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https://www.readbyqxmd.com/read/28334262/discriminating-the-reaction-types-of-plant-type-iii-polyketide-synthases
#1
Yugo Shimizu, Hiroyuki Ogata, Susumu Goto
Motivation: Functional prediction of paralogs is challenging in bioinformatics because of rapid functional diversification after gene duplication events combined with parallel acquisitions of similar functions by different paralogs. Plant type III polyketide synthases (PKSs), producing various secondary metabolites, represent a paralogous family that has undergone gene duplication and functional alteration. Currently, there is no computational method available for the functional prediction of type III PKSs...
March 6, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28329766/complex-pectin-metabolism-by-gut-bacteria-reveals-novel-catalytic-functions
#2
Didier Ndeh, Artur Rogowski, Alan Cartmell, Ana S Luis, Arnaud Baslé, Joseph Gray, Immacolata Venditto, Jonathon Briggs, Xiaoyang Zhang, Aurore Labourel, Nicolas Terrapon, Fanny Buffetto, Sergey Nepogodiev, Yao Xiao, Robert A Field, Yanping Zhu, Malcolm A O'Neill, Breeanna R Urbanowicz, William S York, Gideon J Davies, D Wade Abbott, Marie-Christine Ralet, Eric C Martens, Bernard Henrissat, Harry J Gilbert
The metabolism of carbohydrate polymers drives microbial diversity in the human gut microbiota. It is unclear, however, whether bacterial consortia or single organisms are required to depolymerize highly complex glycans. Here we show that the gut bacterium Bacteroides thetaiotaomicron uses the most structurally complex glycan known: the plant pectic polysaccharide rhamnogalacturonan-II, cleaving all but 1 of its 21 distinct glycosidic linkages. The deconstruction of rhamnogalacturonan-II side chains and backbone are coordinated to overcome steric constraints, and the degradation involves previously undiscovered enzyme families and catalytic activities...
March 22, 2017: Nature
https://www.readbyqxmd.com/read/28325834/structural-model-of-dodecameric-heat-shock-protein-hsp21-flexible-n-terminal-arms-interact-with-client-proteins-while-c-terminal-tails-maintain-the-dodecamer-and-chaperone-activity
#3
Gudrun Rutsdottir, Johan Härmark, Yoran Weide, Hans Hebert, Morten Ib Rasmussen, Sven Wernersson, Michal Respondek, Mikael Akke, Peter Højrup, Philip J B Koeck, Christopher A G Söderberg, Cecilia Emanuelsson
Small heat shock proteins (sHsps) prevent aggregation of thermosensitive client proteins in a first line of defense against cellular stress. The mechanisms by which they perform this function have been hard to define due to limited structural information; currently there is only one high-resolution structure of a plant sHsp published, of the cytosolic Hsp16.9. We took interest in Hsp21, a chloroplast-localized sHsp crucial for plant stress resistance, which has even longer N-terminals arms than Hsp16.9, with a functionally important and conserved methionine-rich motif...
March 21, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28321972/vectorization-of-agrochemicals-via-amino-acid-carriers-influence-of-the-spacer-arm-structure-on-the-phloem-mobility-of-phenylpyrrole-conjugates-in-the-ricinus-system
#4
Sophie Marhadour, Hanxiang Wu, Wen Yang, Cécile Marivingt-Mounir, Jean-Louis Bonnemain, Jean-François Chollet
BACKGROUND: Excessive agrochemical use causes significant threats to environmental safety and human health. Reducing pesticide use without reducing yield is necessary for sustainable agriculture. Therefore we developed a vectorization strategy to enhance agrochemical delivery through plant amino acid carriers. RESULTS: In addition to a fenpiclonil conjugate recently described, three new amino acid conjugates were synthesized by coupling fenpiclonil to an L-α-amino acid...
