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Plant Gene Seeker -PGS
Absolutely Fascinated for plant & genomes
Curated by Andres Zurita
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The Big Data Explosion [infographic]

The Big Data Explosion [infographic] | Plant Gene Seeker -PGS | Scoop.it

Data is everywhere!

Take a look at the data that is being produced throughout the world every day and the sources of the explosion of big data...


Via Lauren Moss
Andres Zurita's insight:

amazing flow of info...

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Ending Hunger | Malnutrition no more

Ending Hunger | Malnutrition no more | Plant Gene Seeker -PGS | Scoop.it

Just like any hot topic, the solution to malnutrition has two dominant schools of thought. Many believe in the power of supplements and fortified foods for tackling undernourishment.


Via Luigi Guarino
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Genes contra el hambre

Genes contra el hambre | Plant Gene Seeker -PGS | Scoop.it
La biotecnología es una herramienta clave para asegurar el futuro alimentario del planeta. La cooperación con los países pobres no debe ser solo económica, sino sobre todo científica

Via Isabel Etayo
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Toxic algae species is full of freeloading cheaters... and why that makes them even deadlier

Toxic algae species is full of freeloading cheaters... and why that makes them even deadlier | Plant Gene Seeker -PGS | Scoop.it
Prymnesium parvum is a single-celled, toxic algae species that wreaks havoc throughout U.S. waters. The toxin is designed to wipe out their competition for sunlight and nutrients...

 

Nice story, here's the article: http://onlinelibrary.wiley.com/doi/10.1111/evo.12030/abstract


Via Mary Williams
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Mary Williams's curator insight, February 1, 2013 12:22 PM

I love this video "Golden algae attacking" - Prymnesium parvum algae ganging up on a marine green alga... http://www.eurekalert.org/pub_releases/2013-01/uoa-tht011813.php. Show your students, they'll love it and want to learn more!

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Temporal Changes in Allocation and Partitioning of New Carbon as 11C Elicited by Simulated Herbivory Suggest that Roots Shape Aboveground Responses in Arabidopsis

Temporal Changes in Allocation and Partitioning of New Carbon as 11C Elicited by Simulated Herbivory Suggest that Roots Shape Aboveground Responses in Arabidopsis | Plant Gene Seeker -PGS | Scoop.it
Andres Zurita's insight:

Using the short-lived isotope 11C (t1/2 = 20.4 min) as 11CO2, we captured temporal changes in whole-plant carbon movement and partitioning of recently fixed carbon into primary and secondary metabolites in a time course (2, 6, and 24 h) following simulated herbivory with the well-known defense elicitor methyl jasmonate (MeJA) to young leaves of Arabidopsis (Arabidopsis thaliana). Both11CO2 fixation and 11C-photosynthate export from the labeled source leaf increased rapidly (2 h) following MeJA treatment relative to controls, with preferential allocation of radiolabeled resources belowground. At the same time,11C-photosynthate remaining in the aboveground sink tissues showed preferential allocation to MeJA-treated, young leaves, where it was incorporated into 11C-cinnamic acid. By 24 h, resource allocation toward roots returned to control levels, while allocation to the young leaves increased. This corresponded to an increase in invertase activity and the accumulation of phenolic compounds, particularly anthocyanins, in young leaves. Induction of phenolics was suppressed in sucrose transporter mutant plants (suc2-1), indicating that this phenomenon may be controlled, in part, by phloem loading at source leaves. However, when plant roots were chilled to 5°C to disrupt carbon flow between above- and belowground tissues, source leaves failed to allocate resources belowground or toward damaged leaves following wounding and MeJA treatment to young leaves, suggesting that roots may play an integral role in controlling how plants respond defensively aboveground.

