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Journal ArticleDOI

Proteomic analysis of the pulvinus, a heliotropic tissue, in Glycine max

23 Jun 2014-Vol. 5, Iss: 1

TL;DR: This study used two-dimensional gel electrophoresis and liquid chromatography-tandom mass spectrometry to separate and identify the proteins located in the soybean pulvinus and found that the most significant terms were related to proton transport.

AbstractCertain plant species respond to light, dark, and other environmental factors by leaf movement. Leguminous plants both track and avoid the sun through turgor changes of the pulvinus tissue at the base of leaves. Mechanisms leading to pulvinar turgor flux, particularly knowledge of the proteins involved, are not well-known. In this study we used two-dimensional gel electrophoresis and liquid chromatography-tandom mass spectrometry to separate and identify the proteins located in the soybean pulvinus. A total of 183 spots were separated and 195 proteins from 165 spots were identified and functionally analyzed using single enrichment analysis for gene ontology terms. The most significant terms were related to proton transport. Comparison with guard cell proteomes revealed similar significant processes but a greater number of pulvinus proteins are required for comparable analysis. To our knowledge, this is a novel report on the analysis of proteins found in soybean pulvinus. These findings provide a better understanding of the proteins required for turgor change in the pulvinus.

Topics: Pulvinus (71%), Proton transport (53%), Turgor pressure (52%)

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Citations
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Journal ArticleDOI
Peter V. Minorsky1
TL;DR: Foliar nyctinasty, much like the enhanced illumination of the full moon, may mitigate feeding by nocturnal herbivores by altering their foraging behaviour and may slow certain types of ectothermic herbivore making them more vulnerable to predation.
Abstract: Foliar nyctinasty is a plant behaviour characterised by a pronounced daily oscillation in leaf orientation. During the day, the blades of nyctinastic plant leaves (or leaflets) assume a more or less horizontal position that optimises their ability to capture sunlight for photosynthesis. At night, the positions that the leaf blades assume, regardless of whether they arise by rising, falling or twisting, are essentially vertical. Among the ideas put forth to explain the raison d'etre of foliar nyctinasty are that it: (i) improves the temperature relations of plants; (ii) helps remove surface water from foliage; (iii) prevents the disruption of photoperiodism by moonlight; and (iv) directly discourages insect herbivory. After discussing these previous hypotheses, a novel tritrophic hypothesis is introduced that proposes that foliar nyctinasty constitutes an indirect plant defence against nocturnal herbivores. It is suggested that the reduction in physical clutter that follows from nocturnal leaf closure may increase the foraging success of many types of animals that prey upon or parasitise herbivores. Predators and parasitoids generally use some combination of visual, auditory or olfactory cues to detect prey. In terrestrial environments, it is hypothesised that the vertical orientation of the blades of nyctinastic plants at night would be especially beneficial to flying nocturnal predators (e.g. bats and owls) and parasitoids whose modus operandi is death from above. The movements of prey beneath a plant with vertically oriented foliage would be visually more obvious to gleaning or swooping predators under nocturnal or crepuscular conditions. Such predators could also detect sounds made by prey better without baffling layers of foliage overhead to damp and disperse the signal. Moreover, any volatiles released by the prey would diffuse more directly to the awaiting olfactory apparatus of the predators or parasitoids. In addition to facilitating the demise of herbivores by carnivores and parasitoids, foliar nyctinasty, much like the enhanced illumination of the full moon, may mitigate feeding by nocturnal herbivores by altering their foraging behaviour. Foliar nyctinasty could also provide a competitive advantage by encouraging herbivores, seeking more cover, to forage on or around non-nyctinastic species. As an added advantage, foliar nyctinasty, by decreasing the temperature between plants through its effects on re-radiation, may slow certain types of ectothermic herbivores making them more vulnerable to predation. Foliar nyctinasty also may not solely be a behavioural adaptation against folivores; by discouraging foraging by granivores, the inclusive fitness of nyctinastic plants may be increased.

