Comparative genomic mapping between a 754 kb region flanking DREB1A in Arabidopsis thaliana and maize

Comparative mapping between model plant species for which the complete genome sequence is known and crop species has been suggested as a new strategy for the isolation of agronomically valuable genes. In this study, we tested whether comparative mapping between Arabidopsisand maize of a small region (754 kb) surrounding the DREB1A gene in Arabidopsis could lead to the identification of an orthologous region in maize containing the DREB1A homologue. The genomic sequence information available for Arabidopsis allowed for the selection of conserved, low-copy genes that were used for the identification of maize homologues in a large EST database. In total, 17 maize homologues were mapped. A second BLAST comparison of these genes to the recently completed Arabidopsis sequence revealed that 15 homologues are likely to be orthologous as the highest similarity score was obtained either with the original Arabidopsis gene or with a highly similar Arabidopsis gene localized on a duplication of the investigated region on chromosome 5. The map position of these genes showed a significant degree of orthology with the Arabidopsis region. Nevertheless, extensive duplications and rearrangements in the Arabidopsisand maize genomes as well as the evolutionary distance between Arabidopsis and maize make it unlikely that orthology and collinearity between these two species are sufficient to aid gene prediction and cloning in maize.     

Integrative approaches to determining Csl function

While there is an ever-increasing amount of information regarding cellulose synthase catalytic subunits (CesA) and their role in the formation of the cell wall, the remainder of the enzymes that synthesize structural cell wall polysaccharides are unknown. The completion of the Arabidopsis genome and the wealth of the sequence information from other plant genome projects provide a rich resource for determining the identity of these enzymes. Arabidopsis contains six families of genes related to cellulose synthase, the cellulose synthase-like (Csl) genes. Our laboratory is taking a multidisciplinary approach to determine the function of the Csl genes, incorporating genomic, genetic and biochemical data. Information from expressed sequence tag (EST) projects has revealed the presence of Csl genes in all plant species with a significant number of ESTs. Certain Csl families appear to be missing from some species. For example, no examples of CslG ESTs have been found in rice or maize. Microarray data and reporter constructs are being used to determine the expression pattern of the CesA and Csl genes in Arabidopsis. Mutations and insertion events have been identified in a majority of the genes in the Arabidopsis CesA superfamily and are being characterized by phenotypic and biochemical analysis. While we cannot yet link the function of any of the Csl genes to their respective products, the expression and localization of these genes is consistent with the expected expression pattern of polysaccharide synthases that contribute to the primary cell wall.     

siRNA介导的ERA1表达下调对拟南芥抗旱性的影响

ERA1是控制植物气孔开闭的一个重要基因,根据其保守域构建RNA干扰(RNAi)载体并转化拟南芥,考察转基因植株的生长、气孔导度、离体叶片失水率以及ERA1和相关基因表达,探讨siRNA介导的ERA1表达下调对拟南芥抗旱性的影响。结果表明:转基因拟南芥株系中ERA1的表达受到明显抑制,其离体叶片失水率低于野生型,但并未出现ERA1缺失突变体的负面生长表型;转基因株系对ABA处理比野生型更敏感,其ABA处理株的根长显著变短,气孔孔径更小;转基因株ABI1、ABI2、ATHB6的表达量降低,而RAB18、RD29B、ADH1的表达量升高,siRNA介导的ERA1表达下调可能会激活RAB18、RD29B等逆境响应元件。研究发现,采用RNAi技术可以有效下调ERA1表达,在没有过多负面生长表型的前提下提高拟南芥的抗旱性,且ERA1表达下调可能通过ABA途径正面影响拟南芥的抗旱性。     

Two WD-repeat genes from cotton are functional homologues of the <Emphasis Type="Italic">Arabidopsis thaliana</Emphasis><Emphasis Type="Italic">TRANSPARENT TESTA GLABRA1</Emphasis> (<Emphasis Type="Italic">TTG1</Emphasis>) gene

Cotton fibres are single, highly elongated cells derived from the outer epidermis of ovules, and are developmentally similar to the trichomes of Arabidopsis thaliana. To identify genes involved in the molecular control of cotton fibre initiation, we isolated four putative homologues of the Arabidopsis trichome-associated gene TRANSPARENT TESTA GLABRA1 (TTG1). All four WD-repeat genes are derived from the ancestral D diploid genome of tetraploid cotton and are expressed in many tissues throughout the plant, including ovules and growing fibres. Two of the cotton genes were able to restore trichome formation in ttg1 mutant Arabidopsis plants. Both these genes also complemented the anthocyanin defect in a white-flowered Matthiola incana ttg1 mutant. These results demonstrate parallels in differentiation between trichomes in cotton and Arabidopsis, and indicate that these cotton genes may be functional homologues of AtTTG1.     