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How plant communities endure stress

How plant communities endure stress | Plant Gene Seeker -PGS | Scoop.it
The Stress Gradient Hypothesis holds that as stress increases in an ecosystem, mutually supportive interactions become more significant and negative interactions, such as competition, become less so.
Andres Zurita's insight:

The idea has been hotly debated but is now backed by a review of hundreds of studies co-authored in Ecology Lettersby Mark Bertness, professor of biology at Brown, who first formally proposed the hypothesis in 1994. The time has come, he said, to test its application and predictive value.

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NatBiotech (2012): Deployment of new biotechnologies in plant breeding

NatBiotech (2012): Deployment of new biotechnologies in plant breeding | Plant Gene Seeker -PGS | Scoop.it

OK, so it's already a year old, but I don't look at Nature Biotechnology all that often. However, this is a great find, especially for teaching. It's a summary of all the "new" technologies for genomic modification in plants, including zinc finger nucleases, cis-genesis, grafting onto GM stocks, etc. Hot topic and good review. (http://www.nature.com/nbt/journal/v30/n3/full/nbt.2142.html)


Via Mary Williams
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Control limits for accumulation of plant metabolites: brute force is no substitute for understanding - Morandini - 2013 - Plant Biotechnology Journal - Wiley Online Library


Via Biswapriya Biswavas Misra
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Biswapriya Biswavas Misra's curator insight, January 30, 2013 6:36 AM
SummaryWhich factors limit metabolite accumulation in plant cells? Are theories on flux control effectiveat explaining the results? Many biotechnologists cling to the idea that every pathway has a ratelimiting enzyme and target such enzymes first in order to modulate fluxes. This often translatesinto large effects on metabolite concentration, but disappointing small increases in flux. Ratelimiting enzymes do exist, but are rare and quite opposite to what predicted by biochemistry. Inmany cases however, flux control is shared among many enzymes. Flux control andconcentration control can (and must) be distinguished and quantified for effective manipulation.Flux control for several ‘building blocks’ of metabolism is placed on the demand side, andtherefore increasing demand can be very successful. Tampering with supply, particularlydesensitizing supply enzymes, is usually not very effective, if not dangerous, because supplyregulatory mechanisms function to control metabolite homeostasis. Some important, but usuallyunnoticed, metabolic constraints shape the responses of metabolic systems to manipulation:mass conservation, cellular resource allocation and, most prominently, energy supply,particularly in heterotrophic tissues. The theoretical basis for this view shall be explored withrecent examples gathered from the manipulation of several metabolites (vitamins,carotenoids, amino acids, sugars, fatty acids, polyhydroxyalkanoates, fructans and sugaralcohols). Some guiding principles are suggested for an even more successful engineering of

plant metabolism

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Scientist/Artist: Experimenting, Reflecting, Creating: Urban Geography, Ecology, and Sustainability

Scientist/Artist: Experimenting, Reflecting, Creating: Urban Geography, Ecology, and Sustainability | Plant Gene Seeker -PGS | Scoop.it
RT @SamHammer: Thinking about ancient irrigation systems in Sri lanka and elsewhere around the world. http://t.co/5Y0aZ9gr

Via Luigi Guarino
Andres Zurita's insight:

A necessary and fruitful link

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Guia de Bolsillo Los cultivos modificados genéticamente en la Unión Europea | Transgénicos

Guia de Bolsillo Los cultivos modificados genéticamente en la Unión Europea | Transgénicos | Plant Gene Seeker -PGS | Scoop.it
[caption id=attachment_11262 align=alignleft width=300 caption= ][/caption] Coincidiendo con el cumplimiento de los 15 años de siembra continuada de

Via Isabel Etayo
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Global Food Crisis Will Worsen as Heat Waves Increase

Global Food Crisis Will Worsen as Heat Waves Increase | Plant Gene Seeker -PGS | Scoop.it
Harvests will fall dramatically during heat waves, predicted to become more likely in coming decades.

Via CIMMYT, Int.
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Lee Pearson's curator insight, February 4, 2013 5:39 AM

"New research, which used corn growing in France as an example, predicts losses of up to 12 percent for maize yields in the next 20 years. A second, longer-term study published on Sunday indicates that, without action against climate change, wheat and soybean harvests will fall by up to 30 percent by 2050 as the world warms."

