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https://www.readbyqxmd.com/read/28651382/assignment-of-sigma-factors-of-rna-polymerase-to-promoters-in-corynebacterium-glutamicum
#1
Hana Dostálová, Jiří Holátko, Tobias Busche, Lenka Rucká, Andrey Rapoport, Petr Halada, Jan Nešvera, Jörn Kalinowski, Miroslav Pátek
Corynebacterium glutamicum is an important industrial producer of various amino acids and other metabolites. The C. glutamicum genome encodes seven sigma subunits (factors) of RNA polymerase: the primary sigma factor SigA (σ(A)), the primary-like σ(B) and five alternative sigma factors (σ(C), σ(D), σ(E), σ(H) and σ(M)). We have developed in vitro and in vivo methods to assign particular sigma factors to individual promoters of different classes. In vitro transcription assays and measurements of promoter activity using the overexpression of a single sigma factor gene and the transcriptional fusion of the promoter to the gfpuv reporter gene enabled us to reliably define the sigma factor dependency of promoters...
December 2017: AMB Express
https://www.readbyqxmd.com/read/28651373/sex-dependent-differences-in-liver-and-gut-metabolomic-profiles-with-acarbose-and-calorie-restriction-in-c57bl-6-mice
#2
Victoria K Gibbs, Rachel A Brewer, Nathan D Miyasaki, Amit Patki, Daniel L Smith
Acarbose, an alpha-glucosidase inhibitor used in treating type 2 diabetes, impairs complex carbohydrate digestion and absorption and extends lifespan in mice (without a requisite reduction in food intake). To assess sex-differential effects coincident with calorie restriction versus a non-restricted longevity enhancing intervention, we evaluated the metabolite profiles (by LC/MS) from livers and cecal contents of C57BL/6J mice (n=4/sex/group,) which were maintained for 10 months under one of three diet treatments: ad libitum control diet (CON), ad libitum control diet containing 0...
June 23, 2017: Journals of Gerontology. Series A, Biological Sciences and Medical Sciences
https://www.readbyqxmd.com/read/28651056/significantly-improved-protein-folding-thermodynamics-using-a-dispersion-corrected-water-model-and-a-new-residue-specific-force-field
#3
Hao-Nan Wu, Fan Jiang, Yun-Dong Wu
An accurate potential energy model is crucial for biomolecular simulations. Despite many recent improvements of classical protein force fields, there are remaining key issues: much weaker temperature-dependence of folding/unfolding equilibrium, and overly collapsed unfolded or disordered states. For the later problem, a new water model (TIP4P-D) has been proposed to correct the significantly underestimated water dispersion interactions. Here, using TIP4P-D, we reveal problems in current force fields through failures in folding model systems (a polyalanine peptide, Trp-cage and the GB1 hairpin)...
June 26, 2017: Journal of Physical Chemistry Letters
https://www.readbyqxmd.com/read/28651002/the-n-terminal-domain-of-mycobacterium-tuberculosis-ppe17-rv1168c-protein-plays-a-dominant-role-in-inducing-antibody-responses-in-active-tb-patients
#4
Philip Raj Abraham, Niteen Pathak, Gourango Pradhan, Gaddam Sumanlatha, Sangita Mukhopadhyay
The PPE (proline-proline-glutamic acid) proteins of Mycobacterium tuberculosis are characterized by a conserved N-terminal domain of approximately 180 amino acids and variable C-terminal domain. Since last decade, these proteins have gained much importance in the serodiagnosis of tuberculosis (TB) as they act as a source of antigenic variation. We have demonstrated earlier that one of the PPE proteins PPE17 (Rv1168c) induces strong B-cell and T-cell responses in active TB disease and also displays a higher antibody titer compared to immunodominant antigens such as ESAT-6, Hsp60 and PPD...
2017: PloS One
https://www.readbyqxmd.com/read/28650991/distinguishing-functional-polymorphism-from-random-variation-in-the-sequences-of-10-000-hla-a-b-and-c-alleles
#5
James Robinson, Lisbeth A Guethlein, Nezih Cereb, Soo Young Yang, Paul J Norman, Steven G E Marsh, Peter Parham
HLA class I glycoproteins contain the functional sites that bind peptide antigens and engage lymphocyte receptors. Recently, clinical application of sequence-based HLA typing has uncovered an unprecedented number of novel HLA class I alleles. Here we define the nature and extent of the variation in 3,489 HLA-A, 4,356 HLA-B and 3,111 HLA-C alleles. This analysis required development of suites of methods, having general applicability, for comparing and analyzing large numbers of homologous sequences. At least three amino-acid substitutions are present at every position in the polymorphic α1 and α2 domains of HLA-A, -B and -C...
