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Plant Flux analysis

Laura Radville, Taryn L Bauerle, Louise H Comas, Katherine A Marchetto, Alan N Lakso, David R Smart, Richard M Dunst, David M Eissenstat
PREMISE OF THE STUDY: Plant phenology influences resource utilization, carbon fluxes, and interspecific interactions. Although controls on aboveground phenology have been studied to some degree, controls on root phenology are exceptionally poorly understood. METHODS: We used minirhizotrons to examine the timing of grape root production over 5 yr in Fredonia, New York, USA, in a humid continental climate; and over 3 yr in Oakville, California, USA, in a Mediterranean climate...
November 2016: American Journal of Botany
Nisar Ahmad, Mario Malagoli, Markus Wirtz, Ruediger Hell
BACKGROUND: Drought is the most important environmental stress that limits crop yield in a global warming world. Despite the compelling evidence of an important role of oxidized and reduced sulfur-containing compounds during the response of plants to drought stress (e.g. sulfate for stomata closure or glutathione for scavenging of reactive oxygen species), the assimilatory sulfate reduction pathway is almost not investigated at the molecular or at the whole plant level during drought...
November 9, 2016: BMC Plant Biology
Ciera C Martinez, Daniel H Chitwood, Richard S Smith, Neelima R Sinha
Leaves in plants with spiral phyllotaxy exhibit directional asymmetries, such that all the leaves originating from a meristem of a particular chirality are similarly asymmetric relative to each other. Models of auxin flux capable of recapitulating spiral phyllotaxis predict handed auxin asymmetries in initiating leaf primordia with empirically verifiable effects on superficially bilaterally symmetric leaves. Here, we extend a similar analysis of leaf asymmetry to decussate and distichous phyllotaxy. We found that our simulation models of these two patterns predicted mirrored asymmetries in auxin distribution in leaf primordia pairs...
December 19, 2016: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
Maciej A Zwieniecki, Katrine S Haaning, C Kevin Boyce, Kaare H Jensen
Stomata are portals in plant leaves that control gas exchange for photosynthesis, a process fundamental to life on Earth. Gas fluxes and plant productivity depend on external factors such as light, water and CO2 availability and on the geometrical properties of the stoma pores. The link between stoma geometry and environmental factors has informed a wide range of scientific fields-from agriculture to climate science, where observed variations in stoma size and density are used to infer prehistoric atmospheric CO2 content...
November 2016: Journal of the Royal Society, Interface
Rachel M Wheatley, Vinoy K Ramachandran, Barney A Geddes, Benjamin J Perry, Chris K Yost, Philip S Poole
: Insertion sequencing (INSeq) analysis of Rhizobium leguminosarum bv. viciae 3841 (Rlv3841) grown on glucose or succinate at both 21% and 1% O2 was used to understand how O2 concentration alters metabolism. Two transcriptional regulators were required for growth on glucose (pRL120207 (eryD) and RL0547 (phoB)), five on succinate (pRL100388, RL1641, RL1642, RL3427 and RL4524 (ecfL)) and three on 1% O2 (pRL110072, RL0545 (phoU) and RL4042). A novel toxin-antitoxin system was identified that could be important for generation of new plasmid-less rhizobial strains...
October 17, 2016: Journal of Bacteriology
Veronique Beckers, Lisa Maria Dersch, Katrin Lotz, Guido Melzer, Oliver Ernst Bläsing, Regine Fuchs, Thomas Ehrhardt, Christoph Wittmann
BACKGROUND: During the last decades, we face an increasing interest in superior plants to supply growing demands for human and animal nutrition and for the developing bio-based economy. Presently, our limited understanding of their metabolism and its regulation hampers the targeted development of desired plant phenotypes. In this regard, systems biology, in particular the integration of metabolic and regulatory networks, is promising to broaden our knowledge and to further explore the biotechnological potential of plants...
October 29, 2016: BMC Systems Biology
B Duarte, M T Cabrita, C Gameiro, A R Matos, R Godinho, J C Marques, I Caçador
A profound analysis of A. tripolium photochemical traits under salinity exposure is lacking in the literature, with very few references focusing on its fatty acid profile role in photophysiology. To address this, the deep photochemical processes were evaluated by Pulse Amplitude Modulated (PAM) Fluorometry coupled with a discrimination of its leaf fatty acid profile. Plants exposed to 125-250 mm NaCl showed higher photochemical light harvesting efficiencies and lower energy dissipation rates. under higher NaCl exposure, there is evident damage of the oxygen evolving complexes (OECs)...
