拟南芥DNA探针的比较基因组原位杂交揭示的拟南芥与远缘植物基因组间的同源性

采用生物素标记的拟南芥基因组DNA探针在75%杂交严谨度下对双子叶植物番茄、蚕豆和单子叶植物水稻、玉米、大麦的染色体进行了比较基因组荧光原位杂交（comparative genomic in situ hybridization,cGISH）分析,以揭示拟南芥与远缘植物基因组间的同源性.cGISH信号代表了拟南芥基因组DNA中的重复DNA与靶物种染色体上同源序列的杂交.探针DNA在所有靶物种的全部染色体上都产生了杂交信号.杂交信号为散在分布,并呈现随基因组增大,杂交信号增多,且分布更加分散的趋势.所有靶物种的核仁组织区（NOR）都显示了明显强于其他区域的杂交信号,表明拟南芥基因组DNA探针可用于植物NOR的物理定位.在所有的靶物种中,信号主要分布在染色体的臂中间区和末端,着丝粒或近着丝粒区有少数信号分布.大麦染色体显示了与C-和N-带不同的独特的cGISH信号带型,表明此探针可用于不同植物染色体的识别.这些结果表明,拟南芥基因组与远缘植物基因组之间,除rDNA和端粒重复序列外,还存在其它同源的重复DNA;一些重复DNA序列在被子植物分歧进化为单子叶和双子叶植物之前就已存在,虽经历了长期的进化过程,至今在远缘物种之间仍保持了较高的同源性.结果还提示,大基因组中古老而保守的重复DNA在进化过程中发生了明显的扩增.     

Role of Genetic Recombination in DNA Replication of Bacteriophage Lambda II. Effect in DNA Replication by Gene Delta

We have studied the effect of delta mutations in phage lambda on DNA synthesis as assayed by the accumulation of lambda DNA in infected cells. We find that delta mutants appear to generate somewhat less DNA than lambda(+) in a rec(+) host, suggesting the wild-type delta gene may act in DNA replication. An additional clue to delta function arises if replication is measured in the gamma-negative situation where concatemer formation is abortive. In this situation, the wild-type delta gene has an "inhibitory" effect on replication. A similar inhibitory effect on replication due to delta is observed after infection of P(2) lysogens. We conclude from these studies that the delta gene may act with alpha, beta, and gamma genes, possibly in a process affecting DNA replication.     

Genetic similarity among Arabidopsis thaliana ecotypes estimated by DNA sequence comparison

DNA polymorphisms among Arabidopsis thaliana ecotypes are widely used as genetic markers in map-based cloning strategies. New PCR-based molecular markers do not only facilitate molecular mapping, but can also be used to obtain reliable sequence information for cladistic analyses. We have used CAPS (cleaved amplified polymorphic sequences) markers and a direct sequencing strategy to estimate genetic similarity among eighteen Arabidopsis ecotypes. Sequences at four loci, two from the nuclear and two from a non-nuclaar genome, were analysed. For each ecotype more than 1000pb of sequence information was obtained, and genetic similarity was calculated from a total of 35 polymorphic sites using a character-based approach. Divergence ranged from zero up to 50 discordant characters among the 72 characters defined by the polymorphisms. Separate calculations based on the nuclear and the non-nuclear sequences were performed and revealed a number of common features, including the existence of small clusters of very closely related ecotypes separated from each other by extensive sequence divergence. Our results provide information useful especially to investigators setting up crosses for chromosome landing strategies.     

拟南芥CHS基因表达的实时荧光定量PCR检测

在简要介绍实时荧光定量PCR反应和定量原理的基础上,采用TaqMan荧光定量PCR技术,研究了UV-B辐射对拟南芥(Arabidopsis thaliana)CHS(查耳酮合成酶基因)表达的诱导,获得了与传统Northern杂交一致的结果.实时荧光定量PCR用于基因表达的定量检测,具有特异性强、自动化程度高、高效快捷,避免使用放射性同位素,能同时对多个样品中的起始模板进行准确定量等特点,因此该方法已逐渐被广泛用于基因表达的定量分析.     

