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ABSTRACT: Microtubules are highly dynamic cytoskeletal polymers of α/β-tubulin heterodimers that undergo multiple posttranslational modifications essential for various cellular functions in eukaryotes. The lysine 40 (K40) is largely conserved in α-tubulins in many eukaryote species, and the post-translational modification by acetylation at K40 is critical for neuronal development in vertebrates. However, the biological function of K40 of α-tubulins in plants remains unexplored. In this study, we show in Arabidopsis thaliana that constitutive expression of mutated forms of α-tubulin6 (TUA6) at K40 (TUA6(K40A) or TUA6(K40Q) ), in which K40 is replaced by alanine or glutamine, result in severely reduced plant size. Phenotypic characterization of the 35S:TUA6(K40A) transgenic plants revealed that both cell proliferation and cell expansion were affected. Cytological and biochemical analyses showed that the accumulation of α- and β-tubulin proteins was significantly reduced in the transgenic plants, and the cortical microtubule arrays were severely disrupted, indicating that K40 of the plant α-tubulin is critical in maintaining microtubule stability. We also constructed 35S:TUA6(K40R) transgenic plants in which K40 of the engineered TUA6 protein is replaced by an arginine, and found that the 35S:TUA6(K40R) plants were phenotypically indistinguishable from the wild-type. Since lysine and arginine are similar in biochemical nature but arginine cannot be acetylated, these results suggest a structural importance for K40 of α-tubulins in cell division and expansion.
Journal of Integrative Plant Biology 11/2012; · 2.53 Impact Factor
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ABSTRACT: During their life cycle, flowering plants must experience a transition from vegetative to reproductive growth. Here, we report that double mutations in the Arabidopsis thaliana IMITATION SWITCH (AtISWI) genes, CHROMATIN REMODELING11 (CHR11) and CHR17, and the plant-specific DDT-domain containing genes, RINGLET1 (RLT1) and RLT2, resulted in plants with similar developmental defects, including the dramatically accelerated vegetative-to-reproductive transition. We demonstrated that AtISWI physically interacts with RLTs in preventing plants from activating the vegetative-to-reproductive transition early by regulating several key genes that contribute to flower timing. In particular, AtISWI and RLTs repress FT, SEP1, SEP3, FUL, and SOC1, but promote FLC in the leaf. Furthermore, AtISWI and RLTs may directly repress FT and SEP3 through associating with the FT and SEP3 loci. Our study reveals that AtISWI and RLTs represent a previously unrecognized genetic pathway that is required for the maintenance of the plant vegetative phase.
The Plant Journal 06/2012; 72(2):261-70. · 6.16 Impact Factor
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ABSTRACT: The Arabidopsis AtMYB103 gene is required for anther development, but whether the homologous gene in rice has the same role is unclear. Sequence analysis
indicated that the rice OsMYB103 gene shares a high sequence similarity with AtMYB103. Therefore, we investigated the functional role of OsMYB103 in anther development using an RNAi approach. The OsMYB103 RNA transcript was expressed most abundantly in flowers, specifically in the tapetum, premeiotic pollen mother cells, and
meiotic PMCs. OsMYB103-RNAi transgenic lines grew normally during their vegetative phase but displayed reduced male fertility,
a phenotype that was associated with downregulated OsMYB103 transcript levels. Expression of OsMS2, an ortholog of the Arabidopsis AtMS2 gene, was also dramatically reduced in the transgenic plants. Knockdown of OsMYB103 led to defects in tapetum development, and most of the microspores in mature anthers lacked exines. Moreover, OsMYB103 could partially rescue the male sterility phenotype of an AtMYB103 knockout mutant ms188. Taken together, these results indicate that OsMYB103 does have an important role in rice tapetum and microspore development.
Keywordsanther development-microspore-
Oryza sativa
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OsMYB103
-tapetum
Chinese Science Bulletin 04/2012; 55(29):3288-3297. · 1.32 Impact Factor
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ABSTRACT: Identification of regulatory relationships between transcription factors (TFs) and their targets is a central problem in post-genomic biology. In this paper, we apply an approach based on the support vector machine (SVM) and gene-expression data to predict the regulatory interactions in Arabidopsis. A set of 125 experimentally validated TF-target interactions and 750 negative regulatory gene pairs are collected as the training data. Their expression profiles data at 79 experimental conditions are fed to the SVM to perform the prediction. Through the jackknife cross-validation test, we find that the overall prediction accuracy of our approach achieves 88.68%. Our approach could help to widen the understanding of Arabidopsis gene regulatory scheme and may offer a cost-effective alternative to construct the gene regulatory network.
Plant Physiology and Biochemistry 03/2011; 49(3):280-3. · 2.84 Impact Factor
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ABSTRACT: Identification of cis-regulatory elements in Arabidopsis is a key step to understanding its transcriptional regulation scheme. In this study, the Arabidopsis gene coexpression network was constructed using the ATTED-II data, and thereafter a subgraph-induced approach and clique-finding algorithm were used to extract gene coexpression groups from the gene coexpression network. A total of 23 large coexpression gene groups were obtained, with each consisting of more than 100 highly correlated genes. Four classical tools were used to predict motifs in the promoter regions of coexpressed genes. Consequently, we detected a large number of candidate biologically relevant regulatory elements, and many of them are consistent with known cis-regulatory elements from AGRIS and AthaMap. Experiments on coexpressed groups, including E2Fa target genes, showed that our method had a high probability of returning the real binding motif. Our study provides the basis for future cis-regulatory module analysis and creates a starting point to unravel regulatory networks of Arabidopsis thaliana.
