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https://www.readbyqxmd.com/read/28527238/a-widespread-family-of-serine-threonine-protein-phosphatases-shares-a-common-regulatory-switch-with-proteasomal-proteases
#1
Niels Bradshaw, Vladimir M Levdikov, Christina M Zimanyi, Rachelle Gaudet, Anthony J Wilkinson, Richard Losick
PP2C phosphatases control biological processes including stress responses, development, and cell division in all kingdoms of life. Diverse regulatory domains adapt PP2C phosphatases to specific functions, but how these domains control phosphatase activity was unknown. We present structures representing active and inactive states of the PP2C phosphatase SpoIIE from Bacillus subtilis. Based on structural analyses and genetic and biochemical experiments, we identify an α-helical switch that shifts a carbonyl oxygen into the active site to coordinate a metal cofactor...
May 20, 2017: ELife
https://www.readbyqxmd.com/read/28527179/making-time-conservation-of-biological-clocks-from-fungi-to-animals
#2
Jay C Dunlap, Jennifer J Loros
The capacity for biological timekeeping arose at least three times through evolution, in prokaryotic cyanobacteria, in cells that evolved into higher plants, and within the group of organisms that eventually became the fungi and the animals. Neurospora is a tractable model system for understanding the molecular bases of circadian rhythms in the last of these groups, and is perhaps the most intensively studied circadian cell type. Rhythmic processes described in fungi include growth rate, stress responses, developmental capacity, and sporulation, as well as much of metabolism; fungi use clocks to anticipate daily environmental changes...
May 2017: Microbiology Spectrum
https://www.readbyqxmd.com/read/28526743/systematic-identification-of-functional-residues-of-artemisia-annua-amorpha-4-11-diene-synthase
#3
Xin Fang, Jian-Xu Li, Jin-Quan Huang, You-Li Xiao, Peng Zhang, Xiao-Ya Chen
Terpene synthases (TPSs) are responsible for the extremely diversified and complex structure of terpenoids. Amorpha-4,11-diene synthase (ADS) has a high (90%) fidelity in generating the sesquiterpene precursor for biosynthesis of artemisinin, an antimalarial drug, however, little is known about how active site residues of ADS involved in the carbocation rearrangement and cyclization reactions. Here, we identify seven residues that are key to most of the catalytic steps in ADS. By structural modeling and amino acid sequence alignments of ADS with two functionally relevant sesquiterpene synthases from Artemisia annua, we performed site-directed mutagenesis and found that a single substitution, T296V, impaired the ring closure activity almost completely, and tetra-substitutions (L374Y/L404V/L405I/G439S) led to an enzyme generating 80% monocyclic bisabolyl-type sesquiterpenes, whereas a double mutant (T399L/T447G) showed compromised activity in regioselective deprotonation to yield 34...
May 19, 2017: Biochemical Journal
https://www.readbyqxmd.com/read/28526529/adding-biological-meaning-to-human-protein-protein-interactions-identified-by-yeast-two-hybrid-screenings-a-guide-through-bioinformatics-tools
#4
Juliana Felgueiras, Joana Vieira Silva, Margarida Fardilha
"A man is known by the company he keeps" is a popular expression that perfectly fits proteins. A common approach to characterize the function of a target protein is to identify its interacting partners and thus infer its roles based on the known functions of the interactors. Protein-protein interaction networks (PPINs) have been created for several organisms, including humans, primarily as results of high-throughput screenings, such as yeast two-hybrid (Y2H). Their unequivocal use to understand events underlying human pathophysiology is promising in identifying genes and proteins associated with diseases...
May 16, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28526268/structural-and-functional-aspects-of-the-nonribosomal-peptide-synthetase-condensation-domain-superfamily-discovery-dissection-and-diversity
#5
REVIEW
Kristjan Bloudoff, T Martin Schmeing
Nonribosomal peptide synthetases (NRPSs) are incredible macromolecular machines that produce a wide range of biologically- and therapeutically-relevant molecules. During synthesis, peptide elongation is performed by the condensation (C) domain, as it catalyzes amide bond formation between the nascent peptide and the amino acid it adds to the chain. Since their discovery more than two decades ago, C domains have been subject to extensive biochemical, bioinformatic, mutagenic, and structural analyses. They are composed of two lobes each with homology to chloramphenicol acetyltransferase, have two binding sites for their two peptidyl carrier protein-bound ligands, and have an active site with conserved motif HHxxxDG located between the two lobes...
