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https://www.readbyqxmd.com/read/28724263/mutagenesis-and-characterization-of-a-bacillus-amyloliquefaciens-strain-for-cinnamomum-camphora-seed-kernel-oil-extraction-by-aqueous-enzymatic-method
#1
Cheng Zeng, Rongbin Zhao, Maomao Ma, Zheling Zeng, Deming Gong
The purpose of the present study was to increase the proteinase activity of the strain NCU116 by combining ultraviolet irradiation and N-methyl-N'-nitro-N-nitroso guanidine treatment, in order to enhance the efficiency of Cinnamomum camphora seed kernel oil (CCSKO) extraction by aqueous enzymatic method (AEM). The mutated strain, designated as NCU116-1, was screened out by the ratio of hydrolytic zone diameter to colony diameter on skim milk plate. The proteinase activity (9116.1 U/ml) of NCU116-1 was increased by 31...
December 2017: AMB Express
https://www.readbyqxmd.com/read/28723955/crystal-structure-and-functional-characterization-of-an-isoaspartyl-dipeptidase-cpsiada-from-colwellia-psychrerythraea-strain-34h
#2
Sun-Ha Park, Chang Woo Lee, Sung Gu Lee, Seung Chul Shin, Hak Jun Kim, Hyun Park, Jun Hyuck Lee
Isoaspartyl dipeptidase (IadA) is an enzyme that catalyzes the hydrolysis of an isoaspartyl dipeptide-like moiety, which can be inappropriately formed in proteins, between the β-carboxyl group side chain of Asp and the amino group of the following amino acid. Here, we have determined the structures of an isoaspartyl dipeptidase (CpsIadA) from Colwellia psychrerythraea, both ligand-free and that complexed with β-isoaspartyl lysine, at 1.85-Å and 2.33-Å resolution, respectively. In both structures, CpsIadA formed an octamer with two Zn ions in the active site...
2017: PloS One
https://www.readbyqxmd.com/read/28723891/the-lysosomal-potassium-channel-tmem175-adopts-a-novel-tetrameric-architecture
#3
Changkeun Lee, Jiangtao Guo, Weizhong Zeng, Sunghoon Kim, Ji She, Chunlei Cang, Dejian Ren, Youxing Jiang
TMEM175 is a lysosomal K(+) channel that is important for maintaining the membrane potential and pH stability in lysosomes. It contains two homologous copies of a six-transmembrane-helix (6-TM) domain, which has no sequence homology to the canonical tetrameric K(+) channels and lacks the TVGYG selectivity filter motif found in these channels. The prokaryotic TMEM175 channel, which is present in a subset of bacteria and archaea, contains only a single 6-TM domain and functions as a tetramer. Here, we present the crystal structure of a prokaryotic TMEM175 channel from Chamaesiphon minutus, CmTMEM175, the architecture of which represents a completely different fold from that of canonical K(+) channels...
July 19, 2017: Nature
https://www.readbyqxmd.com/read/28723202/structure-guided-design-of-protein-biosensors-for-phenolic-pollutants
#4
Shamayeeta Ray, Santosh Panjikar, Ruchi Anand
Phenolic aromatic compounds are a major source of environmental pollution. Currently there are no in situ methods for specifically and selectively detecting these pollutants. Here, we exploit the nature's biosensory machinery by employing Acinetobacter calcoaceticus NCIB8250 protein, MopR, as a model system to develop biosensors for selective detection of a spectrum of these pollutants. The X-ray structure of the sensor domain of MopR was used as a scaffold for logic-based tunable biosensor design. By employing a combination of in silico structure guided approaches, mutagenesis and isothermal calorimetric studies, we were able to generate biosensor templates, that can selectively and specifically sense harmful compounds like chlorophenols, cresols, catechol, and xylenols...
March 24, 2017: ACS Sensors
https://www.readbyqxmd.com/read/28722773/radh-a-versatile-halogenase-for-integration-into-synthetic-pathways
#5
Binuraj Menon, Eileen Brandenburger, Humera Sharif, Ulrike Klemstein, Sarah Shepherd, Michael Greaney, Jason Micklefield
Flavin-dependent halogenases are useful enzymes providing halogenated molecules with improved biological activity or intermediates for synthetic derivatization. Here we demonstrate how the fungal halogenase RadH can be used to regioselectively halogenate a range of bioactive aromatic scaffolds. Site-directed mutagenesis of RadH was used to identify catalytic residues and provide insights into the mechanism of fungal halogenases. A high throughput fluorescence screen was also developed enabling a RadH mutant to be evolved with improved properties...