March 20, 2017: Pest Management Science
https://www.readbyqxmd.com/read/28319155/relationships-between-abiotic-environment-plant-functional-traits-and-animal-body-size-at-mount-kilimanjaro-tanzania
#5
David Schellenberger Costa, Alice Classen, Stefan Ferger, Maria Helbig-Bonitz, Marcell Peters, Katrin Böhning-Gaese, Ingolf Steffan-Dewenter, Michael Kleyer
The effect-response framework states that plant functional traits link the abiotic environment to ecosystem functioning. One ecosystem property is the body size of the animals living in the system, which is assumed to depend on temperature or resource availability, among others. For primary consumers, resource availability may directly be related to plant traits, while for secondary consumers the relationship is indirect. We used plant traits to describe resource availability along an elevational gradient on Mount Kilimanjaro, Tanzania...
2017: PloS One
https://www.readbyqxmd.com/read/28314113/genome-wide-estimation-of-heritability-and-its-functional-components-for-flowering-defense-ionomics-and-developmental-traits-in-a-geographically-diverse-population-of-i-arabidopsis-thaliana-i
#6
Rong-Cai Yang
Narrow-sense heritability (portion of the total phenotypic variation due to additive genetic effect, <i>h</i><sup>2</sup>) is a critical parameter in plant breeding and genetics, but its estimation is difficult for populations with unknown pedigree information. This study applied a marker-based linear mixed model (LMM) analysis to estimate narrow-sense heritability and its seven functional components corresponding to SNPs in coding and noncoding regions for each of 107 flowering, defense, ionomics and developmental traits in an Arabidopsis (<i>Arabidopsis thaliana</i>) population of 199 inbred lines with unknown genetic relatedness...
March 17, 2017: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/28301721/highly-selective-vertically-aligned-nanopores-in-sustainably-derived-polymer-membranes-by-molecular-templating
#7
Xunda Feng, Kohsuke Kawabata, Gilad Kaufman, Menachem Elimelech, Chinedum O Osuji
We describe a combination of molecular templating and directed self-assembly to realize highly selective vertically aligned nanopores in polymer membranes using sustainably derived materials. The approach exploits a structure directing molecule to template the assembly of plant-derived fatty acids into highly ordered columnar mesophases. Directed self-assembly using physical confinement and magnetic fields provides vertical alignment of the columnar nanostructures in large area (several cm(2)) thin films. Chemically crosslinking the mesophase with added conventional vinyl comonomers and removing the molecular template results in a mechanically robust polymer film with vertically aligned 1...
March 16, 2017: ACS Nano
https://www.readbyqxmd.com/read/28300158/the-receptor-like-pseudokinase-mrh1-interacts-with-the-voltage-gated-potassium-channel-akt2
#8
Kamil Sklodowski, Janin Riedelsberger, Natalia Raddatz, Gonzalo Riadi, Julio Caballero, Isabelle Chérel, Waltraud Schulze, Alexander Graf, Ingo Dreyer
The potassium channel AKT2 plays important roles in phloem loading and unloading. It can operate as inward-rectifying channel that allows H(+)-ATPase-energized K(+) uptake. Moreover, through reversible post-translational modifications it can also function as an open, K(+)-selective channel, which taps a 'potassium battery', providing additional energy for transmembrane transport processes. Knowledge about proteins involved in the regulation of the operational mode of AKT2 is very limited. Here, we employed a large-scale yeast two-hybrid screen in combination with fluorescence tagging and null-allele mutant phenotype analysis and identified the plasma membrane localized receptor-like kinase MRH1/MDIS2 (AT4G18640) as interaction partner of AKT2...
March 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28296168/plant-xylem-hydraulics-what-we-understand-current-research-and-future-challenges
#9
Martin D Venturas, John S Sperry, Uwe G Hacke
Herein we review the current state-of-the-art of plant hydraulics in the context of plant physiology, ecology, and evolution, focusing on current and future research opportunities. We explain the physics of water transport in plants and the limits of this transport system, highlighting the relationships between xylem structure and function. We describe the great variety of techniques existing for evaluating xylem resistance to cavitation. We address several methodological issues and their connection with current debates on conduit refilling and exponential shape vulnerability curves...
