as seen in the .

通过与ATG8相互作用在线粒体自噬中发挥关键作用，标记受损线粒体以进行自噬降解，并且对回收过程至关重要。与动物和酵母细胞不同，植物细胞含有可以产生ATP的叶绿体，因此线粒体功能的轻微扰动，正如在...中所见。

trb1trb2

double mutant, may not cause a significant growth defect under normal circumstances

双突变体，在正常情况下可能不会导致显著的生长缺陷。

. It is reported that, the accumulation of

据报道，积累的

TRAB-1

transcript and protein was observed to be higher in the tolerant rice cultivar Nonabokra when subjected to cadmium and salt stresses

在耐受性水稻品种Nonabokra中，当受到镉和盐胁迫时，观察到其转录本和蛋白质水平较高。

，

. Our analysis suggests that the downregulation of TraB family proteins during periods of stress is a significant consequence that causes severe damage to rice plants. However, further investigations, such as conducting experiments where these proteins are overexpressed in stressed plants, are necessary to validate this hypothesis..

我们的分析表明，TraB 家族蛋白在压力时期的下调是一个重要的后果，会导致对水稻植株的严重损害。然而，要进一步验证这一假设，还需要进行更多的研究，例如在受压植物中过度表达这些蛋白的实验。

The prediction of the protein-protein interaction network of

蛋白质-蛋白质相互作用网络的预测

Os10g0111700

(coding POT protein) (Fig.

（编码POT蛋白）（图。

) revealed a connection between the protein and manganese-dependent ADP-ribose/CDP-alcohol diphosphatase (

）揭示了该蛋白与锰依赖性的ADP-核糖/CDP-醇二磷酸酶之间的联系（

OsJ_25650

). Manganese-dependent ADP-ribose/CDP-alcohol diphosphatase (mADPR/CDP-alcohol pyrophosphatase) is an enzyme found in plants that is involved in the metabolism of the signaling molecule ADP-ribose (ADPR). This enzyme can hydrolyze both ADPR and CDP-alcohols, which are important intermediates in nucleotide metabolism.

）。锰依赖性ADP-核糖/CDP-醇二磷酸酶（mADPR/CDP-醇焦磷酸酶）是一种存在于植物中的酶，参与信号分子ADP-核糖（ADPR）的代谢。该酶能够水解ADPR和CDP-醇，这些是核苷酸代谢中的重要中间体。

It has been suggested that mADPR/CDP-alcohol diphosphatase may play a role in regulating plant growth and development, as well as in the response of plants to biotic and abiotic stresses.

有人认为，mADPR/CDP-醇二磷酸酶可能在调节植物生长发育以及植物对生物和非生物胁迫的响应中发挥重要作用。

. Additionally, there is another interaction reported between the POT protein and calcineurin-like phosphoesterase (

此外，还有报道称POT蛋白和钙调神经磷酸酶样磷酸酯酶之间存在另一种相互作用（

OsJ_34100

), which is a family of enzymes found in plants involved in various cellular processes, including the regulation of ion channels and the response to abiotic stresses. Specifically, CAs play a role in regulating the levels of calcium ions (Ca

），这是植物中发现的一类酶家族，参与多种细胞过程，包括离子通道的调节和对非生物胁迫的响应。具体来说，CAs 在调节钙离子（Ca）水平方面发挥着作用。

) in plant cells, which are essential for signal transduction in response to various environmental stresses. CAs achieve this by dephosphorylating certain proteins involved in the transport of calcium ions across membranes in plant cells. Overall, CAs help to maintain calcium homeostasis in plant cells, which is crucial for normal plant growth and development, as well as for the response to various abiotic stresses.

）在植物细胞中，这对于响应各种环境胁迫的信号转导至关重要。CAs通过去磷酸化某些参与植物细胞膜钙离子转运的蛋白质来实现这一功能。总体而言，CAs有助于维持植物细胞中的钙稳态，这对植物的正常生长发育以及对各种非生物胁迫的响应都至关重要。

，

. On the other hand, the protein encoded by the downregulated gene

另一方面，下调基因编码的蛋白质

Os08g0545700

(

IAA6

) shows a confident interaction with molybdenum cofactor sulfurase 3 (

) 显示了与钼辅因子硫化酶 3 的自信互动 (

Os08g0545000

). It is suggested that MCSU3 plays a critical role in maintaining plant growth and development under normal conditions by regulating the activity of enzymes involved in sulfur and molybdenum metabolism. The study also proposed that MCSU3 may be involved in stress response pathways in plants, but further research is needed to confirm this.