July 19, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28722139/structure-based-release-analysis-of-the-jc-virus-agnoprotein-regions-a-role-for-the-hydrophilic-surface-of-the-major-alpha-helix-domain-in-release
#6
A Sami Saribas, Martyn K White, Mahmut Safak
Agnoprotein (Agno) is an important regulatory protein of JC virus (JCV), BK virus (BKV) and simian virus 40 (SV40) and these viruses are unable to replicate efficiently in the absence of this protein. Recent 3D-NMR structural data revealed that Agno contains two alpha-helices (a minor and a major) while the rest of the protein adopts an unstructured conformation (Coric et al., 2017, J Cell Biochem). Previously, release of the JCV Agno from the Agno-positive cells was reported. Here, we have further mapped the regions of Agno responsible for its release by a structure-based systematic mutagenesis approach...
July 19, 2017: Journal of Cellular Physiology
https://www.readbyqxmd.com/read/28720707/intrinsically-disordered-chromatin-protein-nupr1-binds-to-the-c-terminal-region-of-polycomb-ring1b
#7
Patricia Santofimia-Castaño, Bruno Rizzuti, Ángel L Pey, Philippe Soubeyran, Miguel Vidal, Raúl Urrutia, Juan L Iovanna, José L Neira
Intrinsically disordered proteins (IDPs) are ubiquitous in eukaryotes, and they are often associated with diseases in humans. The protein NUPR1 is a multifunctional IDP involved in chromatin remodeling and in the development and progression of pancreatic cancer; however, the details of such functions are unknown. Polycomb proteins are involved in specific transcriptional cascades and gene silencing. One of the proteins of the Polycomb complex is the Ring finger protein 1 (RING1). RING1 is related to aggressive tumor features in multiple cancer types...
July 18, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28720677/synthetic-circulating-cell-free-dna-as-quality-control-materials-for-somatic-mutation-detection-in-liquid-biopsy-for-cancer
#8
Rui Zhang, Rongxue Peng, Ziyang Li, Peng Gao, Shiyu Jia, Xin Yang, Jiansheng Ding, Yanxi Han, Jiehong Xie, Jinming Li
BACKGROUND: Detection of somatic genomic alterations in tumor-derived cell-free DNA (cfDNA) in the plasma is challenging owing to the low concentrations of cfDNA, variable detection methods, and complex workflows. Moreover, no proper quality control materials are available currently. METHODS: We developed a set of synthetic cfDNA quality control materials (SCQCMs) containing spike-in cfDNA on the basis of micrococcal nuclease digestion carrying somatic mutations as simulated cfDNA and matched genomic DNA as genetic background to emulate paired tumor-normal samples in real clinical tests...
July 18, 2017: Clinical Chemistry
https://www.readbyqxmd.com/read/28719838/identification-of-a-prototypical-single-stranded-uracil-dna-glycosylase-from-listeria-innocua
#9
Jing Li, Ye Yang, Jose Guevara, Liangjiang Wang, Weiguo Cao
A recent phylogenetic study on UDG superfamily estimated a new clade of family 3 enzymes (SMUG1-like), which shares a lower homology with canonic SMUG1 enzymes. The enzymatic properties of the newly found putative DNA glycosylase are unknown. To test the potential UDG activity and evaluate phylogenetic classification, we isolated one SMUG1-like glycosylase representative from Listeria innocua (Lin). A biochemical screening of DNA glycosylase activity in vitro indicates that Lin SMUG1-like glycosylase is a single-strand selective uracil DNA glycosylase...
July 8, 2017: DNA Repair
https://www.readbyqxmd.com/read/28719607/stress-induced-mutagenesis-stress-diversity-facilitates-the-persistence-of-mutator-genes
#10
Marta Lukačišinová, Sebastian Novak, Tiago Paixão
Mutator strains are expected to evolve when the availability and effect of beneficial mutations are high enough to counteract the disadvantage from deleterious mutations that will inevitably accumulate. As the population becomes more adapted to its environment, both availability and effect of beneficial mutations necessarily decrease and mutation rates are predicted to decrease. It has been shown that certain molecular mechanisms can lead to increased mutation rates when the organism finds itself in a stressful environment...
