Laser Microdissection of Grapevine Leaves Reveals Site-Specific Regulation of Transcriptional Response to Plasmopara viticola
Grapevine is one of the most important fruit crops in the world, and it is highly susceptible to downy mildew caused by the biotrophic oomycete Plasmopara viticola. Gene expression profiling has been used extensively to investigate the regulation processes of grapevine–P. viticola interaction, but all studies to date have involved the use of whole leaves. However, only a small fraction of host cells is in contact with the pathogen, so highly localized transcriptional changes of infected cells may be masked by the large portion of non-infected cells when analyzing the whole leaf. In order to understand the transcripti...
Source: Plant and Cell Physiology - January 21, 2016 Category: Cytology Authors: Lenzi, L., Caruso, C., Bianchedi, P. L., Pertot, I., Perazzolli, M. Tags: Regular Papers Source Type: research
Genome-Wide Transcriptome Analysis During Anthesis Reveals New Insights into the Molecular Basis of Heat Stress Responses in Tolerant and Sensitive Rice Varieties
In this study, an RNA-sequencing approach of heat- and control-treated reproductive tissues during anthesis was carried out using N22, one of the most heat-tolerant rice cultivars known to date. This analysis revealed that expression of genes encoding a number of transcription factor families, together with signal transduction and metabolic pathway genes, is repressed. On the other hand, expression of genes encoding heat shock factors and heat shock proteins was highly activated. Many of these genes are predominantly expressed at late stages of anther development. Further physiological experiments using heat-tolerant N22 a...
Source: Plant and Cell Physiology - January 21, 2016 Category: Cytology Authors: Gonzalez-Schain, N., Dreni, L., Lawas, L. M. F., Galbiati, M., Colombo, L., Heuer, S., Jagadish, K. S. V., Kater, M. M. Tags: Regular Papers Source Type: research
Distinct Biochemical Properties of Arabidopsis thaliana Actin Isoforms
In this study, we purified four recombinant Arabidopsis actin isoforms, two major vegetative actin isoforms, ACT2 and ACT7, and two major reproductive isoforms, ACT1 and ACT11, and characterized them biochemically. Phalloidin bound normally to the filaments of the two reproductive actins as well as to the filaments of skeletal muscle actin. However, phalloidin bound only weakly to ACT7 filaments and hardly at all to ACT2 filaments, despite the conserved sequence of the phalloidin-binding site. Polymerization and phosphate release rates among these four actin isoforms were also significantly different. Moreover, interaction...
Source: Plant and Cell Physiology - January 21, 2016 Category: Cytology Authors: Kijima, S. T., Hirose, K., Kong, S.-G., Wada, M., Uyeda, T. Q. P. Tags: Regular Papers Source Type: research
TBL3 and TBL31, Two Arabidopsis DUF231 Domain Proteins, are Required for 3-O-Monoacetylation of Xylan
In this report, we demonstrated the essential roles of two other Arabidopsis DUF231 genes, TBL3 and TBL31, in xylan acetylation. The expression of both TBL3 and TBL31 was shown to be induced by overexpression of the secondary wall master transcriptional regulator SND1 (secondary wall-associated NAC domain protein1) and down-regulated by simultaneous mutations of SND1 and its paralog NST1, indicating their involvement in secondary wall biosynthesis. β-Glucurondase (GUS) reporter gene analysis showed that TBL3 and TBL31 were specifically expressed in the xylem and interfascicular fibers in stems and the secondary xylem ...
Source: Plant and Cell Physiology - January 21, 2016 Category: Cytology Authors: Yuan, Y., Teng, Q., Zhong, R., Ye, Z.-H. Tags: Regular Papers Source Type: research
Phloem transcriptome signatures underpin the physiological differentiation of the pedicel, stalk and fruit of cucumber (Cucumis sativus L.)
Cucumber is one of the most important vegetables grown worldwide due to its important economic and nutritional value. The cucumber fruit consists morphologically of the undesirable stalk and the tasty fruit; however, physiological differentiation of these two parts and the underlying molecular basis remain largely unknown. Here we characterized the physiological differences among the pedicel, stalk and fruit, and compared the respective phloem transcriptomes using laser capture microdissection coupled with RNA sequencing (RNA-Seq). We found that the pedicel was characterized by minor cell expansion and a high concentration...