October 17, 2016: Plant Biology
Perrin H Beatty, Matthias S Klein, Jeffrey J Fischer, Ian A Lewis, Douglas G Muench, Allen G Good
A comprehensive understanding of plant metabolism could provide a direct mechanism for improving nitrogen use efficiency (NUE) in crops. One of the major barriers to achieving this outcome is our poor understanding of the complex metabolic networks, physiological factors, and signaling mechanisms that affect NUE in agricultural settings. However, an exciting collection of computational and experimental approaches has begun to elucidate whole-plant nitrogen usage and provides an avenue for connecting nitrogen-related phenotypes to genes...
October 10, 2016: Plants (Basel, Switzerland)
Rémi Peyraud, Ludovic Cottret, Lucas Marmiesse, Jérôme Gouzy, Stéphane Genin
Bacterial pathogenicity relies on a proficient metabolism and there is increasing evidence that metabolic adaptation to exploit host resources is a key property of infectious organisms. In many cases, colonization by the pathogen also implies an intensive multiplication and the necessity to produce a large array of virulence factors, which may represent a significant cost for the pathogen. We describe here the existence of a resource allocation trade-off mechanism in the plant pathogen R. solanacearum. We generated a genome-scale reconstruction of the metabolic network of R...
October 2016: PLoS Pathogens
Vishal Kumar, Mehak Baweja, Puneet K Singh, Pratyoosh Shukla
Microorganisms play a crucial role in the sustainability of the various ecosystems. The characterization of various interactions between microorganisms and other biotic factors is a necessary footstep to understand the association and functions of microbial communities. Among the different microbial interactions in an ecosystem, plant-microbe interaction plays an important role to balance the ecosystem. The present review explores plant-microbe interactions using gene editing and system biology tools toward the comprehension in improvement of plant traits...
2016: Frontiers in Plant Science
Jing Zhang, Yan-Bo Huo, Yan Liu, Jun-Tao Feng, Zhi-Qing Ma, Chuan-Shu Zhu, Xing Zhang
Tripterygium wilfordii Hook. f. is the traditional medicinal plants in China. Triptolide, wilforgine, and wilforine are the bioactive compounds in T. wilfordii. In this study, the contents of three metabolites and transcription levels of 21 genes involved in three metabolites biosynthesis in T. wilfordii were examined using high-performance liquid chromatography and reverse transcription PCR after application of methyl jasmonate (MeJA) on hairy roots in time course experiment (3-24 h). The results indicated that application of MeJA inhibited triptolide accumulation and promoted wilforgine and wilforine metabolites biosynthesis...
September 21, 2016: Journal of Asian Natural Products Research
Shin-Nosuke Hashida, Taketo Itami, Kentaro Takahara, Takayuki Hirabayashi, Hirofumi Uchimiya, Maki Kawai-Yamada
NAD is a well-known co-enzyme that mediates hundreds of redox reactions and is the basis of various processes regulating cell responses to different environmental and developmental cues. The regulatory mechanism that determines the amount of cellular NAD and the rate of NAD metabolism remains unclear. We created Arabidopsis thaliana plants overexpressing the NAD synthase (NADS) gene that participates in the final step of NAD biosynthesis. NADS overexpression enhanced the activity of NAD biosynthesis but not the amounts of NAD(+), NADH, NADP(+), or NADPH...
September 1, 2016: Plant & Cell Physiology
Martin Blaser, Ralf Conrad
While the structure of microbial communities can nowadays be determined by applying molecular analytical tools to soil samples, microbial function can usually only be determined by physiological experiments requiring incubation of samples. However, analysis of stable isotope fractionation might be able to analyse microbial function without incubation in soil samples. We describe the limitations of diagnosing and quantifying carbon flux pathways in soil by using the determination of stable carbon isotope composition in soil compounds and emphasize the importance of determining stable isotope fractionation factors for defined biochemical pathways...
October 2016: Current Opinion in Biotechnology
Jinxin Che, Junling Shi, Zhenhong Gao, Yan Zhang
Alternaria sp. MG1, an endophytic fungus previously isolated from Merlot grape, produces resveratrol from glucose, showing similar metabolic flux to the phenylpropanoid biosynthesis pathway, currently found solely in plants. In order to identify the resveratrol biosynthesis pathway in this strain at the gene level, de novo transcriptome sequencing was conducted using Illumina paired-end sequencing. A total of 22,954,434 high-quality reads were assembled into contigs and 18,570 unigenes were identified. Among these unigenes, 14,153 were annotated in the NCBI non-redundant protein database and 5341 were annotated in the Swiss-Prot database...
