水稻响应盐胁迫关键转录因子的鉴定

盐胁迫是影响水稻生产的重要非生物胁迫之一.本研究以盐胁迫条件下的水稻转录组数据为材料,通过HTSeq和DESeq软件分析转录因子在转录组水平上的表达变化.主要结果如下:水稻在盐胁迫1、3和6h三个时间点共有26个相同的差异表达转录因子,通过蛋白互作筛选出14个基因组成的重要模块;重要模块基因GO分析主要富集在ATP结合...     

基因芯片技术筛选转SlNAC1基因拟南芥差异表达基因

研究已表明植物特有的一些NAC(NAM,ATAF1/2,CUC2)转录因子可提高植物抗逆性,利用基因芯片技术筛选转SlNAC1基因拟南芥与野生型拟南芥间差异表达基因,能够为研究转基因拟南芥非生物胁迫抗性相关基因提供依据。结果显示,在转SlNAC1基因拟南芥43 604个基因中有3 046个差异表达2倍以上的基因。对差异表达5倍以上基因经过GO富集度统计学分析表明,细胞组分相关基因占33.05%;分子功能相关基因占33.95%;生物学过程相关基因占33.00%。对差异表达2倍以上基因进行KEGG信号通路分析,结果表明有2 431个基因涉及到88个不同的信号通路。通过筛选获得转基因拟南芥非生物胁迫抗性相关候选基因,为后续研究NAC转录因子的下游基因及其调控网络的构建提供方向和理论支撑。     

互花米草NHX2基因的克隆与功能鉴定

NHX2属于CPA1基因家族,编码Na~+/H~+逆向转运蛋白,控制液泡膜中活性K~+的摄取,同时调节气孔的关闭。该研究以耐盐植物互花米草为材料,采用PCR技术克隆NHX2基因,并将其转入拟南芥进行相关功能鉴定。结果显示:(1)成功克隆获得互花米草NHX2基因CDS序列(1 602 bp),命名为SaNHX2,该基因编码533个氨基酸,SaNHX2蛋白的分子量约为58.65 kD,定位于细胞核和细胞膜,表明SaNHX2基因可能发挥转录调控的功能。(2) qRT-PCR结果显示,在ABA、NaCl和干旱胁迫处理下,互花米草叶和根中SaNHX2基因的表达量均上调。(3)为进一步鉴定其功能,成功构建植物表达载体,将SaNHX2基因转入拟南芥;经RT-PCR检测结果显示,SaNHX2基因在转基因植株中过表达;高盐胁迫处理后,转SaNHX2基因拟南芥的主根长度、叶绿素总量和相关胁迫应答基因表达量均高于转空载拟南芥,表明转SaNHX2基因拟南芥的耐盐能力显著增强。研究表明,SaNHX2基因可能在盐胁迫调节机制中发挥调控作用,可作为改良农作物耐盐的重要候选基因。     

玉米转录因子 ZmNAC59 调控植物抗盐性

【目的】NAC转录因子家族是植物中研究较多的一类转录因子,在调控植物生长发育和响应非生物胁迫过程中起重要作用。玉米是三大粮食作物之一,其生长过程常会面临各种逆境胁迫,盐害被认为是限制作物生长和生产的主要环境因素之一。因此鉴定玉米抗盐基因,解析其抗盐机制对培育玉米抗逆品种具有重要意义。【方法】研究克隆了玉米转录因子ZmNAC59,并用生物信息学手段分析其保守结构域和系统进化关系,用实时荧光定量PCR方法分析该基因在NaCl和MeJA处理下的表达模式,并用稳定转基因体系将该基因异源表达拟南芥观察表型,同时还用病毒诱导沉默技术将该基因在玉米中沉默后进行盐处理表型观察,并进行酶活性检测。【结果】ZmNAC59能够被NaCl和MeJA诱导上调。病毒诱导沉默ZmNAC59后进行盐胁迫,沉默株系对盐胁迫更敏感,ROS积累更多;而ZmNAC59过表达拟南芥后,过表达株系在盐胁迫处理下存活率更高,活性氧积累更少,Na⁺/K⁺比率低,表明ZmNAC59作为盐胁迫中的正调控因子可以通过调节离子流动提高植物抗盐性。实时荧光定量PCR结果表明拟南芥过表达株系中Na     

