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https://www.readbyqxmd.com/read/28109185/folding-of-intrinsically-disordered-plant-lea-proteins-is-driven-by-glycerol-induced-crowding-and-the-presence-of-membranes
#1
Anne Bremer, Martin Wolff, Anja Thalhammer, Dirk K Hincha
Late embryogenesis abundant (LEA) proteins are related to cellular dehydration tolerance. Most LEA proteins are predicted to have no stable secondary structure in solution, i.e. to be intrinsically disordered proteins (IDPs), but they may acquire α-helical structure upon drying. In the model plant Arabidopsis thaliana the LEA proteins COR15A and COR15B are highly induced upon cold treatment and are necessary for the plants to attain full freezing tolerance. Freezing leads to increased intracellular crowding due to dehydration by extracellular ice crystals...
January 21, 2017: FEBS Journal
https://www.readbyqxmd.com/read/28105941/the-loss-of-photosynthetic-pathways-in-the-plastid-and-nuclear-genomes-of-the-non-photosynthetic-mycoheterotrophic-eudicot-monotropa-hypopitys
#2
Nikolai V Ravin, Eugeny V Gruzdev, Alexey V Beletsky, Alexander M Mazur, Egor B Prokhortchouk, Mikhail A Filyushin, Elena Z Kochieva, Vitaly V Kadnikov, Andrey V Mardanov, Konstantin G Skryabin
BACKGROUND: Chloroplasts of most plants are responsible for photosynthesis and contain a conserved set of about 110 genes that encode components of housekeeping gene expression machinery and photosynthesis-related functions. Heterotrophic plants obtaining nutrients from other organisms and their plastid genomes represent model systems in which to study the effects of relaxed selective pressure on photosynthetic function. The most evident is a reduction in the size and gene content of the plastome, which correlates with the loss of genes encoding photosynthetic machinery which become unnecessary...
November 16, 2016: BMC Plant Biology
https://www.readbyqxmd.com/read/28105917/proclat-a-new-bioinformatics-tool-for-in-silico-protein-reclassification-case-study-of-drab-a-protein-coded-from-the-dratgb-operon-in-azospirillum-brasilense
#3
Elisa Terumi Rubel, Roberto Tadeu Raittz, Nilson Antonio da Rocha Coimbra, Michelly Alves Coutinho Gehlen, Fábio de Oliveira Pedrosa
BACKGROUND: Azopirillum brasilense is a plant-growth promoting nitrogen-fixing bacteria that is used as bio-fertilizer in agriculture. Since nitrogen fixation has a high-energy demand, the reduction of N2 to NH4(+) by nitrogenase occurs only under limiting conditions of NH4(+) and O2. Moreover, the synthesis and activity of nitrogenase is highly regulated to prevent energy waste. In A. brasilense nitrogenase activity is regulated by the products of draG and draT. The product of the draB gene, located downstream in the draTGB operon, may be involved in the regulation of nitrogenase activity by an, as yet, unknown mechanism...
December 15, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/28105914/homology-modeling-and-molecular-dynamics-provide-structural-insights-into-tospovirus-nucleoprotein
#4
Rayane Nunes Lima, Muhammad Faheem, João Alexandre Ribeiro Gonçalves Barbosa, Marcelo Depólo Polêto, Hugo Verli, Fernando Lucas Melo, Renato Oliveira Resende
BACKGROUND: Tospovirus is a plant-infecting genus within the family Bunyaviridae, which also includes four animal-infecting genera: Hantavirus, Nairovirus, Phlebovirus and Orthobunyavirus. Compared to these members, the structures of Tospovirus proteins still are poorly understood. Despite multiple studies have attempted to identify candidate N protein regions involved in RNA binding and protein multimerization for tospovirus using yeast two-hybrid systems (Y2HS) and site-directed mutagenesis, the tospovirus ribonucleocapsids (RNPs) remains largely uncharacterized at the molecular level and the lack of structural information prevents detailed insight into these interactions...