Source: Plant and Cell Physiology - January 21, 2016 Category: Cytology Authors: Zhao, J., Li, Y., Ding, L., Yan, S., Liu, M., Jiang, L., Zhao, W., Wang, Q., Yan, L., Liu, R., Zhang, X. Tags: Regular Papers Source Type: research
The TOR Complex: An Emergency Switch for Root Behavior
Target of rapamycin (TOR) kinase is known to be a controller of cell growth and aging, which determines the fine balance between growth rates and energy availabilities. It has been reported that many eukaryotes express TOR genes. In plants, TOR signaling modifies growth and development in response to a plant’s energy status. An example of TOR action can be found in the root apices, which are active organs that explore the soil environment via vigorous growth and numerous tropisms. The exploratory nature of root apices requires a large energy supply for signaling, as well as for cell division and elongation. In the ca...
Source: Plant and Cell Physiology - January 21, 2016 Category: Cytology Authors: Yokawa, K., Baluska, F. Tags: Mini Reviews Source Type: research
HRGRN: A Graph Search-Empowered Integrative Database of Arabidopsis Signaling Transduction, Metabolism and Gene Regulation Networks
The biological networks controlling plant signal transduction, metabolism and gene regulation are composed of not only tens of thousands of genes, compounds, proteins and RNAs but also the complicated interactions and co-ordination among them. These networks play critical roles in many fundamental mechanisms, such as plant growth, development and environmental response. Although much is known about these complex interactions, the knowledge and data are currently scattered throughout the published literature, publicly available high-throughput data sets and third-party databases. Many ‘unknown’ yet important int...
Source: Plant and Cell Physiology - January 21, 2016 Category: Cytology Authors: Dai, X., Li, J., Liu, T., Zhao, P. X. Tags: Special Online Collection - Database Papers Source Type: research
TOMATOMA Update: Phenotypic and Metabolite Information in the Micro-Tom Mutant Resource
TOMATOMA (http://tomatoma.nbrp.jp/) is a tomato mutant database providing visible phenotypic data of tomato mutant lines generated by ethylmethane sulfonate (EMS) treatment or -ray irradiation in the genetic background of Micro-Tom, a small and rapidly growing variety. To increase mutation efficiency further, mutagenized M3 seeds were subjected to a second round of EMS treatment; M3M1 populations were generated. These plants were self-pollinated, and 4,952 lines of M3M2 mutagenized seeds were generated. We checked for visible phenotypes in the M3M2 plants, and 618 mutant lines with 1,194 phenotypic categories were identifi...
Source: Plant and Cell Physiology - January 21, 2016 Category: Cytology Authors: Shikata, M., Hoshikawa, K., Ariizumi, T., Fukuda, N., Yamazaki, Y., Ezura, H. Tags: Special Online Collection - Database Papers Source Type: research
eHALOPH a Database of Salt-Tolerant Plants: Helping put Halophytes to Work
eHALOPH (http://www.sussex.ac.uk/affiliates/halophytes/) is a database of salt-tolerant plants—halophytes. Records of plant species tolerant of salt concentrations of around 80 mM sodium chloride or more have been collected, along with data on plant type, life form, ecotypes, maximum salinity tolerated, the presence or absence of salt glands, photosynthetic pathway, antioxidants, secondary metabolites, compatible solutes, habitat, economic use and whether there are publications on germination, microbial interactions and mycorrhizal status, bioremediation and of molecular data. The database eHALOPH can be used in the ...
Source: Plant and Cell Physiology - January 21, 2016 Category: Cytology Authors: Santos, J., Al-Azzawi, M., Aronson, J., Flowers, T. J. Tags: Special Online Collection - Database Papers Source Type: research
Finding the Subcellular Location of Barley, Wheat, Rice and Maize Proteins: The Compendium of Crop Proteins with Annotated Locations (cropPAL)
Barley, wheat, rice and maize provide the bulk of human nutrition and have extensive industrial use as agricultural products. The genomes of these crops each contains >40,000 genes encoding proteins; however, the major genome databases for these species lack annotation information of protein subcellular location for >80% of these gene products. We address this gap, by constructing the compendium of crop protein subcellular locations called crop Proteins with Annotated Locations (cropPAL). Subcellular location is most commonly determined by fluorescent protein tagging of live cells or mass spectrometry detection in su...
