杨树MYB转录因子家族基因应答盐胁迫表达特性分析

MYB转录因子家族是植物中数量最多的转录因子家族之一,在植物次生代谢调节、信号转导和抗逆等生物过程起重要作用。根据MYB转录因子结构域组成差异可分4个亚家族：即1R-MYB（MYB-relaed）、R2R3-MYB、3R-MYB和4R-MYB。其中,R2R3-MYB亚家族数量最多,可进一步分为22个亚组;利用生物信息学分析杨树MYB转录因子蛋白序列的保守结构域、系统发生、基因组定位、氨基酸组成和理化性质等;参照拟南芥MYB转录因子功能,预测杨树MYB转录因子功能;基于84K杨转录组测序和RT-qPCR分析,从301个杨树MYB转录因子基因中筛选出69个应答盐胁迫基因（P≤0.05）。其中,上调表达基因32个,下调表达基因37个。该研究可为进一步研究杨树MYB家族基因功能提供参考依据。     

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。     

丹参转录因子SmMYB52的基因克隆、表达分析和亚细胞定位

MYB转录因子家族是植物界最大的转录因子家族之一,在植物生长发育、响应生物、非生物胁迫方面发挥重要作用.本研究分别从gDNA和cDNA水平上克隆得到丹参R2R3-MYB转录因子亚家族第24亚组的基因SmMYB52的全长序列,该基因序列全长1 041 bp,包含2个内含子序列和879 bp完整的CDS(Gen-Bank登录号:KF059406),编码292个氨基酸.运用生物信息学软件对该基因及其编码蛋白进行结构和理化性质分析以及生物信息学分析发现,SmMYB52与拟南芥MYB转录因子AtMYB93亲缘关系最近.利用RT-qPCR测定SmMYB52基因在各器官中的表达,结果显示该基因在根、茎、叶和花中均有表达,根中表达量最高,茎中最低.构建融合表达载体分析SmMYB52蛋白的亚细胞定位,结果显示SmMYB52在细胞核和细胞膜中均有分布.本实验为进一步研究SmMYB52在丹参中的生物学作用提供了科学依据.     

丹参转录因子SmMYB52的基因克隆、表达分析和亚细胞定位

MYB转录因子家族是植物界最大的转录因子家族之一,在植物生长发育、响应生物、非生物胁迫方面发挥重要作用.本研究分别从gDNA和cDNA水平上克隆得到丹参R2R3-MYB转录因子亚家族第24亚组的基因SmMYB52的全长序列,该基因序列全长1 041 bp,包含2个内含子序列和879 bp完整的CDS(Gen-Bank登录号:KF059406),编码292个氨基酸.运用生物信息学软件对该基因及其编码蛋白进行结构和理化性质分析以及生物信息学分析发现,SmMYB52与拟南芥MYB转录因子AtMYB93亲缘关系最近.利用RT-qPCR测定SmMYB52基因在各器官中的表达,结果显示该基因在根、茎、叶和花中均有表达,根中表达量最高,茎中最低.构建融合表达载体分析SmMYB52蛋白的亚细胞定位,结果显示SmMYB52在细胞核和细胞膜中均有分布.本实验为进一步研究SmMYB52在丹参中的生物学作用提供了科学依据.     

大白菜BrMYB34-3基因的3′-RACE克隆及表达

以大白菜叶片为材料,根据NCBI数据库中Br MYB34-3基因序列的已知信息,利用3-RACE获得了Br MYB34-3基因全长,用RT-PCR方法对Br MYB34-3在不同组织中的表达进行分析.结果显示,该基因全长1 135 bp,编码280个氨基酸.Br MYB34-3具有R2R3-MYB(含有2个MYB结构域的转录因子)典型的R2、R3结构域及基序.其氨基酸序列与大白菜的Br MYB34-1和Br MYB34-2、拟南芥的At MYB34具有较高的一致性.Br MYB34-3在莲座叶、当天开的花中表达水平较高,在花序顶端表达水平较低,在根和花序轴中未检测到表达,这与拟南芥At MYB34的表达模式不同.研究表明,Br MYB34-3是大白菜中的MYB34同源基因,在功能上可能与拟南芥At MYB34基因存在差异.     