Journal of plant physiology 10/2010; 168(6):611-8. · 2.50 Impact Factor
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ABSTRACT: Previous reports indicated that AtMYB103 has an important role in tapetum development, callose dissolution, and exine formation in A. thaliana anthers. Here, we further characterized its function in anther development by expression pattern analysis, transmission electron microscopy observation of the knockout mutant, and microarray analysis of downstream genes. A total of 818 genes differentially expressed between ms188 and the wild-type were identified by global expression profiling analysis. Functional classification showed that loss-of-function of AtMYB103 impairs cell wall modification, lipid metabolic pathways, and signal transduction throughout anther development. RNA in situ hybridization confirmed that transcription factors acting downstream of AtMYB103 (At1g06280 and At1g02040) were expressed in the tapetum and microspores at later stages, suggesting that they might have important roles in microsporogenesis. These results indicated that AtMYB103 is a crucial regulator of Arabidopsis anther development.
Science China. Life sciences 09/2010; 53(9):1112-22. · 2.02 Impact Factor
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ABSTRACT: Anther development in Arabidopsis, a popular model plant for plant biology and genetics, is controlled by a complex gene network. Despite the extensive use
of this genus for genetic research, little is known about its regulatory network. In this paper, the direct transcriptional
regulatory relationships between genes expressed in Arabidopsis anther development were predicted with an integrated bioinformatic method that combines mining of microarray data with promoter
analysis. A total of 7710 transcription factor-gene pairs were obtained. The 80 direct regulatory relationships demonstrating
the highest confidence were screened from the initial 7710 pairs; three of the 80 were validated by previous experiments.
The results indicate that our predicted results were reliable. The regulatory relationships revealed by this research and
described in this paper may facilitate further investigation of the molecular mechanisms of anther development. The bioinformatic
method used in this work can also be applied to the prediction of gene regulatory relationships in other organisms.
Chinese Science Bulletin 09/2008; 53(20):3198-3203. · 1.32 Impact Factor
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Jian Cui,
Peng Li,
Guang Li,
Feng Xu,
Chen Zhao,
Yuhua Li, Zhongnan Yang,
Guang Wang,
Qingbo Yu,
Yixue Li,
Tieliu Shi
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ABSTRACT: Arabidopsis thaliana Protein Interactome Database (AtPID) is an object database that integrates data from several bioinformatics prediction methods and manually collected information from the literature. It contains data relevant to protein-protein interaction, protein subcellular location, ortholog maps, domain attributes and gene regulation. The predicted protein interaction data were obtained from ortholog interactome, microarray profiles, GO annotation, and conserved domain and genome contexts. This database holds 28,062 protein-protein interaction pairs with 23,396 pairs generated from prediction methods. Among the rest 4666 pairs, 3866 pairs of them involving 1875 proteins were manually curated from the literature and 800 pairs were from enzyme complexes in KEGG. In addition, subcellular location information of 5562 proteins is available. AtPID was built via an intuitive query interface that provides easy access to the important features of proteins. Through the incorporation of both experimental and computational methods, AtPID is a rich source of information for system-level understanding of gene function and biological processes in A. thaliana. Public access to the AtPID database is available at http://atpid.biosino.org/.
Nucleic Acids Research 02/2008; 36(Database issue):D999-1008. · 8.03 Impact Factor
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Jian Cui,
Peng Li,
Guang Li,
Feng Xu,
Chen Zhao,
Yuhua Li, Zhongnan Yang,
Guang Wang,
Qingbo Yu,
Yi-Xue Li,
Tieliu Shi
Nucleic Acids Research. 01/2008; 36:999-1008.
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ABSTRACT: With the goal of identifying an improved delivery scheme for intracellular tracking and anticancer therapy, we explored a novel double functionalization of a carbon nanotube delivery system containing antisense oligodeoxynucleotides (ASODNs) as a therapeutic gene and CdTe quantum dots as fluorescent labeling probes via electrostatically layer-by-layer assembling. This is the first time that we used mercaptoacetic acid-capped CdTe quantum dots as fluorescent labeling probes for clearly tracking the intracellular transport and evaluating delivery efficiency of ASODNs by functionalized multiwalled carbon nanotubes (MWNTs).
Nano Letters 11/2007; 7(10):2976-80. · 13.20 Impact Factor
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ABSTRACT: The Arabidopsis thaliana ASYMMETRIC LEAVES1 (AS1) and AS2 genes are important for repressing class I KNOTTED1-like homeobox (KNOX) genes and specifying leaf adaxial identity in leaf development. RNA-dependent RNA polymerases (RdRPs) are critical for posttranscriptional and transcriptional gene silencing in eukaryotes; however, very little is known about their functions in plant development. Here, we show that the Arabidopsis RDR6 gene (also called SDE1 and SGS2) that encodes a putative RdRP, together with AS1 and AS2, regulates leaf development. rdr6 single mutant plants displayed only minor phenotypes, whereas rdr6 as1 and rdr6 as2 double mutants showed dramatically enhanced as1 and as2 phenotypes, with severe defects in the leaf adaxial-abaxial polarity and vascular development. In addition, the double mutant plants produced more lobed leaves than the as1 and as2 single mutants and showed leaf-like structures associated on a proportion of leaf blades. The abnormal leaf morphology of the double mutants was accompanied by an extended ectopic expression of a class I KNOX gene BREVIPEDICELLUS (BP) and high levels of microRNA165/166 that may lead to mRNA degradation of genes in the class III HD-ZIP family. Taken together, our data suggest that the Arabidopsis RDR6-associated epigenetic pathway and the AS1-AS2 pathway synergistically repress BP and MIR165/166 for proper plant development.
The Plant Cell 09/2005; 17(8):2157-71. · 8.99 Impact Factor