17 citations


Journal ArticleDOI
TL;DR: Compared with the parental BR 16, P58 copes with drought through better compensation between diaheliotropic and paraheliotropy movements, finer tuning of water-use efficiency, a lower transpiration rate, higher leaf area and higher pod abortion to accomplish the maximum possible grain production under continued drought conditions.
Abstract: Drought stress is one of the most severe environmental constraints on plant production. Under environmental pressures, complex daily heliotropic adjustments of leaflet angles in soybean can help to reduce transpiration losses by diminishing light interception (paraheliotropism), increase diurnal carbon gain in sparse canopies and reduce carbon gain in dense canopies by solar tracking (diaheliotropism). The plant materials studied were cultivar BR 16 and its genetically engineered isoline P58, ectopically overexpressing AtDREB1A, which is involved in abiotic stress responses. We aimed to follow the movements of central and lateral leaflets in vegetative stages V7-V10 and reproductive stages R4-R5, integrating the reversible morphogenetic changes into an estimate of daily plant photosynthesis using three-dimensional modeling, and to analyze the production parameters of BR 16 and P58. The patterns of daily movements of central leaflets of BR 16 in V7-V10 and R4-R5 were similar, expressing fewer diaheliotropic movements under drought stress than under non-limiting water conditions. Daily heliotropic patterns of lateral leaflets in V7-V10 and R4-R5 showed more diaheliotropic movements in drought-stressed P58 plants than in those grown under non-limiting water conditions. Leaf area in R4-R5 was generally higher in P58 than in BR 16. Drought significantly affected gas exchange and vegetative and reproductive architectural features. DREB1A could be involved in various responses to drought stress. Compared with the parental BR 16, P58 copes with drought through better compensation between diaheliotropic and paraheliotropic movements, finer tuning of water-use efficiency, a lower transpiration rate, higher leaf area and higher pod abortion to accomplish the maximum possible grain production under continued drought conditions.

4 citations



References
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Journal ArticleDOI
TL;DR: This assay is very reproducible and rapid with the dye binding process virtually complete in approximately 2 min with good color stability for 1 hr with little or no interference from cations such as sodium or potassium nor from carbohydrates such as sucrose.
Abstract: A protein determination method which involves the binding of Coomassie Brilliant Blue G-250 to protein is described. The binding of the dye to protein causes a shift in the absorption maximum of the dye from 465 to 595 nm, and it is the increase in absorption at 595 nm which is monitored. This assay is very reproducible and rapid with the dye binding process virtually complete in approximately 2 min with good color stability for 1 hr. There is little or no interference from cations such as sodium or potassium nor from carbohydrates such as sucrose. A small amount of color is developed in the presence of strongly alkaline buffering agents, but the assay may be run accurately by the use of proper buffer controls. The only components found to give excessive interfering color in the assay are relatively large amounts of detergents such as sodium dodecyl sulfate, Triton X-100, and commercial glassware detergents. Interference by small amounts of detergent may be eliminated by the use of proper controls.

214,383 citations


Journal ArticleDOI
TL;DR: Silver staining allows a substantial shortening of sample preparation time and may, therefore, be preferable over Coomassie staining, and this work removes a major obstacle to the low-level sequence analysis of proteins separated on polyacrylamide gels.
Abstract: Proteins from silver-stained gels can be digested enzymatically and the resulting peptides analyzed and sequenced by mass spectrometry. Standard proteins yield the same peptide maps when extracted from Coomassie- and silver-stained gels, as judged by electrospray and MALDI mass spectrometry. The low nanogram range can be reached by the protocols described here, and the method is robust. A silver-stained one-dimensional gel of a fraction from yeast proteins was analyzed by nanoelectrospray tandem mass spectrometry. In the sequencing, more than 1000 amino acids were covered, resulting in no evidence of chemical modifications due to the silver staining procedure. Silver staining allows a substantial shortening of sample preparation time and may, therefore, be preferable over Coomassie staining. This work removes a major obstacle to the low-level sequence analysis of proteins separated on polyacrylamide gels.

