萝卜TALE转录因子家族的鉴定与分析

TALE (three-amino acid loop extension)转录因子在植物生长发育及细胞分化过程中起重要作用.在多种植物中均已鉴定出TALE转录因子的家族成员,但是萝卜TALE转录因子家族的研究鲜有报道.文中通过生物信息学手段在象牙白萝卜全基因组中鉴定出了分布于9条染色体上的33个TALE家族基因.研究...     

Computational identification and analysis of immune-associated nucleotide gene family in Arabidopsis thaliana

GTP-binding proteins represent a ubiquitous regulatory mechanism in controlling growth and development in eukaryotes under normal and stress conditions. The IAN/GIMAP proteins belong to a novel family of functionally uncharacterized GTP-binding proteins expressed in both plant and vertebrate cells during anti-pathogenic responses. To gain novel insights into their roles in plants, we did genome-wide analysis of the IAN/GIMAP gene family. We identified 13 Arabidopsis IAN/GIMAP genes, which share similar gene structures and mostly reside in a tandem cluster on chromosomes. Sequence comparison reveals that these genes encode 26–52 kDa proteins with one GTP-binding domain and a conserved box unique to the family. Phylogenetic analysis suggests that the IAN/GIMAP genes of angiosperms and vertebrates may have evolved by independent gene duplication events. GENEVESTIGATOR sources were mined for comprehensive and comparative Arabidopsis IAN/GIMAP gene family expression analysis. These data reveal that IAN/GIMAPs exhibit diverse expression patterns during development and in response to external stimuli, indicating that these paralogous genes are likely involved in complex biological processes in Arabidopsis. Our present findings provide a basis for elucidating the novel GTPase family protein-mediated regulatory mechanisms in the future.     

Molecular identification and characterization of the Arabidopsis AtADF1, AtADF5 and AtADF6 genes

Actin depolymerizing factor (ADF) is a key regulator of the organization of the actin cytoskeleton during various cellular activities. We found that ADF genes in Arabidopsis form a large family consisting of at least nine members, four of which were cloned and sequenced in this study. Comparison of genomic and cDNA sequences showed that the AtADF1, AtADF5, and AtADF6 genes all contain two introns at conserved positions. Analysis of transgenic Arabidopsis plants carrying promoter-GUS fusion constructs revealed that AtADF1 and AtADF6 are expressed in the vascular tissues of all organs, whereas expression of AtADF5 is restricted to the root tip meristem. GFP-AtADF1, GFP-AtADF5, and GFP-AtADF6 fusion proteins were found to bind to actin filaments in vivo, and to reorganize the actin cytoskeleton when transiently expressed in plant cells.     

The Arabidopsis CLV3-like (CLE) genes are expressed in diverse tissues and encode secreted proteins

Members of the receptor-like kinase gene family play crucial regulatory roles in many aspects of plant development, but the ligands to which they bind are largely unknown. In Arabidopsis, the receptor kinase CLAVATA1 (CLV1) binds to the small secreted polypeptide CLV3, and three proteins act as key elements of a signal transduction pathway that regulates shoot apical meristem maintenance. To better understand the signal transduction mechanisms involving small polypeptides, we are studying 25 Arabidopsis CLV3/ESR (CLE) proteins that share a conserved C-terminal domain with CLV3 and three maize ESR proteins. Members of the CLE gene family were identified in database searches and only a few are known to be expressed. We have identified an additional member of the CLE gene family in Arabidopsis, which is more similar in gene structure to CLV3 than the other CLE genes. Phylogenetic analysis reveals that few of the putative CLE gene products are closely related, suggesting there may be little functional overlap between them. We show that 24 of the 25 Arabidopsis CLE genes are transcribed in one or more tissues during development, indicating that they do encode functional products. Many are widely expressed, but others are restricted to one or a few tissue types. We have also determined the sub-cellular localization of several CLE proteins, and find that they are exported to the plasma membrane or extracellular space. Our results suggest that the Arabidopsis CLE proteins, like CLV3, may function as secreted signaling molecules that act in diverse pathways during growth and development.     

Sequence analysis and expression profiling of 14-3-3 genes from the extremophile <Emphasis Type="Italic">Thelungiella salsuginea</Emphasis>, ecotype Yakutsk

Members of the 14-3-3 protein family are known to be important regulators of plant primary metabolism, hormonal signal transduction, and ion homeostasis. We identified nine isoforms of 14-3-3 genes of Thellungiella salsuginea, an extremophile relative of Arabidopsis thaliana. All the identified isoforms were designated according to their Arabidopsis orthologs: Chi, Omega, Psi, Phi, Upsilon, Lambda, Mu, Epsilon, and Omicron. Comparison of the deduced amino acid sequences reveals high degree of identity between the members of this protein family. Isoforms, designated as Ts14-3-3 Chi, Omicron, and Mu, display noticeable differences in their C-terminal domain as compared to their Arabidopsis homologs. Phylogenetic analysis demonstrated that the identified isoforms split into two groups, epsilon and non-epsilon, according to the common classification of the 14-3-3 family genes. The Thellungiella 14-3-3 isoforms are differentially expressed in various plant tissues, and real-time RT-PCR revealed that most of the isoforms are highly expressed even under normal growth conditions. In response to abiotic stress, low temperatures and high concentrations of salts, 14-3-3 genes exhibited different expression patterns. Our data suggest that, due to the high expression levels of the 14-3-3 genes, Thellungiella plants are likely pre-adapted to the stress conditions. Differences between the C-terminal domains of some Thellungiella 14-3-3 proteins and their Arabidopsis homologs may result in differences in target protein specificity.     