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Divide and shape: an endosymbiont in action - Planta

Divide and shape: an endosymbiont in action - Planta | Plant Gene Seeker -PGS | Scoop.it
Andres Zurita's insight:

The endosymbiotic evolution of the plastid within the host cell required development of a mechanism for efficient division of the plastid. Whilst a model for the mechanism of chloroplast division has been constructed, little is known of how other types of plastids divide, especially the proplastid, the progenitor of all plastid types in the cell. It has become clear that plastid shape is highly heterogeneous and dynamic, especially stromules. This article considers how such variation in morphology might be controlled and how such plastids might divide efficiently.

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De Novo Transcriptome Assembly in Chili Pepper (Capsicum frutescens) to Identify Genes Involved in the Biosynthesis of Capsaicinoids

De Novo Transcriptome Assembly in Chili Pepper (Capsicum frutescens) to Identify Genes Involved in the Biosynthesis of Capsaicinoids | Plant Gene Seeker -PGS | Scoop.it
PLOS ONE: an inclusive, peer-reviewed, open-access resource from the PUBLIC LIBRARY OF SCIENCE. Reports of well-performed scientific studies from all disciplines freely available to the whole world.

Via Biswapriya Biswavas Misra
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Biswapriya Biswavas Misra's curator insight, January 28, 2013 3:55 AM
Abstract

The capsaicinoids are a group of compounds produced by chili pepper fruits and are used widely in many fields, especially in medical purposes. The capsaicinoid biosynthetic pathway has not yet been established clearly. To understand more knowledge in biosynthesis of capsaicinoids, we applied RNA-seq for the mixture of placenta and pericarp of pungent pepper (Capsicum frutescens L.). We have assessed the effect of various assembly parameters using different assembly software, and obtained one of the best strategies for de novo assembly of transcriptome data. We obtained a total 54,045 high-quality unigenes (transcripts) using Trinity software. About 92.65% of unigenes showed similarity to the public protein sequences, genome of potato and tomato and pepper (C. annuum) ESTs databases. Our results predicted 3 new structural genes (DHAD, TD, PAT), which filled gaps of the capsaicinoid biosynthetic pathway predicted by Mazourek, and revealed new candidate genes involved in capsaicinoid biosynthesis based on KEGG (Kyoto Encyclopedia of Genes and Genomes) analysis. A significant number of SSR (Simple Sequence Repeat) and SNP (Single Nucleotide Polymorphism) markers were predicted in C. frutescens and C. annuum sequences, which will be helpful in the identification of polymorphisms within chili pepper populations. These data will provide new insights to the pathway of capsaicinoid biosynthesis and subsequent research of chili peppers. In addition, our strategy of de novo transcriptome assembly is applicable to a wide range of similar studies.

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How plants sense gravity: New look at the roles of genetics and the cytoskeleton

How plants sense gravity: New look at the roles of genetics and the cytoskeleton | Plant Gene Seeker -PGS | Scoop.it
The general response to gravity in plants is well known: roots respond positively, growing down, into the soil, and stems respond negatively, growing upward, to reach the sunlight.

Via R K Upadhyay
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Jennifer Mach's comment, February 5, 2013 8:58 AM
Here's the article, http://www.amjbot.org/content/100/1/143, published in July but receiving press in Feb-- interesting strategy or substantial lag by Science Daily?
Andres Zurita's comment, February 5, 2013 9:17 AM
good question! I have no clue, since they indeed publish recently printed papers, but as we receive this info curated from several different sources, they might reach us with delay.
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Planting trees may not reverse climate change but it will help locally

Planting trees may not reverse climate change but it will help locally | Plant Gene Seeker -PGS | Scoop.it

What would be the long-term impacts of planting trees in Europe?

 

"Large contiguous forest blocks can have distinctive biogeophysical effect on the climate on regional and local scale. In certain regions of the temperate zone, climate change signal due to greenhouse gas emission can be reduced by afforestation due to the dominant evaporative cooling effect during summer."