番茄E8基因启动子的克隆及其在拟南芥中的表达

利用PCR技术从番茄基因组DNA中克隆长约1.1kb的E8基因启动子与517bp的E8基因片段,将其二者连接构建植物表达载体,导入农杆菌,通过花序侵染法转化拟南芥,得到转基因拟南芥。用RT-PCR分析转基因拟南芥中E8基因启动子驱动E8基因小片段的结果表明,E8基因小片段mRNA仅在转基因拟南芥长角果中转录,根、茎、叶、花中不转录,提示E8基因的1.1kb启动子在异源植物拟南芥中仍具有驱动外源基因果实特异性表达的特性。     

MYB 转录因子在植物抗逆胁迫中的作用及其分子机理

摘要: 在植物抗逆反应体系中, 通过转录因子调控功能基因的表达, 是植物逆境应答反应的关键环节。作为植物体内最大的转录因子家族之一, MYB(v-myb avian myeloblastosis viral oncogene homolog)类转录因子在植物抗逆胁迫过程中起着重要的作用。文章论述了MYB转录因子的结构特征、功能特性及其分子机理, 并结合研究进展着重讨论了它们在植物抗逆胁迫中的作用。     

植物非生物胁迫诱导启动子顺式元件及转录因子研究进展

顺式作用元件(cix-acting element)是与结构基因串联的特定DNA序列,是转录因子的结合位点,它们通过与转录因子结合调控基因转录的精确起始和转录效率,在植物基因表达调控过程中起着重要的作用.非生物胁迫诱导基因的表达受其上游启动子顺式作用元件及转录因子的调控,目前已发现了多种与非生物胁迫相关的顺势作用元件及转录因子,如DRE元件及DREB类转录因子、MYB元件及MYB类转录因子、GT-1元件及GT-1类转录因子等.顺式作用元件及转录因子的研究对研究植物非生物胁迫相关基因的表达调控具有重要意义,综述植物非生物胁迫诱导启动子功能元件及转录因子的研究进展.     

植物逆境抗性相关转录因子的研究进展

植物各种诱导性基因的表达主要受特定转录因子在转录水平的调控.转录因子也称反式作用因子,通过与靶基因启动子中的顺式作用元件结合发挥调节作用.根据与DNA结合的区域不同,转录因子分为若干个家族.本文综述了与植物逆境抗性相关的4个转录因子家族:bZIP类、WRKY类、AP2/EREBP类和MYB类在逆境信号转导中的作用以及它们在植物抗逆基因工程改良中的应用现状.     

水稻MYB cDNA的克隆和表达分析

根据植物MYB类转录因子DNA结合功能域的保守区设计一对简并引物 ,以水稻根、小苗和未成熟种子中的RNA为材料 ,用RT PCR方法扩增出约 180bp的片段。序列分析表明 ,它们与MYB基因的保守区有很好的同源性。以未成熟种子中获得的这一 180bp片段作探针 ,从水稻未成熟种子cDNA文库中分离到 5个新的MYB基因家族成员 ,它们是OsMYB12、13、14、15和5 1。在酵母系统中证实OsMYB13、OsMYB15和Os MYB5 1蛋白具有转录激活功能。Northern印迹分析表明 ,OsMYB5 1主要在未成熟种子中表达 ,在根和小苗中表达水平较低。RT PCR分析表明 ,OsMYB15在根、茎、小穗、叶片和种子中有低水平的表达     

Tomato responds to green peach aphid infestation with the activation of trehalose metabolism and starch accumulation

The disaccharide trehalose and trehalose-6-phosphate that are present in trace amounts are suggested to have a signaling function in plants. Recently, it was demonstrated that trehalose metabolism contributes to Arabidopsis thaliana defense against the green peach aphid (GPA; Myzus persicae Sülzer), an important insect pest of a large variety of plants. TPS11 (TREHALOSE PHOSPHATE SYNTHASE11)-dependent trehalose metabolism was shown to curtail GPA infestation by promoting starch accumulation and expression of the PAD4 (PHYTOALEXIN-DEFICIENT4) gene, which has important roles in regulating antibiosis and antixenosis against GPA. Here we show that trehalose metabolism is similarly activated in leaves of GPA-infested tomato (Solanum lycopersicum) plants and likely contributes to tomato defense against GPA. GPA-infested leaves of tomato accumulated trehalose, which was accompanied by the transient upregulation of SlTPS11, a homolog of the Arabidopsis TPS11. GPA-infestation was also accompanied by starch accumulation and the upregulation of SlPAD4, the tomato homolog of Arabidopsis PAD4. Furthermore, trehalose application induced SlPAD4 expression and starch accumulation, and curtailed GPA infestation, suggesting that like in Arabidopsis trehalose contributes to tomato defense against GPA.     