Molecules and morphology: comparative developmental genetics of the Brassicaceae

For approximately 20 years Arabidopsis has been a model system to investigate developmental and physiological questions in plant biology, leading to the identification of genes and genetic systems involved in many processes. Extending ideas arising from knowledge of developmental genetic systems in Arabidopsis to other species of the Brassicaceae will require the application of genomics technologies developed in Arabidopsis and the establishment of additional genetic systems and resources in other species. Morphological variation in all plant organs, as well as in growth habit, mating systems, and physiology are represented in the breadth of Brassicaceae species offering ample opportunity to investigate the molecular basis of morphological evolution in this family. In addition, the frequent recent hybridization events in Brassica and Arabidopsis facilitate study of this pervasive force in the evolution of all plants.     

Constitutive expression of a meiotic recombination protein gene homolog, OsTOP6A1, from rice confers abiotic stress tolerance in transgenic Arabidopsis plants

Plant productivity is greatly influenced by various environmental stresses, such as high salinity and drought. Earlier, we reported the isolation of topoisomerase 6 homologs from rice and showed that over expression of OsTOP6A3 and OsTOP6B confers abiotic stress tolerance in transgenic Arabidopsis plants. In this study, we have assessed the function of nuclear-localized topoisomerase 6 subunit A homolog, OsTOP6A1, in transgenic Arabidopsis plants. The over expression of OsTOP6A1 in transgenic Arabidopsis plants driven by cauliflower mosaic virus-35S promoter resulted in pleiotropic effects on plant growth and development. The transgenic Arabidopsis plants showed reduced sensitivity to stress hormone, abscisic acid (ABA), and tolerance to high salinity and dehydration at the seed germination; seedling and adult stages as reflected by the percentage of germination, fresh weight of seedlings and leaf senescence assay, respectively. Concomitantly, the expression of many stress-responsive genes was enhanced under various stress conditions in transgenic Arabidopsis plants. Moreover, microarray analysis revealed that the expression of a large number of genes involved in various processes of plant growth and development and stress responses was altered in transgenic plants. Although AtSPO11-1, the homolog of OsTOP6A1 in Arabidopsis, has been implicated in meiotic recombination; the present study demonstrates possible additional role of OsTOP6A1 and provides an effective tool for engineering crop plants for tolerance to different environmental stresses. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Different cell-wall components from Phytophthora megasperma f. sp. glycinea elicit phytoalexin production in soybean and parsley

Different components of a crude cell-wall preparation from the phytopathogenic fungus, Phytophthora megasperma f. sp. glycinea, act as elicitors of phytoalexin accumulation in parsley (Petroselinum crispum) and soybean (Glycine max). Treatments of cultured parsley cells and protoplasts or soybean cells and cotyledons with proteinase-digested or deglycosylated elicitor preparations identify proteinaceous constituents as active eliciting compounds in parsley, which are inactive in soybean. The proteinase-treated elicitor as well as a defined heptaglucan are active in soybean but do not stimulate phytoalexin synthesis in parsley. Soybean and parsley cells therefore not only perceive different signals from cell walls of Phytophthora megasperma f. sp. glycinea, but are unable to respond to the fungal compounds primarily recognized by the other plant.Abbreviations Pmg Phytophthora megasperma f. sp. glycinea     