基于基因芯片技术的转Slnac2基因拟南芥差异表达基因分析

NAC转录因子,对植物的生长发育及抵御逆境胁迫起着重要的作用。实验室前期克隆了辽宁碱蓬(Suaeda liaotungensis)Slnac2基因,转Slnac2拟南芥(Arabidopsis thaliana)提高了抵御盐胁迫的能力。本研究利用基因芯片技术筛选转SlNAC2拟南芥差异表达基因,共筛选出差异表达2倍以上的基因1 258个。GO富集度分析结果显示,分子功能相关基因占34.06%,细胞组分相关基因占33.13%,生物学过程相关基因占32.81%。KEGG分析表明,差异表达基因涉及63个信号通路,主要有植物激素信号转导、核糖体、植物病原物相互作用和抗坏血酸代谢等。通过实时荧光定量PCR对部分差异基因进行验证,所得结果与基因芯片结果一致。本研究揭示,SlNAC2可调控多个下游基因的表达,提高植物在逆境胁迫下的生存能力。     

拟南芥MYB转录因子家族研究进展

在长期的进化过程中,植物形成了复杂的基因调控网络,调节其生长发育及生理代谢,以适应外界环境的变化,其中一种重要的方式是通过转录因子在转录水平上调控目的基因的表达。MYB转录因子作为拟南芥中最大的转录因子家族之一,广泛参与调节拟南芥的不同生理活动。现对拟南芥MYB转录因子的分类和生物学功能进行综述,其中重点阐述了其在细胞周期控制、次生代谢及不同逆境胁迫中的作用。     

互花米草NAC转录因子家族的鉴定与表达分析

互花米草(Spartina alterniflora)作为一种海岸带盐生植物,高度耐盐胁迫,但因为缺少参考基因组,其耐盐的分子机制却尚未见报道。NAC家族蛋白是植物特有的转录因子,调控植物的生长发育和胁迫应答。为了鉴定互花米草NAC蛋白(SaNAC)并探究它们与互花米草生长发育及胁迫响应之间的关系,本研究以互花米草三代全长转录组数据为参考,通过与水稻(Oryza sativa)、拟南芥(Arabidopsis thaliana)和玉米(Zea mays)NAC蛋白序列进行比对,并结合保守功能域进一步筛选,最终找到62个SaNAC蛋白。从蛋白序列比对、进化、motif预测、同源性比较、亚细胞定位、组织表达以及非生物胁迫下的基因差异表达等方面分别对互花米草NAC家族成员进行分析,结果发现SaNAC蛋白均含有保守的NAM结构域,且在进化上与水稻NAC家族具有一定的相似性;SaNAC家族中的两个蛋白SaNAC9和SaNAC49在细胞核表达;另外,本研究还发现互花米草SaNAC基因表达具有高度组织和胁迫应答差异性。这些结果表明互花米草NAC转录因子家族不仅具有保守的功能域,而且在调控互花米草的生长发育和非生物胁迫响应过程中具有重要的作用。     

毛竹MYB转录因子PeMYB2的克隆与功能分析

MYB类转录因子在调控逆境应答基因的表达起着重要的作用, 是最大的植物转录因子之一。文章通过同源基因克隆方法和RACE(Rapid-amplification of cDNA ends)技术, 以毛竹幼苗为材料, 获得一个MYB类转录因子, 命名PeMYB2。氨基酸序列分析表明, PeMYB2具有典型的R2R3-MYB特征, N端含有两个串联重复保守结构域, C端含有一个膜蛋白DUF3651; 进化树分析表明, PeMYB2与水稻OsMYB18序列相似性最高, 达到85.98%; 酵母单杂实验表明, PeMYB2具有转录激活功能。将PeMYB2转化拟南芥对其功能进行分析, 获得7株转基因纯合体植株。比较转基因和野生型拟南芥表型发现, PeMYB2的过量表达使转基因拟南芥出现矮化、晚花的现象; 非生物胁迫处理(盐胁迫、干旱胁迫、低温胁迫)结果表明, 转基因拟南芥中PeMYB2的过量表达, 导致转基因植株对盐胁迫和低温胁迫有更高的耐性, 但是对低温胁迫的耐受性没有明显的变化; 进一步通过盐胁迫信号通路相关Marker基因(NXH1、SOS1、RD29A、COR15A)的定量PCR实验验证, 发现PeMYB2对下游这些抗逆基因的表达具有调控作用。上述实验结果表明, 毛竹PeMYB2可参与非生物胁迫调控, 对毛竹盐胁迫和低温胁迫的响应起着重要的作用。     