Homologies to the tomato endopolygalacturonase gene in the peach genome

Abstract. Peach endopolygalacturonase was isolated from the mesocarp tissue of soft ripe, freestone peach fruit, but was not detectable in mature pre-ripening fruit. It is a basic protein with a M_r of approximately 45000 Da, and cross-reacts with antibody to tomato endopolygalacturonase. Using a cDNA to the tomato enzyme as a probe, a fragment of peach genomic DNA was isolated which encoded about 50% of the peach enzyme. The nucleotide sequence of the fragment was determined and the amino acid sequence of part of the peach endopolygalacturonase peptide derived. Coding regions of the peach gene show extensive homology with related regions of the tomato gene. Introns are dissimilar. Endopolygalacturonase activity occurs in ripe 'freestone'peaches but not in the firmer 'clingstone'varieties. Hybridization studies identified a similar gene fragment in freestone, semi-freestone and clingstone peach varieties.     

Macrostructure of the tomato telomeres.

The macrostructure of the tomato telomeres has been investigated by in situ hybridization, genomic sequencing, and pulsed-field gel electrophoresis. In situ hybridizations with a cloned telomeric sequence from Arabidopsis thaliana indicated that the telomeric repeat of tomato cross-hybridizes with that of Arabidopsis and is located at all telomeres. Bal31 digestion kinetics confirmed that the tomato telomeric repeat represents the outermost DNA sequence of each tomato chromosome. Genomic sequencing of enriched tomato telomeric sequences, using primers derived from the Arabidopsis sequence, revealed that the consensus sequence of the tomato telomeric repeat is TT(T/A)AGGG compared with the Arabidopsis consensus sequence of TTTAGGG. Furthermore, as shown by pulsed-field gel electrophoresis, the telomeric repeat of tomato is separated by not more than a few hundred kilobases from a previously described 162-base pair satellite DNA repeat of tomato (TGR I) at 20 of the 24 telomeres. Together, these sequences are found in the heterochromatic terminal knob observed in pachytene chromosomes. Therefore, these two repeats determine the structure of 20 of the 24 tomato chromosome ends over approximately 2% of the total chromosome length.     

The SELF-PRUNING gene family in tomato

The SELF PRUNING (SP) gene controls the regularity of the vegetative-reproductive switch along the compound shoot of tomato and thus conditions the 'determinate' (sp/sp) and 'indeterminate' (SP_) growth habits of the plant. SP is a developmental regulator which is homologous to CENTRORADIALIS (CEN) from Antirrhinum and TERMINAL FLOWER 1 (TFL1) and FLOWERING LOCUS T (FT) from Arabidopsis. Here we report that SP is a member of a gene family in tomato composed of at least six genes, none of which is represented in the tomato EST collection. Sequence analysis of the SP gene family revealed that its members share homology along their entire coding regions both among themselves and with the six members of the Arabidopsis family. Furthermore, members of the gene family in the two species display a common genomic organization (intron-exon pattern). In tomato, phylogenetically close homologues diverged considerably with respect to their organ expression patterns while SP2I and its closest homologue from Arabidopsis (MFT) exhibited constitutive expression. This research focusing on a plant of sympodial growth habit sets the stage for a functional analysis of this weakly expressed gene family which plays a key role in determining plant architecture.     

Sequence and Analysis of the Tomato JOINTLESS Locus

A 119-kb bacterial artificial chromosome from the JOINTLESS locus on the tomato (Lycopersicon esculentum) chromosome 11 contained 15 putative genes. Repetitive sequences in this region include one copia-like LTR retrotransposon, 13 simple sequence repeats, three copies of a novel type III foldback transposon, and four putative short DNA repeats. Database searches showed that the foldback transposon and the short DNA repeats seemed to be associated preferably with genes. The predicted tomato genes were compared with the complete Arabidopsis genome. Eleven out of 15 tomato open reading frames were found to be colinear with segments on five Arabidopsis bacterial artificial chromosome/P1-derived artificial chromosome clones. The synteny patterns, however, did not reveal duplicated segments in Arabidopsis, where over half of the genome is duplicated. Our analysis indicated that the microsynteny between the tomato and Arabidopsis genomes was still conserved at a very small scale but was complicated by the large number of gene families in the Arabidopsis genome.     