Comprehensive approach to genes involved in cell wall modifications in <Emphasis Type="Italic">Arabidopsis thaliana</Emphasis>

The plant cell wall is of supermolecular architecture, and is composed of various types of heterogeneous polymers. A few thousand enzymes and structural proteins are directly involved in the construction processes, and in the functional aspects of the dynamic architecture in Arabidopsis thaliana. Most of these proteins are encoded by multigene families, and most members within each family share significant similarities in structural features, but often exhibit differing expression profiles and physiological functions. Thus, for the molecular dissection of cell wall dynamics, it is necessary to distinguish individual members within a family of proteins. As a first step towards characterizing the processes involved in cell wall dynamics, we have manufactured a gene-specific 70-mer oligo microarray that consists of 765 genes classified into 30 putative families of proteins that are implicated in the cell wall dynamics of Arabidopsis. By using this array system, we identified several sets of genes that exhibit organ preferential expression profiles. We also identified gene sets that are expressed differentially at certain specific growth stages of the Arabidopsis inflorescence stem. Our results indicate that there is a division of roles among family members within each of the putative cell wall-related gene families.     

Activation of hypersensitive cell death by pathogen-induced receptor-like protein kinases from <Emphasis Type="Italic">Arabidopsis</Emphasis>

In Arabidopsis, there is a family of receptor-like protein kinases (RLKs) containing novel cysteine-rich repeats in their extracellular domains. Genes encoding many of these cysteine-rich RLKs (CRKs) are induced by pathogen infection, suggesting a possible role in plant defense responses. We have previously generated Arabidopsis plants expressing four pathogen-regulated CRK genes (CRK5, 6, 10 and 11) under control of a steroid-inducible promoter and found that induced expression of CRK5, but not the other three CRK genes, triggered hypersensitive response-like cell death in transgenic plants. In the present study, we have analyzed the structural relationship of the CRK family and identified three CRKs (CRK4, 19 and 20) that are structurally closely related to CRK5. Genes encoding these three CRKs are all induced by salicylic acid and pathogen infection. Furthermore, induced expression of CRK4, 19and 20 all activates rapid cell death in transgenic plants. Thus, the activity of inducing rapid cell death is shared by these structurally closely related CRKs. We have also performed yeast two-hybrid screens and identified proteins that interact with the kinase domains of CRKs. One of the identified CRK-interacting proteins is the kinase-associated type 2C protein phospohatase known to interact with a number of other RLKs through its kinase-interacting FHA domain. Other CRK-interacting proteins include a second protein with a FHA domain and another type 2C protein phosphatase. Interactions of CRKs with these three proteins in vivo were demonstrated through co-immunoprecipitation. These CRK-interacting proteins may play roles in the regulation and signaling of CRKs.     

森林草莓SUN基因家族的鉴定及其对逆境的响应

SUN基因是调控植物生长发育的关键基因。本研究鉴定了二倍体森林草莓(Fragaria vesca)的SUN基因家族,并对各成员的理化性质、基因结构、系统进化以及基因表达进行了分析。结果表明,森林草莓有31个FvSUN基因,其编码蛋白可聚类为7个组,同一组内成员具有高度相似的基因结构与编码蛋白保守域;FvSUNs蛋白的亚细胞定位主要在细胞核中。共线性分析表明森林草莓FvSUNs基因家族主要通过染色体片段复制产生,拟南芥与森林草莓存在23对直系同源基因。利用森林草莓的转录组数据,对FvSUNs基因的组织表达特征进行分析,发现主要可归为3类：各组织均表达、组织中几乎不表达、组织特异性表达,并通过实时荧光定量PCR (quantitative real-time polymerase chain reaction, qRT-PCR)进一步验证结果。此外,还对森林草莓进行不同的逆境胁迫处理,qRT-PCR分析了31个FvSUNs基因的表达情况,发现大部分基因均在不同程度上受低温、高盐或干旱胁迫的诱导表达。这些研究结果为深入揭示草莓SUN基因的生物学功能及其分子机制奠定了基础。     

The <Emphasis Type="Italic">FT/TFL1</Emphasis> gene family in grapevine

The FT/TFL1 gene family encodes proteins with similarity to phosphatidylethanolamine binding proteins which function as flowering promoters and repressors. We show here that the FT/TFL1 gene family in Vitis vinifera is composed of at least five genes. Sequence comparisons with homologous genes identified in other dicot species group them in three major clades, the FT, MFT and TFL1 subfamilies, the latter including three of the Vitis sequences. Gene expression patterns are in agreement with a role of VvFT and VvMFT as flowering promoters; while VvTFL1A, VvTFL1B and VvTFL1C could be associated with vegetative development and maintenance of meristem indetermination. Overexpression of VvFT in transgenic Arabidopsis plants generates early flowering phenotypes similar to those produced by FT supporting a role for this gene in flowering promotion. Overexpression of VvTFL1A does not affect flowering time but the determination of flower meristems, strongly altering inflorescence structure, which is consistent with the biological roles assigned to similar genes in other species.     

