The Increasing Impact of Activity-Based Protein Profiling in Plant Science
The active proteome dictates plant physiology. Yet, active proteins are difficult to predict based on transcript or protein levels, because protein activities are regulated post-translationally in their microenvironments. Over the past 10 years, activity-based protein profiling (ABPP) is increasingly used in plant science. ABPP monitors the activities of hundreds of plant proteins using tagged chemical probes that react with the active site of proteins in a mechanism-dependent manner. Since labeling is covalent and irreversible, labeled proteins can be detected and identified on protein gels and by mass spectrometry using ...
Source: Plant and Cell Physiology - March 14, 2016 Category: Cytology Authors: Morimoto, K., van der Hoorn, R. A. L. Tags: Invited Reviews Source Type: research
Plant Morphology of Heterotrimeric G Protein Mutants
The heterotrimeric G protein complex, comprising Gα, G and G subunits, is an evolutionarily conserved signaling molecular machine that transmits signals from transmembrane receptors to downstream target proteins. Plants conserved the core G protein elements, while developing their own regulatory systems differently from animals. Genetic evidence supports the conclusion that the heterotrimeric G proteins regulate shoot, root and epidermis development, as well as sugar sensing, hormone responsiveness and abiotic and biotic stress tolerance. This review is a compendium of the known morphological changes conferred by los...
Source: Plant and Cell Physiology - March 14, 2016 Category: Cytology Authors: Urano, D., Miura, K., Wu, Q., Iwasaki, Y., Jackson, D., Jones, A. M. Tags: Invited Reviews Source Type: research
A Low Glutathione Redox State Couples with a Decreased Ascorbate Redox Ratio to Accelerate Flowering in Oncidium Orchid
In conclusion, our results provide evidence that the decreased GSH redox state is linked to the decline in the AsA redox ratio and mediated by down-regulated expression of GSH metabolism-related genes to affect flowering time in Oncidium orchid. (Source: Plant and Cell Physiology)
Source: Plant and Cell Physiology - February 23, 2016 Category: Cytology Authors: Chin, D.-C., Hsieh, C.-C., Lin, H.-Y., Yeh, K.-W. Tags: Regular Papers Source Type: research
Combining -Omics to Unravel the Impact of Copper Nutrition on Alfalfa (Medicago sativa) Stem Metabolism
In this study, alfalfa is exposed to different levels of copper availability, from deficiency to slight excess, and the impact on the metabolism of the stem is assessed by a non-targeted proteomics study and by the expression analysis of key genes controlling plant stem development. Under copper deficiency, the plant stem accumulates specific copper chaperones, the expression of genes involved in stem development is decreased and the concentrations of zinc and molybdenum are increased in comparison with the optimum copper level. At the optimal copper level, the expression of cell wall-related genes increases and proteins p...
Source: Plant and Cell Physiology - February 23, 2016 Category: Cytology Authors: Printz, B., Guerriero, G., Sergeant, K., Audinot, J.-N., Guignard, C., Renaut, J., Lutts, S., Hausman, J.-F. Tags: Regular Papers Source Type: research
Identification of a Major Lipid Droplet Protein in a Marine Diatom Phaeodactylum tricornutum
Various kinds of organisms, including microalgae, accumulate neutral lipids in distinct intracellular compartments called lipid droplets. Generally, lipid droplets are generated from the endoplasmic reticulum, and particular proteins localize on their surface. Some of these proteins function as structural proteins to prevent fusion between the lipid droplets, and the others could have an enzymatic role or might be involved in intracellular membrane trafficking. However, information about lipid droplet proteins in microalgae is scarce as compared with that in animals and land plants. We focused on the oil-producing, marine,...
Source: Plant and Cell Physiology - February 23, 2016 Category: Cytology Authors: Yoneda, K., Yoshida, M., Suzuki, I., Watanabe, M. M. Tags: Regular Papers Source Type: research
Efficient Gene Induction and Endogenous Gene Repression Systems for the Filamentous Cyanobacterium Anabaena sp. PCC 7120
In the last decade, many studies have been conducted to employ genetically engineered cyanobacteria in the production of various metabolites. However, the lack of a strict gene regulation system in cyanobacteria has hampered these attempts. The filamentous cyanobacterium Anabaena sp. PCC 7120 performs both nitrogen and carbon fixation and is, therefore, a good candidate organism for such production. To employ Anabaena cells for this purpose, we intended to develop artificial gene regulation systems to alter the cell metabolic pathways efficiently. We introduced into Anabaena a transcriptional repressor TetR, widely used in...