）。研究表明，MCSU3通过调节参与硫和钼代谢的酶的活性，在正常条件下对维持植物生长发育起着关键作用。该研究还提出MCSU3可能参与植物的胁迫响应途径，但需要进一步研究来证实这一点。

。

Conclusion

结论

The results of transcriptome meta-analysis of rice under multiple stresses indicate the single stress-specific and common responses. Two and twelve genes were up- and downregulated in all stress conditions. Non-ABC transporters including

对水稻在多种胁迫下的转录组荟萃分析结果表明，单一胁迫特异性响应和共同响应存在差异。在所有胁迫条件下，分别有2个和12个基因被上调和下调。非ABC转运蛋白包括

POT

锅

，

OsAAP7C

and

和

OsGT1

were downregulated, a phenomenon that is resulted to inability of the plant to uptake and transfer nitrate and amino acids under stressful conditions, and hence, is resulted to decrease of plant growth which is obvious from turning the green tissues to yellow color. On this basis, preventing the reduction of the expression of these genes under stress conditions, especially through the control of their upstream transcription factor genes, can help reduce the adverse effects of abiotic stress in reducing the absorption and transfer of nitrogen or amino acids..

被下调，这种现象导致植物在胁迫条件下无法吸收和转运硝酸盐和氨基酸，因此导致植物生长减缓，这从绿色组织变黄的现象中可以明显看出。基于此，防止这些基因在胁迫条件下的表达降低，特别是通过控制其上游转录因子基因，可以帮助减轻非生物胁迫对氮或氨基酸吸收和转运的不利影响。

Data availability

数据可用性

Data is provided within the manuscript or supplementary information files or available from the corresponding author upon reasonable request.

数据在手稿或补充信息文件中提供，或可在合理要求下从通讯作者处获得。

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周，H. 等。多个R2R3-MYB转录因子参与调控桃花中花青素的积累。

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植物科学前沿

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Acknowledgements

致谢

The work was supported by annual grants from Shahid Beheshti University.

这项工作得到了沙希德·贝赫什提大学的年度资助支持。

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作者与所属机构

Department of Cellular and Molecular Biology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran

伊朗德黑兰沙希德·贝赫什提大学生命科学与生物技术学院细胞与分子生物学系

Asadollah Ahmdikhah, Mehdi Safaeizadeh & Alireza S. Tehranian

阿萨杜拉·艾哈迈迪赫、迈赫迪·萨法伊扎德和阿里礼萨·S·德黑兰尼

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Asadollah Ahmdikhah

阿萨杜拉·艾哈迈迪赫

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Mehdi Safaeizadeh

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Alireza S. Tehranian

阿里礼萨·S·德黑兰尼安

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Contributions

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A.A. collected the transcriptome material and conducted the analyses. M.S. conducted qRT-PCR and contributed in analyses. A.S.T. prepared the MS draft and contributed in analyses. All authors read and approved the final MS.

A.A. 收集了转录组材料并进行了分析。M.S. 进行了qRT-PCR并参与了分析。A.S.T. 撰写了初稿并参与了分析。所有作者阅读并批准了最终稿件。

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Mehdi Safaeizadeh

梅赫迪·萨法伊扎德

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The authors declare no competing interests.

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Ahmdikhah, A., Safaeizadeh, M. & Tehranian, A.S. Responses of rice plant to multiple abiotic stresses revealed by transcriptome meta-analysis and identification of novel genetic factors.

Ahmdikhah, A., Safaeizadeh, M. & Tehranian, A.S. 通过转录组荟萃分析揭示水稻对多种非生物胁迫的响应并鉴定新的遗传因子。

Sci Rep

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, 8248 (2025). https://doi.org/10.1038/s41598-025-92527-2

`, 8248 (2025). https://doi.org/10.1038/s41598-025-92527-2`

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12 January 2024

2024年1月12日