Source: Plant and Cell Physiology - January 21, 2016 Category: Cytology Authors: Hooper, C. M., Castleden, I. R., Aryamanesh, N., Jacoby, R. P., Millar, A. H. Tags: Special Online Collection - Database Papers Source Type: research
CANTATAdb: A Collection of Plant Long Non-Coding RNAs
Long non-coding RNAs (lncRNAs) represent a class of potent regulators of gene expression that are found in a wide array of eukaryotes; however, our knowledge about these molecules in plants is still very limited. In particular, a number of model plant species still lack comprehensive data sets of lncRNAs and their annotations, and very little is known about their biological roles. To meet these shortcomings, we created an online database of lncRNAs in 10 model plant species. The lncRNAs were identified computationally using dozens of publicly available RNA sequencing (RNA-Seq) libraries. Expression values, coding potential...
Source: Plant and Cell Physiology - January 21, 2016 Category: Cytology Authors: Szczesniak, M. W., Rosikiewicz, W., Makałowska, I. Tags: Special Online Collection - Database Papers Source Type: research
TENOR: Database for Comprehensive mRNA-Seq Experiments in Rice
Here we present TENOR (Transcriptome ENcyclopedia Of Rice, http://tenor.dna.affrc.go.jp), a database that encompasses large-scale mRNA sequencing (mRNA-Seq) data obtained from rice under a wide variety of conditions. Since the elucidation of the ability of plants to adapt to various growing conditions is a key issue in plant sciences, it is of great interest to understand the regulatory networks of genes responsible for environmental changes. We used mRNA-Seq and performed a time-course transcriptome analysis of rice, Oryza sativa L. (cv. Nipponbare), under 10 abiotic stress conditions (high salinity; high and low phosphat...
Source: Plant and Cell Physiology - January 21, 2016 Category: Cytology Authors: Kawahara, Y., Oono, Y., Wakimoto, H., Ogata, J., Kanamori, H., Sasaki, H., Mori, S., Matsumoto, T., Itoh, T. Tags: Special Online Collection - Database Papers Source Type: research
Pleurochrysome: A Web Database of Pleurochrysis Transcripts and Orthologs Among Heterogeneous Algae
Pleurochrysis is a coccolithophorid genus, which belongs to the Coccolithales in the Haptophyta. The genus has been used extensively for biological research, together with Emiliania in the Isochrysidales, to understand distinctive features between the two coccolithophorid-including orders. However, molecular biological research on Pleurochrysis such as elucidation of the molecular mechanism behind coccolith formation has not made great progress at least in part because of lack of comprehensive gene information. To provide such information to the research community, we built an open web database, the Pleurochrysome (http://...
Source: Plant and Cell Physiology - January 21, 2016 Category: Cytology Authors: Yamamoto, N., Kudo, T., Fujiwara, S., Takatsuka, Y., Hirokawa, Y., Tsuzuki, M., Takano, T., Kobayashi, M., Suda, K., Asamizu, E., Yokoyama, K., Shibata, D., Tabata, S., Yano, K. Tags: Special Online Collection - Database Papers Source Type: research
ATTED-II in 2016: A Plant Coexpression Database Towards Lineage-Specific Coexpression
ATTED-II (http://atted.jp) is a coexpression database for plant species with parallel views of multiple coexpression data sets and network analysis tools. The user can efficiently find functional gene relationships and design experiments to identify gene functions by reverse genetics and general molecular biology techniques. Here, we report updates to ATTED-II (version 8.0), including new and updated coexpression data and analysis tools. ATTED-II now includes eight microarray- and six RNA sequencing-based coexpression data sets for seven dicot species (Arabidopsis, field mustard, soybean, barrel medick, poplar, tomato and ...
Source: Plant and Cell Physiology - January 21, 2016 Category: Cytology Authors: Aoki, Y., Okamura, Y., Tadaka, S., Kinoshita, K., Obayashi, T. Tags: Special Online Collection - Database Papers Source Type: research
Boosting AthaMap Database Content with Data from Protein Binding Microarrays
The AthaMap database generates a map of predicted transcription factor binding sites (TFBS) and small RNA target sites for the whole Arabidopsis thaliana genome. With the advent of protein binding microarrays (PBM), the number of known TFBS for A. thaliana transcription factors (TFs) has increased dramatically. Using 113 positional weight matrices (PWMs) generated from a single PBM study and representing a total number of 68 different TFs, the number of predicted TFBS in AthaMap was now increased by about 3.8 x 107 to 4.9 x 107. The number of TFs with PWM-predicted TFBS annotated in AthaMap has increased to 126, representi...
Source: Plant and Cell Physiology - January 21, 2016 Category: Cytology Authors: Hehl, R., Norval, L., Romanov, A., Bülow, L. Tags: Special Online Collection - Database Papers Source Type: research