May 16, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28525753/the-u6-snrna-m-6-a-methyltransferase-mettl16-regulates-sam-synthetase-intron-retention
#6
Kathryn E Pendleton, Beibei Chen, Kuanqing Liu, Olga V Hunter, Yang Xie, Benjamin P Tu, Nicholas K Conrad
Maintenance of proper levels of the methyl donor S-adenosylmethionine (SAM) is critical for a wide variety of biological processes. We demonstrate that the N(6)-adenosine methyltransferase METTL16 regulates expression of human MAT2A, which encodes the SAM synthetase expressed in most cells. Upon SAM depletion by methionine starvation, cells induce MAT2A expression by enhanced splicing of a retained intron. Induction requires METTL16 and its methylation substrate, a vertebrate conserved hairpin (hp1) in the MAT2A 3' UTR...
May 18, 2017: Cell
https://www.readbyqxmd.com/read/28524091/chemical-diversity-biological-activity-and-genetic-aspects-of-three-ocotea-species-from-the-amazon
#7
Joyce Kelly da Silva, Rafaela da Trindade, Edith Cibelle Moreira, José Guilherme S Maia, Noura S Dosoky, Rebecca S Miller, Leland J Cseke, William N Setzer
Ocotea species present economic importance and biological activities attributed to their essential oils (EOs) and extracts. For this reason, various strategies have been developed for their conservation. The chemical compositions of the essential oils and matK DNA sequences of O. caudata, O. cujumary, and O. caniculata were subjected to comparison with data from O. floribunda, O. veraguensis, and O. whitei, previously reported. The multivariate analysis of chemical composition classified the EOs into two main clusters...
May 18, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28523997/differences-in-relative-levels-of-88-micrornas-in-various-regions-of-the-normal-adult-human-brain
#8
Elena Vladislavovna Filatova, Anelya Khanlarovna Alieva, Maria Igorevna Shadrina, Petr Andreevich Slominsky
AIM OF STUDY: Since the discovery of microRNAs (miRNAs) in the 1990s, our knowledge about their biology has grown considerably. The increasing number of studies addressing the role of miRNAs in development and in various diseases emphasizes the need for a comprehensive catalogue of accurate sequence, expression and conservation information regarding the large number of miRNAs proposed recently in all organs and tissues. The objective of this study was to provide data on the levels of miRNA expression in 15 tissues of the normal human brain...
May 19, 2017: MicroRNA
https://www.readbyqxmd.com/read/28522996/interfering-satellite-rnas-of-bamboo-mosaic-virus
#9
REVIEW
Kuan-Yu Lin, Na-Sheng Lin
Satellite RNAs (satRNAs) are sub-viral agents that may interact with their cognate helper virus (HV) and host plant synergistically and/or antagonistically. SatRNAs totally depend on the HV for replication, so satRNAs and HV usually evolve similar secondary or tertiary RNA structures that are recognized by a replication complex, although satRNAs and HV do not share an appreciable sequence homology. The satRNAs of Bamboo mosaic virus (satBaMV), the only satRNAs of the genus Potexvirus, have become one of the models of how satRNAs can modulate HV replication and virus-induced symptoms...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28522851/mouse-rif1-is-a-regulatory-subunit-of-protein-phosphatase-1-pp1
#10
Rasa Sukackaite, Daniela Cornacchia, Malene Ringkjøbing Jensen, Philippe J Mas, Martin Blackledge, Elin Enervald, Guangyou Duan, Tania Auchynnikava, Maja Köhn, Darren J Hart, Sara B C Buonomo
Rif1 is a conserved protein that plays essential roles in orchestrating DNA replication timing, controlling nuclear architecture, telomere length and DNA repair. However, the relationship between these different roles, as well as the molecular basis of Rif1 function is still unclear. The association of Rif1 with insoluble nuclear lamina has thus far hampered exhaustive characterization of the associated protein complexes. We devised a protocol that overcomes this problem, and were thus able to discover a number of novel Rif1 interactors, involved in chromatin metabolism and phosphorylation...