Genome-wide analysis of intronless genes in rice and <Emphasis Type="Italic">Arabidopsis</Emphasis>

Intronless genes, a characteristic feature of prokaryotes, constitute a significant portion of the eukaryotic genomes. Our analysis revealed the presence of 11,109 (19.9%) and 5,846 (21.7%) intronless genes in rice and Arabidopsis genomes, respectively, belonging to different cellular role and gene ontology categories. The distribution and conservation of rice and Arabidopsis intronless genes among different taxonomic groups have been analyzed. A total of 301 and 296 intronless genes from rice and Arabidopsis, respectively, are conserved among organisms representing the three major domains of life, i.e., archaea, bacteria, and eukaryotes. These evolutionarily conserved proteins are predicted to be involved in housekeeping cellular functions. Interestingly, among the 68% of rice and 77% of Arabidopsis intronless genes present only in eukaryotic genomes, approximately 51% and 57% genes have orthologs only in plants, and thus may represent the plant-specific genes. Furthermore, 831 and 144 intronless genes of rice and Arabidopsis, respectively, referred to as ORFans, do not exhibit homology to any of the genes in the database and may perform species-specific functions. These data can serve as a resource for further comparative, evolutionary, and functional analysis of intronless genes in plants and other organisms. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Cloning and expression analysis of candidate genes involved in wax deposition along the growing barley (<Emphasis Type="Italic">Hordeum vulgare</Emphasis>) leaf

The aim of the present study was to isolate clones of genes which are likely to be involved in wax deposition on barley leaves. Of particular interest were those genes which encode proteins that take part in the synthesis and further modification of very long chain fatty acids (VLCFAs), the precursors of waxes. Previously, it had been shown that wax deposition commences within a spatially well-defined developmental zone along the growing barley leaf (Richardson et al. in Planta 222:472–483, 2005). In the present study, a barley microarray approach was used to screen for candidate contig-sequences (www.barleybase.org) that are expressed particularly in those leaf zones where wax deposition occurs and which are expressed specifically within the epidermis, the site of wax synthesis. Candidate contigs were used to screen an established in-house cDNA library of barley. Six full-length coding sequences clones were isolated. Based on sequence homologies, three clones were related to Arabidopsis CER6/CUT1, and these clones were termed HvCUT1;1, HvCUT1;2 and HvCUT1;3. A fourth clone, which was related to Arabidopsis Fiddlehead (FDH), was termed HvFDH1;1. These clones are likely to be involved in synthesis of VLCFAs. A fifth and sixth clone were related to Arabidopsis CER1, and were termed HvCER1;1 and HvCER1;2. These clones are likely to be involved in the decarbonylation pathway of VLCFAs. Semi-quantitative RT-PCR confirmed microarray expression data. In addition, expression analyses at 10-mm resolution along the blade suggest that HvCUT1;1 (and possibly HvCUT1;2) and HvCER1;1 are involved in commencement of wax deposition during barley leaf epidermal cell development. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Molecular analysis of the<Emphasis Type="Italic"> CRINKLY4</Emphasis> gene family in<Emphasis Type="Italic"> Arabidopsis thaliana</Emphasis>

The maize (Zea mays L.) CRINKLY4 (CR4) gene encodes a serine/threonine receptor-like kinase that controls an array of developmental processes in the plant and endosperm. The Arabidopsis thaliana (L.) Heynh. genome encodes an ortholog of CR4, ACR4, and four CRINKLY4-RELATED (CRR) proteins: AtCRR1, AtCRR2, AtCRR3 and AtCRK1. The available genome sequence of rice (Oryza sativa L.) encodes a CR4 ortholog, OsCR4, and four CRR proteins: OsCRR1, OsCRR2, OsCRR3 and OsCRR4, not necessarily orthologous to the Arabidopsis CRRs. A phylogenetic study showed that AtCRR1 and AtCRR2 form a clade closest to the CR4 group while all the other CRRs form a separate cluster. The five Arabidopsis genes are differentially expressed in various tissues. A construct formed by fusion of the ACR4 promoter and the GUS reporter, ACR4::GUS, is expressed primarily in developing tissues of the shoot. The ACR4 cytoplasmic domain functions in vitro as a serine/threonine kinase, while the AtCRR1 and AtCRR2 kinases are not active. The ability of ACR4 to phosphorylate AtCRR2 suggests that they might function in the same signal transduction pathway. T-DNA insertions were obtained in ACR4, AtCRR1, AtCRR2, AtCRR3 and AtCRK1. Mutations in acr4 show a phenotype restricted to the integuments and seed coat, suggesting that Arabidopsis might contain a redundant function that is lacking in maize. The lack of obvious mutant phenotypes in the crr mutants indicates they are not required for the hypothetical redundant function.