March 14, 2017: Journal of Integrative Plant Biology
https://www.readbyqxmd.com/read/28289427/the-arabidopsis-lipid-transfer-protein-2-atltp2-is-involved-in-cuticle-cell-wall-interface-integrity-and-in-etiolated-hypocotyl-permeability
#10
Adélaïde Jacq, Clémentine Pernot, Yves Martinez, Frédéric Domergue, Bruno Payré, Elisabeth Jamet, Vincent Burlat, Valérie B Pacquit
Plant non-specific lipid transfer proteins (nsLTPs) belong to a complex multigenic family implicated in diverse physiological processes. However, their function and mode of action remain unclear probably because of functional redundancy. Among the different roles proposed for nsLTPs, it has long been suggested that they could transport cuticular precursor across the cell wall during the formation of the cuticle, which constitutes the first physical barrier for plant interactions with their aerial environment...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28283658/multitrait-successional-forest-dynamics-enable-diverse-competitive-coexistence
#11
Daniel S Falster, Åke Brännström, Mark Westoby, Ulf Dieckmann
To explain diversity in forests, niche theory must show how multiple plant species coexist while competing for the same resources. Although successional processes are widespread in forests, theoretical work has suggested that differentiation in successional strategy allows only a few species stably to coexist, including only a single shade tolerant. However, this conclusion is based on current niche models, which encode a very simplified view of plant communities, suggesting that the potential for niche differentiation has remained unexplored...
March 10, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28279524/two-residues-determine-the-product-profile-of-the-class-ii-diterpene-synthases-tps14-and-tps21-of-tripterygium-wilfordii
#12
Nikolaj L Hansen, Jakob N Nissen, Björn Hamberger
The medicinal plant Tripterygium wilfordii (Celastraceae) contains a pair of class II diterpene synthases (diTPS) of specialized labdane-type metabolism that, despite remarkably close homology, form strikingly different products. TwTPS21 catalyzes bicyclization of the linear C20 precursor geranylgeranyl diphosphate to ent-copal-8-ol diphosphate, while TwTPS14 forms kolavenyl diphosphate. To determine the amino acid signature controlling the functional divergence of the homologues, we modeled their structures based on an existing crystal structure of the Arabidopsis ent-copalyl diphosphate synthase, archetypal of diTPSs in general metabolism of gibberellin phytohormones...
March 6, 2017: Phytochemistry
https://www.readbyqxmd.com/read/28279171/single-amino-acid-substitutions-in-the-selectivity-filter-render-nbxip1-1%C3%AE-aquaporin-water-permeable
#13
Henry Ampah-Korsah, Yonathan Sonntag, Angelica Engfors, Andreas Kirscht, Per Kjellbom, Urban Johanson
BACKGROUND: Aquaporins (AQPs) are integral membrane proteins that facilitate transport of water and/or other small neutral solutes across membranes in all forms of life. The X Intrinsic Proteins (XIPs) are the most recently recognized and the least characterized aquaporin subfamily in higher plants. XIP1s have been shown to be impermeable to water but permeable to boric acid, glycerol, hydrogen peroxide and urea. However, uncertainty regarding the determinants for selectivity and lack of an activity that is easy to quantify have hindered functional investigations...
March 9, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/28276177/circumpolar-arctic-tundra-biomass-and-productivity-dynamics-in-response-to-projected-climate-change-and-herbivory
#14
Qin Yu, Howard Epstein, Ryan Engstrom, Donald Walker
Satellite remote sensing data have indicated a general 'greening' trend in the arctic tundra biome. However, the observed changes based on remote sensing are the result of multiple environmental drivers, and the effects of individual controls such as warming, herbivory, and other disturbances on changes in vegetation biomass, community structure, and ecosystem function remain unclear. We apply ArcVeg, an arctic tundra vegetation dynamics model, to estimate potential changes in vegetation biomass and net primary production (NPP) at the plant community and functional type levels...