Via R K Upadhyay, Mary Williams
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The Rice Genome Knowledgebase (RGKbase): an annotation database for rice comparative genomics and evolutionary biology

The Rice Genome Knowledgebase (RGKbase): an annotation database for rice comparative genomics and evolutionary biology | Plant Gene Seeker -PGS | Scoop.it

Rice is the first genome sequenced crop in the world and its improvement of harvest and trait can significantly benefit to humans. Furthermore, we carried out the parallel intricate gene annotation pipelines and integrated microarray, RNA-Seq and population data of 1000 rice genomes.

We not only pay attention on the gene structure, repetitive elements, alternatively-splicing events, transcriptome, proteomics and phenotype, but also study the evolutionary polymorphism variations within and between species (chromosomes, genes and segments combination and separation).

We tried to carry out the studies on specific subspecies of rice genome in a precise scope and hope that this database can help the biology scientists understand the essential evolution mechanisms of rice lineages, and facilitate the breeding and cultivation.


Via Elsa Ballini
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Elsa Ballini's comment, February 1, 2013 10:17 AM
Full text available here: http://nar.oxfordjournals.org/content/41/D1/D1199.full
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Role of the Putative Osmosensor Arabidopsis Histidine Kinase1 in Dehydration Avoidance and Low-Water-Potential Response

Role of the Putative Osmosensor Arabidopsis Histidine Kinase1 in Dehydration Avoidance and Low-Water-Potential Response | Plant Gene Seeker -PGS | Scoop.it
Andres Zurita's insight:

The molecular basis of plant osmosensing remains unknown. Arabidopsis (Arabidopsis thaliana) Histidine Kinase1 (AHK1) can complement the osmosensitivity of yeast (Saccharomyces cerevisiae) osmosensor mutants lacking Synthetic Lethal of N-end rule1 and SH3-containing Osmosensor and has been proposed to act as a plant osmosensor. We found that ahk1 mutants in either the Arabidopsis Nossen-0 or Columbia-0 background had increased stomatal density and stomatal index consistent with greater transpirational water loss. However, the growth of ahk1 mutants was not more sensitive to controlled moderate low water potential (ψw) or to salt stress. Also, ahk1 mutants had increased, rather than reduced, solute accumulation across a range of low ψw severities. ahk1mutants had reduced low ψw induction of Δ1-Pyrroline-5-Carboxylate Synthetase1 (P5CS1) and 9-cis-Epoxycarotenoid Dioxygenase3, which encode rate-limiting enzymes in proline and abscisic acid (ABA) synthesis, respectively. However, neither Pro nor ABA accumulation was reduced in ahk1 mutants at lowψw. P5CS1 protein level was not reduced in ahk1 mutants. This indicated that proline accumulation was regulated in part by posttranscriptional control of P5CS1 that was not affected by AHK1. Expression of AHK1 itself was reduced by low ψw, in contrast to previous reports. These results define a role of AHK1 in controlling stomatal density and the transcription of stress-responsive genes. These phenotypes may be mediated in part by reduced ABA sensitivity. More rapid transpiration and water depletion can also explain the previously reported sensitivity of ahk1 to uncontrolled soil drying. The unimpaired growth, ABA, proline, and solute accumulation of ahk1 mutants at low ψw suggest that AHK1 may not be the main plant osmosensor required for low ψw tolerance.