一个园艺植物基因组序列和注释的在线批量实时提取平台

目前, 大量园艺植物基因组测序已经完成或接近尾声, 它们的基因组序列和注释数据极大地促进了功能基因组学研究。为给科研人员提供批量下载特定的基因组区段序列和注释平台, 笔者开发了一个称为OBRRP的生物信息学工具。OBRRP具有提取葡萄(Vitis vinifera)、桃(Prunus persica)、草莓(Fragaria vesca)、黄瓜(Cucumis sativus)、西瓜(Citrullus lanatus)、番茄(Solanum lycopersicum)、甜橙(Citrus sinensis)、苹果(Malus x domestica)、猕猴桃(Actinidia chinensis)、马铃薯(Solanum tuberosum)、香蕉(Musa acuminata)和拟南芥(Arabidopsis thaliana) 12种植物基因组序列及注释数据的功能; 同时, 也具有扩展到其它Gbrowser浏览器架构的数据库功能。测试结果表明, OBRRP是一个快捷简便的在线、批量和实时提取工具, 其登录地址为http://bioinfo.jit.edu.cn/OBRRP/。     

Comparative sequence analysis reveals extensive microcolinearity in the lateral suppressor regions of the tomato, Arabidopsis, and Capsella genomes

A 57-kb region of tomato chromosome 7 harboring five different genes was compared with the sequence of the Arabidopsis genome to search for microsynteny between the genomes of these two species. For all five genes, homologous sequences could be identified in a 30-kb region located on Arabidopsis chromosome 1. Only two inversion events distinguish the arrangement of the five genes in tomato from that in Arabidopsis. Inversions were not detected when the arrangement of the five Arabidopsis genes was compared with the arrangement in the orthologous region of Capsella, a plant closely related to Arabidopsis. These results provide evidence for microcolinearity between closely and distantly related dicotyledonous species. The degree of microcolinearity found can be exploited to localize orthologous genes in Arabidopsis and tomato in an unambiguous way.     

Analysis of sequence, map position, and gene expression reveals conserved essential genes for iron uptake in Arabidopsis and tomato

Arabidopsis (Arabidopsis thaliana) and tomato (Lycopersicon esculentum) show similar physiological responses to iron deficiency, suggesting that homologous genes are involved. Essential gene functions are generally considered to be carried out by orthologs that have remained conserved in sequence and map position in evolutionarily related species. This assumption has not yet been proven for plant genomes that underwent large genome rearrangements. We addressed this question in an attempt to deduce functional gene pairs for iron reduction, iron transport, and iron regulation between Arabidopsis and tomato. Iron uptake processes are essential for plant growth. We investigated iron uptake gene pairs from tomato and Arabidopsis, namely sequence, conserved gene content of the regions containing iron uptake homologs based on conserved orthologous set marker analysis, gene expression patterns, and, in two cases, genetic data. Compared to tomato, the Arabidopsis genome revealed more and larger gene families coding for the iron uptake functions. The number of possible homologous pairs was reduced if functional expression data were taken into account in addition to sequence and map position. We predict novel homologous as well as partially redundant functions of ferric reductase-like and iron-regulated transporter-like genes in Arabidopsis and tomato. Arabidopsis nicotianamine synthase genes encode a partially redundant family. In this study, Arabidopsis gene redundancy generally reflected the presumed genome duplication structure. In some cases, statistical analysis of conserved gene regions between tomato and Arabidopsis suggested a common evolutionary origin. Although involvement of conserved genes in iron uptake was found, these essential genes seem to be of paralogous rather than orthologous origin in tomato and Arabidopsis.     

Detection of Phytoplasma from deferent infected hosts in Jordan based on PCR amplification of the 16S rDNA sequences

Sixteen leaf samples, both healthy and Phytoplasma diseased, were collected from different plants such as grape, peach, almond, tomato, paper, squash, apple and pear in northern Jordan. Extracted DNA from diseased grape, peach, almond, tomato, paper and squash plus from infected periwinkle (Catharanthus roseus) samples were amplified with the Phytoplasma universal 16S rDNA sequences primer pairs. Extracted DNA samples from healthy and diseased apple and pear plants were not amplified with the same primer pairs. All the PCR-amplified DNA samples show a common band with size of 558 bp, indicating Phytoplasma pathogens as a disease-causative agent for grape, peach, almond, tomato, paper and squash plants. The restriction fragment length polymorphisms of Alu1 enzyme for the amplified 16S rDNA sequences shows the same DNA fragment patterns indicating no or a limited diversity among the DNA of the detected Phytoplasma pathogens.