December 15, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/28104373/novel-multilayer-microcapsules-based-on-soy-protein-isolate-fibrils-and-high-methoxyl-pectin-production-characterization-and-release-modeling
#5
Elham Ansarifar, Mohebbat Mohebbi, Fakhri Shahidi, Arash Koocheki, Navid Ramezanian
In this study, novel microcapsules were produced through the layer by layer adsorption of food-grade and plant-based polyelectrolytes, soy protein isolate (SPI) fibrils and high methoxyl pectin (HMP). The physical properties of the fibrils were investigated by TEM and AFM and the properties of the microcapsules such as size, uniformity, zeta potential, morphology, functional groups, modeling and the release kinetics of limonene were examined. The results revealed that SPI-fibrils had a thickness varying from 1 to 10nm and strand like structure...
January 16, 2017: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/28103421/structure-of-the-arabidopsis-thaliana-nadph-cytochrome-p450-reductase-2-atr2-provides-insight-into-its-function
#6
Guoqi Niu, Shun Zhao, Lei Wang, Wei Dong, Lin Liu, Yikun He
Members of the cytochrome P450 family catalyze a variety of monooxygenase reactions, and for the eukaryotic membrane-bound members, NADPH is typically used as the reducing agent. The flavoprotein NADPH-cytochrome P450 reductase (CPR) enables electron transfer from NADPH to cytochrome P450 via its flavin cofactors. ATR2 is one of the two authentic CPR genes in the genome of the model plant Arabidopsis thaliana, and its product has been physiologically and kinetically characterized. Here, we report the 2.3-Å structure of ATR2 and find that the position of the two flavin cofactors differs from that of other known CPR structures...
January 19, 2017: FEBS Journal
https://www.readbyqxmd.com/read/28103252/comparative-and-evolutionary-analysis-of-grass-pollen-allergens-using-brachypodium-distachyon-as-a-model-system
#7
Akanksha Sharma, Niharika Sharma, Prem Bhalla, Mohan Singh
Comparative genomics have facilitated the mining of biological information from a genome sequence, through the detection of similarities and differences with genomes of closely or more distantly related species. By using such comparative approaches, knowledge can be transferred from the model to non-model organisms and insights can be gained in the structural and evolutionary patterns of specific genes. In the absence of sequenced genomes for allergenic grasses, this study was aimed at understanding the structure, organisation and expression profiles of grass pollen allergens using the genomic data from Brachypodium distachyon as it is phylogenetically related to the allergenic grasses...
2017: PloS One
https://www.readbyqxmd.com/read/28100609/sterol-binding-by-the-tombusviral-replication-proteins-is-essential-for-replication-in-yeast-and-plants
#8
Kai Xu, Peter D Nagy
: Membranous structures derived from various organelles are important for replication of plus-stranded RNA viruses. Although the important roles of co-opted host proteins in RNA virus replication have been appreciated for a decade, the equally important functions of cellular lipids in virus replication are gaining full attention only recently. Previous works with Tomato bushy stunt tombusvirus (TBSV) in model host yeast have revealed essential roles for phosphatidylethanolamine and sterols in viral replication...
January 18, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28100184/cnvs-into-the-wild-screening-the-genomes-of-conifer-trees-picea-spp-reveals-fewer-gene-copy-number-variations-in-hybrids-and-links-to-adaptation
#9
Julien Prunier, Sébastien Caron, John MacKay
BACKGROUND: Copy number variations (CNVs) have been linked to different phenotypes in human, including many diseases. A genome-scale understanding of CNVs is available in a few plants but none are wild species, leaving a knowledge gap regarding their genome biology and evolutionary role. We developed a reliable CNV detection method for species lacking contiguous reference genome. We selected multiple probes within 14,078 gene sequences and developed comparative genome hybridization on arrays...
January 18, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28097084/the-calcium-dependent-protein-kinase-cdpk-and-cdpk-related-kinase-gene-families-in-hevea-brasiliensis-comparison-with-five-other-plant-species-in-structure-evolution-and-expression
#10
Xiao-Hu Xiao, Meng Yang, Jin-Lei Sui, Ji-Yan Qi, Yong-Jun Fang, Song-Nian Hu, Chao-Rong Tang
Calcium-dependent protein kinases (CDPKs or CPKs) play important roles in various physiological processes of plants, including growth and development, stress responses and hormone signaling. Although the CDPK gene family has been characterized in several model plants, little is known about this gene family in Hevea brasiliensis (the Para rubber tree). Here, we characterize the entire H. brasiliensis CDPK and CDPK-related kinase (CRK) gene families comprising 30 CDPK genes (HbCPK1 to 30) and nine CRK genes (HbCRK1 to 9)...