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Global shifts towards positive species interactions with increasing environmental stress - He - 2013 - Ecology Letters -

Global shifts towards positive species interactions with increasing environmental stress - He - 2013 - Ecology Letters - | Plant Gene Seeker -PGS | Scoop.it
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Abstract

The study of positive species interactions is a rapidly evolving field in ecology. Despite decades of research, controversy has emerged as to whether positive and negative interactions predictably shift with increasing environmental stress as hypothesised by the stress-gradient hypothesis (SGH). Here, we provide a synthesis of 727 tests of the SGH in plant communities across the globe to examine its generality across a variety of ecological factors. Our results show that plant interactions change with stress through an outright shift to facilitation (survival) or a reduction in competition (growth and reproduction). In a limited number of cases, plant interactions do not respond to stress, but they never shift towards competition with stress. These findings are consistent across stress types, plant growth forms, life histories, origins (invasive vs. native), climates, ecosystems and methodologies, though the magnitude of the shifts towards facilitation with stress is dependent on these factors. We suggest that future studies should employ standardised definitions and protocols to test the SGH, take a multi-factorial approach that considers variables such as plant traits in addition to stress, and apply the SGH to better understand how species and communities will respond to environmental change.

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PhilTransRoySoc: Catch up on thylakoids with this special issue

PhilTransRoySoc: Catch up on thylakoids with this special issue | Plant Gene Seeker -PGS | Scoop.it

In case you missed it, there's a special issue on 'The plant thylakoid membrane: structure, organization, assembly and dynamic response to the environment' in Dec 2012 Phil Trans Roy Soc B. Lots of fine reviews!

 

http://rstb.royalsocietypublishing.org/content/367/1608.toc


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Nitric oxide in plants: an assessment of the current state of knowledge

Andres Zurita's insight:

Background and aims After a series of seminal works during the last decade of the 20th century, nitric oxide (NO) is now firmly placed in the pantheon of plant signals. Nitric oxide acts in plant–microbe interactions, responses to abiotic stress, stomatal regulation and a range of developmental processes. By considering the recent advances in plant NO biology, this review will highlight certain key aspects that require further attention.

Scope and conclusions The following questions will be considered. While cytosolic nitrate reductase is an important source of NO, the contributions of other mechanisms, including a poorly defined arginine oxidizing activity, need to be characterized at the molecular level. Other oxidative pathways utilizing polyamine and hydroxylamine also need further attention. Nitric oxide action is dependent on its concentration and spatial generation patterns. However, no single technology currently available is able to provide accurate in planta measurements of spatio-temporal patterns of NO production. It is also the case that pharmaceutical NO donors are used in studies, sometimes with little consideration of the kinetics of NO production. We here include in planta assessments of NO production from diethylamine nitric oxide, S-nitrosoglutathione and sodium nitroprusside following infiltration of tobacco leaves, which could aid workers in their experiments. Further, based on current data it is difficult to define a bespoke plant NO signalling pathway, but rather NO appears to act as a modifier of other signalling pathways. Thus, early reports that NO signalling involves cGMP—as in animal systems—require revisiting. Finally, as plants are exposed to NO from a number of external sources, investigations into the control of NO scavenging by such as non-symbiotic haemoglobins and other sinks for NO should feature more highly. By crystallizing these questions the authors encourage their resolution through the concerted efforts of the plant NO community.

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PLOS Biology: Transforming a Stem into a Bush

PLOS Biology: Transforming a Stem into a Bush | Plant Gene Seeker -PGS | Scoop.it
PLOS Biology is an open-access, peer-reviewed journal that features works of exceptional significance in all areas of biological science, from molecules to ecosystems, including works at the interface with other disciplines.

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Genotypic recognition and spatial responses by rice roots

Genotypic recognition and spatial responses by rice roots | Plant Gene Seeker -PGS | Scoop.it
Andres Zurita's insight:

