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https://www.readbyqxmd.com/read/27914200/assembling-the-tat-protein-translocase
#1
Felicity Alcock, Phillip J Stansfeld, Hajra Basit, Johann Habersetzer, Matthew Ab Baker, Tracy Palmer, Mark I Wallace, Ben C Berks
The twin-arginine protein translocation system (Tat) transports folded proteins across the bacterial cytoplasmic membrane and the thylakoid membranes of plant chloroplasts. The Tat transporter is assembled from multiple copies of the membrane proteins TatA, TatB, and TatC. We combine sequence co-evolution analysis, molecular simulations, and experimentation to define the interactions between the Tat proteins of Escherichia coli at molecular-level resolution. In the TatBC receptor complex the transmembrane helix of each TatB molecule is sandwiched between two TatC molecules, with one of the inter-subunit interfaces incorporating a functionally important cluster of interacting polar residues...
December 3, 2016: ELife
https://www.readbyqxmd.com/read/27913751/new-fungal-defensin-like-peptides-provide-evidence-for-fold-change-of-proteins-in-evolution
#2
Yucheng Wu, Bin Gao, Shunyi Zhu
Defensins containing a consensus cystine framework, Cys[1]..Cys[2]X3Cys[3]..Cys[4]..Cys[5]X1Cys[6] ("X", any amino acids normally except Cys; "...", variable residue numbers), are extensively distributed in a variety of multicellular organisms (plants, fungi and invertebrates) and essentially involved in immunity as microbicidal agents. This framework is a prerequisite for forming a cystine-stabilized α-helix and β-sheet (CSαβ) fold, in which the two invariant motifs, Cys[2]X3Cys[3]/Cys[5]X1Cys[6], are key determinants of fold formation...
December 2, 2016: Bioscience Reports
https://www.readbyqxmd.com/read/27913746/anti-trachea-inflammatory-effects-of-diosgenin-from-dioscorea-nipponica-through-interactions-with-glucocorticoid-receptor-%C3%AE
#3
Yang Junchao, Wang Zhen, Wang Yuan, Xu Liying, Jiang Libin, Zhu Yuanhong, Zhao Wei, Chen Ruilin, Zhai Lu
Asthma is a heterogeneous disease characterized by symptoms of chronic inflammation and airway structural and functional changes. It affects about 300 million people worldwide and causes 250 000 deaths annually, but its symptoms can be greatly relieved by regular use of inhaled glucocorticoids (GCs). GCs exert their function through interacting with glucocorticoid receptors (GRs). Diosgenin is a naturally occurring steroidal saponin abundantly present in many medicinal plants, including Dioscorea nipponica, which shares a similar steroidal structure with GC...
December 2, 2016: Journal of International Medical Research
https://www.readbyqxmd.com/read/27911995/allometry-data-and-equations-for-coastal-marsh-plants
#4
Meng Lu, Joshua S Caplan, Jonathan D Bakker, J Adam Langley, Thomas J Mozdzer, Bert G Drake, J Patrick Megonigal
Coastal marshes are highly valued for ecosystem services such as protecting inland habitats from storms, sequestering carbon, removing nutrients and other pollutants from surface water, and providing habitat for fish, shellfish, and birds. Because plants largely determine the structure and function of coastal marshes, quantifying plant biomass is essential for evaluating these ecosystem services, understanding the biogeochemical processes that regulate ecosystem function, and forecasting tidal wetland responses to accelerated sea level rise...
December 2016: Ecology
https://www.readbyqxmd.com/read/27911919/few-ant-species-play-a-central-role-linking-different-plant-resources-in-a-network-in-rupestrian-grasslands
#5
Fernanda V Costa, Marco A R Mello, Judith L Bronstein, Tadeu J Guerra, Renata L Muylaert, Alice C Leite, Frederico S Neves
Ant-plant associations are an outstanding model to study the entangled ecological interactions that structure communities. However, most studies of plant-animal networks focus on only one type of resource that mediates these interactions (e.g, nectar or fruits), leading to a biased understanding of community structure. New approaches, however, have made possible to study several interaction types simultaneously through multilayer networks models. Here, we use this approach to ask whether the structural patterns described to date for ant-plant networks hold when multiple interactions with plant-derived food rewards are considered...