June 26, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28650988/transcriptomic-analysis-to-uncover-genes-affecting-cold-resistance-in-the-chinese-honey-bee-apis-cerana-cerana
#6
Kai Xu, Qingsheng Niu, Huiting Zhao, Yali Du, Yusuo Jiang
The biological activity and geographical distribution of honey bees is strongly temperature-dependent, due to their ectothermic physiology. In China, the endemic Apis cerana cerana exhibits stronger cold hardiness than Western honey bees, making the former species important pollinators of winter-flowering plants. Although studies have examined behavioral and physiological mechanisms underlying cold resistance in bees, data are scarce regarding the exact molecular mechanisms. Here, we investigated gene expression in A...
2017: PloS One
https://www.readbyqxmd.com/read/28650855/intermittent-vs-continuous-enteral-feeding-to-prevent-catabolism-in-acutely-ill-adult-and-pediatric-patients
#7
Filippo G Di Girolamo, Roberta Situlin, Nicola Fiotti, Gianni Biolo
PURPOSE OF REVIEW: In clinical management of acutely ill adults and children, continuous enteral feeding (CEF), being considered the most tolerable approach, in comparison to other temporal patterns of nutrient administration (i.e. intermittent, cyclic and bolus), is the most frequently applied method. However, uncertainties remain about the most efficient approach to counteract protein catabolism. RECENT FINDINGS: In critically ill adults, protein loss is mainly driven by increased protein breakdown whereas, in pediatric patients, acute illness is mainly characterized by blunted regulation of protein synthesis and stunted growth...
June 24, 2017: Current Opinion in Clinical Nutrition and Metabolic Care
https://www.readbyqxmd.com/read/28650653/growth-and-metabolic-responses-of-rice-oryza-sativa-l-cultivated-in-phosphorus-deficient-soil-amended-with-tio2-nanoparticles
#8
Zahra Zahra, Naima Waseem, Rubab Zahra, Hwanhui Lee, Mohsin Ali Badshah, Arshad Mehmood, Hyung-Kyoon Choi, Muhammad Arshad
Plants have natural ability to withstand stress conditions through metabolic adjustments. The present study aimed at investigating effects of Titanium dioxide nanoparticles (TiO2 NPs) application (0, 25, 50, 150, 250, 500 and 750 mg kg-1) in phosphorus deficient soil in terms of growth responses, P contents and metabolic alterations in rice. TiO2 NPs application increased shoot length up to 14.5%. Phosphorus contents in rice roots, shoots, and grains were increased by 2.6-, 2.4-, and 1.3-fold, respectively at 750 mg kg-1 of TiO2 NPs...
June 26, 2017: Journal of Agricultural and Food Chemistry
https://www.readbyqxmd.com/read/28650636/orthogonal-electric-field-measurements-near-the-green-fluorescent-protein-fluorophore-through-stark-effect-spectroscopy-and-pka-shifts-provide-a-unique-benchmark-for-electrostatics-models
#9
Joshua D Slocum, Jeremy T First, Lauren J Webb
Measurement of the magnitude, direction, and functional importance of electric fields in biomolecules has been a longstanding experimental challenge. pKa shifts of titratable residues have been the most widely implemented measurements of local electrostatic environment around the labile proton, and experimental data sets of pKa shifts in a variety of systems have been used to test and refine computational prediction capabilities of protein electrostatic fields. A more direct and increasingly popular technique to measure electric fields in proteins is Stark effect spectroscopy, where the change in absorption energy of a chromophore relative to a reference state is related to the change in electric field felt by the chromophore...
June 26, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28650592/om-lv20-a-novel-peptide-from-odorous-frog-skin-accelerates-wound-healing-in-vitro-and-in-vivo
#10
Xiaojie Li, Ying Wang, Zhirong Zou, Meifeng Yang, Chunyun Wu, Yunshan Su, Jing Tang, Xinwang Yang
The healing of chronic wounds remains a considerable challenge in clinical trials and imposes severe financial and physiological burdens on patients. Many works are being tried to find ideal clinical promoting-wound-healing biomaterials. Small bioactive peptides with low cost and easy production, store and transfer become excellent candidates. Here, we identified a novel peptide (named OM-LV20) from skin secretions of odorous frog Odorrana margaretae. The peptide had an amino acid sequence of 'LVGKLLKGAVGDVCGLLPIC', contained an intramolecular disulfide bridge at the C-terminus, and was produced by posttranslational processing of a 71-residue prepropeptide...