2016: Frontiers in Microbiology
Abigail L S Swann, Forrest M Hoffman, Charles D Koven, James T Randerson
Rising atmospheric CO2 will make Earth warmer, and many studies have inferred that this warming will cause droughts to become more widespread and severe. However, rising atmospheric CO2 also modifies stomatal conductance and plant water use, processes that are often are overlooked in impact analysis. We find that plant physiological responses to CO2 reduce predictions of future drought stress, and that this reduction is captured by using plant-centric rather than atmosphere-centric metrics from Earth system models (ESMs)...
September 6, 2016: Proceedings of the National Academy of Sciences of the United States of America
Ciera C Martinez, Daniel Koenig, Daniel H Chitwood, Neelima R Sinha
The spatiotemporal localization of the plant hormone auxin acts as a positional cue during early leaf and flower organogenesis. One of the main contributors to auxin localization is the auxin efflux carrier PIN-FORMED1 (PIN1). Phylogenetic analysis has revealed that PIN1 genes are split into two sister clades; PIN1 and the relatively uncharacterized Sister-Of-PIN1 (SoPIN1). In this paper we identify entire-2 as a loss-of-function SlSoPIN1a (Solyc10g078370) mutant in Solanum lycopersicum. The entire-2 plants are unable to specify proper leaf initiation leading to a frequent switch from the wild type spiral phyllotactic pattern to distichous and decussate patterns...
August 20, 2016: Developmental Biology
Chun-Juan Dong, Ning Cao, Liang Li, Qing-Mao Shang
Salicylic acid (SA) is an important phytohormone that plays vital regulatory roles in plant growth, development, and stress responses. However, studies on the molecular mechanism of SA, especially during the early SA responses, are lagging behind. In this study, we initiated a comprehensive isobaric tag for relative and absolute quantitation (iTRAQ)-based proteomic analysis to explore the early and late SA-responsive proteins in leaves of cucumber (Cucumis sativus L.) seedlings. Upon SA application through the roots, endogenous SA accumulated in cucumber leaves...
2016: PloS One
Tingting Li, Maarit Raivonen, Pavel Alekseychik, Mika Aurela, Annalea Lohila, Xunhua Zheng, Qing Zhang, Guocheng Wang, Ivan Mammarella, Janne Rinne, Lijun Yu, Baohua Xie, Timo Vesala, Wen Zhang
Boreal/arctic wetlands are dominated by diverse plant species, which vary in their contribution to CH4 production, oxidation and transport processes. Earlier studies have often lumped the processes all together, which may induce large uncertainties into the results. We present a novel model, which includes three vegetation classes and can be used to simulate CH4 emissions from boreal and arctic treeless wetlands. The model is based on an earlier biogeophysical model, CH4MODwetland. We grouped the vegetation as graminoids, shrubs and Sphagnum and recalibrated the vegetation parameters according to their different CH4 production, oxidation and transport capacities...
August 10, 2016: Science of the Total Environment
Quentin Schorpp, Catharina Riggers, Dominika Lewicka-Szczebak, Anette Giesemann, Reinhard Well, Stefan Schrader
RATIONALE: The gaseous N losses mediated by soil denitrifiers are generally inferred by measuring N2 O fluxes, but should include associated N2 emissions, which may be affected by abiotic soil characteristics and biotic interactions. Soil fauna, particularly anecic earthworms and euedaphic collembola, alter the activity of denitrifiers, creating hotspots for denitrification. These soil fauna are abundant in perennial agroecosystems intended to contribute to more sustainable production of bioenergy...
November 15, 2016: Rapid Communications in Mass Spectrometry: RCM
Ulrike Baetz, Cornelia Eisenach, Takayuki Tohge, Enrico Martinoia, Alexis De Angeli
The ability to control the cytoplasmic environment is a prerequisite for plants to cope with changing environmental conditions. During salt stress, for instance, Na(+) and Cl(-) are sequestered into the vacuole to help maintain cytosolic ion homeostasis and avoid cellular damage. It has been observed that vacuolar ion uptake is tied to fluxes across the plasma membrane. The coordination of both transport processes and relative contribution to plant adaptation, however, is still poorly understood. To investigate the link between vacuolar anion uptake and whole-plant ion distribution during salinity, we used mutants of the only vacuolar Cl(-) channel described to date: the Arabidopsis (Arabidopsis thaliana) ALMT9...
October 2016: Plant Physiology
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