May 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28521626/experimental-evolution-of-resistance-against-bacillus-thuringiensis-in-the-insect-model-host-galleria-mellonella-results-in-epigenetic-modifications
#11
Krishnendu Mukherjee, Ekaterina Grizanova, Ekaterina Chertkova, Ruediger Lehmann, Ivan Dubovskiy, Andreas Vilcinskas
Epigenetic mechanisms have been proposed to translate environmental stimuli into heritable transgenerational phenotypic variations that can significantly influence natural selection. An intriguing example is exposure to pathogens, which imposes selection for host resistance. To test this hypothesis, we used larvae of the greater wax moth Galleria mellonella as model host to experimentally select for resistance to Bacillus thuringiensis (Bt), the most widely used bacterial agent for the biological control of pest insects...
May 19, 2017: Virulence
https://www.readbyqxmd.com/read/28521193/issues-raised-by-the-reference-doses-for-perfluorooctane-sulfonate-and-perfluorooctanoic-acid
#12
Zhaomin Dong, Md Mezbaul Bahar, Joytishna Jit, Bruce Kennedy, Brian Priestly, Jack Ng, Dane Lamb, Yanju Liu, Luchun Duan, Ravi Naidu
On 25th May 2016, the U.S. EPA released reference doses (RfDs) for Perfluorooctane Sulfonate (PFOS) and Perfluorooctanoic Acid (PFOA) of 20ng/kg/day, which were much more conservative than previous values. These RfDs rely on the choices of animal point of departure (PoD) and the toxicokinetics (TK) model. At this stage, considering that the human evidence is not strong enough for RfD determination, using animal data may be appropriate but with more uncertainties. In this article, the uncertainties concerning RfDs from the choices of PoD and TK models are addressed...
May 15, 2017: Environment International
https://www.readbyqxmd.com/read/28521013/flagellin-peptide-flg22-gains-access-to-long-distance-trafficking-in-arabidopsis-via-its-receptor-fls2
#13
Joanna Jelenska, Sandra M Davern, Robert F Standaert, Saed Mirzadeh, Jean T Greenberg
Diverse pathogen-derived molecules, such as bacterial flagellin and its conserved peptide flg22, are recognized in plants via plasma membrane receptors and induce both local and systemic immune responses. The fate of such ligands was unknown: whether and by what mechanism(s) they enter plant cells and whether they are transported to distal tissues. We used biologically active fluorophore and radiolabeled peptides to establish that flg22 moves to distal organs with the closest vascular connections. Remarkably, entry into the plant cell via endocytosis together with the FLS2 receptor is needed for delivery to vascular tissue and long-distance transport of flg22...
March 1, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/28515878/a-multispecies-dependent-double-observer-model-a-new-method-for-estimating-multispecies-abundance
#14
Jessie D Golding, J Joshua Nowak, Victoria J Dreitz
Conservation of biological communities requires accurate estimates of abundance for multiple species. Recent advances in estimating abundance of multiple species, such as Bayesian multispecies N-mixture models, account for multiple sources of variation, including detection error. However, false-positive errors (misidentification or double counts), which are prevalent in multispecies data sets, remain largely unaddressed. The dependent-double observer (DDO) method is an emerging method that both accounts for detection error and is suggested to reduce the occurrence of false positives because it relies on two observers working collaboratively to identify individuals...
May 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/28515874/universal-expressions-of-population-change-by-the-price-equation-natural-selection-information-and-maximum-entropy-production
#15
Steven A Frank
The Price equation shows the unity between the fundamental expressions of change in biology, in information and entropy descriptions of populations, and in aspects of thermodynamics. The Price equation partitions the change in the average value of a metric between two populations. A population may be composed of organisms or particles or any members of a set to which we can assign probabilities. A metric may be biological fitness or physical energy or the output of an arbitrarily complicated function that assigns quantitative values to members of the population...