January 2017: FEBS Open Bio
https://www.readbyqxmd.com/read/28096492/identification-of-glutaminyl-cyclase-genes-involved-in-pyroglutamate-modification-of-fungal-lignocellulolytic-enzymes
#11
Vincent W Wu, Craig M Dana, Anthony T Iavarone, Douglas S Clark, N Louise Glass
: The breakdown of plant biomass to simple sugars is essential for the production of second-generation biofuels and high-value bioproducts. Currently, enzymes produced from filamentous fungi are used for deconstructing plant cell wall polysaccharides into fermentable sugars for biorefinery applications. A post-translational N-terminal pyroglutamate modification observed in some of these enzymes occurs when N-terminal glutamine or glutamate is cyclized to form a five-membered ring. This modification has been shown to confer resistance to thermal denaturation for CBH-1 and EG-1 cellulases...
January 17, 2017: MBio
https://www.readbyqxmd.com/read/28093983/an-approach-towards-structure-based-antimicrobial-peptide-design-for-use-in-development-of-transgenic-plants-a-strategy-for-plant-disease-management
#12
Humaira Ilyas, Aritreyee Datta, Anirban Bhunia
Antimicrobial peptides (AMPs), also known as host defense peptides (HDPs), are ubiquitous and vital components of innate defense response that present themselves as potential candidates for drug design, aimed to control plant and animal diseases. Though their application for plant disease management has long been studied with natural AMPs, cytotoxicity and stability related shortcomings for the development of transgenic plants limits their usage. Newer technologies like molecular modelling, NMR spectroscopy and combinatorial chemistry allow screening for potent candidates and provide new avenues for the generation of rationally designed synthetic AMPs with multiple biological functions...
January 16, 2017: Current Medicinal Chemistry
https://www.readbyqxmd.com/read/28092811/towards-the-structure-of-the-tir-domain-signalosome
#13
REVIEW
Surekha Nimma, Thomas Ve, Simon J Williams, Bostjan Kobe
TIR (Toll/interleukin-1 receptor/resistance protein) domains feature in animal, plant and bacterial proteins involved in innate immunity pathways and associated processes. They function through protein:protein interactions, in particular self-association and homotypic association with other TIR domains. Structures of TIR domains from all phyla have been determined, but common association modes have only emerged for plant and bacterial TIR domains, and not for mammalian TIR domains. Numerous attempts involving hybrid approaches, which have combined structural, computational, mutagenesis and biophysical data, have failed to converge onto common models of how these domains associate and function...
January 13, 2017: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/28088302/the-cyp79a1-catalyzed-conversion-of-tyrosine-to-e-p-hydroxyphenylacetaldoxime-unravelled-using-an-improved-method-for-homology-modeling
#14
Dario Vazquez-Albacete, Marco Montefiori, Stefan Kol, Mohammed Saddik Motawia, Birger Lindberg Møller, Lars Olsen, Morten H H Nørholm
The vast diversity and membrane-bound nature of plant P450s makes it challenging to study the structural characteristics of this class of enzymes especially with respect to accurate intermolecular enzyme-substrate interactions. To address this problem we here apply a modified hybrid structure strategy for homology modeling of plant P450s. This allows for structural elucidation based on conserved motifs in the protein sequence and secondary structure predictions. We modeled the well-studied Sorghum bicolor cytochrome P450 CYP79A1 catalyzing the first step in the biosynthesis of the cyanogenic glucoside dhurrin...
January 11, 2017: Phytochemistry
https://www.readbyqxmd.com/read/28087663/evolution-and-structural-diversification-of-nictaba-like-lectin-genes-in-food-crops-with-a-focus-on-soybean-glycine-max
#15
Sofie Van Holle, Pierre Rougé, Els J M Van Damme
BACKGROUND AND AIMS: The Nictaba family groups all proteins that show homology to Nictaba, the tobacco lectin. So far, Nictaba and an Arabidopsis thaliana homologue have been shown to be implicated in the plant stress response. The availability of more than 50 sequenced plant genomes provided the opportunity for a genome-wide identification of Nictaba-like genes in 15 species, representing members of the Fabaceae, Poaceae, Solanaceae, Musaceae, Arecaceae, Malvaceae and Rubiaceae. Additionally, phylogenetic relationships between the different species were explored...