Source: Plant and Cell Physiology - February 23, 2016 Category: Cytology Authors: Higo, A., Isu, A., Fukaya, Y., Hisabori, T. Tags: Regular Papers Source Type: research
Metabolic consequences of knocking out UGT85B1, the gene encoding the glucosyltransferase required for synthesis of dhurrin in Sorghum bicolor (L. Moench)
Many important food crops produce cyanogenic glucosides as natural defense compounds to protect against herbivory or pathogen attack. It has also been suggested that these nitrogen-based secondary metabolites act as storage reserves of nitrogen. In sorghum, three key genes, CYP79A1, CYP71E1 and UGT85B1, encode two Cytochrome P450s and a glycosyltransferase, respectively, the enzymes essential for synthesis of the cyanogenic glucoside dhurrin. Here, we report the use of targeted induced local lesions in genomes (TILLING) to identify a line with a mutation resulting in a premature stop codon in the N-terminal region of UGT85...
Source: Plant and Cell Physiology - February 23, 2016 Category: Cytology Authors: Blomstedt, C. K., ODonnell, N. H., Bjarnholt, N., Neale, A. D., Hamill, J. D., Moller, B. L., Gleadow, R. M. Tags: Regular Papers Source Type: research
Profiling and Characterization of Small RNAs in the Liverwort, Marchantia polymorpha, Belonging to the First Diverged Land Plants
MicroRNAs (miRNAs) have important roles in gene regulation during plant development. Previous studies revealed that some miRNAs are highly shared by most land plants. Recently, the liverwort, Marchantia polymorpha, has been studied by molecular genetic approaches, and sequencing of its genome is currently underway. The expression pattern and the detailed functions of miRNAs during Marchantia development are unknown. Here, we profiled the small RNAs expressed in thalli, antheridiophores and archegoniophores of M. polymorpha using high-throughput RNA sequencing. We revealed that a limited number of miRNAs are shared between ...
Source: Plant and Cell Physiology - February 23, 2016 Category: Cytology Authors: Tsuzuki, M., Nishihama, R., Ishizaki, K., Kurihara, Y., Matsui, M., Bowman, J. L., Kohchi, T., Hamada, T., Watanabe, Y. Tags: Special Focus Issue - Regular Papers Source Type: research
Identification of miRNAs and Their Targets in the Liverwort Marchantia polymorpha by Integrating RNA-Seq and Degradome Analyses
This study provides a foundation for further investigations of the RNA-mediated silencing mechanism in M. polymorpha as well as of the evolution of this gene silencing pathway in embryophytes. (Source: Plant and Cell Physiology)
Source: Plant and Cell Physiology - February 23, 2016 Category: Cytology Authors: Lin, P.-C., Lu, C.-W., Shen, B.-N., Lee, G.-Z., Bowman, J. L., Arteaga-Vazquez, M. A., Liu, L.-Y. D., Hong, S.-F., Lo, C.-F., Su, G.-M., Kohchi, T., Ishizaki, K., Zachgo, S., Althoff, F., Takenaka, M., Yamato, K. T., Lin, S.-S. Tags: Special Focus Issue - Regular Papers Source Type: research
Transcriptional Framework of Male Gametogenesis in the Liverwort Marchantia polymorpha L.
This study provides a transcriptional framework on which to study the molecular mechanism of plant motile sperm development in M. polymorpha as a model. (Source: Plant and Cell Physiology)
Source: Plant and Cell Physiology - February 23, 2016 Category: Cytology Authors: Higo, A., Niwa, M., Yamato, K. T., Yamada, L., Sawada, H., Sakamoto, T., Kurata, T., Shirakawa, M., Endo, M., Shigenobu, S., Yamaguchi, K., Ishizaki, K., Nishihama, R., Kohchi, T., Araki, T. Tags: Special Focus Issue - Regular Papers Source Type: research
SNARE Molecules in Marchantia polymorpha: Unique and Conserved Features of the Membrane Fusion Machinery
We examined the subcellular distribution of a major portion of these SNARE proteins by expressing Citrine-tagged SNARE proteins in M. polymorpha, and the results showed that some of the SNARE proteins were targeted to different compartments from their orthologous products in Arabidopsis thaliana. For example, MpSYP12B was localized to the surface of the oil body, which is a unique organelle in liverworts. Furthermore, we identified three VAMP72 members with distinctive structural characteristics, whose N-terminal extensions contain consensus sequences for N-myristoylation. These results suggest that M. polymorpha has acqui...