May 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/28515778/evolution-of-movement-rate-increases-the-effectiveness-of-marine-reserves-for-the-conservation-of-pelagic-fishes
#16
Jonathan A Mee, Sarah P Otto, Daniel Pauly
Current debates about the efficacy of no-take marine reserves (MR) in protecting large pelagic fish such as tuna and sharks have usually not considered the evolutionary dimension of this issue, which emerges because the propensity to swim away from a given place, like any other biological trait, will probably vary in a heritable fashion among individuals. Here, based on spatially explicit simulations, we investigated whether selection to remain in MRs to avoid higher fishing mortality can lead to the evolution of more philopatric fish...
June 2017: Evolutionary Applications
https://www.readbyqxmd.com/read/28515321/flavin-containing-monooxygenases-in-aging-and-disease-emerging-roles-for-ancient-enzymes
#17
Ryan Rossner, Matt Kaeberlein, Scott F Leiser
Flavin- containing monooxygenases (FMOs) are primarily studied as xenobiotic metabolizing enzymes with a prominent role in drug metabolism. In contrast, endogenous functions and substrates of FMOs are less well understood. A growing body of recent evidence, however, implicates FMOs in aging, several diseases, and metabolic pathways. The evidence suggests an important role for these well- conserved proteins in multiple processes and raises questions about the endogenous substrate(s) and regulation of FMOs. Here, we present an overview of evidence for FMOs' involvement in aging and disease, discussing the biological context and arguing for increased investigation into the function of these enzymes...
May 17, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28515169/osmoregulation-bioenergetics-and-oxidative-stress-in-coastal-marine-invertebrates-raising-the-questions-for-future-research
#18
REVIEW
Georgina A Rivera-Ingraham, Jehan-Hervé Lignot
Osmoregulation is by no means an energetically cheap process, and its costs have been extensively quantified in terms of respiration and aerobic metabolism. Common products of mitochondrial activity are reactive oxygen and nitrogen species, which may cause oxidative stress by degrading key cell components, while playing essential roles in cell homeostasis. Given the delicate equilibrium between pro- and antioxidants in fueling acclimation responses, the need for a thorough understanding of the relationship between salinity-induced oxidative stress and osmoregulation arises as an important issue, especially in the context of global changes and anthropogenic impacts on coastal habitats...
May 15, 2017: Journal of Experimental Biology
https://www.readbyqxmd.com/read/28513415/the-fungal-cell-wall-structure-biosynthesis-and-function
#19
Neil A R Gow, Jean-Paul Latge, Carol A Munro
The molecular composition of the cell wall is critical for the biology and ecology of each fungal species. Fungal walls are composed of matrix components that are embedded and linked to scaffolds of fibrous load-bearing polysaccharides. Most of the major cell wall components of fungal pathogens are not represented in humans, other mammals, or plants, and therefore the immune systems of animals and plants have evolved to recognize many of the conserved elements of fungal walls. For similar reasons the enzymes that assemble fungal cell wall components are excellent targets for antifungal chemotherapies and fungicides...
May 2017: Microbiology Spectrum
https://www.readbyqxmd.com/read/28513076/a-computational-assessment-of-the-predicted-structures-of-human-macrophage-migration-inhibitory-factor-1-orthologs-in-parasites-and-its-affinity-to-human-cd74-receptor
#20
REVIEW
Claudia Machicado, Luis A Marcos
The human macrophage migration inhibitory factor 1 (Hu-MIF-1) is a protein involved in the inflammatory and immunology response to parasite infection. In the present study, the existence of Hu-MIF-1 from parasites have been explored by mining WormBase. A total of 35 helminths were found to have Hu-MIF-1 homologs, including some parasites of importance for public health. Physicochemical, structural, and biological properties of Hu-MIF-1 were compared with its orthologs in parasites showing that most of these are secretory proteins, with positive net charge and presence of the Cys-Xaa-Xaa-Cys motif that is critical for its oxidoreductase activity...
May 17, 2017: Journal of Molecular Recognition: JMR
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