拟南芥CHS 基因表达的实时荧光定量PCR 检测

在简要介绍实时荧光定量PCR反应和定量原理的基础上, 采用TaqMan荧光定量PCR技术, 研究了UV-B辐射对拟南芥(Arabidopsis thaliana)CHS(查耳酮合成酶基因)表达的诱导, 获得了与传统Northern杂交一致的结果。实时荧光定量PCR用于基因表达的定量检测, 具有特异性强、自动化程度高、高效快捷, 避免使用放射性同位素, 能同时对多个样品中的起始模板进行准确定量等特点, 因此该方法已逐渐被广泛用于基因表达的定量分析。     

Internet Resources for Gene Expression Analysis in Arabidopsis thaliana

The number of online databases and web-tools for gene expression analysis in Arabidopsis thaliana has increased tremendously during the last years. These resources permit the database-assisted identification of putative cis-regulatory DNA sequences, their binding proteins, and the determination of common cis-regulatory motifs in coregulated genes. DNA binding proteins may be predicted by the type of cis-regulatory motif. Further questions of combinatorial control based on the interaction of DNA binding proteins and the colocalization of cis-regulatory motifs can be addressed. The database-assisted spatial and temporal expression analysis of DNA binding proteins and their target genes may help to further refine experimental approaches. Signal transduction pathways upstream of regulated genes are not yet fully accessible in databases mainly because they need to be manually annotated. This review focuses on the use of the AthaMap and PathoPlant^® databases for gene expression regulation analysis and discusses similar and complementary online databases and web-tools. Online databases are helpful for the development of working hypothesis and for designing subsequent experiments.     

拟南芥白化突变体心口的基因定位与分析

EMS30是拟南芥经甲基磺酸乙酯（EMS）诱变得到的白化突变体。该突变体的叶绿体结构存在严重缺陷,同时伴随叶绿素缺失。遗传分析显示EMS30突变体的突变表型受隐性单基因控制。采用图位克隆的方法对EMS30突变基因进行定位的结果显示,该基因位于拟南芥第一条染色体的分子标记F21M12和F14N23之间的96kb区间内,该区间包含25个基因。通过生物信息学分析发现,该区间内有3个基因定位在叶绿体或与叶绿体发育相关。这些结果有助于该基因的克隆,为阐释叶绿体发育提供线索。     

Role of Genetic Recombination in DNA Replication of Bacteriophage Lambda I. Genetic Characterization of the Delta Gene

We describe the isolation and genetic characterization of point mutations in gene delta, including a temperature-sensitive mutation (del(206)). Genetic methods enable the extraction of a delta mutation from the triple mutant (del,red,gam) and the construction of new genotypes, including del,red and del,gam double mutants. Tests of plating efficiency indicate gene delta is essential for normal phase growth on the polA host. The possible association of delta in a system involving alpha, beta, and gamma is considered.     

Genomic Recombination of the Mitochondrial atp6 Gene in Arabidopsis thaliana at the Protein Processing Site Creates Two Different Presequences

In the mitochondrial genome of the flowering plant Arabidopsisthaliana the atp6 open reading frame is located on the borderof one of the repeats resulting in two copies with differentpresequence extensions. The two presequences of 135 and 97 aminoacids respectively show no similarity to each other, while themature protein sequences are identical. Both preproteins aremost likely synthesized in Arabidopsis mitochondria from promoterelements upstream of each copy. The presence of two arrangementsin the mitochondrial genome of fertile Arabidopsis plants suggeststhis recombination to be unrelated to a cytoplasmic male sterilephenotype. This recombination precisely at the mature proteinterminus is reminiscent of the domain shuffling model in proteinevolution.     