March 8, 2017: Global Change Biology
https://www.readbyqxmd.com/read/28263426/linking-river-flow-regimes-to-riparian-plant-guilds-a-community-wide-modeling-approach
#15
David A Lytle, David M Merritt, Jonathan D Tonkin, Julian D Olden, Lindsay V Reynolds
Modeling riparian plant dynamics along rivers is complicated by the fact that plants have different edaphic and hydrologic requirements at different life-stages. With intensifying human demands for water and continued human alteration of rivers, there is a growing need for predicting responses of vegetation to flow alteration, including responses related to climate change and river flow management. We developed a coupled structured population model that coombines stage-specific responses of plant guilds with specific attributes of river hydrologic regime...
March 6, 2017: Ecological Applications: a Publication of the Ecological Society of America
https://www.readbyqxmd.com/read/28261471/environmental-control-of-the-microfaunal-community-structure-in-tropical-bromeliads
#16
Pavel Kratina, Jana S Petermann, Nicholas A C Marino, Andrew A M MacDonald, Diane S Srivastava
Ecological communities hosted within phytotelmata (plant compartments filled with water) provide an excellent opportunity to test ecological theory and to advance our understanding of how local and global environmental changes affect ecosystems. However, insights from bromeliad phytotelmata communities are currently limited by scarce accounts of microfauna assemblages, even though these assemblages are critical in transferring, recycling, and releasing nutrients in these model ecosystems. Here, we analyzed natural microfaunal communities in leaf compartments of 43 bromeliads to identify the key environmental filters underlying their community structures...
March 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/28261464/intraspecific-functional-diversity-of-common-species-enhances-community-stability
#17
Connor M Wood, Shawn T McKinney, Cynthia S Loftin
Common species are fundamental to the structure and function of their communities and may enhance community stability through intraspecific functional diversity (iFD). We measured among-habitat and within-habitat iFD (i.e., among- and within-plant community types) of two common small mammal species using stable isotopes and functional trait dendrograms, determined whether iFD was related to short-term population stability and small mammal community stability, and tested whether spatially explicit trait filters helped explain observed patterns of iFD...
March 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/28255663/towards-quantitative-root-hydraulic-phenotyping-novel-mathematical-functions-to-calculate-plant-scale-hydraulic-parameters-from-root-system-functional-and-structural-traits
#18
F Meunier, V Couvreur, X Draye, J Vanderborght, M Javaux
Predicting root water uptake and plant transpiration is crucial for managing plant irrigation and developing drought-tolerant root system ideotypes (i.e. ideal root systems). Today, three-dimensional structural functional models exist, which allows solving the water flow equation in the soil and in the root systems under transient conditions and in heterogeneous soils. Yet, these models rely on the full representation of the three-dimensional distribution of the root hydraulic properties, which is not always easy to access...
March 2, 2017: Journal of Mathematical Biology
https://www.readbyqxmd.com/read/28248229/mitochondrial-proteome-studies-in-seeds-during-germination
#19
REVIEW
Malgorzata Czarna, Marta Kolodziejczak, Hanna Janska
Seed germination is considered to be one of the most critical phases in the plant life cycle, establishing the next generation of a plant species. It is an energy-demanding process that requires functioning mitochondria. One of the earliest events of seed germination is progressive development of structurally simple and metabolically quiescent promitochondria into fully active and cristae-containing mitochondria, known as mitochondrial biogenesis. This is a complex and tightly regulated process, which is accompanied by sequential and dynamic gene expression, protein synthesis, and post-translational modifications...
June 21, 2016: Proteomes
https://www.readbyqxmd.com/read/28241737/eco-evolution-in-size-structured-ecosystems-simulation-case-study-of-rapid-morphological-changes-in-alewife
#20
Jung Koo Kang, Xavier Thibert-Plante
BACKGROUND: Over the last 300 years, interactions between alewives and zooplankton communities in several lakes in the U.S. have caused the alewives' morphology to transition rapidly from anadromous to landlocked. Lakes with landlocked alewives contain smaller-bodied zooplankton than those without alewives. Landlocked adult alewives display smaller body sizes, narrower gapes, smaller inter-gill-raker spacings, reach maturity at an earlier age, and are less fecund than anadromous alewives...
February 27, 2017: BMC Evolutionary Biology
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