过量表达棉花CBF2基因提高转基因拟南芥抗旱耐盐能力

CBF/DREB是一类植物中特有的转录因子,在植物抵抗逆境胁迫过程中发挥重要功能。本研究从陆地棉(Gossypium hirsutum L.)Coker 312中克隆获得1个棉花CBF/DREB基因,命名为Gh CBF2,该基因编码一个由216个氨基酸组成的CBF蛋白。序列分析结果显示,Gh CBF2与其他植物的CBF蛋白类似,含有AP2转录因子典型的保守结构域。干旱或高盐胁迫处理明显增加了Gh CBF2基因的表达量。亚细胞定位分析结果发现Gh CBF2定位在细胞核中。将Gh CBF2基因构建到由35S启动子调控的植物表达载体p MD上并转化拟南芥(Arabidopsis thaliana L.),结果表明,在干旱和盐胁迫条件下,过量表达Gh CBF2基因拟南芥的成活率显著高于野生型,并且游离脯氨酸和可溶性糖含量也高于野生型,说明转Gh CBF2基因提高了拟南芥的耐盐抗旱能力。采用实时荧光定量PCR方法分析胁迫相关标记基因COR15A、RD29A和ERD6的表达情况,结果显示转基因株系中的表达量显著高于野生型,说明Gh CBF2参与调控拟南芥干旱和盐胁迫相关基因的表达。     

小黑杨HD-Zip转录因子家族生物信息学及应答盐胁迫分析

HD-Zip转录因子基因是植物中特有的一类蛋白家族,在植物生长发育和逆境应答胁迫过程中发挥重要作用。HD-Zip转录因子基因是由高度保守的同源异型结构域（HD）和亮氨酸拉链域（LZ）结构域构成的特殊结构模型。杨树HD-Zip转录因子家族共有63个基因,可被分为HD-ZipⅠ、HD-ZipⅡ、HD-ZipⅢ和HD-ZipⅣ四个亚家族。本文利用RNA-Seq分析了盐胁迫条件下HD-Zip基因家族在小黑杨根、茎、叶等不同组织的基因表达差异,从转录组水平揭示其应答胁迫环境的分子机制,结果表明,盐胁迫下在叶中有25个HD-Zip基因下调表达,21个基因上调表达;茎中有42个基因下调表达,11个基因上调表达;根中有26个基因下调表达,24个基因上调表达。另外,本文根据拟南芥HD-Zip转录因子家族基因的已知功能,预测了杨树HD-Zip转录因子同源基因的功能,并利用生物信息学方法分析了杨树HD-Zip转录因子蛋白序列的保守结构域、氨基酸组成和理化性质等,为进一步研究杨树HD-Zip转录因子基因功能提供参考。     

Genetic analysis of salt tolerance in arabidopsis. Evidence for a critical role of potassium nutrition.

A large genetic screen for sos (for salt overly sensitive) mutants was performed in an attempt to isolate mutations in any gene with an sos phenotype. Our search yielded 28 new alleles of sos1, nine mutant alleles of a newly identified locus, SOS2, and one allele of a third salt tolerance locus, SOS3. The sos2 mutations, which are recessive, were mapped to the lower arm of chromosome V, approximately 2.3 centimorgans away from the marker PHYC. Growth measurements demonstrated that sos2 mutants are specifically hypersensitive to inhibition by Na+ or Li+ and not hypersensitive to general osmotic stresses. Interestingly, the SOS2 locus is also necessary for K+ nutrition because sos2 mutants were unable to grow on a culture medium with a low level of K+. The expression of several salt-inducible genes was superinduced in sos2 plants. The salt tolerance of sos1, sos2, and sos3 mutants correlated with their K+ tissue content but not their Na+ tissue content. Double mutant analysis indicated that the SOS genes function in the same pathway. Based on these results, a genetic model for salt tolerance mechanisms in Arabidopsis is presented in which SOS1, SOS2, and SOS3 are postulated to encode regulatory components controlling plant K+ nutrition that in turn is essential for salt tolerance.     

水稻OsRPK2基因的克隆及功能初步鉴定

类受体蛋白激酶基因OsRPK1在水稻的抗逆信号传导中起着重要作用。本研究扩增获得与OsRPK1高度同源的OsRPK2基因,构建p1300:35S:OsRPK2过表达载体后转化拟南芥。对35S:OsRPK2纯合体拟南芥进行抗逆性分析表明,在盐、ABA、PEG胁迫下,OsRPK2过表达拟南芥萌发率都明显低于野生型拟南芥,其幼苗的根长生长和成株生长状况方面比野生型拟南芥表现出更为明显的受抑现象。生理检测表明,盐胁迫处理后,与野生型拟南芥相比,35S:OsRPK2转基因拟南芥中叶绿素含量下降更为明显,脯氨酸上升量较小,丙二醛含量上升更为明显,这些内在生理机制使得OsRPK2过表达拟南芥抗逆性明显下降。通过对35S:OsRPK2拟南芥的qRTPCR检测发现,OsRPK2的过量表达使拟南芥抗逆信号通路下游的SAD、SOS3和FRY基因表达明显受到抑制,OsRPK2基因可能通过SOS和CDPK信号通路影响拟南芥的抗逆性。     