July 18, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28718782/prediction-of-protein-hotspots-from-whole-protein-sequences-by-a-random-projection-ensemble-system
#11
Jinjian Jiang, Nian Wang, Peng Chen, Chunhou Zheng, Bing Wang
Hotspot residues are important in the determination of protein-protein interactions, and they always perform specific functions in biological processes. The determination of hotspot residues is by the commonly-used method of alanine scanning mutagenesis experiments, which is always costly and time consuming. To address this issue, computational methods have been developed. Most of them are structure based, i.e., using the information of solved protein structures. However, the number of solved protein structures is extremely less than that of sequences...
July 18, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28718734/pullulan-production-from-synthetic-medium-by-a-new-mutant-of-aureobasidium-pullulans
#12
Guoqiang Chen, Jiming Wang, Yulong Su, Youshuang Zhu, Ge Zhang, Hongwei Zhao, Haobao Liu, Ying Yang, Rui Nian, Haibo Zhang, Yuxi Wei, Mo Xian
Pullulan with different molecular-weight could be applied in various fields. A UV-induced mutagenesis Aureobasidium pullulans UVMU6-1 was obtained from the strain A. pullulans CGMCC3.933 for the production of low-molecular-weight pullulan. Firstly, the obtained polysaccharide from A. pullulans UVMU6-1 was purified and identified to be pullulan with TLC, FT-IR and NMR. Then, culture medium and conditions for this strain were optimized by flask fermentation. Based on the optimized medium and culture conditions (pH 4, addition of 4 g/L Tween 80 for 96 h of cultivation), continuously fermentation was performed...
July 18, 2017: Preparative Biochemistry & Biotechnology
https://www.readbyqxmd.com/read/28718413/intrinsic-molecular-processes-impact-on-mutagenesis
#13
REVIEW
Byungho Lim, Jihyeob Mun, Seon-Young Kim
Mutations provide resources for genome evolution by generating genetic variability. In addition, mutations act as a driving force leading to disease pathogenesis, and thus have important implications for disease diagnosis, prognosis, and treatment. Understanding the mechanisms underlying how mutations occur is therefore of prime importance for elucidating evolutionary and pathogenic processes. Recent genomics studies have revealed that mutations occur non-randomly across the human genome. In particular, the distribution of mutations is highly associated with intrinsic molecular processes including transcription, chromatin organization, DNA replication timing, and DNA repair...
May 2017: Trends in Cancer
https://www.readbyqxmd.com/read/28717217/tki-addicted-ros1-rearranged-cells-are-destined-to-survival-or-death-by-the-intensity-of-ros1-kinase-activity
#14
Hayato Ogura, Yuka Nagatake-Kobayashi, Jun Adachi, Takeshi Tomonaga, Naoya Fujita, Ryohei Katayama
ROS1 rearrangement is observed in 1-2% of non-small cell lung cancers (NSCLC). The ROS1 tyrosine kinase inhibitor (TKI) crizotinib has induced marked tumour shrinkage in ROS1-rearranged cancers. However, emergence of acquired resistance to TKI is inevitable within a few years. Previous findings indicate that cabozantinib overcomes secondary mutation-mediated crizotinib-resistance in ROS1-fusion-positive cells. Here we attempted to establish cabozantinib-resistant cells by N-ethyl-N-nitrosourea mutagenesis screening using CD74-ROS1-expressing Ba/F3 cells...
July 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28717216/random-mutagenesis-analysis-and-identification-of-a-novel-c2h2-type-transcription-factor-from-the-nematode-trapping-fungus-arthrobotrys-oligospora
#15
Dewei Jiang, Jing Zhou, Guizhen Bai, Xinjing Xing, Liyan Tang, Xuewei Yang, Juan Li, Ke-Qin Zhang, Jinkui Yang
Arthrobotrys oligospora is a typical nematode-trapping fungus. In this study, 37 transformants of A. oligospora were obtained by REMI (restriction enzyme mediated integration) method and phenotypic properties of nine transformants were analyzed. The nine transformants showed differences in growth, conidiation, trap formation, stress tolerance, and/or pathogenicity among each other and with those of the parental wild-type strain (WT). The insertional sites of the hph cassette were identified in transformants X5 and X13...