Root system growth and development is highly plastic and is influenced by the surrounding environment. Roots frequently grow in heterogeneous environments that include interactions from neighboring plants and physical impediments in the rhizosphere. To investigate how planting density and physical objects affect root system growth, we grew rice in a transparent gel system in close proximity with another plant or a physical object. Root systems were imaged and reconstructed in three dimensions. Root–root interaction strength was calculated using quantitative metrics that characterize the extent to which the reconstructed root systems overlap each other. Surprisingly, we found the overlap of root systems of the same genotype was significantly higher than that of root systems of different genotypes. Root systems of the same genotype tended to grow toward each other but those of different genotypes appeared to avoid each other. Shoot separation experiments excluded the possibility of aerial interactions, suggesting root communication. Staggered plantings indicated that interactions likely occur at root tips in close proximity. Recognition of obstacles also occurred through root tips, but through physical contact in a size-dependent manner. These results indicate that root systems use two different forms of communication to recognize objects and alter root architecture: root-root recognition, possibly mediated through root exudates, and root-object recognition mediated by physical contact at the root tips. This finding suggests that root tips act as local sensors that integrate rhizosphere information into global root architectural changes.

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Maps - climate change impacts, from PLOS ONE and NOAA

Maps - climate change impacts, from PLOS ONE and NOAA | Plant Gene Seeker -PGS | Scoop.it

Check out both of these - here are some global maps of threatened areas: http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0054839

 

and here is what NOAA shows as threatened areas of the US:

http://www.noaanews.noaa.gov/stories2013/20130125_coastalclimateimpacts.html

 

(no wonder the inland "red states" don't care!)


Via Mary Williams
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Karen Johnson's curator insight, January 30, 2013 6:14 AM

Interesting information from PLoS and NOAA.  Thanks for the link Mary, you have some great scoops on your site :)

Mary Williams's comment, January 31, 2013 10:06 AM
Thanks Karen!
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How do plants make mitochondria? - Planta

How do plants make mitochondria? - Planta | Plant Gene Seeker -PGS | Scoop.it
Andres Zurita's insight:

Plant mitochondria can differ in size, shape, number and protein content across different tissue types and over development. These differences are a result of signaling and regulatory processes that ensure mitochondrial function is tuned in a cell-specific manner to support proper plant growth and development. In the last decade, the processes involved in mitochondrial biogenesis are becoming clearer, including; how dormant seeds transition from empty promitochondria to fully functional mitochondria with extensive cristae structures and various biochemical activities, the regulation of nuclear genes encoding mitochondrial proteins via regulators of the diurnal cycle in plants, the mitochondrial stress response, the targeting of proteins to mitochondria and other organelles and connections between the respiratory chain and protein import complexes. All these findings indicate that mitochondrial function is a part of an integrated cellular network, and communication between mitochondria and other cellular processes extends beyond the known exchange or transport of metabolites. Our current knowledge now needs to be used to gain more insight into the molecular components at various levels of this hierarchical and complex regulatory and communication network, so that mitochondrial function can be predicted and modified in a rational manner.

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Protein tyrosine nitration in pea roots during development and senescence

Protein tyrosine nitration in pea roots during development and senescence | Plant Gene Seeker -PGS | Scoop.it
Andres Zurita's insight:

Protein tyrosine nitration is a post-translational modification mediated by reactive nitrogen species (RNS) that is associated with nitro-oxidative damage. No information about this process is available in relation to higher plants during development and senescence. Using pea plants at different developmental stages (ranging from 8 to 71 days), tyrosine nitration in the main organs (roots, stems, leaves, flowers, and fruits) was analysed using immunological and proteomic approaches. In the roots of 71-day-old senescent plants, nitroproteome analysis enabled the identification a total of 16 nitrotyrosine-immunopositive proteins. Among the proteins identified, NADP-isocitrate dehydrogenase (ICDH), an enzyme involved in the carbon and nitrogen metabolism, redox regulation, and responses to oxidative stress, was selected to evaluate the effect of nitration. NADP-ICDH activity fell by 75% during senescence. Analysis showed that peroxynitrite inhibits recombinant cytosolic NADP-ICDH activity through a process of nitration. Of the 12 tyrosines present in this enzyme, mass spectrometric analysis of nitrated recombinant cytosolic NADP-ICDH enabled this study to identify the Tyr392 as exclusively nitrated by peroxynitrite. The data as a whole reveal that protein tyrosine nitration is a nitric oxide-derived PTM prevalent throughout root development and intensifies during senescence.

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