拟南芥AHAl基因启动子的表达特性分析

从拟南芥中分离到编码质膜H^＋-ATPase的AHA1基因启动子序列813bp,并构建了此种启动子与GUS嵌合的重组载体,通过农杆菌介导转化拟南芥,得到转基因拟南芥。用组织化学方法分析AHA1基因启动子驱动GUS转基因拟南芥的结果表明,GUS基因在转基因的拟南芥根、茎、叶、花和荚的维管组织中均有表达,且不同发育时间内GUS基因表达也不同。以上研究表明拟南芥AHA1基因可能参与植物的生长发育与抗逆胁迫反应。     

Genetic variation within and among populations of Arabidopsis thaliana.

We investigated levels of nucleotide polymorphism within and among populations of the highly self-fertilizing Brassicaceous species, Arabidopsis thaliana. Four-cutter RFLP data were collected at one mitochondrial and three nuclear loci from 115 isolines representing 11 worldwide population collections, as well as from seven commonly used ecotypes. The collections include multiple populations from North America and Eurasia, as well as two pairs of collections from locally proximate sites, and thus allow a hierarchical geographic analysis of polymorphism. We found no variation at the mitochondrial locus Nad5 and very low levels of intrapopulation nucleotide diversity at Adh, Dhs1, and Gpa1. Interpopulation nucleotide diversity was also consistently low among the loci, averaging 0.0014. gst, a measure of population differentiation, was estimated to be 0.643. Interestingly, we found no association between geographical distance between populations and genetic distance. Most haplotypes have a worldwide distribution, suggesting a recent expansion of the species or long-distance gene flow. The low level of polymorphism found in this study is consistent with theoretical models of neutral mutations and background selection in highly self-fertilizing species.     

A Genetic Analysis of Chloroplast Division and Expansion in Arabidopsis thaliana

A nuclear recessive mutant of Arabidopsis thaliana, arc5, has been isolated in which there is no significant increase in chloroplast number during leaf mesophyll cell expansion and in which there are only 13 chloroplasts per mesophyll cell compared with 121 in wild-type cells. Mature arc5 chloroplasts in fully expanded mesophyll cells are 6-fold larger than in wild-type cells. A large proportion of arc5 chloroplasts also show some degree of central constriction, suggesting that the mutation has prevented the completion of the chloroplast division process. To examine the interaction of arc loci, a double mutant was constructed between arc1, a mutant possessing many small chloroplasts, and arc5. A second double mutant was also constructed between arc3, a previously discovered mutant also possessing few large chloroplasts per cell, and arc1. Analysis of these double mutants shows that chloroplast number per mesophyll cell is greater when arc5 and arc3 mutations are expressed in the arc1 background than when expressed alone. The cell-specific nature of arc mutants was also analyzed. The phenotypic traits characteristic of arc3 and arc5 are a reduction in chloroplast number and an increase in chloroplast size in mesophyll cells: these changes are also observed in reduced form in the epidermal and guard cell chloroplasts of arc3 and arc5 plants. Analysis of parenchyma sheath cell chloroplasts suggests that in leaves of arc1 plants the normal developmental distinction between mesophyll and parenchyma sheath chloroplasts is perturbed. The relevance of these findings to the analysis of the control of chloroplast division in mesophyll cells is discussed.     

拟南芥IQM3基因的表达分析及其突变体的鉴定

对拟南芥(Arabidopsis thaliana)IQM3基因的功能进行了分析.结果表明,推定IQM3的启动子中存在多种光、非生物胁迫和植物激素反应的顺式作用元件,可能参与植物对环境变化的反应.RT-PCR分析表明,IQM3在拟南芥莲座叶、花序叶、茎、花和根中的表达较强,但在荚果中的表达很弱;IQM3基因的T-DNA插入突变体iqm3-1和iqm3-2分别是功能缺失和超表达突变体,对这些突变体的表型分析表明,IQM3基因与种子萌发及幼苗子叶膨大有密切关系.     