2016: PloS One
https://www.readbyqxmd.com/read/27900472/tissue-specific-expression-of-telomerase-reverse-transcriptase-gene-variants-in-nicotiana-tabacum
#6
Jana Fišerová Jurečková, Eva Sýkorová, Said Hafidh, David Honys, Jiří Fajkus, Miloslava Fojtová
In tobacco, three sequence variants of the TERT gene have been described. We revealed unbalanced levels of TERT variant transcripts in vegetative tobacco tissues and enhanced TERT transcription and telomerase activity in reproductive tissues. Telomerase is a ribonucleoprotein complex responsible for the maintenance of telomeres, structures delimiting ends of linear eukaryotic chromosomes. In the Nicotiana tabacum (tobacco) allotetraploid plant, three sequence variants (paralogs) of the gene coding for the telomerase reverse transcriptase subunit (TERT) have been described, two of them derived from the maternal N...
November 29, 2016: Planta
https://www.readbyqxmd.com/read/27894701/design-of-a-new-pid-controller-using-predictive-functional-control-optimization-for-chamber-pressure-in-a-coke-furnace
#7
Jianming Zhang
An improved proportional-integral-derivative (PID) controller based on predictive functional control (PFC) is proposed and tested on the chamber pressure in an industrial coke furnace. The proposed design is motivated by the fact that PID controllers for industrial processes with time delay may not achieve the desired control performance because of the unavoidable model/plant mismatches, while model predictive control (MPC) is suitable for such situations. In this paper, PID control and PFC algorithm are combined to form a new PID controller that has the basic characteristic of PFC algorithm and at the same time, the simple structure of traditional PID controller...
November 25, 2016: ISA Transactions
https://www.readbyqxmd.com/read/27893157/brown-world-forests-increased-ungulate-browsing-keeps-temperate-trees-in-recruitment-bottlenecks-in-resource-hotspots
#8
Marcin Churski, Jakub W Bubnicki, Bogumiła Jędrzejewska, Dries P J Kuijper, Joris P G M Cromsigt
Plant biomass consumers (mammalian herbivory and fire) are increasingly seen as major drivers of ecosystem structure and function but the prevailing paradigm in temperate forest ecology is still that their dynamics are mainly bottom-up resource-controlled. Using conceptual advances from savanna ecology, particularly the demographic bottleneck model, we present a novel view on temperate forest dynamics that integrates consumer and resource control. We used a fully factorial experiment, with varying levels of ungulate herbivory and resource (light) availability, to investigate how these factors shape recruitment of five temperate tree species...
November 28, 2016: New Phytologist
https://www.readbyqxmd.com/read/27886144/cuticular-lipids-as-a-cross-talk-among-ants-plants-and-butterflies
#9
REVIEW
Francesca Barbero
Even though insects and plants are distantly related organisms, they developed an integument which is functionally and structurally similar. Besides functioning as a physical barrier to cope with abiotic and biotic stress, this interface, called cuticle, is also a source of chemical signaling. Crucial compounds with this respect are surface lipids and especially cuticular hydrocarbons (CHCs). This review is focused on the role of CHCs in fostering multilevel relationships among ants, plants and Lepidoptera (primarily butterflies)...
November 24, 2016: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/27884467/elucidating-ozonation-mechanisms-of-organic-micropollutants-based-on-dft-calculations-taking-sulfamethoxazole-as-a-case
#10
Siyu Zhang, Gang Yu, Jingwen Chen, Qing Zhao, Xuejiao Zhang, Bin Wang, Jun Huang, Shubo Deng, Yujue Wang
Ozonation is widely used in wastewater treatment plants to remove diverse organic micropollutants. As molecular structures of organic micropollutants contain multiple ozone-preferred reaction sites, and moreover intermediate products can react with ozone again, ozonation mechanism is complex. A fast increasing number of organic micropollutants and a great demand of ecological risk assessments call for an in silico method to provide insights into the ozonation mechanism of organic micropollutants. Here, an in silico model was developed to unveil ozonation mechanisms of organic micropollutants...