January 12, 2017: Annals of Botany
https://www.readbyqxmd.com/read/28081202/characterization-and-functional-analysis-of-five-mads-box-b-class-genes-related-to-floral-organ-identification-in-tagetes-erecta
#16
Ye Ai, Chunling Zhang, Yalin Sun, Weining Wang, Yanhong He, Manzhu Bao
According to the floral organ development ABC model, B class genes specify petal and stamen identification. In order to study the function of B class genes in flower development of Tagetes erecta, five MADS-box B class genes were identified and their expression and putative functions were studied. Sequence comparisons and phylogenetic analyses indicated that there were one PI-like gene-TePI, two euAP3-like genes-TeAP3-1 and TeAP3-2, and two TM6-like genes-TeTM6-1 and TeTM6-2 in T. erecta. Strong expression levels of these genes were detected in stamens of the disk florets, but little or no expression was detected in bracts, receptacles or vegetative organs...
2017: PloS One
https://www.readbyqxmd.com/read/28074936/hygroscopic-motions-of-fossil-conifer-cones
#17
Simon Poppinga, Nikolaus Nestle, Andrea Šandor, Bruno Reible, Tom Masselter, Bernd Bruchmann, Thomas Speck
Conifer cones represent natural, woody compliant structures which move their scales as passive responses to changes in environmental humidity. Here we report on water-driven opening and closing motions in coalified conifer cones from the Eemian Interglacial (approx. 126,000-113,000 years BP) and from the Middle Miocene (approx. 16.5 to 11.5 million years BP). These cones represent by far the oldest documented evidence of plant parts showing full functionality of such passive hydraulically actuated motion. The functional resilience of these structures is far beyond the biological purpose of seed dispersal and protection and is because of a low level of mineralization of the fossils...
January 11, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28072861/identification-of-the-molecular-clockwork-of-the-oyster-crassostrea-gigas
#18
Mickael Perrigault, Damien Tran
Molecular clock system constitutes the origin of biological rhythms that allow organisms to anticipate cyclic environmental changes and adapt their behavior and physiology. Components of the molecular clock are largely conserved across a broad range of species but appreciable diversity in clock structure and function is also present especially in invertebrates. The present work aimed at identify and characterize molecular clockwork components in relationship with the monitoring of valve activity behavior in the oyster Crassostrea gigas...
2017: PloS One
https://www.readbyqxmd.com/read/28065919/force-of-habit-shrubs-trees-and-contingent-evolution-of-wood-anatomical-diversity-using-croton-euphorbiaceae-as-a-model-system
#19
Rafael Arévalo, Benjamin W van Ee, Ricarda Riina, Paul E Berry, Alex C Wiedenhoeft
BACKGROUND AND AIMS: Wood is a major innovation of land plants, and is usually a central component of the body plan for two major plant habits: shrubs and trees. Wood anatomical syndromes vary between shrubs and trees, but no prior work has explicitly evaluated the contingent evolution of wood anatomical diversity in the context of these plant habits. METHODS: Phylogenetic comparative methods were used to test for contingent evolution of habit, habitat and wood anatomy in the mega-diverse genus Croton (Euphorbiaceae), across the largest and most complete molecular phylogeny of the genus to date...
January 8, 2017: Annals of Botany
https://www.readbyqxmd.com/read/28064392/chemical-composition-structural-properties-and-source-apportionment-of-organic-macromolecules-in-atmospheric-pm10-in-a-coastal-city-of-southeast-china
#20
Yanting Chen, Wenjiao Du, Jinsheng Chen, Youwei Hong, Jinping Zhao, Lingling Xu, Hang Xiao
Particulate matter (PM10) associated with the fractions of organic macromolecules, including humic acid (HA), kerogen + black carbon (KB), and black carbon (BC), was determined during summer and winter at urban and suburban sites in a coastal city of southeast China. The organic macromolecules were characterized by elemental analysis (EA), scanning electron microscopy (SEM), and Fourier transform infrared spectroscopy (FTIR), and their sources were identified by using stable carbon/nitrogen isotope (δ(13)C/δ(15)N) and the Hybrid Single Particle Lagrangian Integrated Trajectory (HYSPLIT) Model...
January 7, 2017: Environmental Science and Pollution Research International
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