Uptake of isolated plant chromosomes by plant protoplasts

For mass isolation of plant metaphase chromosomes, cultured cells of wheat (Triticum monococcum) and parsley (Petroselinum hortense) were synchronized by hydroxyurea and colchicine treatment. This synchronization procedure resulted in high mitotic synchrony, especially in suspension cultures of parsley in which 80% of the cells were found to be at the metaphase stage. Mitotic protoplasts isolated from these synchronized cell cultures served as a source for isolation of chromosomes. The described isolation and purification method yielded relatively pure chromosome suspension. The uptake of the isolated plant chromosomes into recipient wheat, parsley, and maize protoplasts was induced by polyethylene-glycol treatment. Cytological studies provided evidences for uptake of plant chromosomes into plant protoplasts.Abbreviations PEG polyethylene glycol - HU hydroxyruea - C colchicine - HUC hydroxyurea and colchicine - CIM chromosome isolation medium - TCM Tris chromosome medium     

Identification of more than 200 glucose-responsive <Emphasis Type="Italic">Arabidopsis</Emphasis> genes none of which responds to 3-O-methylglucose or 6-deoxyglucose

The response of some plant genes to glucose analogues 3-O-methylglucose (3OMG) or 6-deoxyglucose (6DOG) has been cited as evidence for metabolism-independent glucose signalling. To analyse such signalling using a genetic approach, we sought to identify Arabidopsis glucose-responsive genes which also respond to 3OMG and 6DOG in seedlings. Microarray analysis of gene expression in glucose-treated seedlings and RT-PCR analysis of glucose-treated leaf sections identified more than 200 glucose-responsive genes, but none responded to 3OMG or 6DOG. These data together with other published data on individual genes fail to identify any Arabidopsis sugar-responsive genes which also respond to 3OMG or 6DOG.     

二氧化硫增强拟南芥植株对干旱的适应性

以模式植物拟南芥为材料,研究SO_2对植物干旱适应性的影响。采用分光光度法检测植物干旱生理指标的变化,并用半定量RT-PCR技术分析了拟南芥热激基因和干旱响应基因的转录水平。研究发现:4周龄拟南芥植株暴露于30mg/m3的SO_2后,6—72h间叶面气孔开度显著低于对照并逐渐减小,在暴露48h和72h时,热激转录因子HsfA2和热激基因Hsp17.7、Hsp17.6B、Hsp17.6C转录上调,干旱响应基因DREB2A、DREB2B和RD29A表达增强;在SO_2熏气72h后进行干旱胁迫,干旱期间SO_2预暴露植株的叶片相对含水量高于非熏气干旱处理组,植株萎蔫程度比后者明显减轻,且SO_2预暴露植株的地上组织中可溶性糖和脯氨酸含量升高,超氧化物歧化酶活性提高,丙二醛含量降低。结果表明:SO_2能降低气孔开度、提高抗氧化能力、上调热激基因和干旱响应基因转录,并能促进干旱期间植物细胞内渗透调节物质的合成和积累,促使抗氧化酶活性提高,从而降低干旱胁迫对植株造成的氧化损伤,增强拟南芥对干旱的适应性。植物通过基因转录应答、酶活性改变、渗透调节物质积累等,在适应环境高浓度SO_2的同时,提高了对干旱的适应性。     

The Arabidopsis thaliana 4-coumarate:CoA ligase (4CL) gene: stress and developmentally regulated expression and nucleotide sequence of its cDNA

An Arabidopsis cDNA clone encoding 4-coumarate:CoA ligase (4CL), a key enzyme of phenylpropanoid metabolism, was identified and sequenced. The predicted amino acid sequence is similar to those of other cloned 4CL genes. Southern blot analysis indicated that 4CL is single-copy gene in Arabidopsis. Northern blots showed that 4CL expression was activated early during seedling development. The onset of 4CL expression was correlated with the onset of lignin deposition in cotyledons and roots 2–3 days after germination. The timing of the expression of a parsley 4CL1-GUS fusion in transgenic Arabidopsis seedlings was examined in parallel and was very similar to that of endogenous 4CL. In mature plants, highest 4CL expression was observed in bolting stems, where relatively large amounts of lignin accumulate. Both 4CL and 4CL1-GUS mRNA accumulation was strongly and transiently activated by wounding of mature Arabidopsis leaves. 4CL expression was specifically activated within 6 h after infiltration of Arabidopsis ecotype Columbia leaves with a Pseudomonas syringae pv. maculicola strain harboring the bacterial avirulence gene avrB, which causes in incompatible interaction. The timing of 4CL activation was identical to the previously observed activation of PAL gene expression in this interaction. No activation of 4CL expression was observed in a compatible interaction caused by a Pseudomonas syringae pv. maculicola strain without avrB.     