November 21, 2016: Environmental Pollution
https://www.readbyqxmd.com/read/27881986/the-parenchyma-of-secondary-xylem-and-its-critical-role-in-tree-defense-against-fungal-decay-in-relation-to-the-codit-model
#11
REVIEW
Hugh Morris, Craig Brodersen, Francis W M R Schwarze, Steven Jansen
This review examines the roles that ray and axial parenchyma (RAP) plays against fungal pathogens in the secondary xylem of wood within the context of the CODIT model (Compartmentalization of Decay in Trees), a defense concept first conceived in the early 1970s by Alex Shigo. This model, simplistic in its design, shows how a large woody perennial is highly compartmented. Anatomical divisions in place at the time of infection or damage, (physical defense) alongside the 'active' response by the RAP during and after wounding work together in forming boundaries that function to restrict air or decay spread...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/27881680/structures-and-short-linear-motif-of-disordered-transcription-factor-regions-provide-clues-to-the-interactome-of-the-cellular-hub-radical-induced-cell-death1
#12
Charlotte O'Shea, Lasse Staby, Sidsel Krogh Bendsen, Frederik Grønbæk Tidemand, Andreas Redsted, Martin Willemoës, Birthe B Kragelund, Karen Skriver
Intrinsically disordered protein regions (IDRs) lack a well-defined three-dimensional structure, but often facilitate key protein functions. Some interactions between IDRs and folded protein domains rely on short linear motifs (SLiMs). These motifs are challenging to identify, but once found can point to larger networks of interactions, such as with proteins that serve as hubs for essential cellular functions. The stress-associated plant protein Radical-Induced Cell Death1 (RCD1) is one such hub, interacting with many transcription factors via their flexible IDRs...
November 23, 2016: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/27871361/recreating-the-synthesis-of-starch-granules-in-yeast
#13
Barbara Pfister, Antoni Sánchez-Ferrer, Ana Diaz, Kuanjen Lu, Caroline Otto, Mirko Holler, Farooque Razvi Shaik, Florence Meier, Raffaele Mezzenga, Samuel C Zeeman
Starch, as the major nutritional component of our staple crops and a feedstock for industry, is a vital plant product. It is composed of glucose polymers that form massive semi-crystalline granules. Its precise structure and composition determine its functionality and thus applications; however, there is no versatile model system allowing the relationships between the biosynthetic apparatus, glucan structure and properties to be explored. Here, we expressed the core Arabidopsis starch-biosynthesis pathway in Saccharomyces cerevisiae purged of its endogenous glycogen-metabolic enzymes...
November 22, 2016: ELife
https://www.readbyqxmd.com/read/27870885/a-negative-relationship-between-foliar-carbon-isotope-composition-and-mass-based-nitrogen-concentration-on-the-eastern-slope-of-mount-gongga-china
#14
Jiazhu Li, Guoan Wang, Runan Zhang, Li Li
Plants adopt ecological strategy to resist environmental changes and increase their resource-use efficiency. The ecological strategy includes changes in physiological traits and leaf morphology, which may result in simultaneous variations in foliar N concentration and the ratio of intercellular CO2 concentration to ambient CO2 concentration (ci/ca). This in turn links to foliar carbon isotope discrimination, and thus, a relationship between foliar N concentration and foliar carbon isotope composition (δ13C) is expected...
2016: PloS One
https://www.readbyqxmd.com/read/27864511/root-nodule-symbiosis-in-lotus-japonicus-drives-the-establishment-of-distinctive-rhizosphere-root-and-nodule-bacterial-communities
#15
Rafal Zgadzaj, Ruben Garrido-Oter, Dorthe Bodker Jensen, Anna Koprivova, Paul Schulze-Lefert, Simona Radutoiu
Lotus japonicus has been used for decades as a model legume to study the establishment of binary symbiotic relationships with nitrogen-fixing rhizobia that trigger root nodule organogenesis for bacterial accommodation. Using community profiling of 16S rRNA gene amplicons, we reveal that in Lotus, distinctive nodule- and root-inhabiting communities are established by parallel, rather than consecutive, selection of bacteria from the rhizosphere and root compartments. Comparative analyses of wild-type (WT) and symbiotic mutants in Nod factor receptor5 (nfr5), Nodule inception (nin) and Lotus histidine kinase1 (lhk1) genes identified a previously unsuspected role of the nodulation pathway in the establishment of different bacterial assemblages in the root and rhizosphere...