8,201 citations


"Proteomic analysis of the pulvinus,..." refers methods in this paper

  • ...Trypsin digestion of selected spots was based on methods by Shevchenko et al. (1996) and Gharahdaghi et al. (1999).19,20 Spots were excised and rinsed twice with 50% methanol, ten minutes each....

    [...]


Journal ArticleDOI
Zhou Du1, Xin Zhou1, Yi Ling1, Zhenhai Zhang1, Zhen Su1 
Abstract: Gene Ontology (GO), the de facto standard in gene functionality description, is used widely in functional annotation and enrichment analysis. Here, we introduce agriGO, an integrated web-based GO analysis toolkit for the agricultural community, using the advantages of our previous GO enrichment tool (EasyGO), to meet analysis demands from new technologies and research objectives. EasyGO is valuable for its proficiency, and has proved useful in uncovering biological knowledge in massive data sets from high-throughput experiments. For agriGO, the system architecture and website interface were redesigned to improve performance and accessibility. The supported organisms and gene identifiers were substantially expanded (including 38 agricultural species composed of 274 data types). The requirement on user input is more flexible, in that user-defined reference and annotation are accepted. Moreover, a new analysis approach using Gene Set Enrichment Analysis strategy and customizable features is provided. Four tools, SEA (Singular enrichment analysis), PAGE (Parametric Analysis of Gene set Enrichment), BLAST4ID (Transfer IDs by BLAST) and SEACOMPARE (Cross comparison of SEA), are integrated as a toolkit to meet different demands. We also provide a cross-comparison service so that different data sets can be compared and explored in a visualized way. Lastly, agriGO functions as a GO data repository with search and download functions; agriGO is publicly accessible at http://bioinfo.cau.edu.cn/agriGO/.

2,089 citations


Journal ArticleDOI
TL;DR: By using the destaining method, the sensitivity and quality of mass spectra is increased for matrix‐assisted laser desorption ionization‐time of flight (MALDI‐TOF) mass spectrometric analysis, permitting more proteins to be identified by peptide mass database analysis.
Abstract: Mass spectrometry is a powerful technique for the identification of proteins at nanogram quantities. However, some degree of sample preparation prior to mass spectrometry is required, and silver-stained protein gel samples are most problematic. Here we report our strategy to obtain peptide mass profiles from silver-stained protein gel samples from one- or two-dimensional gels by destaining prior to enzymatic digestion. This study demonstrates that by using the destaining method, the sensitivity and quality of mass spectra is increased for matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometric analysis, permitting more proteins to be identified by peptide mass database analysis.

892 citations


"Proteomic analysis of the pulvinus,..." refers methods in this paper

  • ...Trypsin digestion of selected spots was based on methods by Shevchenko et al. (1996) and Gharahdaghi et al. (1999).19,20 Spots were excised and rinsed twice with 50% methanol, ten minutes each....

    [...]


Journal ArticleDOI
29 Jan 1998-Nature
TL;DR: Analysis of the sequence revealed an average gene density of one gene every 4.8 kilobases, and 54% of the predicted genes had significant similarity to known genes, and other interesting features were found, such as the sequence of a disease-resistance gene locus, the distribution of retroelements, and the frequent occurrence of clustered gene families.
Abstract: The plant Arabidopsis thaliana (Arabidopsis) has become an important model species for the study of many aspects of plant biology. The relatively small size of the nuclear genome and the availability of extensive physical maps of the five chromosomes provide a feasible basis for initiating sequencing of the five chromosomes. The YAC (yeast artificial chromosome)-based physical map of chromosome 4 was used to construct a sequence-ready map of cosmid and BAC (bacterial artificial chromosome) clones covering a 1.9-megabase (Mb) contiguous region, and the sequence of this region is reported here. Analysis of the sequence revealed an average gene density of one gene every 4.8 kilobases (kb), and 54% of the predicted genes had significant similarity to known genes. Other interesting features were found, such as the sequence of a disease-resistance gene locus, the distribution of retroelements, the frequent occurrence of clustered gene families, and the sequence of several classes of genes not previously encountered in plants.

814 citations