June 26, 2017: Chemical Biology & Drug Design
https://www.readbyqxmd.com/read/28650572/cloning-and-characterization-of-nitrate-reductase-gene-in-ulva-prolifera-ulvophyceae-chlorophyta
#11
Yang Guo, Hao Zhe Wang, Chun Hui Wu, Hui Hui Fu, Peng Jiang
Ulva spp. dominates green tides around the world, which are occurring at an accelerated rate. The competitive nitrogen assimilation efficiency in Ulva is suggested to result in ecological success against other seaweeds. However, molecular characterization of genes involved in nitrogen assimilation have not been conducted. Here, we describe the identification of the nitrate reductase (NR) gene from a green seaweed Ulva prolifera, an alga which is responsible for the world's largest green tide in the Yellow Sea...
June 26, 2017: Journal of Phycology
https://www.readbyqxmd.com/read/28650495/syntheses-of-potent-teixobactin-analogues-against-methicillin-resistant-staphylococcus-aureus-mrsa-through-the-replacement-of-l-allo-enduracididine-with-its-isosteres
#12
Anish Parmar, Abhishek Iyer, Daniel G Lloyd, Charlotte S Vincent, Stephen H Prior, Annemieke Madder, Edward J Taylor, Ishwar Singh
The recently discovered cyclic depsipeptide, teixobactin, is a highly potent antibiotic against multi-drug resistant pathogens such as methicillin-resistant Staphylococcus aureus (MRSA) and Mycobaterium tuberculosis. It comprises of 4 D amino acids and a rare l-allo-enduracididine amino acid. The synthesis of a properly protected l-allo-enduracididine amino acid and its incorporation into teixobactin is time consuming, synthetically challenging and low yielding and is therefore a major bottleneck in the development of potent analogues of teixobactin...
June 26, 2017: Chemical Communications: Chem Comm
https://www.readbyqxmd.com/read/28650492/exploiting-the-biosynthetic-machinery-of-streptomyces-pilosus-to-engineer-a-water-soluble-zirconium-iv-chelator
#13
Tomas Richardson-Sanchez, William Tieu, Michael P Gotsbacher, Thomas J Telfer, Rachel Codd
The water solubility of a natural product-inspired octadentate hydroxamic acid chelator designed to coordinate Zr(iv)-89 has been improved by using a combined microbiological-chemical approach to engineer four ether oxygen atoms into the main-chain region of a methylene-containing analogue. First, an analogue of the trimeric hydroxamic acid desferrioxamine B (DFOB) that contained three main-chain ether oxygen atoms (DFOB-O3) was generated from cultures of the native DFOB-producer Streptomyces pilosus supplemented with oxybis(ethanamine) (OBEA), which competed against the native 1,5-diaminopentane (DP) substrate during DFOB assembly...
June 26, 2017: Organic & Biomolecular Chemistry
https://www.readbyqxmd.com/read/28650100/tautomerization-and-dissociation-of-molecular-peptide-radical-cations
#14
REVIEW
Xiaoyan Mu, Tao Song, Chi-Kit Siu, Ivan K Chu
Radical-mediated dissociations of peptide radical cations have intriguing unimolecular gas phase chemistry, with cleavages of almost every bond of the peptide backbone and amino acid side chains in a competitive and apparently "stochastic" manner. Challenges of unraveling mechanistic details are related to complex tautomerizations prior to dissociations. Recent conjunctions of experimental and theoretical investigations have revealed the existence of non-interconvertible isobaric tautomers with a variety of radical-site-specific initial structures, generated from dissociative electron transfer of ternary metal-ligand-peptide complexes...
June 26, 2017: Chemical Record: An Official Publication of the Chemical Society of Japan ... [et Al.]
https://www.readbyqxmd.com/read/28650092/photoactivatable-mussel-based-underwater-adhesive-proteins-by-an-expanded-genetic-code
#15
Mathias Hauf, Florian Richter, Tobias Schneider, Thomas Faidt, Berta M Martins, Tobias Baumann, Patrick Durkin, Holger Dobbek, Karin Jacobs, Andreas Möglich, Nediljko Budisa
Marine mussels exhibit potent underwater adhesion abilities under hostile conditions employing 3,4-dihydroxy-phenylalanine (Dopa)-rich mussel-adhesive proteins (MAPs). However, their recombinant production is a major biotechnological challenge. Here, we have developed a novel strategy based on genetic code expansion by engineering efficient aminoacyl-tRNA synthetases (aaRSs) for the photocaged non-canonical amino acid (ncAA) ortho-nitrobenzyl Dopa (ONB-Dopa). The engineered ONB-DopaRS enables in vivo production of MAP type 5 site-specifically equipped with multiple instances of ONB-Dopa yielding spatiotemporally controlled underwater adhesives...