拟南芥丝氨酸羧肽酶类蛋白家族的基因组学分析

基于隐马可夫模型,利用已知丝氨酸羧肽酶（Serine Carboxypeptidases,SCP）氨基酸序列作为训练集,搜索拟南芥全蛋白质组数据库,鉴定了54个推定的SCPL（丝氨酸羧肽酶类,Serine Carboxypeptidase-Like）基因,详细分析了各基因的结构特征、染色体定位与编码的蛋白质序列,发现7个可能最近发生复制事件的基因簇聚区,并且其SCPL基因广泛存在交替剪接方式。系统进化分析表明,88．9％基因编码的蛋白质属于双链羧肽酶Ⅰ或Ⅱ亚族,仅11．1％蛋白质属于单链羧肽酶Ⅲ亚族,暗示SCP蛋白不仅具有独特拓扑结构的催化中心与高度保守的“α/β水解酶折叠”三级结构,其DNA或蛋白质序列特征也可以作为系统进化研究依据。     

利用RNAi技术抑制拟南芥NHX1基因家族的表达

采用RNAi抑制NHX1基因家族的表达,并观察其对拟南芥耐盐性和耐旱性的影响.根据从拟南芥(Ara-bidopsis thaliana)cDNA中扩增出编码Na /H 反向转运蛋白基因AtNHX1长度为210 bp高度保守序列作为RNAi的靶标区,并正反2个方向插入载体pHANNIBAL中,2个片段用intron连接;将RNAi表达框连入具有NPTⅡ筛选标记基因的表达载体pART27中,构建以拟南芥NHX1基因家族为靶标的RNAi载体.采用农杆菌介导的真空渗透法转化拟南芥,得到T0代转基因拟南芥种子.对转基因阳性植株进行RT-PCR检测以及耐盐性和耐旱性分析.结果表明,利用本实验构建的NHX1基因家族RNAi载体,拟南芥NHX1基因家族表达被成功地抑制;耐盐和耐旱分析表明RNAi技术对基因表达沉默是有效的.     

拟南芥ABC转运类蛋白家族的分子进化、表达模式和蛋白功能网络预测分析

ABC转运蛋白又称腺苷三磷酸结合盒转运蛋白(ATP-binding cassette transporters),该基因家族是目前已知最大、最古老的蛋白家族之一,在植物中ABC转运蛋白种类繁多、结构复杂、功能多样,涉及植物一切的生命活动过程。本研究系统介绍了拟南芥中131个ABC转运蛋白的亚家族分类、系统命名、蛋白大小以及蛋白亚细胞定位等基因信息,在此基础上,分析了ABC转运蛋白基因在染色体分布以及进化过程中发生的复制事件;其次在47个组织器官或发育阶段中聚类分析了ABC转运蛋白的表达模式和各个亚家族分布规律,结果表明ABC转运蛋白基因的表达具有明显的组织特异性和时空特异性,说明在进化过程中该类蛋白功能也进一步发生分化;我们以花药发育过程为例,说明ABC转运蛋白在花药发育过程中具有较高的协调性,在时空和组织上表达受到严格的调控;最后我们分析了ABC转运蛋白亚家族内部和各个亚家族之间可能存在的蛋白相互作用关系,推测ABC半分子转运蛋白形成同源或异源二聚体发挥功能的可能性,进一步说明ABC转运蛋白在蛋白互作水平上也存在功能多样性和严格的调控关系。     

Genetic characterization of late-flowering traits induced by DNA hypomethylation mutation in Arabidopsis thaliana

Arabidopsis DNA hypomethylation mutation, ddm1 , results in a variety of developmental abnormalities by slowly inducing heritable lesions at unlinked loci. Here, late-flowering traits observed at high frequencies in independently-established ddm1 lines were genetically characterized. In all of the four late-flowering lines examined the traits were dominant and mapped to the same chromosomal region, which is close or possibly identical to the FWA locus. The ddm1 -induced phenotypic onsets are apparently not random mutation events, but specific to a group of genes, suggesting the underlying epigenetic mechanism. The DNA methylation mutant provide useful system for identifying epigenetically-regulated genes important for plant development.