The complexity of gene expression dynamics revealed by permutation entropy

Background

High complexity is considered a hallmark of living systems. Here we investigate the complexity of temporal gene expression patterns using the concept of Permutation Entropy (PE) first introduced in dynamical systems theory. The analysis of gene expression data has so far focused primarily on the identification of differentially expressed genes, or on the elucidation of pathway and regulatory relationships. We aim to study gene expression time series data from the viewpoint of complexity.

Results

Applying the PE complexity metric to abiotic stress response time series data in Arabidopsis thaliana, genes involved in stress response and signaling were found to be associated with the highest complexity not only under stress, but surprisingly, also under reference, non-stress conditions. Genes with house-keeping functions exhibited lower PE complexity. Compared to reference conditions, the PE of temporal gene expression patterns generally increased upon stress exposure. High-complexity genes were found to have longer upstream intergenic regions and more cis-regulatory motifs in their promoter regions indicative of a more complex regulatory apparatus needed to orchestrate their expression, and to be associated with higher correlation network connectivity degree. Arabidopsis genes also present in other plant species were observed to exhibit decreased PE complexity compared to Arabidopsis specific genes.

Conclusions

We show that Permutation Entropy is a simple yet robust and powerful approach to identify temporal gene expression profiles of varying complexity that is equally applicable to other types of molecular profile data.     

The putative plasma membrane Na(+)/H(+) antiporter SOS1 controls long-distance Na(+) transport in plants

The salt tolerance locus SOS1 from Arabidopsis has been shown to encode a putative plasma membrane Na(+)/H(+) antiporter. In this study, we examined the tissue-specific pattern of gene expression as well as the Na(+) transport activity and subcellular localization of SOS1. When expressed in a yeast mutant deficient in endogenous Na(+) transporters, SOS1 was able to reduce Na(+) accumulation and improve salt tolerance of the mutant cells. Confocal imaging of a SOS1-green fluorescent protein fusion protein in transgenic Arabidopsis plants indicated that SOS1 is localized in the plasma membrane. Analysis of SOS1 promoter-beta-glucuronidase transgenic Arabidopsis plants revealed preferential expression of SOS1 in epidermal cells at the root tip and in parenchyma cells at the xylem/symplast boundary of roots, stems, and leaves. Under mild salt stress (25 mM NaCl), sos1 mutant shoot accumulated less Na(+) than did the wild-type shoot. However, under severe salt stress (100 mM NaCl), sos1 mutant plants accumulated more Na(+) than did the wild type. There also was greater Na(+) content in the xylem sap of sos1 mutant plants exposed to 100 mM NaCl. These results suggest that SOS1 is critical for controlling long-distance Na(+) transport from root to shoot. We present a model in which SOS1 functions in retrieving Na(+) from the xylem stream under severe salt stress, whereas under mild salt stress it may function in loading Na(+) into the xylem.     

Comparative network analysis reveals that tissue specificity and gene function are important factors influencing the mode of expression evolution in Arabidopsis and rice

Microarray experiments have yielded massive amounts of expression information measured under various conditions for the model species Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa). Expression compendia grouping multiple experiments make it possible to define correlated gene expression patterns within one species and to study how expression has evolved between species. We developed a robust framework to measure expression context conservation (ECC) and found, by analyzing 4,630 pairs of orthologous Arabidopsis and rice genes, that 77% showed conserved coexpression. Examples of nonconserved ECC categories suggested a link between regulatory evolution and environmental adaptations and included genes involved in signal transduction, response to different abiotic stresses, and hormone stimuli. To identify genomic features that influence expression evolution, we analyzed the relationship between ECC, tissue specificity, and protein evolution. Tissue-specific genes showed higher expression conservation compared with broadly expressed genes but were fast evolving at the protein level. No significant correlation was found between protein and expression evolution, implying that both modes of gene evolution are not strongly coupled in plants. By integration of cis-regulatory elements, many ECC conserved genes were significantly enriched for shared DNA motifs, hinting at the conservation of ancestral regulatory interactions in both model species. Surprisingly, for several tissue-specific genes, patterns of concerted network evolution were observed, unveiling conserved coexpression in the absence of conservation of tissue specificity. These findings demonstrate that orthologs inferred through sequence similarity in many cases do not share similar biological functions and highlight the importance of incorporating expression information when comparing genes across species.