July 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28716925/symmetry-related-proton-transfer-pathways-in-respiratory-complex-i
#16
Andrea Di Luca, Ana P Gamiz-Hernandez, Ville R I Kaila
Complex I functions as the initial electron acceptor in aerobic respiratory chains of most organisms. This gigantic redox-driven enzyme employs the energy from quinone reduction to pump protons across its complete approximately 200-Å membrane domain, thermodynamically driving synthesis of ATP. Despite recently resolved structures from several species, the molecular mechanism by which complex I catalyzes this long-range proton-coupled electron transfer process, however, still remains unclear. We perform here large-scale classical and quantum molecular simulations to study the function of the proton pump in complex I from Thermus thermophilus The simulations suggest that proton channels are established at symmetry-related locations in four subunits of the membrane domain...
July 17, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28716862/gene-therapy-for-wiskott-aldrich-syndrome-in-a-severely-affected-adult
#17
Emma C Morris, Thomas Fox, Ronjon Chakraverty, Rita Tendeiro, Katie Snell, Christine Rivat, Sarah Grace, Kimberly Gilmour, Sarita Workman, Karen Buckland, Katie Butler, Ronnie Chee, Alan D Salama, Hazem Ibrahim, Havinder Hara, Cecile Duret, Fulvio Mavilio, Frances Male, Frederick D Bushman, Anne Galy, Siobhan O Burns, H Bobby Gaspar, Adrian J Thrasher
Until recently hematopoietic stem cell transplantation was the only curative option for Wiskott-Aldrich syndrome (WAS). The first attempts at gene therapy for WAS using a ϒ-retroviral vector improved immunological parameters substantially but were complicated by acute leukemia as a result of insertional mutagenesis in a high proportion of patients. More recently treatment of children with a state-of-the-art self-inactivating lentiviral vector (LV-w1.6 WASp) has resulted in significant clinical benefit without inducing selection of clones harbouring integrations near oncogenes...
July 17, 2017: Blood
https://www.readbyqxmd.com/read/28715793/monitoring-in-vivo-metabolic-flux-with-a-designed-whole-cell-metabolite-biosensor-of-shikimic-acid
#18
Heng Li, Chaoning Liang, Wei Chen, Jian-Ming Jin, Shuang-Yan Tang, Yong Tao
Knowledge of intracellular metabolite levels is important for the understanding of metabolic flux distributions. Whole-cell biosensors of key metabolites are ideal for the monitoring of carbon flow in important metabolic pathways, thus guiding metabolic engineering for microbial improvement. However, lack of biosensors for metabolites of interests has limited their applications. In this study, a genetically encoded whole-cell biosensor specifically responding to shikimic acid has been developed by screening a site-saturation mutagenesis library of the binding pocket of a uric acid-responsive regulatory protein...
July 11, 2017: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/28715414/kinesin-1-promotes-chondrocyte-maintenance-during-skeletal-morphogenesis
#19
Adrian Santos-Ledo, Marina Garcia-Macia, Philip D Campbell, Marta Gronska, Florence L Marlow
During skeletal morphogenesis diverse mechanisms are used to support bone formation. This can be seen in the bones that require a cartilage template for their development. In mammals the cartilage template is removed, but in zebrafish the cartilage template persists and the bone mineralizes around the cartilage scaffold. Remodeling of unmineralized cartilage occurs via planar cell polarity (PCP) mediated cell rearrangements that contribute to lengthening of elements; however, the mechanisms that maintain the chondrocyte template that supports perichondral ossification remain unclear...
July 17, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28715115/membrane-topology-and-identification-of-key-residues-of-eadact-a-plant-mboat-with-unusual-substrate-specificity
#20
Tam N T Tran, Jennifer Shelton, Susan Brown, Timothy P Durrett
Euonymus alatus diacylglycerol acetyltransferase (EaDAcT) catalyzes the transfer of an acetyl group from acetyl-CoA to the sn-3 position of diacylglycerol (DAG) to form 3-acetyl-1,2-diacyl-sn-glycerol (acetyl-TAG). EaDAcT belongs to a small, plant-specific subfamily of the membrane bound O-acyltransferases (MBOAT) that acylate different lipid substrates. Sucrose gradient density centrifugation revealed that EaDAcT colocalizes to the same fractions as an endoplasmic reticulum specific marker. By mapping the membrane topology of EaDAcT, we obtained an experimentally determined topology model for a plant MBOAT...
July 17, 2017: Plant Journal: for Cell and Molecular Biology
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