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Meng Y.,State Key Laboratory of Plant Physiology and Biochemistry | Meng Y.,Zhejiang University | Mao C.,State Key Laboratory of Plant Physiology and Biochemistry | Jin Y.,Zhejiang University | And 2 more authors.
Nucleic Acids Research

MicroRNAs (miRNAs), one type of small RNAs (sRNAs) in plants, play an essential role in gene regulation. Several miRNA databases were established; however, successively generated new datasets need to be collected, organized and analyzed. To this end, we have constructed a plant miRNA knowledge base (PmiRKB) that provides four major functional modules. In the 'SNP' module, single nucleotide polymorphism (SNP) data of seven Arabidopsis (Arabidopsis thaliana) accessions and 21 rice (Oryza sativa) subspecies were collected to inspect the SNPs within pre-miRNAs (precursor microRNAs) and miRNA-target RNA duplexes. Depending on their locations, SNPs can affect the secondary structures of pre-miRNAs, or interactions between miRNAs and their targets. A second module, 'Pri-miR', can be used to investigate the tissue-specific, transcriptional contexts of pre- and pri-miRNAs (primary microRNAs), based on massively parallel signature sequencing data. The third module, 'MiR-Tar', was designed to validate thousands of miRNA-target pairs by using parallel analysis of RNA end (PARE) data. Correspondingly, the fourth module, 'Self-reg', also used PARE data to investigate the metabolism of miRNA precursors, including precursor processing and miRNA- or miRNA*-mediated self-regulation effects on their host precursors. PmiRKB can be freely accessed at http://bis.zju.edu. cn/pmirkb/. © The Author(s) 2010. Source

Zhu X.F.,State Key Laboratory of Plant Physiology and Biochemistry | Zheng C.,State Key Laboratory of Plant Physiology and Biochemistry | Zheng C.,Zhejiang University | Hu Y.T.,State Key Laboratory of Plant Physiology and Biochemistry | And 7 more authors.
Plant, Cell and Environment

The mechanisms of heavy metal resistance in plants can be classified into internal tolerance and exclusion mechanisms, but exclusion of heavy metals with the help of organic acids secretion has not been well documented. Here we demonstrated the contribution of oxalate secretion to cadmium (Cd) exclusion and resistance in tomato. Different Cd resistance between two tomato cultivars was evaluated by relative root elongation (RRE) and Cd accumulation. Cultivar 'Micro-Tom' showed better growth and lower Cd content in roots than 'Hezuo903' at different Cd concentrations not only in short-term hydroponic experiment but also in long-term hydroponic and soil experiments, indicating that the genotypic difference in Cd resistance is related to the exclusion of Cd from roots. 'Micro-Tom' had greater ability to secrete oxalate, suggesting that oxalate secretion might contribute to Cd resistance. Cd-induced secretion of oxalate was localized to root apex at which the majority of Cd accumulated. Phenylglyoxal, an anion-channel inhibitor, effectively blocked Cd-induced oxalate secretion and aggravated Cd toxicity while exogenous oxalate supply ameliorated Cd toxicity efficiently. These results indicated that the oxalate secreted from the root apex helps to exclude Cd from entering tomato roots, thus contributes to Cd resistance in the Cd-resistant tomato cultivar. © 2011 Blackwell Publishing Ltd. Source

Sun P.,China Agricultural University | Sun P.,State Key Laboratory of Plant Physiology and Biochemistry | Sun P.,National Center for Evaluation of Agricultural Wild Plant Rice | Sun P.,Beijing Key Laboratory of Crop Genetic Improvement and Genome of Ministry of Agriculture | And 25 more authors.
Indian Journal of Genetics and Plant Breeding

An F8 recombinant inbred lines (RIL) population was used to identify quantitative trait loci (QTLs) for potassium chlorate (KClO3) resistance and low temperature tolerance (LTT), two key physiological traits to distinguish rice subspecies, indica and japonica. Four traits were measured for KClO3 resistance including shoot length, root length, shoot length and root length ratios of treatment and control conditions, and four traits for LTT including shoot length, root length and germination rate in 15° and 28°. A total of six QTLs were identified on chromosomes 2, 4, 7 and 10 for KClO3, including a major QTL qSLratio-2, which accounted for 40% of the phenotypic variance. On the other hand, a total of four QTLs for LTT were identified on chromosomes 2 and 4. These results will be useful in marker-assisted selections for these two important traits. Source

Meng Q.,State Key Laboratory of Plant Physiology and Biochemistry | Du J.,State Key Laboratory of Plant Physiology and Biochemistry | Li J.,State Key Laboratory of Plant Physiology and Biochemistry | Lu X.,State Key Laboratory of Plant Physiology and Biochemistry | And 3 more authors.
Plant Molecular Biology

Three genes that encode MAP65-1 family proteins have been identified in the Nicotiana tabacum genome. In this study, NtMAP65-1c fusion protein was shown to bind and bundle microtubules (MTs). Further in vitro investigations demonstrated that NtMAP65-1c not only alters MT assembly and nucleation, but also exhibits high MT stabilizing activity against cold or katanin-induced destabilization. Analysis of NtMAP65-1c-GFP expressing BY-2 cells clearly demonstrated that NtMAP65-1c was able to bind to MTs during specific stages of the cell cycle. Furthermore, in vivo, NtMAP65-1c-GFP-bound cortical MTs displayed an increase in resistance against the MT-disrupting drug, propyzamide, as well as against cold temperatures. Taken together, these results strongly suggest that NtMAP65-1c stabilizes MTs and is involved in the regulation of MT organization and cellular dynamics. © 2010 Springer Science+Business Media B.V. Source

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