June 26, 2017: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/28650040/synthesis-functionalisation-and-post-synthetic-modification-of-bismuth-metal-organic-frameworks
#16
M Köppen, O Beyer, S Wuttke, U Lüning, N Stock
Two new bismuth metal-organic frameworks (Bi-MOFs) were discovered using high throughput experiments employing bismuth(iii) nitrate pentahydrate and triazine-2,4,6-triyl-tribenzoic acid (H3TATB). The reaction was carried out for long reaction times (∼5 d) in a water/DMF-mixture and resulted in the formation of [Bi2(O)(OH)(TATB)]·H2O (denoted as CAU-35). By switching to short reaction times and a methanol/DMF-mixture as the solvent, an analogue of CAU-7-BTB with the composition [Bi(TATB)]·DMF·6H2O (denoted as CAU-7-TATB) was obtained...
June 26, 2017: Dalton Transactions: An International Journal of Inorganic Chemistry
https://www.readbyqxmd.com/read/28649989/an-l-threonine-transaldolase-is-required-for-l-threo-%C3%AE-hydroxy-%C3%AE-amino-acid-assembly-during-obafluorin-biosynthesis
#17
Thomas A Scott, Daniel Heine, Zhiwei Qin, Barrie Wilkinson
β-Lactone natural products occur infrequently in nature but possess a variety of potent and valuable biological activities. They are commonly derived from β-hydroxy-α-amino acids, which are themselves valuable chiral building blocks for chemical synthesis and precursors to numerous important medicines. However, despite a number of excellent synthetic methods for their asymmetric synthesis, few effective enzymatic tools exist for their preparation. Here we report cloning of the biosynthetic gene cluster for the β-lactone antibiotic obafluorin and delineate its biosynthetic pathway...
June 26, 2017: Nature Communications
https://www.readbyqxmd.com/read/28649967/structural-perturbations-on-huntingtin-n17-domain-during-its-folding-on-2d-nanomaterials
#18
Leili Zhang, Mei Feng, Ruhong Zhou, Binquan Luan
A globular protein's folded structure in its physiological environment is largely determined by its amino acid sequence. Recently, newly discovered transformer proteins as well as intrinsically disordered proteins may adopt the folding-upon-binding mechanism where their secondary structures are highly dependent on their binding partners. Due to the various applications of nanomaterials in biological sensors and potential wearable devices, it is important to discover possible conformational changes of proteins on nanomaterials...
June 26, 2017: Nanotechnology
https://www.readbyqxmd.com/read/28649795/geometry-retentive-c-alkenylation-of-lithiated-%C3%AE-aminonitriles-quaternary-%C3%AE-alkenyl-amino-acids-and-hydantoins
#19
Josep Mas-Roselló, Shuji Hachisu, Jonathan Clayden
α-Amino nitriles tethered to alkenes through a urea linkage undergo intramolecular C-alkenylation on treatment with base by attack of the lithionitrile derivatives on the N'-alkenyl group. The geometry-retentive alkene shift affords stereospecifically the E or Z isomer of the 5-alkenyl-4-iminohydantoin products from the corresponding starting E- or Z-N'-alkenyl urea, each of which may be formed from the same N-allyl precursor by stereodivergent alkene isomerisation. The reaction, formally a nucleophilic substitution at an sp2 carbon atom, allows the direct regioselective incorporation of mono-, di-, tri- and tetrasubstituted olefins at the α-carbon of amino acid derivatives...
June 26, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28649782/heterozygous-variants-in-actl6a-encoding-a-component-of-the-baf-complex-are-associated-with-intellectual-disability
#20
Ronit Marom, Mahim Jain, Lindsay C Burrage, I-Wen Song, Brett H Graham, Chester W Brown, Servi J C Stevens, Alexander P A Stegmann, Andrew T Gunter, Julie D Kaplan, Ralitza H Gavrilova, Marwan Shinawi, Jill A Rosenfeld, Yangjin Bae, Alyssa A Tran, Yuqing Chen, James T Lu, Richard A Gibbs, Christine Eng, Yaping Yang, Justine Rousseau, Bert B A de Vries, Philippe M Campeau, Brendan Lee
Pathogenic variants in genes encoding components of the BAF chromatin remodeling complex have been associated with intellectual disability syndromes. We identified heterozygous, novel variants in ACTL6A, a gene encoding a component of the BAF complex, in three subjects with varying degrees of intellectual disability. Two subjects have missense variants affecting highly conserved amino acid residues within the actin-like domain. Missense mutations in the homologous region in yeast actin were previously reported to be dominant lethal and were associated with impaired binding of the human ACTL6A to β-actin and BRG1...
June 25, 2017: Human Mutation
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