Source: Plant and Cell Physiology - February 23, 2016 Category: Cytology Authors: Kanazawa, T., Era, A., Minamino, N., Shikano, Y., Fujimoto, M., Uemura, T., Nishihama, R., Yamato, K. T., Ishizaki, K., Nishiyama, T., Kohchi, T., Nakano, A., Ueda, T. Tags: Special Focus Issue - Regular Papers Source Type: research
Cryopreservation of Gemmae from the Liverwort Marchantia polymorpha L.
The liverwort Marchantia polymorpha L. is one of the key model plants in evo–devo studies, and an increasing number of transgenic and mutant lines have been established. For reliable long-term preservation of M. polymorpha plants, spores have been used, but crossing is indispensable to obtain them. Gemmae, however, are vegetative clones and readily available in large numbers without crossing, thereby enabling the clonal preservation and rapid propagation of transgenic or mutant lines. Here, we report a simple cryopreservation protocol for in vitro grown M. polymorpha gemmae using aluminum cryoplates. Gemmae were pre-...
Source: Plant and Cell Physiology - February 23, 2016 Category: Cytology Authors: Tanaka, D., Ishizaki, K., Kohchi, T., Yamato, K. T. Tags: Special Focus Issue - Regular Papers Source Type: research
A Cyan Fluorescent Reporter Expressed from the Chloroplast Genome of Marchantia polymorpha
We report the design of a codon-optimized gfp varian, mturq2cp, which allowed successful expression of a cyan fluorescent protein under control of the tobacco psbA promoter from the chloroplast genome of M. polymorpha. We demonstrate the utility of mturq2cp in (i) early screening for transplastomic events following biolistic transformation of M. polymorpha spores; (ii) visualization of stromules as elements of plastid structure in Marchantia; and (iii) quantitative microscopy for the analysis of promoter activity. (Source: Plant and Cell Physiology)
Source: Plant and Cell Physiology - February 23, 2016 Category: Cytology Authors: Boehm, C. R., Ueda, M., Nishimura, Y., Shikanai, T., Haseloff, J. Tags: Special Focus Issue - Regular Papers Source Type: research
Efficient and Inducible Use of Artificial MicroRNAs in Marchantia polymorpha
We describe the efficient use of artificial microRNAs (amiRs) in Marchantia polymorpha using both endogenous and heterologous primary microRNA (pri-miR) hairpin backbones. Targeting of two transcription factor genes, MpARF1 and MpRR-B, mediating different hormonal responses, demonstrated that amiRs can create specific and reproducible physiological and morphological defects, facilitating interpretation of gene function. A third amiR was designed to target a gene encoding a component of the Polycomb recessive complex 2, MpE(z), and constitutive expression of this amiR results in sporeling lethality. Adaptation of an estroge...
Source: Plant and Cell Physiology - February 23, 2016 Category: Cytology Authors: Flores-Sandoval, E., Dierschke, T., Fisher, T. J., Bowman, J. L. Tags: Special Focus Issue - Regular Papers Source Type: research
Conditional Gene Expression/Deletion Systems for Marchantia polymorpha Using its Own Heat-Shock Promoter and Cre/loxP-Mediated Site-Specific Recombination
The liverwort Marchantia polymorpha is an emerging model plant suitable for addressing, using genetic approaches, various evolutionary questions in the land plant lineage. Haploid dominancy in its life cycle facilitates genetic analyses, but conversely limits the ability to isolate mutants of essential genes. To overcome this issue and to be employed in cell lineage, mosaic and cell autonomy analyses, we developed a system that allows conditional gene expression and deletion using a promoter of a heat-shock protein (HSP) gene and the Cre/loxP site-specific recombination system. Because the widely used promoter of the Arabi...
Source: Plant and Cell Physiology - February 23, 2016 Category: Cytology Authors: Nishihama, R., Ishida, S., Urawa, H., Kamei, Y., Kohchi, T. Tags: Special Focus Issue - Regular Papers Source Type: research