Domain-Specific Positive Selection Contributes to the Evolution of Arabidopsis Leucine-Rich Repeat Receptor-Like Kinase (LRR RLK) Genes

Leucine-rich repeat receptor-like kinases (LRR RLKs) comprise the largest group within the plant receptor-like kinase (RLK) superfamily, and the Arabidopsis genome alone contains over 200 LRR RLK genes. Although there is clear evidence for diverse roles played by individual LRR RLK genes in Arabidopsis growth and development, the evolutionary mechanism for this functional diversification is currently unclear. In this study, we focused on the LRRII RLK subfamily to investigate the molecular mechanisms that might have led to the functional differentiation of Arabidopsis LRR RLK genes. Phylogenetic analysis of 14 genes in this subfamily revealed three well-supported groups (I, II, and III). RT-PCR analysis did not find many qualitative differences in expression among these 14 genes in various Arabidopsis tissues, suggesting that evolution of regulatory sequences did not play a major role in their functional divergence. We analyzed substitution patterns in the predicted ligand-binding regions of these genes to examine if positive selection has acted to produce novel ligand-binding specificities, using the nonsynonymous/synonymous rate ratio (d _N/d _S) as an indicator of selective pressure. Estimates of d _N/d _S ratios from multiple methods indicate that nonsynonymous substitutions accumulated during divergence of the three lineages. Positive selection is likely to have occurred along the lineages ancestral to groups II and III. We suggest that positive selection on the ligand-binding sites of LRRII RLKs promoted diversification of ligand-binding specificities and thus contributed to the functional differentiation of Arabidopsis LRRII RLK genes during evolution. [Reviewing Editor: Dr. Martin Kreitman]     

Plant development going MADS

It has been known for a decade that the plant MADS genesare important regulators of meristem and floral organ identity. The MADS family in Arabidopsis consists of more than 80 members and, until recently, the function of the majority of these genes was unknown. With the enhanced ability to generate loss-of-function mutants and over-expression lines, the function of the MADS gene family members is beginning to be elucidated. Recent progress demonstrates that MADS genes in Arabidopsis are important regulators not only of meristem and floral organ identity but also of flowering timing and cell-type specification in floral organs.     

The Peroxidase Gene Family in Plants: A Phylogenetic Overview

The 73 class III peroxidase genes in Arabidopsis thaliana were used for surveying the evolutionary relationships among peroxidases in the plant kingdom. In Arabidopsis, the 73 genes were clustered in robust similarity groups. Comparison to peroxidases from other angiosperms showed that the diversity observed in Arabidopsis preceded the radiation of dicots, whereas some clusters were absent from grasses. Grasses contained some unique peroxidase clusters not seen in dicot plants. We found peroxidases in other major groups of land plants but not in algae. This might indicate that the class III peroxidase gene family appeared with the colonization of land by plants. The present survey may be used as a rational basis for further investigating the functional roles of class III peroxidases.     

绿豆VrWOX基因家族鉴定及表达分析北大核心CSCD

WOX(WUSCHEL-related homebox)基因家族是植物特有的一类转录因子,是同源盒(homeobox,HB)转录因子超家族中的重要成员。WOX基因在植物干细胞调节及生殖发育过程中具有重要作用,其功能已在多个植物物种中鉴定。然而绿豆(Vigna radiate)VrWOX基因家族信息尚不清楚。本研究通过同源比对和聚类分析,在绿豆基因组中鉴定了42个VrWOX基因。VrWOX基因在绿豆染色体中分布不均,其中7号染色体含有的VrWOX数量最多。VrWOX基因分为古老进化支(19个VrWOX)、中等进化支(12个VrWOX)和年轻进化支(WUSCHEL进化支,11个VrWOX)3个亚类。种内和种间共线性分析发现,VrWOX基因共有12个重复事件,与拟南芥(Arabidopsis thaliana)AtWOX有15个同源基因对,与菜豆(Phaseolus vulgaris)PvWOX有22个同源基因对。VrWOX基因在基因结构、保守基序等方面存在很大差异,因而可能存在功能差异。VrWOX基因启动子区域含有不同种类和不同数量的顺式作用元件,导致VrWOX基因在不同组织中表现出不同的基因表达模式。本研究对VrWOX基因家族信息和表达模式进行了分析,为绿豆VrWOX基因功能和调控网络的解析奠定了一定的理论依据。     