November 18, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27862469/araport11-a-complete-reannotation-of-the-arabidopsis-thaliana-reference-genome
#16
Chia-Yi Cheng, Vivek Krishnakumar, Agnes Chan, Françoise Thibaud-Nissen, Seth Schobel, Christopher D Town
The flowering plant Arabidopsis thaliana is a dicot model organism for research in many aspects of plant biology. A comprehensive annotation of its genome paves the way for understanding the functions and activities of all types of transcripts, including mRNA, the various classes of non-coding RNA, and small RNA. The TAIR10 annotation update had a profound impact on Arabidopsis research but was released more than five years ago. Maintaining the accuracy of the annotation continues to be a prerequisite for future progress...
November 8, 2016: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/27857941/septin-organization-and-functions-in-budding-yeast
#17
REVIEW
Oliver Glomb, Thomas Gronemeyer
The septins are a conserved family of GTP-binding proteins present in all eukaryotic cells except plants. They were originally discovered in the baker's yeast Saccharomyces cerevisiae that serves until today as an important model organism for septin research. In yeast, the septins assemble into a highly ordered array of filaments at the mother bud neck. The septins are regulators of spatial compartmentalization in yeast and act as key players in cytokinesis. This minireview summarizes the recent findings about structural features and cell biology of the yeast septins...
2016: Frontiers in Cell and Developmental Biology
https://www.readbyqxmd.com/read/27830985/teaching-an-old-dog-new-tricks-suppressing-activation-of-specific-mitogen-activated-kinases-as-a-potential-virulence-function-of-the-bacterial-avrrpt2-effector-protein
#18
Lennart Eschen-Lippold, Dierk Scheel, Justin Lee
AvrRpt2 is one of the first Pseudomonas syringae effector proteins demonstrated to be delivered into host cells. It suppresses plant immunity by modulating auxin signaling and cleavage of the membrane-localized defense regulator RIN4. We recently uncovered a novel potential virulence function of AvrRpt2, where it specifically blocked activation of mitogen-activated protein kinases, MPK4 and MPK11, but not of MPK3 and MPK6. Putative AvrRpt2 homologs from different phytopathogens and plant-associated bacteria showed distinct activities with respect to MPK4/11 activation suppression and RIN4 cleavage...
November 10, 2016: Plant Signaling & Behavior
https://www.readbyqxmd.com/read/27825302/arabidopsis-thaliana-population-analysis-reveals-high-plasticity-of-the-genomic-region-spanning-msh2-at3g18530-and-at3g18535-genes-and-provides-evidence-for-nahr-driven-recurrent-cnv-events-occurring-in-this-location
#19
Agnieszka Zmienko, Anna Samelak-Czajka, Piotr Kozlowski, Maja Szymanska, Marek Figlerowicz
BACKGROUND: Intraspecies copy number variations (CNVs), defined as unbalanced structural variations of specific genomic loci, ≥1 kb in size, are present in the genomes of animals and plants. A growing number of examples indicate that CNVs may have functional significance and contribute to phenotypic diversity. In the model plant Arabidopsis thaliana at least several hundred protein-coding genes might display CNV; however, locus-specific genotyping studies in this plant have not been conducted...
November 8, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27822186/structure-and-protein-protein-interactions-of-human-udp-glucuronosyltransferases
#20
REVIEW
Ryoichi Fujiwara, Tsuyoshi Yokoi, Miki Nakajima
Mammalian UDP-glucuronosyltransferases (UGTs) catalyze the transfer of glucuronic acid from UDP-glucuronic acid to various xenobiotics and endobiotics. Since UGTs comprise rate-limiting enzymes for metabolism of various compounds, co-administration of UGT-inhibiting drugs and genetic deficiency of UGT genes can cause an increased blood concentration of these compounds. During the last few decades, extensive efforts have been made to advance the understanding of gene structure, function, substrate specificity, and inhibition/induction properties of UGTs...
2016: Frontiers in Pharmacology
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