Constitutive expression of two apple (Malus x domestica Borkh.) homolog genes of LIKE HETEROCHROMATIN PROTEIN1 affects flowering time and whole-plant growth in transgenic Arabidopsis

Fruit trees, such as apple (Malus × domestica Borkh.), are woody perennial plants with a long juvenile phase. The biological analysis for the regulation of flowering time provides insights into the reduction of juvenile phase and the acceleration of breeding in fruit trees. In Arabidopsis, LIKE HETEROCHROMATIN PROTEIN1 (LHP1) is involved in epigenetic silencing of the target genes such as flowering genes. We isolated and characterized twin apple LHP1 homolog genes, MdLHP1a and MdLHP1b. These genes may have been generated as a result of ancient genome duplication. Although the putative MdLHP1 proteins showed lower similarity to any other known plant LHP1 homologs, a chromo domain, a chromo shadow domain, and the nuclear localization signal motifs were highly conserved among them. RT-PCR analysis showed that MdLHP1a and MdLHP1b were expressed constantly in developing shoot apices of apple trees throughout the growing season. Constitutive expression of MdLHP1a or MdLHP1b could compensate for the pleiotropic phenotype of lhp1/tfl2 mutant, suggesting that apple LHP1 homolog genes are involved in the regulation of flowering time and whole-plant growth. Based on these results, LHP1 homolog genes might have rapidly evolved among plant species, but the protein functions were conserved, at least between Arabidopsis and apple. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

The<Emphasis Type="Italic"> GAOLAOZHUANGREN2</Emphasis> gene is required for normal glucose response and development of<Emphasis Type="Italic"> Arabidopsis</Emphasis>

Recent studies of glucose (Glc) sensing and signaling have revealed that Glc acts as a critical signaling molecule in higher plants. Several Glc sensing-defective Arabidopsis mutants have been characterized in detail, and the corresponding genes encoding Glc-signaling proteins have been isolated. However, the full complexity of Glc signaling in higher plants is not yet fully understood. Here, we report the identification and characterization of a new Glc-insensitive mutant, gaolaozhuangren2 (glz2), which was isolated from transposon mutagenesis experiments in Arabidopsis. In addition to its insensitivity to Glc, the glz2 plant exhibits several developmental defects such as short stature with reduced apical dominance, short roots, small and dark-green leaves, late flowering and female sterility. Treatment with 4% Glc blocked expression of the OE33 gene in wild-type plants, whereas expression of this gene was unchanged in the glz2 mutant plants. Taken together, our results suggest that the GLZ2 gene is required for normal glucose response and development of Arabidopsis.Mingjie Chen and Xiaoxiang Xia contributed equally to this work.     

CENTRORADIALIS/TERMINAL FLOWER 1 gene homolog is conserved inN. tabacum, a determinate inflorescence plant

A mutation in theCENTRORADIALIS (CEN) gene ofAntirrhinum and in theTERMINAL FLOWER 1 (TFL1) gene ofArabidopsis causes their indeterminate inflorescence to determinate. We clonedCEN/TFL1 homologs fromNicotiana tabacum, the wild-type of which has a determinate inflorescence. TheCEN gene was expressed in the inflorescnece meristem and kept its inflorescence meristem identity, whereas the tobacco homolog (NCH) was expressed at a low level throughout the plant’s development. AlthoughCEN andNCH are highly homologous genes, they may have been recruited to different developmental functions during their evolution. TwoNCH genes are derived from amphidiploidN. tabacum, but both of them hybridized with its diploid parents,N. sylvestris andN. tomentosiformis. Southern blotting, and the genomic organization ofTFL1 inArabidopsis revealed that anotherCEN homolog exists in the genome ofArabidopsis. These results suggest that there are two copies of theCEN homolog per diploid plant. The extended abstract of a paper presented at the 13th International Symposium in Conjugation with Award of the International Prize for Biology “Frontier of Plant Biology” These two authors contributed to this work equally.